From fb60b04cd59946d9b580d455ec6ffa63c3e5be20 Mon Sep 17 00:00:00 2001
From: Piotr Gawron <piotr.gawron@uni.lu>
Date: Thu, 23 Aug 2018 14:22:13 +0200
Subject: [PATCH] jsdoc type definition added
---
frontend-js/src/main/js/Configuration.js | 155 ++++++++++++++++-
.../src/main/js/ConfigurationOption.js | 55 ++++++
frontend-js/src/main/js/Functions.js | 68 ++++++++
frontend-js/src/main/js/GuiConnector.js | 57 +++++-
.../src/main/js/InvalidArgumentError.js | 6 +
.../src/main/js/InvalidCredentialsError.js | 6 +
frontend-js/src/main/js/NetworkError.js | 11 ++
.../src/main/js/ObjectWithListeners.js | 5 +
frontend-js/src/main/js/SecurityError.js | 6 +
frontend-js/src/main/js/SessionData.js | 162 +++++++++++++----
frontend-js/src/main/js/ValidationError.js | 6 +
.../src/main/js/gui/AddOverlayDialog.js | 22 ++-
frontend-js/src/main/js/gui/CommentDialog.js | 132 +++++++++++++-
frontend-js/src/main/js/gui/ContextMenu.js | 39 +++++
.../src/main/js/gui/GuiMessageError.js | 6 +
frontend-js/src/main/js/gui/Header.js | 43 +++++
frontend-js/src/main/js/gui/Legend.js | 44 +++++
frontend-js/src/main/js/gui/LoginDialog.js | 41 ++++-
frontend-js/src/main/js/gui/MapContextMenu.js | 30 +++-
frontend-js/src/main/js/gui/OptionsMenu.js | 34 ++++
frontend-js/src/main/js/gui/OverviewDialog.js | 33 ++++
frontend-js/src/main/js/gui/Panel.js | 70 ++++++++
frontend-js/src/main/js/gui/PluginDialog.js | 39 +++++
.../src/main/js/gui/SelectionContextMenu.js | 21 +++
.../js/gui/admin/AbstractAnnotatorsDialog.js | 12 ++
.../js/gui/admin/ChooseAnnotatorsDialog.js | 42 +++++
.../main/js/gui/admin/CommentsAdminPanel.js | 31 ++++
.../src/main/js/gui/admin/LogListDialog.js | 40 +++++
.../src/main/js/gui/admin/MapsAdminPanel.js | 78 ++++++++-
frontend-js/src/main/js/gui/admin/ZipEntry.js | 34 ++++
.../main/js/gui/export/AbstractExportPanel.js | 131 ++++++++++++++
.../main/js/gui/export/ElementExportPanel.js | 30 ++++
.../main/js/gui/export/GraphicsExportPanel.js | 40 +++++
.../main/js/gui/export/NetworkExportPanel.js | 39 ++++-
.../main/js/gui/leftPanel/AbstractDbPanel.js | 40 ++++-
.../main/js/gui/leftPanel/ChemicalPanel.js | 37 ++++
.../src/main/js/gui/leftPanel/DrugPanel.js | 27 +++
.../js/gui/leftPanel/GenericSearchPanel.js | 30 ++++
.../src/main/js/gui/leftPanel/LeftPanel.js | 60 +++++++
.../src/main/js/gui/leftPanel/MiRnaPanel.js | 38 ++++
.../src/main/js/gui/leftPanel/OverlayPanel.js | 9 +-
.../main/js/gui/leftPanel/ProjectInfoPanel.js | 48 +++++-
.../js/gui/leftPanel/PublicationListDialog.js | 32 ++++
.../src/main/js/gui/leftPanel/SubmapPanel.js | 38 ++++
.../src/main/js/gui/topMenu/TopMenu.js | 44 +++++
frontend-js/src/main/js/map/CustomMap.js | 3 +
.../src/main/js/map/CustomMapOptions.js | 9 +
frontend-js/src/main/js/map/OverlayParser.js | 4 +
frontend-js/src/main/js/map/Submap.js | 3 +
frontend-js/src/main/js/map/data/Annotator.js | 72 ++++++++
.../src/main/js/map/data/DataOverlay.js | 8 +
.../src/main/js/map/data/IdentifiedElement.js | 45 ++++-
.../src/main/js/map/data/KineticLaw.js | 49 ++++++
.../src/main/js/map/data/LayoutAlias.js | 64 +++++++
.../src/main/js/map/data/LayoutReaction.js | 64 +++++--
frontend-js/src/main/js/map/data/MapModel.js | 163 +++++++++++++++++-
frontend-js/src/main/js/map/data/Mesh.js | 53 ++++++
frontend-js/src/main/js/map/data/MiRna.js | 6 +
.../src/main/js/map/data/MiriamType.js | 54 ++++++
.../main/js/map/data/ModificationStateType.js | 49 +++++-
frontend-js/src/main/js/map/data/Modifier.js | 29 ++++
frontend-js/src/main/js/map/data/PointData.js | 4 +
.../src/main/js/map/data/PrivilegeType.js | 48 ++++++
frontend-js/src/main/js/map/data/Product.js | 26 ++-
frontend-js/src/main/js/map/data/Project.js | 33 +++-
.../src/main/js/map/data/ProjectStatistics.js | 59 +++++--
frontend-js/src/main/js/map/data/Reactant.js | 30 +++-
frontend-js/src/main/js/map/data/Reaction.js | 113 ++++++++++++
.../src/main/js/map/data/ReferenceGenome.js | 17 ++
.../js/map/data/ReferenceGenomeGeneMapping.js | 15 ++
.../src/main/js/map/data/SbmlFunction.js | 68 +++++++-
.../src/main/js/map/data/SbmlParameter.js | 65 +++++++
.../main/js/map/data/SearchBioEntityGroup.js | 136 ++++++++++++++-
frontend-js/src/main/js/map/data/Target.js | 73 ++++++--
.../main/js/map/data/TargettingStructure.js | 37 ++++
.../src/main/js/map/data/UserPreferences.js | 19 ++
.../src/main/js/map/marker/AliasMarker.js | 4 +
.../main/js/map/overlay/AbstractDbOverlay.js | 113 +++++++++++-
.../overlay/AbstractTargettingDbOverlay.js | 37 +++-
.../main/js/map/overlay/ChemicalDbOverlay.js | 16 ++
.../main/js/map/overlay/CommentDbOverlay.js | 54 ++++--
.../js/map/overlay/DbOverlayCollection.js | 6 +
.../src/main/js/map/overlay/DrugDbOverlay.js | 16 ++
.../src/main/js/map/overlay/MiRnaDbOverlay.js | 16 ++
.../main/js/map/overlay/SearchDbOverlay.js | 33 +++-
.../src/main/js/map/overlay/UserDbOverlay.js | 54 ++++++
.../src/main/js/map/structure/MolArt.js | 35 +++-
.../src/main/js/map/surface/AliasSurface.js | 5 +
.../src/main/js/map/window/AliasInfoWindow.js | 3 +
frontend-js/src/main/js/minerva.js | 64 ++++++-
.../src/main/js/plugin/MinervaPluginProxy.js | 92 +++++++++-
frontend-js/src/main/js/plugin/Plugin.js | 59 +++++++
.../src/main/js/plugin/PluginManager.js | 13 ++
93 files changed, 3877 insertions(+), 132 deletions(-)
diff --git a/frontend-js/src/main/js/Configuration.js b/frontend-js/src/main/js/Configuration.js
index be283044b0..912bd07f4a 100644
--- a/frontend-js/src/main/js/Configuration.js
+++ b/frontend-js/src/main/js/Configuration.js
@@ -27,6 +27,29 @@ var ModificationStateType = require('./map/data/ModificationStateType');
*
*/
+/**
+ * @typedef {Object} ImageConverter
+ * @property {string} name
+ * @property {string} handler
+ */
+
+/**
+ * @typedef {Object} ModelConverter
+ * @property {string} name
+ * @property {string} handler
+ */
+
+/**
+ * @typedef {Object} MapType
+ * @property {string} id
+ * @property {string} name
+ */
+
+/**
+ * @typedef {Object} MapCanvasType
+ * @property {string} id
+ * @property {string} name
+ */
/**
*
@@ -184,26 +207,58 @@ Configuration.prototype.getOverlayTypes = function () {
return this._overlayTypes;
};
+/**
+ *
+ * @param {ImageConverter[]} imageConverters
+ */
Configuration.prototype.setImageConverters = function (imageConverters) {
this._imageConverters = imageConverters;
};
+
+/**
+ *
+ * @returns {ImageConverter[]}
+ */
Configuration.prototype.getImageConverters = function () {
return this._imageConverters;
};
+/**
+ *
+ * @param {ModelConverter[]} modelConverters
+ */
Configuration.prototype.setModelConverters = function (modelConverters) {
this._modelConverters = modelConverters;
};
+
+/**
+ *
+ * @returns {ModelConverter[]}
+ */
Configuration.prototype.getModelConverters = function () {
return this._modelConverters;
};
+/**
+ *
+ * @param {BioEntityType[]} elementTypes
+ */
Configuration.prototype.setElementTypes = function (elementTypes) {
this._elementTypes = elementTypes;
};
+
+/**
+ *
+ * @returns {BioEntityType[]}
+ */
Configuration.prototype.getElementTypes = function () {
return this._elementTypes;
};
+
+/**
+ *
+ * @returns {string[]}
+ */
Configuration.prototype.getElementTypeNames = function () {
var result = [];
for (var i = 0; i < this._elementTypes.length; i++) {
@@ -212,6 +267,11 @@ Configuration.prototype.getElementTypeNames = function () {
return result;
};
+/**
+ *
+ * @param {BioEntityType} elementType
+ * @returns {BioEntityType|null}
+ */
Configuration.prototype.getParentType = function (elementType) {
var i;
for (i = 0; i < this._elementTypes.length; i++) {
@@ -227,6 +287,10 @@ Configuration.prototype.getParentType = function (elementType) {
return null;
};
+/**
+ *
+ * @returns {string[]}
+ */
Configuration.prototype.getSimpleElementTypeNames = function () {
var classesToBeExcluded = {};
var i;
@@ -242,14 +306,27 @@ Configuration.prototype.getSimpleElementTypeNames = function () {
return result;
};
-
+/**
+ *
+ * @param {BioEntityType[]} reactionTypes
+ */
Configuration.prototype.setReactionTypes = function (reactionTypes) {
this._reactionTypes = reactionTypes;
};
+
+/**
+ *
+ * @returns {BioEntityType[]}
+ */
Configuration.prototype.getReactionTypes = function () {
return this._reactionTypes;
};
+
+/**
+ *
+ * @param {Object<string,MiriamTypeOptions>} miriamTypes
+ */
Configuration.prototype.setMiriamTypes = function (miriamTypes) {
this._miriamTypes = [];
for (var key in miriamTypes) {
@@ -268,16 +345,25 @@ Configuration.prototype.setMiriamTypes = function (miriamTypes) {
);
};
+/**
+ *
+ * @param {MapType[]} mapTypes
+ */
Configuration.prototype.setMapTypes = function (mapTypes) {
this._mapTypes = mapTypes;
};
+
+/**
+ *
+ * @returns {MapType[]}
+ */
Configuration.prototype.getMapTypes = function () {
return this._mapTypes;
};
/**
*
- * @param {Array}mapCanvasTypes
+ * @param {MapCanvasType[]} mapCanvasTypes
*/
Configuration.prototype.setMapCanvasTypes = function (mapCanvasTypes) {
this._mapCanvasTypes = mapCanvasTypes;
@@ -285,12 +371,16 @@ Configuration.prototype.setMapCanvasTypes = function (mapCanvasTypes) {
/**
*
- * @returns {Array}
+ * @returns {MapCanvasType[]}
*/
Configuration.prototype.getMapCanvasTypes = function () {
return this._mapCanvasTypes;
};
+/**
+ *
+ * @param {Object<string,PrivilegeTypeOptions>} privilegeTypes
+ */
Configuration.prototype.setPrivilegeTypes = function (privilegeTypes) {
this._privilegeTypes = [];
for (var key in privilegeTypes) {
@@ -311,7 +401,7 @@ Configuration.prototype.getPrivilegeTypes = function () {
/**
*
- * @param name
+ * @param {string} name
* @returns {PrivilegeType}
*/
Configuration.prototype.getPrivilegeType = function (name) {
@@ -326,6 +416,11 @@ Configuration.prototype.getPrivilegeType = function (name) {
return null;
};
+/**
+ *
+ * @param {string} name
+ * @returns {MiriamType|null}
+ */
Configuration.prototype.getMiriamTypeByName = function (name) {
var self = this;
for (var i = 0; i < self._miriamTypes.length; i++) {
@@ -337,10 +432,18 @@ Configuration.prototype.getMiriamTypeByName = function (name) {
return null;
};
+/**
+ *
+ * @returns {MiriamType[]}
+ */
Configuration.prototype.getMiriamTypes = function () {
return this._miriamTypes;
};
+/**
+ *
+ * @param {Object<string,ModificationStateTypeOptions>} modificationStateTypes
+ */
Configuration.prototype.setModificationStateTypes = function (modificationStateTypes) {
this._modificationStateTypes = [];
for (var key in modificationStateTypes) {
@@ -350,9 +453,20 @@ Configuration.prototype.setModificationStateTypes = function (modificationStateT
}
}
};
+
+/**
+ *
+ * @returns {ModificationStateType[]}
+ */
Configuration.prototype.getModificationStateTypes = function () {
return this._modificationStateTypes;
};
+
+/**
+ *
+ * @param {string} name
+ * @returns {ModificationStateType}
+ */
Configuration.prototype.getModificationStateTypeByName = function (name) {
var self = this;
for (var i = 0; i < self._modificationStateTypes.length; i++) {
@@ -364,6 +478,10 @@ Configuration.prototype.getModificationStateTypeByName = function (name) {
return null;
};
+/**
+ *
+ * @param {AnnotatorOptions[]} annotators
+ */
Configuration.prototype.setAnnotators = function (annotators) {
this._annotators = [];
for (var key in annotators) {
@@ -374,17 +492,36 @@ Configuration.prototype.setAnnotators = function (annotators) {
}
};
+/**
+ *
+ * @returns {Array}
+ */
Configuration.prototype.getPluginsData = function () {
return this._pluginsData;
};
+
+/**
+ *
+ * @param {Array} pluginsData
+ */
Configuration.prototype.setPluginsData = function (pluginsData) {
this._pluginsData = pluginsData;
};
+/**
+ *
+ * @returns {Annotator[]}
+ */
Configuration.prototype.getAnnotators = function () {
return this._annotators;
};
+/**
+ *
+ * @param {BioEntityType} [type] - element type for which we want to get annotators, if empty all annotators will
+ * be returned
+ * @returns {Array}
+ */
Configuration.prototype.getElementAnnotators = function (type) {
if (type === undefined) {
return this._annotators;
@@ -413,6 +550,12 @@ Configuration.prototype.getElementAnnotators = function (type) {
return result;
};
+/**
+ *
+ * @param {T} original
+ * @returns {T}
+ * @template T
+ */
function createCopy(original) {
if (Object.prototype.toString.call(original) === '[object Array]') {
var result = [];
@@ -425,6 +568,10 @@ function createCopy(original) {
}
}
+/**
+ *
+ * @param {Configuration} original
+ */
Configuration.prototype.update = function (original) {
var self = this;
var i;
diff --git a/frontend-js/src/main/js/ConfigurationOption.js b/frontend-js/src/main/js/ConfigurationOption.js
index d7ce2f8fd3..e8a0328f38 100644
--- a/frontend-js/src/main/js/ConfigurationOption.js
+++ b/frontend-js/src/main/js/ConfigurationOption.js
@@ -4,6 +4,21 @@ var ObjectWithListeners = require('./ObjectWithListeners');
var logger = require('./logger');
+/**
+ * @typedef {Object} ConfigurationOptionParam
+ * @property {string} type
+ * @property {string} commonName
+ * @property {string} group
+ * @property {string} value
+ * @property {string} valueType
+ */
+
+/**
+ *
+ * @param {ConfigurationOption|ConfigurationOptionParam} data
+ * @constructor
+ * @extends ObjectWithListeners
+ */
function ConfigurationOption(data) {
// call super constructor
ObjectWithListeners.call(this);
@@ -27,42 +42,82 @@ function ConfigurationOption(data) {
ConfigurationOption.prototype = Object.create(ObjectWithListeners.prototype);
ConfigurationOption.prototype.constructor = ConfigurationOption;
+/**
+ *
+ * @param {string} type
+ */
ConfigurationOption.prototype.setType = function (type) {
this._type = type;
};
+/**
+ *
+ * @returns {string}
+ */
ConfigurationOption.prototype.getType = function () {
return this._type;
};
+/**
+ *
+ * @param {string} value
+ */
ConfigurationOption.prototype.setValue = function (value) {
this._value = value;
};
+/**
+ *
+ * @returns {string}
+ */
ConfigurationOption.prototype.getValue = function () {
return this._value;
};
+/**
+ *
+ * @param {string} valueType
+ */
ConfigurationOption.prototype.setValueType = function (valueType) {
this._valueType = valueType;
};
+/**
+ *
+ * @returns {string}
+ */
ConfigurationOption.prototype.getValueType = function () {
return this._valueType;
};
+/**
+ *
+ * @param {string} commonName
+ */
ConfigurationOption.prototype.setCommonName = function (commonName) {
this._commonName = commonName;
};
+/**
+ *
+ * @returns {string}
+ */
ConfigurationOption.prototype.getCommonName = function () {
return this._commonName;
};
+/**
+ *
+ * @param {string} group
+ */
ConfigurationOption.prototype.setGroup = function (group) {
this._group = group;
};
+/**
+ *
+ * @returns {string}
+ */
ConfigurationOption.prototype.getGroup = function () {
return this._group;
};
diff --git a/frontend-js/src/main/js/Functions.js b/frontend-js/src/main/js/Functions.js
index b233ee58d6..2eefe04ecd 100644
--- a/frontend-js/src/main/js/Functions.js
+++ b/frontend-js/src/main/js/Functions.js
@@ -61,14 +61,29 @@ Functions.prototype.bound = function (value, minVal, maxVal) {
return value;
};
+/**
+ *
+ * @param {number} deg
+ * @returns {number}
+ */
Functions.prototype.degreesToRadians = function (deg) {
return deg * (Math.PI / 180);
};
+/**
+ *
+ * @param {number} rad
+ * @returns {number}
+ */
Functions.prototype.radiansToDegrees = function (rad) {
return rad / (Math.PI / 180);
};
+/**
+ *
+ * @param {number} value
+ * @returns {string}
+ */
Functions.prototype.intToColorString = function (value) {
/* jslint bitwise: true */
var trimmedValue = (value & 0xFFFFFF);
@@ -295,6 +310,12 @@ Functions.prototype.overlayToColor = function (elementOverlay) {
}
};
+/**
+ *
+ * @param {HTMLElement} element
+ * @param {string} name
+ * @returns {HTMLElement}
+ */
Functions.prototype.getElementByName = function (element, name) {
if (element !== undefined) {
if (element.getAttribute("name") === name) {
@@ -395,14 +416,32 @@ Functions.prototype.createElement = function (params) {
return result;
};
+/**
+ *
+ * @param {number} x
+ * @returns {number}
+ */
function sqr(x) {
return x * x;
}
+/**
+ *
+ * @param {Point} v
+ * @param {Point} w
+ * @returns {number}
+ */
function dist2(v, w) {
return sqr(v.x - w.x) + sqr(v.y - w.y);
}
+/**
+ *
+ * @param {Point} p
+ * @param {Point} v
+ * @param {Point} w
+ * @returns {number}
+ */
function distToSegmentSquared(p, v, w) {
var l2 = dist2(v, w);
@@ -422,6 +461,12 @@ function distToSegmentSquared(p, v, w) {
return dist2(p, new Point(v.x + t * (w.x - v.x), v.y + t * (w.y - v.y)));
}
+/**
+ *
+ * @param {Point} p1
+ * @param {Point| {start:Point, end:Point}} el2
+ * @returns {number}
+ */
Functions.prototype.distance = function (p1, el2) {
if (el2 instanceof Point) {
var p2 = el2;
@@ -431,6 +476,10 @@ Functions.prototype.distance = function (p1, el2) {
}
};
+/**
+ *
+ * @param {HTMLElement} element
+ */
Functions.prototype.removeChildren = function (element) {
while (element.firstChild) {
element.removeChild(element.firstChild);
@@ -438,6 +487,7 @@ Functions.prototype.removeChildren = function (element) {
};
/**
+ * @param {string} url
*
* @returns {Promise} resolved after javascript is loaded
*/
@@ -464,6 +514,11 @@ Functions.prototype.loadScript = function (url) {
});
};
+/**
+ *
+ * @param {string} s
+ * @returns {string}
+ */
Functions.prototype.computeMD5 = function (s) {
function L(k, d) {
return (k << d) | (k >>> (32 - d))
@@ -476,10 +531,13 @@ Functions.prototype.computeMD5 = function (s) {
I = (G & 1073741824);
d = (k & 1073741824);
x = (G & 1073741823) + (k & 1073741823);
+ // noinspection JSBitwiseOperatorUsage
if (I & d) {
return (x ^ 2147483648 ^ F ^ H)
}
+ // noinspection JSBitwiseOperatorUsage
if (I | d) {
+ // noinspection JSBitwiseOperatorUsage
if (x & 1073741824) {
return (x ^ 3221225472 ^ F ^ H)
} else {
@@ -549,6 +607,11 @@ Functions.prototype.computeMD5 = function (s) {
return aa
}
+ /**
+ *
+ * @param {number} x
+ * @returns {string}
+ */
function B(x) {
var k = "", F = "", G, d;
for (d = 0; d <= 3; d++) {
@@ -597,6 +660,7 @@ Functions.prototype.computeMD5 = function (s) {
E = X;
v = W;
g = V;
+ // noinspection PointlessArithmeticExpressionJS
Y = u(Y, X, W, V, C[P + 0], S, 3614090360);
V = u(V, Y, X, W, C[P + 1], Q, 3905402710);
W = u(W, V, Y, X, C[P + 2], N, 606105819);
@@ -616,6 +680,7 @@ Functions.prototype.computeMD5 = function (s) {
Y = f(Y, X, W, V, C[P + 1], A, 4129170786);
V = f(V, Y, X, W, C[P + 6], z, 3225465664);
W = f(W, V, Y, X, C[P + 11], y, 643717713);
+ // noinspection PointlessArithmeticExpressionJS
X = f(X, W, V, Y, C[P + 0], w, 3921069994);
Y = f(Y, X, W, V, C[P + 5], A, 3593408605);
V = f(V, Y, X, W, C[P + 10], z, 38016083);
@@ -638,6 +703,7 @@ Functions.prototype.computeMD5 = function (s) {
W = D(W, V, Y, X, C[P + 7], l, 4139469664);
X = D(X, W, V, Y, C[P + 10], j, 3200236656);
Y = D(Y, X, W, V, C[P + 13], o, 681279174);
+ // noinspection PointlessArithmeticExpressionJS
V = D(V, Y, X, W, C[P + 0], m, 3936430074);
W = D(W, V, Y, X, C[P + 3], l, 3572445317);
X = D(X, W, V, Y, C[P + 6], j, 76029189);
@@ -645,6 +711,7 @@ Functions.prototype.computeMD5 = function (s) {
V = D(V, Y, X, W, C[P + 12], m, 3873151461);
W = D(W, V, Y, X, C[P + 15], l, 530742520);
X = D(X, W, V, Y, C[P + 2], j, 3299628645);
+ // noinspection PointlessArithmeticExpressionJS
Y = t(Y, X, W, V, C[P + 0], U, 4096336452);
V = t(V, Y, X, W, C[P + 7], T, 1126891415);
W = t(W, V, Y, X, C[P + 14], R, 2878612391);
@@ -666,6 +733,7 @@ Functions.prototype.computeMD5 = function (s) {
W = K(W, v);
V = K(V, g)
}
+ // noinspection JSSuspiciousNameCombination
var i = B(Y) + B(X) + B(W) + B(V);
return i.toLowerCase()
};
diff --git a/frontend-js/src/main/js/GuiConnector.js b/frontend-js/src/main/js/GuiConnector.js
index 137259eee3..dfaa7c33f6 100644
--- a/frontend-js/src/main/js/GuiConnector.js
+++ b/frontend-js/src/main/js/GuiConnector.js
@@ -25,6 +25,11 @@ function GuiConnector() {
this.getParams = [];
}
+/**
+ *
+ * @param {GuiConnector} object
+ * @returns {GuiConnector}
+ */
function returnThisOrSingleton(object) {
if (object === undefined || object === null) {
return GuiConnector.singleton;
@@ -46,6 +51,7 @@ GuiConnector.prototype.init = function () {
return d >= 0 && this.lastIndexOf(pattern) === d;
};
}
+ // noinspection PointlessBooleanExpressionJS
var isIE = /* @cc_on!@ */false || !!document.documentMode;
if (isIE) {
@@ -103,10 +109,18 @@ GuiConnector.prototype.init = function () {
}
};
+/**
+ *
+ * @param {function} handler
+ */
GuiConnector.prototype.addWindowResizeEvent = function (handler) {
this._windowResizeEvents.push(handler);
};
+/**
+ *
+ * @param {function} handler
+ */
GuiConnector.prototype.removeWindowResizeEvent = function (handler) {
var events = this._windowResizeEvents;
var index = events.indexOf(handler);
@@ -123,6 +137,7 @@ GuiConnector.prototype.removeWindowResizeEvent = function (handler) {
* @param bigLogo
* {@link Boolean} value determining if we want to have big logo or
* small one
+ * @returns {string}
*/
GuiConnector.prototype.getLcsbLogoImg = function (bigLogo) {
if (bigLogo) {
@@ -135,18 +150,23 @@ GuiConnector.prototype.getLcsbLogoImg = function (bigLogo) {
/**
* Returns name of the file with image that should be presented when we are
* waiting for data to be loaded.
+ * @returns {string}
*/
GuiConnector.prototype.getLoadingImg = function () {
return "icons/ajax-loader.gif";
};
-
+/**
+ *
+ * @returns {string}
+ */
GuiConnector.prototype.getEmptyTileUrl = function () {
return "resources/images/empty_tile.png";
};
/**
* Returns home directory for images in the application.
+ * @returns {string}
*/
GuiConnector.prototype.getImgPrefix = function () {
return "resources/images/";
@@ -154,6 +174,9 @@ GuiConnector.prototype.getImgPrefix = function () {
/**
* Updates coordinates of the mouse in the browser.
+ *
+ * @param {number} x
+ * @param {number} y
*/
GuiConnector.prototype.updateMouseCoordinates = function (x, y) {
var self = returnThisOrSingleton(this);
@@ -161,6 +184,10 @@ GuiConnector.prototype.updateMouseCoordinates = function (x, y) {
self.yPos = y;
};
+/**
+ *
+ * @param {string} messageText
+ */
GuiConnector.prototype.showProcessing = function (messageText) {
var self = returnThisOrSingleton(this);
if (self._processingDialog === undefined) {
@@ -192,11 +219,19 @@ GuiConnector.prototype.showProcessing = function (messageText) {
$(self._processingDialog).dialog("open");
};
+/**
+ *
+ */
GuiConnector.prototype.hideProcessing = function () {
var self = returnThisOrSingleton(this);
$(self._processingDialog).dialog("close");
};
+/**
+ *
+ * @param {string} error
+ * @param {boolean} [redirectIfSecurityError]
+ */
GuiConnector.prototype.alert = function (error, redirectIfSecurityError) {
if (redirectIfSecurityError === undefined) {
redirectIfSecurityError = false;
@@ -224,6 +259,11 @@ GuiConnector.prototype.alert = function (error, redirectIfSecurityError) {
}
};
+/**
+ *
+ * @param {Error|string} error
+ * @returns {string}
+ */
GuiConnector.prototype.getErrorMessageForError = function (error) {
var message = error;
if (message instanceof SecurityError) {
@@ -243,6 +283,10 @@ GuiConnector.prototype.getErrorMessageForError = function (error) {
return message;
};
+/**
+ *
+ * @param {string} message
+ */
GuiConnector.prototype.info = function (message) {
var self = returnThisOrSingleton(this);
if (self._infoDialog === undefined) {
@@ -263,6 +307,10 @@ GuiConnector.prototype.info = function (message) {
};
+/**
+ *
+ * @param {{message:string, [title]:string}} params
+ */
GuiConnector.prototype.showConfirmationDialog = function (params) {
var message = params.message;
var title = params.title;
@@ -292,6 +340,9 @@ GuiConnector.prototype.showConfirmationDialog = function (params) {
});
};
+/**
+ *
+ */
GuiConnector.prototype.destroy = function () {
var self = returnThisOrSingleton(this);
@@ -315,6 +366,10 @@ GuiConnector.prototype.destroy = function () {
};
+/**
+ *
+ * @param {string} message
+ */
GuiConnector.prototype.warn = function (message) {
var self = GuiConnector;
logger.warn(message);
diff --git a/frontend-js/src/main/js/InvalidArgumentError.js b/frontend-js/src/main/js/InvalidArgumentError.js
index b016647977..41fb1e1140 100644
--- a/frontend-js/src/main/js/InvalidArgumentError.js
+++ b/frontend-js/src/main/js/InvalidArgumentError.js
@@ -4,6 +4,12 @@
var logger = require('./logger');
+/**
+ *
+ * @param {string} message
+ * @constructor
+ * @extends Error
+ */
function InvalidArgumentError(message) {
this.message = message;
this.stack = (new Error()).stack;
diff --git a/frontend-js/src/main/js/InvalidCredentialsError.js b/frontend-js/src/main/js/InvalidCredentialsError.js
index 7e5f85ce4f..ccbed75899 100644
--- a/frontend-js/src/main/js/InvalidCredentialsError.js
+++ b/frontend-js/src/main/js/InvalidCredentialsError.js
@@ -6,6 +6,12 @@ var logger = require('./logger');
var SecurityError = require("./SecurityError");
+/**
+ *
+ * @param {string} message
+ * @constructor
+ * @extends SecurityError
+ */
function InvalidCredentialsError(message) {
this.message = message;
this.stack = (new Error()).stack;
diff --git a/frontend-js/src/main/js/NetworkError.js b/frontend-js/src/main/js/NetworkError.js
index 0b693ae0ba..75cbb6f19b 100644
--- a/frontend-js/src/main/js/NetworkError.js
+++ b/frontend-js/src/main/js/NetworkError.js
@@ -5,6 +5,17 @@
// noinspection JSUnusedLocalSymbols
var logger = require('./logger');
+/**
+ *
+ * @param {string} message
+ * @param {Object} [connectionParams]
+ * @param {number} connectionParams.statusCode
+ * @param {string} connectionParams.url
+ * @param {string} connectionParams.content
+ *
+ * @constructor
+ * @extends Error
+ */
function NetworkError(message, connectionParams) {
this.message = message;
this.stack = (new Error()).stack;
diff --git a/frontend-js/src/main/js/ObjectWithListeners.js b/frontend-js/src/main/js/ObjectWithListeners.js
index c930048dd6..41b332c6d2 100644
--- a/frontend-js/src/main/js/ObjectWithListeners.js
+++ b/frontend-js/src/main/js/ObjectWithListeners.js
@@ -170,6 +170,11 @@ ObjectWithListeners.prototype.callListeners = function (type, arg) {
return Promise.all(promises);
};
+/**
+ *
+ * @param {string} type
+ * @returns {function[]}
+ */
ObjectWithListeners.prototype.getListeners = function (type) {
if (this._validListeners[type] === undefined) {
throw new Error("Unknown listener type: " + type);
diff --git a/frontend-js/src/main/js/SecurityError.js b/frontend-js/src/main/js/SecurityError.js
index c5755cafbf..e388bd04d4 100644
--- a/frontend-js/src/main/js/SecurityError.js
+++ b/frontend-js/src/main/js/SecurityError.js
@@ -4,6 +4,12 @@
var logger = require('./logger');
+/**
+ *
+ * @param {string} message
+ * @constructor
+ * @extends Error
+ */
function SecurityError(message) {
this.message = message;
this.stack = (new Error()).stack;
diff --git a/frontend-js/src/main/js/SessionData.js b/frontend-js/src/main/js/SessionData.js
index 30b8d32347..d09649faf3 100644
--- a/frontend-js/src/main/js/SessionData.js
+++ b/frontend-js/src/main/js/SessionData.js
@@ -9,6 +9,11 @@ var Cookies = require('js-cookie');
var logger = require('./logger');
+/**
+ *
+ * @param {Project} project
+ * @constructor
+ */
function SessionData(project) {
if (project === undefined) {
throw new Error("Project must be passed as an argument");
@@ -16,29 +21,55 @@ function SessionData(project) {
this.setProject(project);
}
-SessionData.prototype.setProject = function(project) {
+/**
+ *
+ * @param {Project} project
+ */
+SessionData.prototype.setProject = function (project) {
this._project = project;
};
-SessionData.prototype.getProject = function() {
+/**
+ *
+ * @returns {Project}
+ */
+SessionData.prototype.getProject = function () {
return this._project;
};
-SessionData.prototype.getProjectId = function() {
+/**
+ *
+ * @returns {string}
+ */
+SessionData.prototype.getProjectId = function () {
return this._project.getProjectId();
};
-SessionData.prototype.getShowComments = function() {
+/**
+ *
+ * @returns {boolean}
+ */
+SessionData.prototype.getShowComments = function () {
var key = this.getKey(SessionObjectType.SHOW_COMMENT);
return Cookies.get(key) === "true";
};
-SessionData.prototype.setSearchQuery = function(value) {
+/**
+ *
+ * @param {Object} value
+ */
+SessionData.prototype.setSearchQuery = function (value) {
var key = this.getKey(SessionObjectType.SEARCH_QUERY);
Cookies.set(key, JSON.stringify(value));
};
-SessionData.prototype.setQuery = function(param) {
+/**
+ *
+ * @param {Object} param
+ * @param {string} param.type
+ * @param {Object} param.query
+ */
+SessionData.prototype.setQuery = function (param) {
if (param.type === "drug") {
this.setDrugQuery(param.query);
} else if (param.type === "search") {
@@ -52,7 +83,11 @@ SessionData.prototype.setQuery = function(param) {
}
};
-SessionData.prototype.getSearchQuery = function() {
+/**
+ *
+ * @returns {any}
+ */
+SessionData.prototype.getSearchQuery = function () {
var key = this.getKey(SessionObjectType.SEARCH_QUERY);
var result = Cookies.get(key);
if (result !== undefined) {
@@ -61,12 +96,20 @@ SessionData.prototype.getSearchQuery = function() {
return result;
};
-SessionData.prototype.setDrugQuery = function(value) {
+/**
+ *
+ * @param {Object} value
+ */
+SessionData.prototype.setDrugQuery = function (value) {
var key = this.getKey(SessionObjectType.DRUG_QUERY);
Cookies.set(key, JSON.stringify(value));
};
-SessionData.prototype.getDrugQuery = function() {
+/**
+ *
+ * @returns {any}
+ */
+SessionData.prototype.getDrugQuery = function () {
var key = this.getKey(SessionObjectType.DRUG_QUERY);
var result = Cookies.get(key);
if (result !== undefined) {
@@ -75,12 +118,20 @@ SessionData.prototype.getDrugQuery = function() {
return result;
};
-SessionData.prototype.setMiRnaQuery = function(value) {
+/**
+ *
+ * @param {Object} value
+ */
+SessionData.prototype.setMiRnaQuery = function (value) {
var key = this.getKey(SessionObjectType.MI_RNA_QUERY);
Cookies.set(key, JSON.stringify(value));
};
-SessionData.prototype.getMiRnaQuery = function() {
+/**
+ *
+ * @returns {any}
+ */
+SessionData.prototype.getMiRnaQuery = function () {
var key = this.getKey(SessionObjectType.MI_RNA_QUERY);
var result = Cookies.get(key);
if (result !== undefined) {
@@ -89,12 +140,20 @@ SessionData.prototype.getMiRnaQuery = function() {
return result;
};
-SessionData.prototype.setChemicalQuery = function(value) {
+/**
+ *
+ * @param {Object} value
+ */
+SessionData.prototype.setChemicalQuery = function (value) {
var key = this.getKey(SessionObjectType.CHEMICAL_QUERY);
Cookies.set(key, JSON.stringify(value));
};
-SessionData.prototype.getChemicalQuery = function() {
+/**
+ *
+ * @returns {any}
+ */
+SessionData.prototype.getChemicalQuery = function () {
var key = this.getKey(SessionObjectType.CHEMICAL_QUERY);
var result = Cookies.get(key);
if (result !== undefined) {
@@ -103,22 +162,38 @@ SessionData.prototype.getChemicalQuery = function() {
return result;
};
-SessionData.prototype.setShowComments = function(value) {
+/**
+ *
+ * @param {boolean} value
+ */
+SessionData.prototype.setShowComments = function (value) {
var key = this.getKey(SessionObjectType.SHOW_COMMENT);
Cookies.set(key, value + "");
};
-SessionData.prototype.getSelectedBackgroundOverlay = function() {
+/**
+ *
+ * @returns {number}
+ */
+SessionData.prototype.getSelectedBackgroundOverlay = function () {
var key = this.getKey(SessionObjectType.SELECTED_BACKGROUND_OVERLAY);
return Cookies.get(key);
};
-SessionData.prototype.setSelectedBackgroundOverlay = function(value) {
+/**
+ *
+ * @param {number} value
+ */
+SessionData.prototype.setSelectedBackgroundOverlay = function (value) {
var key = this.getKey(SessionObjectType.SELECTED_BACKGROUND_OVERLAY);
Cookies.set(key, value + "");
};
-SessionData.prototype.getVisibleOverlays = function() {
+/**
+ *
+ * @returns {number[]}
+ */
+SessionData.prototype.getVisibleOverlays = function () {
var key = this.getKey(SessionObjectType.VISIBLE_OVERLAYS);
var value = Cookies.get(key);
if (value === undefined || value === "") {
@@ -129,7 +204,11 @@ SessionData.prototype.getVisibleOverlays = function() {
return value;
};
-SessionData.prototype.setVisibleOverlays = function(value) {
+/**
+ *
+ * @param {string} value
+ */
+SessionData.prototype.setVisibleOverlays = function (value) {
var key = this.getKey(SessionObjectType.VISIBLE_OVERLAYS);
Cookies.set(key, value + "");
};
@@ -139,8 +218,8 @@ SessionData.prototype.setVisibleOverlays = function(value) {
* @param {MapModel} model
* @param {number} value
*/
-SessionData.prototype.setZoomLevel = function(model, value) {
- var key = this.getKey(SessionObjectType.ZOOM_LEVEL, [ model.getId() ]);
+SessionData.prototype.setZoomLevel = function (model, value) {
+ var key = this.getKey(SessionObjectType.ZOOM_LEVEL, [model.getId()]);
Cookies.set(key, value + "");
};
@@ -149,8 +228,8 @@ SessionData.prototype.setZoomLevel = function(model, value) {
* @param {MapModel} model
* @returns {number}
*/
-SessionData.prototype.getZoomLevel = function(model) {
- var key = this.getKey(SessionObjectType.ZOOM_LEVEL, [ model.getId() ]);
+SessionData.prototype.getZoomLevel = function (model) {
+ var key = this.getKey(SessionObjectType.ZOOM_LEVEL, [model.getId()]);
var value = Cookies.get(key);
if (value !== undefined) {
value = parseInt(value);
@@ -158,7 +237,11 @@ SessionData.prototype.getZoomLevel = function(model) {
return value;
};
-SessionData.prototype.setToken = function(token) {
+/**
+ * TODO remove this method
+ * @param {string} token
+ */
+SessionData.prototype.setToken = function (token) {
var key = SessionObjectType.TOKEN;
if (token === undefined) {
Cookies.remove(key);
@@ -167,12 +250,20 @@ SessionData.prototype.setToken = function(token) {
}
};
-SessionData.prototype.getToken = function() {
+/**
+ * TODO remove this method
+ * @returns {string}
+ */
+SessionData.prototype.getToken = function () {
var key = SessionObjectType.TOKEN;
return Cookies.get(key);
};
-SessionData.prototype.setLogin = function(login) {
+/**
+ *
+ * @param {string} login
+ */
+SessionData.prototype.setLogin = function (login) {
var key = SessionObjectType.LOGIN;
if (login === undefined) {
Cookies.remove(key);
@@ -181,13 +272,22 @@ SessionData.prototype.setLogin = function(login) {
}
};
-SessionData.prototype.getLogin = function() {
+/**
+ *
+ * @returns {string}
+ */
+SessionData.prototype.getLogin = function () {
var key = SessionObjectType.LOGIN;
return Cookies.get(key);
};
-SessionData.prototype.setCenter = function(model, value) {
- var key = this.getKey(SessionObjectType.CENTER, [ model.getId() ]);
+/**
+ *
+ * @param {MapModel} model
+ * @param {Point} value
+ */
+SessionData.prototype.setCenter = function (model, value) {
+ var key = this.getKey(SessionObjectType.CENTER, [model.getId()]);
Cookies.set(key, value.x + "," + value.y);
};
@@ -196,8 +296,8 @@ SessionData.prototype.setCenter = function(model, value) {
* @param {MapModel} model
* @returns {Point}
*/
-SessionData.prototype.getCenter = function(model) {
- var key = this.getKey(SessionObjectType.CENTER, [ model.getId() ]);
+SessionData.prototype.getCenter = function (model) {
+ var key = this.getKey(SessionObjectType.CENTER, [model.getId()]);
var value = Cookies.get(key);
if (value !== undefined) {
var tmp = value.split(",");
@@ -212,7 +312,7 @@ SessionData.prototype.getCenter = function(model) {
* @param {Array} [args]
* @returns {string}
*/
-SessionData.prototype.getKey = function(type, args) {
+SessionData.prototype.getKey = function (type, args) {
if (type === undefined) {
throw new Error("Undefined type");
}
diff --git a/frontend-js/src/main/js/ValidationError.js b/frontend-js/src/main/js/ValidationError.js
index aaa83e2edf..2a1bec9469 100644
--- a/frontend-js/src/main/js/ValidationError.js
+++ b/frontend-js/src/main/js/ValidationError.js
@@ -4,6 +4,12 @@
var logger = require('./logger');
+/**
+ *
+ * @param {string} message
+ * @constructor
+ * @extends Error
+ */
function ValidationError(message) {
this.message = message;
this.stack = (new Error()).stack;
diff --git a/frontend-js/src/main/js/gui/AddOverlayDialog.js b/frontend-js/src/main/js/gui/AddOverlayDialog.js
index d4d8871d96..1754a7c1ed 100644
--- a/frontend-js/src/main/js/gui/AddOverlayDialog.js
+++ b/frontend-js/src/main/js/gui/AddOverlayDialog.js
@@ -120,6 +120,11 @@ AddOverlayDialog.prototype.createGui = function () {
self.getElement().appendChild(content);
};
+/**
+ *
+ * @param file
+ * @returns {Promise}
+ */
AddOverlayDialog.prototype.processFile = function (file) {
var self = this;
self.setFileContent(null);
@@ -172,6 +177,11 @@ AddOverlayDialog.prototype.processFile = function (file) {
}
};
+
+/**
+ *
+ * @param {string} fileContent
+ */
AddOverlayDialog.prototype.setFileContent = function (fileContent) {
if (typeof fileContent === 'string' || fileContent instanceof String) {
fileContent = new TextEncoder("UTF8").encode(fileContent);
@@ -180,6 +190,10 @@ AddOverlayDialog.prototype.setFileContent = function (fileContent) {
this._fileContent = fileContent;
};
+/**
+ *
+ * @returns {string|null}
+ */
AddOverlayDialog.prototype.getFileContent = function () {
var self = this;
var contentInput = $("[name='overlay-content']", self.getElement())[0];
@@ -205,7 +219,10 @@ AddOverlayDialog.prototype.init = function () {
return Promise.resolve();
};
-
+/**
+ *
+ * @returns {Promise}
+ */
AddOverlayDialog.prototype.addOverlay = function () {
var self = this;
var nameInput = $("[name='overlay-name']", self.getElement())[0];
@@ -250,6 +267,9 @@ AddOverlayDialog.prototype.destroy = function () {
return Promise.resolve();
};
+/**
+ *
+ */
AddOverlayDialog.prototype.open = function () {
var self = this;
var div = self.getElement();
diff --git a/frontend-js/src/main/js/gui/CommentDialog.js b/frontend-js/src/main/js/gui/CommentDialog.js
index 4a9dea6082..41bf2073ba 100644
--- a/frontend-js/src/main/js/gui/CommentDialog.js
+++ b/frontend-js/src/main/js/gui/CommentDialog.js
@@ -11,6 +11,19 @@ var Reaction = require('../map/data/Reaction');
var logger = require('../logger');
var Functions = require('../Functions');
+/**
+ *
+ * @param {Object} params
+ * @param {HTMLElement} params.element
+ * @param {CustomMap} params.customMap
+ * @param {Configuration} params.configuration
+ * @param {Project} params.project
+ * @param {ServerConnector} [params.serverConnector]
+ *
+ * @constructor
+ *
+ * @extends AbstractGuiElement
+ */
function CommentDialog(params) {
AbstractGuiElement.call(this, params);
var self = this;
@@ -28,6 +41,11 @@ CommentDialog.prototype.constructor = CommentDialog;
CommentDialog.GENERAL = "<General>";
+/**
+ *
+ * @param {HTMLElement} elements
+ * @returns {HTMLTableRowElement}
+ */
function createRow(elements) {
var row = document.createElement('tr');
for (var i = 0; i < elements.length; i++) {
@@ -38,6 +56,11 @@ function createRow(elements) {
return row;
}
+/**
+ *
+ * @param {IdentifiedElement[]} identifiedElements
+ * @returns {Promise}
+ */
CommentDialog.prototype.open = function (identifiedElements) {
var self = this;
self.setTypes([CommentDialog.GENERAL]);
@@ -66,6 +89,10 @@ CommentDialog.prototype.open = function (identifiedElements) {
});
};
+/**
+ *
+ * @private
+ */
CommentDialog.prototype._createGui = function () {
var self = this;
@@ -160,6 +187,11 @@ CommentDialog.prototype._createGui = function () {
detailDiv.innerHTML = text;
};
};
+
+/**
+ *
+ * @param {Array<BioEntity|string>} types
+ */
CommentDialog.prototype.setTypes = function (types) {
var typeOptions = this.getTypeOptions();
while (typeOptions.firstChild) {
@@ -185,14 +217,26 @@ CommentDialog.prototype.setTypes = function (types) {
typeOptions.onchange();
};
+/**
+ *
+ * @returns {Array<BioEntity|string>}
+ */
CommentDialog.prototype.getTypes = function () {
return this._types;
};
+/**
+ *
+ * @returns {BioEntity|string}
+ */
CommentDialog.prototype.getSelectedType = function () {
return this._types[this.getTypeOptions().value];
};
+/**
+ *
+ * @param {number} value
+ */
CommentDialog.prototype.setSelectedType = function (value) {
if (Functions.isInt(value)) {
this.getTypeOptions().value = value;
@@ -202,65 +246,138 @@ CommentDialog.prototype.setSelectedType = function (value) {
}
};
+/**
+ *
+ * @returns {HTMLElement}
+ */
CommentDialog.prototype.getTypeOptions = function () {
return this._typeOptions;
};
+
+/**
+ *
+ * @param {HTMLElement} typeOptions
+ */
CommentDialog.prototype.setTypeOptions = function (typeOptions) {
this._typeOptions = typeOptions;
};
+
+/**
+ *
+ * @param {HTMLElement} contentInput
+ */
CommentDialog.prototype.setContentInput = function (contentInput) {
this._contentInput = contentInput;
};
+
+/**
+ *
+ * @returns {HTMLElement}
+ */
CommentDialog.prototype.getContentInput = function () {
return this._contentInput;
};
+
+/**
+ *
+ * @param {HTMLElement} nameInput
+ */
CommentDialog.prototype.setNameInput = function (nameInput) {
this._nameInput = nameInput;
};
+
+/**
+ *
+ * @returns {HTMLElement}
+ */
CommentDialog.prototype.getNameInput = function () {
return this._nameInput;
};
+
+/**
+ *
+ * @param {HTMLElement} emailInput
+ */
CommentDialog.prototype.setEmailInput = function (emailInput) {
this._emailInput = emailInput;
};
+
+/**
+ *
+ * @returns {HTMLElement}
+ */
CommentDialog.prototype.getEmailInput = function () {
return this._emailInput;
};
+
+/**
+ *
+ * @param {HTMLElement} pinnedCheckbox
+ */
CommentDialog.prototype.setPinnedCheckbox = function (pinnedCheckbox) {
this._pinnedCheckbox = pinnedCheckbox;
};
+/**
+ *
+ * @returns {HTMLElement}
+ */
CommentDialog.prototype.getPinnedCheckbox = function () {
return this._pinnedCheckbox;
};
-CommentDialog.prototype.getTypes = function () {
- return this._types;
-};
-
+/**
+ *
+ * @param {string} name
+ */
CommentDialog.prototype.setName = function (name) {
this.getNameInput().value = name;
};
+/**
+ *
+ * @returns {string}
+ */
CommentDialog.prototype.getName = function () {
return this.getNameInput().value;
};
+/**
+ *
+ * @returns {string}
+ */
CommentDialog.prototype.getEmail = function () {
return this.getEmailInput().value;
};
+/**
+ *
+ * @param {string} email
+ */
CommentDialog.prototype.setEmail = function (email) {
this.getEmailInput().value = email;
};
+/**
+ *
+ * @returns {string}
+ */
CommentDialog.prototype.getContent = function () {
return this.getContentInput().value;
};
+/**
+ *
+ * @returns {boolean}
+ */
CommentDialog.prototype.isPinned = function () {
return this.getPinnedCheckbox().checked;
};
+
+/**
+ *
+ * @returns {number | string}
+ */
CommentDialog.prototype.getSelectedTypeId = function () {
var selected = this.getSelectedType();
if (selected instanceof Alias) {
@@ -272,6 +389,10 @@ CommentDialog.prototype.getSelectedTypeId = function () {
}
};
+/**
+ *
+ * @returns {string}
+ */
CommentDialog.prototype.getSelectedTypeClass = function () {
var selected = this.getSelectedType();
if (selected instanceof Alias) {
@@ -310,6 +431,9 @@ CommentDialog.prototype.addComment = function () {
});
};
+/**
+ *
+ */
CommentDialog.prototype.destroy = function () {
$(this.getElement()).dialog("destroy");
};
diff --git a/frontend-js/src/main/js/gui/ContextMenu.js b/frontend-js/src/main/js/gui/ContextMenu.js
index f8fdbc8c05..6437fe197c 100644
--- a/frontend-js/src/main/js/gui/ContextMenu.js
+++ b/frontend-js/src/main/js/gui/ContextMenu.js
@@ -12,6 +12,19 @@ var logger = require('../logger');
var MARGIN = 5;
+/**
+ *
+ * @param {Object} params
+ * @param {HTMLElement} params.element
+ * @param {CustomMap} params.customMap
+ * @param {Configuration} params.configuration
+ * @param {Project} params.project
+ * @param {ServerConnector} [params.serverConnector]
+ *
+ * @constructor
+ *
+ * @extends AbstractGuiElement
+ */
function ContextMenu(params) {
AbstractGuiElement.call(this, params);
var self = this;
@@ -42,12 +55,21 @@ function ContextMenu(params) {
ContextMenu.prototype = Object.create(AbstractGuiElement.prototype);
ContextMenu.prototype.constructor = ContextMenu;
+/**
+ *
+ */
ContextMenu.prototype.destroy = function () {
var self = this;
$(document).off('click', self._documentClickListener);
$(document).off('touchstart', self._documentClickListener);
};
+/**
+ *
+ * @param {string|SubMenu} name
+ * @param {function} [handler]
+ * @param {boolean} [disabled]
+ */
ContextMenu.prototype.addOption = function (name, handler, disabled) {
if (!disabled) disabled = false;
var self = this;
@@ -109,6 +131,10 @@ ContextMenu.prototype.open = function (x, y, timestamp) {
});
};
+/**
+ *
+ * @param {number} timestamp
+ */
ContextMenu.prototype.hide = function (timestamp) {
var self = this;
if (self._handledTimeStamp < timestamp) {
@@ -117,6 +143,11 @@ ContextMenu.prototype.hide = function (timestamp) {
}
};
+/**
+ *
+ * @param {DataOverlay[]} dataOverlays
+ * @returns {number[]}
+ */
function extractDataOverlayIds(dataOverlays) {
var ids = [];
for (var i = 0; i < dataOverlays.length; i++) {
@@ -125,6 +156,10 @@ function extractDataOverlayIds(dataOverlays) {
return ids;
}
+/**
+ *
+ * @returns {Promise}
+ */
ContextMenu.prototype.createExportAsImageSubmenu = function () {
var self = this;
return self.getMap().getServerConnector().getImageConverters().then(function (converters) {
@@ -160,6 +195,10 @@ ContextMenu.prototype.createExportAsImageSubmenu = function () {
});
};
+/**
+ *
+ * @returns {Promise}
+ */
ContextMenu.prototype.createExportAsModelSubmenu = function () {
var self = this;
return self.getMap().getServerConnector().getModelConverters().then(function (converters) {
diff --git a/frontend-js/src/main/js/gui/GuiMessageError.js b/frontend-js/src/main/js/gui/GuiMessageError.js
index 9cb6b8367a..e978ff15b3 100644
--- a/frontend-js/src/main/js/gui/GuiMessageError.js
+++ b/frontend-js/src/main/js/gui/GuiMessageError.js
@@ -4,6 +4,12 @@
var logger = require('../logger');
+/**
+ *
+ * @param {string} message
+ * @constructor
+ * @extends {Error}
+ */
function GuiMessageError(message) {
this.message = message;
this.stack = (new Error()).stack;
diff --git a/frontend-js/src/main/js/gui/Header.js b/frontend-js/src/main/js/gui/Header.js
index 2e2eeab613..c41db05d06 100644
--- a/frontend-js/src/main/js/gui/Header.js
+++ b/frontend-js/src/main/js/gui/Header.js
@@ -13,6 +13,19 @@ var Promise = require("bluebird");
var logger = require('../logger');
var xss = require('xss');
+/**
+ *
+ * @param {Object} params
+ * @param {HTMLElement} params.element
+ * @param {CustomMap} params.customMap
+ * @param {Configuration} params.configuration
+ * @param {Project} params.project
+ * @param {ServerConnector} [params.serverConnector]
+ *
+ * @constructor
+ *
+ * @extends AbstractGuiElement
+ */
function Header(params) {
AbstractGuiElement.call(this, params);
var self = this;
@@ -31,6 +44,13 @@ function Header(params) {
Header.prototype = Object.create(AbstractGuiElement.prototype);
Header.prototype.constructor = Header;
+/**
+ *
+ * @param {Object} guiParams
+ * @param {boolean} guiParams.adminLink
+ * @param {boolean} guiParams.optionsMenu
+ * @private
+ */
Header.prototype._createHeaderGui = function (guiParams) {
var self = this;
self.getElement().className = "minerva-header";
@@ -103,10 +123,19 @@ Header.prototype._createHeaderGui = function (guiParams) {
self.getElement().appendChild(homeLink);
};
+/**
+ *
+ * @param {string} message
+ */
Header.prototype.addLoadMessage = function (message) {
var self = this;
self._loadMessages.push(message);
};
+
+/**
+ *
+ * @param {string} message
+ */
Header.prototype.removeLoadMessage = function (message) {
var self = this;
var index = self._loadMessages.indexOf(message);
@@ -117,6 +146,9 @@ Header.prototype.removeLoadMessage = function (message) {
}
};
+/**
+ * return {Promise}
+ */
Header.prototype.init = function () {
var self = this;
return new Promise(function (resolve) {
@@ -143,6 +175,9 @@ Header.prototype.init = function () {
});
};
+/**
+ *
+ */
Header.prototype.destroy = function () {
var self = this;
if (self._onDataLoadStart) {
@@ -154,6 +189,10 @@ Header.prototype.destroy = function () {
}
};
+/**
+ *
+ * @param {PluginManager} pluginManager
+ */
Header.prototype.setPluginManager = function (pluginManager) {
var self = this;
self._pluginManager = pluginManager;
@@ -162,6 +201,10 @@ Header.prototype.setPluginManager = function (pluginManager) {
}
};
+/**
+ *
+ * @returns {PluginManager}
+ */
Header.prototype.getPluginManager = function () {
return this._pluginManager;
};
diff --git a/frontend-js/src/main/js/gui/Legend.js b/frontend-js/src/main/js/gui/Legend.js
index be280e8225..6be26eeed2 100644
--- a/frontend-js/src/main/js/gui/Legend.js
+++ b/frontend-js/src/main/js/gui/Legend.js
@@ -8,6 +8,18 @@ var PanelControlElementType = require('./PanelControlElementType');
// noinspection JSUnusedLocalSymbols
var logger = require('../logger');
+/**
+ *
+ * @param {Object} params
+ * @param {HTMLElement} params.element
+ * @param {CustomMap} params.customMap
+ * @param {Configuration} params.configuration
+ * @param {Project} params.project
+ * @param {ServerConnector} [params.serverConnector]
+ *
+ * @constructor
+ * @extends AbstractGuiElement
+ */
function Legend(params) {
AbstractGuiElement.call(this, params);
@@ -17,6 +29,10 @@ function Legend(params) {
Legend.prototype = Object.create(AbstractGuiElement.prototype);
Legend.prototype.constructor = Legend;
+/**
+ *
+ * @private
+ */
Legend.prototype._initializeGui = function () {
var self = this;
@@ -69,9 +85,16 @@ Legend.prototype._initializeGui = function () {
legendDiv.appendChild(rightButton);
};
+/**
+ *
+ */
Legend.prototype.hide = function () {
this.getElement().style.display = "none";
};
+
+/**
+ *
+ */
Legend.prototype.show = function () {
var maxZIndex = Math.max.apply(null,
$.map($('body *'), function (e) {
@@ -84,6 +107,12 @@ Legend.prototype.show = function () {
$(this.getElement()).css('z-index', maxZIndex + 1);
};
+/**
+ *
+ * @param {string} file
+ * @param {number} index
+ * @returns {HTMLLIElement}
+ */
function createLegendIndicator(file, index) {
var result = document.createElement("li");
result.setAttribute("data-target", "legend");
@@ -94,6 +123,12 @@ function createLegendIndicator(file, index) {
return result;
}
+/**
+ *
+ * @param {string} file
+ * @param {number} index
+ * @returns {HTMLDivElement}
+ */
function createLegendSlide(file, index) {
var result = document.createElement("div");
if (index === 0) {
@@ -107,6 +142,11 @@ function createLegendSlide(file, index) {
return result;
}
+/**
+ *
+ * @param {string[]}legendFiles
+ * @returns {Promise<string[]>}
+ */
function getValidLegendFiles(legendFiles) {
var result = [];
@@ -130,6 +170,10 @@ function getValidLegendFiles(legendFiles) {
});
}
+/**
+ *
+ * @returns {Promise}
+ */
Legend.prototype.init = function () {
var self = this;
var element = self.getElement();
diff --git a/frontend-js/src/main/js/gui/LoginDialog.js b/frontend-js/src/main/js/gui/LoginDialog.js
index a32a49e44f..ab627c505d 100644
--- a/frontend-js/src/main/js/gui/LoginDialog.js
+++ b/frontend-js/src/main/js/gui/LoginDialog.js
@@ -11,19 +11,31 @@ var ConfigurationType = require("../ConfigurationType");
var Functions = require('../Functions');
var logger = require('../logger');
+/**
+ *
+ * @param {Object} params
+ * @param {HTMLElement} params.element
+ * @param {CustomMap} params.customMap
+ * @param {Configuration} params.configuration
+ * @param {Project} params.project
+ * @param {ServerConnector} [params.serverConnector]
+ *
+ * @constructor
+ * @extends AbstractGuiElement
+ */
function LoginDialog(params) {
AbstractGuiElement.call(this, params);
var self = this;
self._createLoginTab();
var loginButton = self.getControlElement(PanelControlElementType.USER_TAB_LOGIN_BUTTON);
- loginButton.onclick = function() {
+ loginButton.onclick = function () {
var login = self.getControlElement(PanelControlElementType.USER_TAB_LOGIN_INPUT_TEXT).value;
var password = self.getControlElement(PanelControlElementType.USER_TAB_PASSWORD_INPUT_TEXT).value;
- return ServerConnector.login(login, password).then(function() {
+ return ServerConnector.login(login, password).then(function () {
window.location.reload(false);
- }).then(null, function(error) {
+ }).then(null, function (error) {
if (error instanceof InvalidCredentialsError) {
GuiConnector.alert("invalid credentials");
} else {
@@ -37,6 +49,11 @@ function LoginDialog(params) {
LoginDialog.prototype = Object.create(AbstractGuiElement.prototype);
LoginDialog.prototype.constructor = LoginDialog;
+/**
+ *
+ * @param {HTMLElement[]} elements
+ * @returns {HTMLElement}
+ */
LoginDialog.prototype.createTableRow = function (elements) {
var row = Functions.createElement({
type: "div",
@@ -45,8 +62,8 @@ LoginDialog.prototype.createTableRow = function (elements) {
for (var i = 0; i < elements.length; i++) {
var cell = Functions.createElement({
- type : "div",
- style : "display: table-cell;"
+ type: "div",
+ style: "display: table-cell;"
});
cell.appendChild(elements[i]);
row.appendChild(cell);
@@ -54,6 +71,10 @@ LoginDialog.prototype.createTableRow = function (elements) {
return row;
};
+/**
+ *
+ * @private
+ */
LoginDialog.prototype._createLoginTab = function () {
var self = this;
@@ -114,6 +135,10 @@ LoginDialog.prototype._createLoginTab = function () {
};
+/**
+ *
+ * @returns {Promise}
+ */
LoginDialog.prototype.init = function () {
var self = this;
return ServerConnector.getConfigurationParam(ConfigurationType.REQUEST_ACCOUNT_EMAIL).then(function (value) {
@@ -122,6 +147,9 @@ LoginDialog.prototype.init = function () {
});
};
+/**
+ *
+ */
LoginDialog.prototype.open = function () {
var self = this;
var div = self.getElement();
@@ -136,6 +164,9 @@ LoginDialog.prototype.open = function () {
$(div).dialog("open");
};
+/**
+ *
+ */
LoginDialog.prototype.destroy = function () {
var self = this;
if ($(self.getElement()).hasClass("ui-dialog-content")) {
diff --git a/frontend-js/src/main/js/gui/MapContextMenu.js b/frontend-js/src/main/js/gui/MapContextMenu.js
index 048e16d10b..1bc7ba8719 100644
--- a/frontend-js/src/main/js/gui/MapContextMenu.js
+++ b/frontend-js/src/main/js/gui/MapContextMenu.js
@@ -6,6 +6,19 @@ var ContextMenu = require('./ContextMenu');
var logger = require('../logger');
+/**
+ *
+ * @param {Object} params
+ * @param {HTMLElement} params.element
+ * @param {CustomMap} params.customMap
+ * @param {Configuration} params.configuration
+ * @param {Project} params.project
+ * @param {ServerConnector} [params.serverConnector]
+ *
+ * @constructor
+ *
+ * @extends ContextMenu
+ */
function MapContextMenu(params) {
ContextMenu.call(this, params);
var self = this;
@@ -17,7 +30,10 @@ function MapContextMenu(params) {
MapContextMenu.prototype = Object.create(ContextMenu.prototype);
MapContextMenu.prototype.constructor = MapContextMenu;
-
+/**
+ *
+ * @private
+ */
MapContextMenu.prototype._createMapContextMenuGui = function() {
var self = this;
self.addOption("Add comment", function() {
@@ -28,6 +44,10 @@ MapContextMenu.prototype._createMapContextMenuGui = function() {
});
};
+/**
+ *
+ * @returns {Promise}
+ */
MapContextMenu.prototype.init = function() {
var self = this;
return self.createExportAsImageSubmenu().then(function(submenu){
@@ -38,10 +58,18 @@ MapContextMenu.prototype.init = function() {
});
};
+/**
+ *
+ * @param {MolArt} molArt
+ */
MapContextMenu.prototype.setMolArt = function(molArt){
this._molArt = molArt;
};
+/**
+ *
+ * @returns {MolArt}
+ */
MapContextMenu.prototype.getMolArt = function(){
return this._molArt;
};
diff --git a/frontend-js/src/main/js/gui/OptionsMenu.js b/frontend-js/src/main/js/gui/OptionsMenu.js
index 178fa188ae..03b1bec4b4 100644
--- a/frontend-js/src/main/js/gui/OptionsMenu.js
+++ b/frontend-js/src/main/js/gui/OptionsMenu.js
@@ -4,6 +4,19 @@ var ContextMenu = require('./ContextMenu');
var PluginDialog = require('./PluginDialog');
var Promise = require('bluebird');
+/**
+ *
+ * @param {Object} params
+ * @param {HTMLElement} params.element
+ * @param {CustomMap} params.customMap
+ * @param {Configuration} params.configuration
+ * @param {Project} params.project
+ * @param {ServerConnector} [params.serverConnector]
+ *
+ * @constructor
+ *
+ * @extends ContextMenu
+ */
function OptionsMenu(params) {
ContextMenu.call(this, params);
var self = this;
@@ -15,6 +28,10 @@ OptionsMenu.prototype = Object.create(ContextMenu.prototype);
OptionsMenu.prototype.constructor = OptionsMenu;
+/**
+ *
+ * @private
+ */
OptionsMenu.prototype._createMenuGui = function () {
var self = this;
self.addOption("Plugins", function () {
@@ -33,9 +50,18 @@ OptionsMenu.prototype._createMenuGui = function () {
});
};
+/**
+ *
+ * @returns {Promise}
+ */
OptionsMenu.prototype.init = function () {
return Promise.resolve();
};
+
+/**
+ *
+ * @returns {Promise}
+ */
OptionsMenu.prototype.destroy = function () {
var self = this;
var promises = [];
@@ -45,10 +71,18 @@ OptionsMenu.prototype.destroy = function () {
return Promise.all(promises);
};
+/**
+ *
+ * @param {PluginManager} pluginManager
+ */
OptionsMenu.prototype.setPluginManager = function (pluginManager) {
this._pluginManager = pluginManager;
};
+/**
+ *
+ * @returns {PluginManager}
+ */
OptionsMenu.prototype.getPluginManager = function () {
return this._pluginManager;
};
diff --git a/frontend-js/src/main/js/gui/OverviewDialog.js b/frontend-js/src/main/js/gui/OverviewDialog.js
index 864743375a..6dabef39ae 100644
--- a/frontend-js/src/main/js/gui/OverviewDialog.js
+++ b/frontend-js/src/main/js/gui/OverviewDialog.js
@@ -9,6 +9,19 @@ var Point = require('../map/canvas/Point');
var functions = require('../Functions');
var logger = require('../logger');
+
+/**
+ *
+ * @param {Object} params
+ * @param {HTMLElement} params.element
+ * @param {CustomMap} params.customMap
+ * @param {Configuration} params.configuration
+ * @param {Project} params.project
+ * @param {ServerConnector} [params.serverConnector]
+ *
+ * @constructor
+ * @extends AbstractGuiElement
+ */
function OverviewDialog(params) {
AbstractGuiElement.call(this, params);
var self = this;
@@ -21,6 +34,10 @@ function OverviewDialog(params) {
OverviewDialog.prototype = Object.create(AbstractGuiElement.prototype);
OverviewDialog.prototype.constructor = OverviewDialog;
+/**
+ *
+ * @param {number} overviewImageId
+ */
OverviewDialog.prototype.showOverview = function (overviewImageId) {
var self = this;
var map = self.getMap();
@@ -174,6 +191,14 @@ OverviewDialog.prototype.showOverview = function (overviewImageId) {
$(self.getElement()).dialog("open");
};
+/**
+ *
+ * @param {Object} link
+ * @param {string} link.type
+ * @param {number} [link.modelLinkId]
+ * @param {number} [link.imageLinkId]
+ * @returns {Promise}
+ */
OverviewDialog.prototype.openLink = function (link) {
var self = this;
var map = self.getMap();
@@ -201,6 +226,11 @@ OverviewDialog.prototype.openLink = function (link) {
}
};
+/**
+ *
+ * @param {HTMLCanvasElement} canvas
+ * @param {number} ratio
+ */
OverviewDialog.prototype.drawClickableShapes = function (canvas, ratio) {
var ctx = canvas.getContext("2d");
// clear canvas
@@ -220,6 +250,9 @@ OverviewDialog.prototype.drawClickableShapes = function (canvas, ratio) {
}
};
+/**
+ *
+ */
OverviewDialog.prototype.destroy = function () {
$(this.getElement()).dialog("destroy");
};
diff --git a/frontend-js/src/main/js/gui/Panel.js b/frontend-js/src/main/js/gui/Panel.js
index 309fc1c674..f9208296ff 100644
--- a/frontend-js/src/main/js/gui/Panel.js
+++ b/frontend-js/src/main/js/gui/Panel.js
@@ -67,12 +67,19 @@ function Panel(params) {
Panel.prototype = Object.create(AbstractGuiElement.prototype);
Panel.prototype.constructor = Panel;
+/**
+ *
+ */
Panel.prototype.createHelpButton = function () {
var self = this;
var helpTipButton = self.getGuiUtils().createHelpButton(self.getHelpTip());
self.getElement().appendChild(helpTipButton);
};
+/**
+ *
+ * @param {string} message
+ */
Panel.prototype.disablePanel = function (message) {
var self = this;
@@ -90,19 +97,36 @@ Panel.prototype.disablePanel = function (message) {
$(self.getElement()).prepend(hideReasonDiv);
};
+/**
+ *
+ * @returns {boolean}
+ */
Panel.prototype.isDisabled = function () {
var self = this;
var searchQueryElement = self.getControlElement(PanelControlElementType.SEARCH_DIV);
return searchQueryElement.style.visibility === "hidden";
};
+
+/**
+ *
+ * @param {CustomMap} map
+ */
Panel.prototype.setMap = function (map) {
this._map = map;
};
+/**
+ *
+ * @param {string} panelName
+ */
Panel.prototype.setPanelName = function (panelName) {
this._panelName = panelName;
};
+/**
+ *
+ * @returns {string}
+ */
Panel.prototype.getPanelName = function () {
return this._panelName;
};
@@ -126,6 +150,12 @@ Panel.prototype.getElement = function () {
return this._element;
};
+/**
+ *
+ * @param {HTMLElement} element
+ * @param {string} name
+ * @returns {HTMLElement}
+ */
Panel.prototype.getElementByName = function (element, name) {
if (element !== undefined) {
if (element.getAttribute("name") === name) {
@@ -143,6 +173,11 @@ Panel.prototype.getElementByName = function (element, name) {
return undefined;
};
+/**
+ *
+ * @param {string} id
+ * @returns {HTMLElement}
+ */
Panel.prototype.getDialogDiv = function (id) {
var dialogs = this.getElementByName(this.getElement(), "dialogs");
if (dialogs === undefined) {
@@ -171,6 +206,11 @@ Panel.prototype.getDialogDiv = function (id) {
return dialogDiv;
};
+/**
+ *
+ * @param {HTMLElement} div
+ * @param params
+ */
Panel.prototype.assignDialogOptions = function (div, params) {
var dialog = $(div);
for (var key in params) {
@@ -194,6 +234,11 @@ Panel.prototype.assignDialogOptions = function (div, params) {
}
};
+/**
+ *
+ * @param {string} content
+ * @param options
+ */
Panel.prototype.openDialog = function (content, options) {
if (options === undefined) {
options = {};
@@ -225,14 +270,25 @@ Panel.prototype.openDialog = function (content, options) {
$(div).dialog("open");
};
+/**
+ *
+ */
Panel.prototype.init = function () {
throw new Error(this.getPanelName() + " Not implemented");
};
+/**
+ *
+ * @param {AbstractGuiElement} parent
+ */
Panel.prototype.setParent = function (parent) {
this._parent = parent;
};
+/**
+ *
+ * @returns {AbstractGuiElement}
+ */
Panel.prototype.getParent = function () {
return this._parent;
};
@@ -253,6 +309,10 @@ Panel.prototype.getGuiUtils = function () {
return this._guiUtils;
};
+/**
+ *
+ * @param {string} helpTip
+ */
Panel.prototype.setHelpTip = function (helpTip) {
if (this._helpTip === undefined && helpTip !== undefined) {
this._helpTip = helpTip;
@@ -260,10 +320,17 @@ Panel.prototype.setHelpTip = function (helpTip) {
}
};
+/**
+ *
+ * @returns {string}
+ */
Panel.prototype.getHelpTip = function () {
return this._helpTip;
};
+/**
+ *
+ */
Panel.prototype.onresize = function () {
var self = this;
var footerPosition = window.innerHeight;
@@ -295,6 +362,9 @@ Panel.prototype.onresize = function () {
};
+/**
+ *
+ */
Panel.prototype.destroy = function () {
for (var id in this._dialogs) {
if (this._dialogs.hasOwnProperty(id)) {
diff --git a/frontend-js/src/main/js/gui/PluginDialog.js b/frontend-js/src/main/js/gui/PluginDialog.js
index 0837775528..572c5c6c11 100644
--- a/frontend-js/src/main/js/gui/PluginDialog.js
+++ b/frontend-js/src/main/js/gui/PluginDialog.js
@@ -5,6 +5,19 @@ var GuiUtils = require('./leftPanel/GuiUtils');
var Functions = require('../Functions');
+/**
+ *
+ * @param {Object} params
+ * @param {HTMLElement} params.element
+ * @param {CustomMap} params.customMap
+ * @param {Configuration} params.configuration
+ * @param {Project} params.project
+ * @param {ServerConnector} [params.serverConnector]
+ *
+ * @constructor
+ *
+ * @extends AbstractGuiElement
+ */
function PluginDialog(params) {
AbstractGuiElement.call(this, params);
var self = this;
@@ -15,6 +28,10 @@ function PluginDialog(params) {
PluginDialog.prototype = Object.create(AbstractGuiElement.prototype);
PluginDialog.prototype.constructor = PluginDialog;
+/**
+ *
+ * @private
+ */
PluginDialog.prototype._createPluginGui = function () {
var self = this;
var guiUtils = new GuiUtils();
@@ -112,6 +129,10 @@ PluginDialog.prototype._createPluginGui = function () {
}
};
+/**
+ *
+ * @returns {Promise}
+ */
PluginDialog.prototype.init = function () {
var self = this;
return ServerConnector.getConfiguration().then(function (configuration) {
@@ -123,6 +144,9 @@ PluginDialog.prototype.init = function () {
});
};
+/**
+ *
+ */
PluginDialog.prototype.open = function () {
var self = this;
self._createPluginGui();
@@ -138,11 +162,18 @@ PluginDialog.prototype.open = function () {
$(div).dialog('option', 'title', 'PLUGINS');
$(div).dialog("open");
};
+
+/**
+ *
+ */
PluginDialog.prototype.close = function () {
var self = this;
$(self.getElement()).dialog("close");
};
+/**
+ *
+ */
PluginDialog.prototype.destroy = function () {
var self = this;
var div = self.getElement();
@@ -151,10 +182,18 @@ PluginDialog.prototype.destroy = function () {
}
};
+/**
+ *
+ * @param {PluginManager} pluginManager
+ */
PluginDialog.prototype.setPluginManager = function (pluginManager) {
this._pluginManager = pluginManager;
};
+/**
+ *
+ * @returns {PluginManager}
+ */
PluginDialog.prototype.getPluginManager = function () {
return this._pluginManager;
};
diff --git a/frontend-js/src/main/js/gui/SelectionContextMenu.js b/frontend-js/src/main/js/gui/SelectionContextMenu.js
index 1c22528851..86faf78f93 100644
--- a/frontend-js/src/main/js/gui/SelectionContextMenu.js
+++ b/frontend-js/src/main/js/gui/SelectionContextMenu.js
@@ -6,6 +6,19 @@ var ContextMenu = require('./ContextMenu');
var logger = require('../logger');
+/**
+ *
+ * @param {Object} params
+ * @param {HTMLElement} params.element
+ * @param {CustomMap} params.customMap
+ * @param {Configuration} params.configuration
+ * @param {Project} params.project
+ * @param {ServerConnector} [params.serverConnector]
+ *
+ * @constructor
+ *
+ * @extends ContextMenu
+ */
function SelectionContextMenu(params) {
ContextMenu.call(this, params);
var self = this;
@@ -16,6 +29,10 @@ function SelectionContextMenu(params) {
SelectionContextMenu.prototype = Object.create(ContextMenu.prototype);
SelectionContextMenu.prototype.constructor = SelectionContextMenu;
+/**
+ *
+ * @returns {Promise}
+ */
SelectionContextMenu.prototype.init = function () {
var self = this;
return self.createExportAsImageSubmenu().then(function (submenu) {
@@ -26,6 +43,10 @@ SelectionContextMenu.prototype.init = function () {
});
};
+/**
+ *
+ * @private
+ */
SelectionContextMenu.prototype._createSelectionContextMenuGui = function () {
var self = this;
self.addOption("Remove Selection", function () {
diff --git a/frontend-js/src/main/js/gui/admin/AbstractAnnotatorsDialog.js b/frontend-js/src/main/js/gui/admin/AbstractAnnotatorsDialog.js
index 275de12a40..d13c51e060 100644
--- a/frontend-js/src/main/js/gui/admin/AbstractAnnotatorsDialog.js
+++ b/frontend-js/src/main/js/gui/admin/AbstractAnnotatorsDialog.js
@@ -7,6 +7,18 @@ var AbstractGuiElement = require('../AbstractGuiElement');
// noinspection JSUnusedLocalSymbols
var logger = require('../../logger');
+/**
+ *
+ * @param {Object} params
+ * @param {HTMLElement} params.element
+ * @param {CustomMap} [params.customMap]
+ * @param {Configuration} params.configuration
+ * @param {Project} [params.project]
+ * @param {ServerConnector} [params.serverConnector]
+ *
+ * @constructor
+ * @extends AbstractGuiElement
+ */
function AbstractAnnotatorsDialog(params) {
AbstractGuiElement.call(this, params);
}
diff --git a/frontend-js/src/main/js/gui/admin/ChooseAnnotatorsDialog.js b/frontend-js/src/main/js/gui/admin/ChooseAnnotatorsDialog.js
index 63bc240de4..a43363dbea 100644
--- a/frontend-js/src/main/js/gui/admin/ChooseAnnotatorsDialog.js
+++ b/frontend-js/src/main/js/gui/admin/ChooseAnnotatorsDialog.js
@@ -11,6 +11,18 @@ var Functions = require('../../Functions');
// noinspection JSUnusedLocalSymbols
var logger = require('../../logger');
+/**
+ *
+ * @param {Object} params
+ * @param {HTMLElement} params.element
+ * @param {CustomMap} [params.customMap]
+ * @param {Configuration} params.configuration
+ * @param {Project} [params.project]
+ * @param {ServerConnector} [params.serverConnector]
+ *
+ * @constructor
+ * @extends AbstractAnnotatorsDialog
+ */
function ChooseAnnotatorsDialog(params) {
AbstractAnnotatorsDialog.call(this, params);
var self = this;
@@ -20,6 +32,9 @@ function ChooseAnnotatorsDialog(params) {
ChooseAnnotatorsDialog.prototype = Object.create(AbstractAnnotatorsDialog.prototype);
ChooseAnnotatorsDialog.prototype.constructor = ChooseAnnotatorsDialog;
+/**
+ *
+ */
ChooseAnnotatorsDialog.prototype.createGui = function () {
var self = this;
var content = Functions.createElement({
@@ -44,6 +59,12 @@ ChooseAnnotatorsDialog.prototype.createGui = function () {
self.getElement().appendChild(content);
};
+/**
+ *
+ * @param {HTMLElement} element
+ * @param {User} user
+ * @returns {Promise}
+ */
function onChangeParameterValue(element, user) {
var name = $(element).siblings(".minerva-annotator-param-name")[0].childNodes[0].nodeValue;
var annotatorClassName = $(element).parent().parent().attr('name');
@@ -59,6 +80,12 @@ function onChangeParameterValue(element, user) {
return ServerConnector.updateUserPreferences({user: user, preferences: data}).then(null, GuiConnector.alert);
}
+/**
+ *
+ * @param {BioEntityType[][]} elementTypes
+ * @param {string[]} selectedAnnotators
+ * @returns {Promise}
+ */
ChooseAnnotatorsDialog.prototype.saveAnnotatorsInfo = function (elementTypes, selectedAnnotators) {
selectedAnnotators = selectedAnnotators.slice();
return ServerConnector.getLoggedUser().then(function (user) {
@@ -81,6 +108,11 @@ ChooseAnnotatorsDialog.prototype.saveAnnotatorsInfo = function (elementTypes, se
}).catch(GuiConnector.alert);
};
+/**
+ *
+ * @param {BioEntityTypeTreeNode} elementType
+ * @returns {Promise}
+ */
ChooseAnnotatorsDialog.prototype.setElementType = function (elementType) {
var self = this;
@@ -313,6 +345,10 @@ ChooseAnnotatorsDialog.prototype.setElementType = function (elementType) {
};
+/**
+ *
+ * @returns {Promise}
+ */
ChooseAnnotatorsDialog.prototype.init = function () {
var self = this;
return ServerConnector.getConfiguration().then(function (configuration) {
@@ -334,10 +370,16 @@ ChooseAnnotatorsDialog.prototype.init = function () {
});
};
+/**
+ *
+ */
ChooseAnnotatorsDialog.prototype.destroy = function () {
$(this.getElement()).dialog("destroy");
};
+/**
+ *
+ */
ChooseAnnotatorsDialog.prototype.open = function () {
var self = this;
var div = self.getElement();
diff --git a/frontend-js/src/main/js/gui/admin/CommentsAdminPanel.js b/frontend-js/src/main/js/gui/admin/CommentsAdminPanel.js
index 5c9f1c7791..5d42c41079 100644
--- a/frontend-js/src/main/js/gui/admin/CommentsAdminPanel.js
+++ b/frontend-js/src/main/js/gui/admin/CommentsAdminPanel.js
@@ -11,6 +11,17 @@ var logger = require('../../logger');
var Promise = require("bluebird");
var xss = require('xss');
+/**
+ *
+ * @param {Object} params
+ * @param {HTMLElement} params.element
+ * @param {Configuration} params.configuration
+ * @param {Project} [params.project]
+ * @param {ServerConnector} [params.serverConnector]
+ *
+ * @constructor
+ * @extends AbstractGuiElement
+ */
function CommentsAdminPanel(params) {
params.customMap = null;
AbstractGuiElement.call(this, params);
@@ -21,6 +32,10 @@ function CommentsAdminPanel(params) {
CommentsAdminPanel.prototype = Object.create(AbstractGuiElement.prototype);
CommentsAdminPanel.prototype.constructor = CommentsAdminPanel;
+/**
+ *
+ * @private
+ */
CommentsAdminPanel.prototype._createGui = function () {
var self = this;
@@ -53,11 +68,19 @@ CommentsAdminPanel.prototype._createGui = function () {
};
+/**
+ *
+ * @returns {Promise}
+ */
CommentsAdminPanel.prototype.init = function () {
var self = this;
return self.refreshProjects();
};
+/**
+ *
+ * @returns {Promise}
+ */
CommentsAdminPanel.prototype.refreshComments = function () {
var self = this;
@@ -91,6 +114,11 @@ CommentsAdminPanel.prototype.refreshComments = function () {
});
};
+/**
+ *
+ * @param {Comment} comment
+ * @returns {string[]}
+ */
CommentsAdminPanel.prototype.commentToTableRow = function (comment) {
var self = this;
var projectId = self.getProject().getProjectId();
@@ -139,6 +167,9 @@ CommentsAdminPanel.prototype.commentToTableRow = function (comment) {
toYesNo(comment.isPinned())];
};
+/**
+ *
+ */
CommentsAdminPanel.prototype.destroy = function () {
var self = this;
var table = $("[name='commentsTable']", self.getElement())[0];
diff --git a/frontend-js/src/main/js/gui/admin/LogListDialog.js b/frontend-js/src/main/js/gui/admin/LogListDialog.js
index 14dd795f50..6bc07a0f0b 100644
--- a/frontend-js/src/main/js/gui/admin/LogListDialog.js
+++ b/frontend-js/src/main/js/gui/admin/LogListDialog.js
@@ -10,6 +10,18 @@ var Functions = require('../../Functions');
var GuiConnector = require('../../GuiConnector');
+/**
+ *
+ * @param {Object} params
+ * @param {HTMLElement} params.element
+ * @param {CustomMap} [params.customMap]
+ * @param {Configuration} params.configuration
+ * @param {Project} [params.project]
+ * @param {ServerConnector} [params.serverConnector]
+ *
+ * @constructor
+ * @extends AbstractGuiElement
+ */
function LogListDialog(params) {
AbstractGuiElement.call(this, params);
var self = this;
@@ -21,6 +33,9 @@ function LogListDialog(params) {
LogListDialog.prototype = Object.create(AbstractGuiElement.prototype);
LogListDialog.prototype.constructor = LogListDialog;
+/**
+ *
+ */
LogListDialog.prototype.createLogListDialogGui = function () {
var self = this;
var head = Functions.createElement({
@@ -76,6 +91,13 @@ LogListDialog.prototype.createLogListDialogGui = function () {
};
+/**
+ *
+ * @param {Object} data
+ * @param {function} callback
+ * @returns {Promise}
+ * @private
+ */
LogListDialog.prototype._dataTableAjaxCall = function (data, callback) {
var self = this;
return ServerConnector.getProjectLogs({
@@ -105,6 +127,12 @@ LogListDialog.prototype._dataTableAjaxCall = function (data, callback) {
});
};
+/**
+ *
+ * @param {Object} data
+ * @param {function} callback
+ * @returns {Promise}
+ */
LogListDialog.prototype.downloadAll = function (data, callback) {
var self = this;
return ServerConnector.getProjectLogs({
@@ -152,6 +180,10 @@ LogListDialog.prototype.open = function () {
};
+/**
+ *
+ * @returns {Array}
+ */
LogListDialog.prototype.getColumnsDefinition = function () {
return [{
name: "id"
@@ -160,9 +192,17 @@ LogListDialog.prototype.getColumnsDefinition = function () {
}];
};
+/**
+ *
+ * @returns {Promise}
+ */
LogListDialog.prototype.init = function () {
return Promise.resolve();
};
+
+/**
+ *
+ */
LogListDialog.prototype.destroy = function () {
var self = this;
var div = self.getElement();
diff --git a/frontend-js/src/main/js/gui/admin/MapsAdminPanel.js b/frontend-js/src/main/js/gui/admin/MapsAdminPanel.js
index 56f74f8883..16eeb4efd8 100644
--- a/frontend-js/src/main/js/gui/admin/MapsAdminPanel.js
+++ b/frontend-js/src/main/js/gui/admin/MapsAdminPanel.js
@@ -16,6 +16,18 @@ var Functions = require('../../Functions');
var GuiConnector = require('../../GuiConnector');
var Promise = require("bluebird");
+/**
+ *
+ * @param {Object} params
+ * @param {HTMLElement} params.element
+ * @param {CustomMap} [params.customMap]
+ * @param {Configuration} params.configuration
+ * @param {Project} [params.project]
+ * @param {ServerConnector} [params.serverConnector]
+ *
+ * @constructor
+ * @extends AbstractGuiElement
+ */
function MapsAdminPanel(params) {
var self = this;
AbstractAdminPanel.call(self, params);
@@ -28,6 +40,10 @@ function MapsAdminPanel(params) {
MapsAdminPanel.prototype = Object.create(AbstractAdminPanel.prototype);
MapsAdminPanel.prototype.constructor = MapsAdminPanel;
+/**
+ *
+ * @private
+ */
MapsAdminPanel.prototype._createGui = function () {
var self = this;
var projectsDiv = Functions.createElement({
@@ -47,6 +63,11 @@ MapsAdminPanel.prototype._createGui = function () {
};
+/**
+ *
+ * @returns {HTMLElement}
+ * @private
+ */
MapsAdminPanel.prototype._createMenuRow = function () {
var self = this;
var menuRow = Functions.createElement({
@@ -78,6 +99,11 @@ MapsAdminPanel.prototype._createMenuRow = function () {
return menuRow;
};
+/**
+ *
+ * @returns {HTMLElement}
+ * @private
+ */
MapsAdminPanel.prototype._createProjectTableRow = function () {
var self = this;
var projectsRow = Functions.createElement({
@@ -213,6 +239,11 @@ MapsAdminPanel.prototype.projectToTableRow = function (project, row, user) {
return row;
};
+/**
+ *
+ * @param {Annotation} annotation
+ * @returns {string}
+ */
MapsAdminPanel.prototype.getHtmlStringLink = function (annotation) {
var self = this;
if (annotation !== undefined && annotation !== null) {
@@ -250,6 +281,11 @@ MapsAdminPanel.prototype.setProjects = function (projects) {
});
};
+/**
+ *
+ * @param {Project} project
+ * @param {Array} dataTableRow
+ */
MapsAdminPanel.prototype.addUpdateListener = function (project, dataTableRow) {
var self = this;
@@ -273,6 +309,10 @@ MapsAdminPanel.prototype.addUpdateListener = function (project, dataTableRow) {
project.addListener("onreload", listener);
};
+/**
+ *
+ * @returns {Promise}
+ */
MapsAdminPanel.prototype.onAddClicked = function () {
var self = this;
var dialog = self._addDialog;
@@ -299,6 +339,10 @@ MapsAdminPanel.prototype.onAddClicked = function () {
}
};
+/**
+ *
+ * @returns {Promise}
+ */
MapsAdminPanel.prototype.destroy = function () {
var promises = [];
var self = this;
@@ -325,6 +369,10 @@ MapsAdminPanel.prototype.destroy = function () {
return Promise.all(promises);
};
+/**
+ *
+ * @returns {Promise}
+ */
MapsAdminPanel.prototype.onRefreshClicked = function () {
var self = this;
return ServerConnector.getProjects(true).then(function (projects) {
@@ -342,6 +390,11 @@ MapsAdminPanel.prototype.onRefreshClicked = function () {
});
};
+/**
+ *
+ * @param project
+ * @returns {*}
+ */
MapsAdminPanel.prototype.getDialog = function (project) {
var self = this;
if (self._dialogs === undefined) {
@@ -356,7 +409,7 @@ MapsAdminPanel.prototype.getDialog = function (project) {
project: project,
configuration: self.getConfiguration(),
customMap: null,
- serverConnector:self.getServerConnector()
+ serverConnector: self.getServerConnector()
});
self._dialogs[project.getProjectId()] = dialog;
return dialog.init().then(function () {
@@ -371,6 +424,12 @@ MapsAdminPanel.prototype.getDialog = function (project) {
}
};
+/**
+ *
+ * @param {string} projectId
+ * @param {string} level
+ * @returns {Promise<LogListDialog>}
+ */
MapsAdminPanel.prototype.getLogDialog = function (projectId, level) {
var self = this;
if (self._logDialogs === undefined) {
@@ -395,6 +454,11 @@ MapsAdminPanel.prototype.getLogDialog = function (projectId, level) {
}
};
+/**
+ *
+ * @param {string} id projectId
+ * @returns {Promise}
+ */
MapsAdminPanel.prototype.showEditDialog = function (id) {
var self = this;
GuiConnector.showProcessing();
@@ -410,6 +474,12 @@ MapsAdminPanel.prototype.showEditDialog = function (id) {
});
};
+/**
+ *
+ * @param {string} id projectId
+ * @param {string} level
+ * @returns {Promise<LogListDialog>}
+ */
MapsAdminPanel.prototype.showLogs = function (id, level) {
var self = this;
GuiConnector.showProcessing();
@@ -423,7 +493,11 @@ MapsAdminPanel.prototype.showLogs = function (id, level) {
});
};
-
+/**
+ *
+ * @param {string} id projectId
+ * @returns {Promise}
+ */
MapsAdminPanel.prototype.removeProject = function (id) {
var self = this;
return ServerConnector.removeProject(id).then(function () {
diff --git a/frontend-js/src/main/js/gui/admin/ZipEntry.js b/frontend-js/src/main/js/gui/admin/ZipEntry.js
index d774a22332..9a4c40d851 100644
--- a/frontend-js/src/main/js/gui/admin/ZipEntry.js
+++ b/frontend-js/src/main/js/gui/admin/ZipEntry.js
@@ -2,6 +2,14 @@
var types = ["IMAGE", "OVERLAY", "MAP"];
+/**
+ *
+ * @param {Object} params
+ * @param {string} params.type
+ * @param {string} params.filename
+ * @param {string} params.data
+ * @constructor
+ */
function ZipEntry(params) {
var self = this;
self.setType(params.type);
@@ -9,27 +17,53 @@ function ZipEntry(params) {
self.setData(params.data);
}
+/**
+ *
+ * @param {string} type
+ */
ZipEntry.prototype.setType = function (type) {
if (types.indexOf(type) === -1) {
throw new Error("Unknown ZipEntryType: " + type + ".")
}
this._type = type;
};
+
+/**
+ *
+ * @returns {string}
+ */
ZipEntry.prototype.getType = function () {
return this._type;
};
+/**
+ *
+ * @param {string} filename
+ */
ZipEntry.prototype.setFilename = function (filename) {
this._filename = filename;
};
+/**
+ *
+ * @returns {string}
+ */
ZipEntry.prototype.getFilename = function () {
return this._filename;
};
+/**
+ *
+ * @param {string} data
+ */
ZipEntry.prototype.setData = function (data) {
this._data = data;
};
+
+/**
+ *
+ * @returns {string}
+ */
ZipEntry.prototype.getData = function () {
return this._data;
};
diff --git a/frontend-js/src/main/js/gui/export/AbstractExportPanel.js b/frontend-js/src/main/js/gui/export/AbstractExportPanel.js
index b38d50a2c1..74db8cafbb 100644
--- a/frontend-js/src/main/js/gui/export/AbstractExportPanel.js
+++ b/frontend-js/src/main/js/gui/export/AbstractExportPanel.js
@@ -10,6 +10,19 @@ var Functions = require('../../Functions');
var DualListbox = require('dual-listbox').DualListbox;
var Promise = require("bluebird");
+/**
+ *
+ * @param {Configuration} [params.configuration]
+ * @param {HTMLElement} params.element
+ * @param {Project} params.project
+ * @param {CustomMap} params.customMap
+ * @param {string} params.panelName
+ * @param {string} [params.helpTip]
+ * @param params.parent
+ *
+ * @constructor
+ * @extends Panel
+ */
function AbstractExportPanel(params) {
params.scrollable = true;
Panel.call(this, params);
@@ -19,10 +32,19 @@ function AbstractExportPanel(params) {
AbstractExportPanel.prototype = Object.create(Panel.prototype);
AbstractExportPanel.prototype.constructor = AbstractExportPanel;
+/**
+ *
+ */
AbstractExportPanel.prototype.init = function () {
};
+/**
+ *
+ * @param {Object} val1
+ * @param {Object} val2
+ * @returns {number}
+ */
function compareSimple(val1, val2) {
if (val1 < val2) {
return -1;
@@ -33,6 +55,12 @@ function compareSimple(val1, val2) {
}
}
+/**
+ *
+ * @param annotations
+ * @returns {HTMLElement}
+ * @private
+ */
AbstractExportPanel.prototype._createMiriamTypeDiv = function (annotations) {
var self = this;
var typeDiv = Functions.createElement({
@@ -80,6 +108,11 @@ AbstractExportPanel.prototype._createMiriamTypeDiv = function (annotations) {
return typeDiv;
};
+/**
+ *
+ * @param {HTMLElement} selectElement
+ * @returns {DualListbox}
+ */
AbstractExportPanel.prototype.createDualListbox = function (selectElement) {
return new DualListbox(selectElement, {
availableTitle: 'Available',
@@ -91,6 +124,12 @@ AbstractExportPanel.prototype.createDualListbox = function (selectElement) {
});
};
+/**
+ *
+ * @param {BioEntityType[]} elementTypes
+ * @returns {HTMLElement}
+ * @private
+ */
AbstractExportPanel.prototype._createSelectTypeDiv = function (elementTypes) {
var typeDiv = Functions.createElement({
type: "div",
@@ -132,6 +171,10 @@ AbstractExportPanel.prototype._createSelectTypeDiv = function (elementTypes) {
return typeDiv;
};
+/**
+ *
+ * @returns {Promise<BioEntityType[]>}
+ */
AbstractExportPanel.prototype.getSelectedTypes = function () {
var self = this;
@@ -153,13 +196,28 @@ AbstractExportPanel.prototype.getSelectedTypes = function () {
return Promise.resolve(result);
};
+/**
+ *
+ * @param {DualListbox} dualListbox
+ */
AbstractExportPanel.prototype.setMiriamTypesDualListbox = function (dualListbox) {
this._miriamTypesDualListbox = dualListbox;
};
+
+/**
+ *
+ * @returns {DualListbox}
+ */
AbstractExportPanel.prototype.getMiriamTypesDualListbox = function () {
return this._miriamTypesDualListbox;
};
+/**
+ *
+ * @param {{columnName:string, name:string}[]} columnTypes
+ * @returns {HTMLElement}
+ * @private
+ */
AbstractExportPanel.prototype._createSelectColumnDiv = function (columnTypes) {
var columnDiv = Functions.createElement({
type: "div",
@@ -193,6 +251,10 @@ AbstractExportPanel.prototype._createSelectColumnDiv = function (columnTypes) {
return columnDiv;
};
+/**
+ *
+ * @returns {Promise<MiriamType[]>}
+ */
AbstractExportPanel.prototype.getSelectedMiriamTypes = function () {
var self = this;
return ServerConnector.getConfiguration().then(function (configuration) {
@@ -206,6 +268,10 @@ AbstractExportPanel.prototype.getSelectedMiriamTypes = function () {
});
};
+/**
+ *
+ * @returns {Promise}
+ */
AbstractExportPanel.prototype.getSelectedColumns = function () {
var self = this;
@@ -235,6 +301,11 @@ AbstractExportPanel.prototype.getSelectedColumns = function () {
return Promise.resolve(result);
};
+/**
+ *
+ * @returns {Promise<string[]>}
+ * @private
+ */
AbstractExportPanel.prototype._getCompartmentNames = function () {
var self = this;
var compartments = [];
@@ -252,10 +323,19 @@ AbstractExportPanel.prototype._getCompartmentNames = function () {
});
};
+/**
+ *
+ * @returns {MapModel[]}
+ */
AbstractExportPanel.prototype.getModels = function () {
return this.getProject().getModels();
};
+/**
+ *
+ * @returns {Promise}
+ * @private
+ */
AbstractExportPanel.prototype._getAllCompartments = function () {
var self = this;
var compartments = [];
@@ -278,6 +358,11 @@ AbstractExportPanel.prototype._getAllCompartments = function () {
});
};
+/**
+ *
+ * @returns {HTMLElement}
+ * @private
+ */
AbstractExportPanel.prototype._createDownloadButton = function () {
var self = this;
var downloadDiv = Functions.createElement({
@@ -310,11 +395,20 @@ AbstractExportPanel.prototype._createDownloadButton = function () {
return downloadDiv;
};
+/**
+ *
+ * @returns {string}
+ */
AbstractExportPanel.prototype.getSaveFilename = function () {
var self = this;
return self.getProject().getProjectId() + "-" + self.getPanelName() + ".txt";
};
+/**
+ *
+ * @returns {Promise<HTMLElement>}
+ * @private
+ */
AbstractExportPanel.prototype._createSelectIncludedCompartmentDiv = function () {
var self = this;
var typeDiv = Functions.createElement({
@@ -348,6 +442,11 @@ AbstractExportPanel.prototype._createSelectIncludedCompartmentDiv = function ()
});
};
+/**
+ *
+ * @returns {Promise<HTMLElement>}
+ * @private
+ */
AbstractExportPanel.prototype._createSelectExcludedCompartmentDiv = function () {
var self = this;
var typeDiv = Functions.createElement({
@@ -381,13 +480,26 @@ AbstractExportPanel.prototype._createSelectExcludedCompartmentDiv = function ()
});
};
+/**
+ *
+ * @param {DualListbox} dualListbox
+ */
AbstractExportPanel.prototype.setIncludedCompartmentsDualListbox = function (dualListbox) {
this._includedCompartmentsDualListbox = dualListbox;
};
+
+/**
+ *
+ * @returns {DualListbox}
+ */
AbstractExportPanel.prototype.getIncludedCompartmentsDualListbox = function () {
return this._includedCompartmentsDualListbox;
};
+/**
+ *
+ * @returns {Promise<Array>}
+ */
AbstractExportPanel.prototype.getSelectedIncludedCompartments = function () {
var self = this;
var list = self.getIncludedCompartmentsDualListbox().selected;
@@ -408,13 +520,26 @@ AbstractExportPanel.prototype.getSelectedIncludedCompartments = function () {
});
};
+/**
+ *
+ * @param {DualListbox} dualListbox
+ */
AbstractExportPanel.prototype.setExcludedCompartmentsDualListbox = function (dualListbox) {
this._excludedCompartmentsDualListbox = dualListbox;
};
+
+/**
+ *
+ * @returns {DualListbox}
+ */
AbstractExportPanel.prototype.getExcludedCompartmentsDualListbox = function () {
return this._excludedCompartmentsDualListbox;
};
+/**
+ *
+ * @returns {Promise<Array>}
+ */
AbstractExportPanel.prototype.getSelectedExcludedCompartments = function () {
var self = this;
var list = self.getExcludedCompartmentsDualListbox().selected;
@@ -435,6 +560,12 @@ AbstractExportPanel.prototype.getSelectedExcludedCompartments = function () {
});
};
+/**
+ *
+ * @param {{name:string}[]} columns
+ * @param {MiriamType[]> miriamTypes
+ * @returns {string}
+ */
AbstractExportPanel.prototype.createResponseHeader = function (columns, miriamTypes) {
var stringBuilder = [];
var i;
diff --git a/frontend-js/src/main/js/gui/export/ElementExportPanel.js b/frontend-js/src/main/js/gui/export/ElementExportPanel.js
index 5b1b0ae483..ceb0ddd96d 100644
--- a/frontend-js/src/main/js/gui/export/ElementExportPanel.js
+++ b/frontend-js/src/main/js/gui/export/ElementExportPanel.js
@@ -9,6 +9,17 @@ var logger = require('../../logger');
var Promise = require("bluebird");
+/**
+ *
+ * @param {Configuration} [params.configuration]
+ * @param {HTMLElement} params.element
+ * @param {Project} params.project
+ * @param {string} [params.helpTip]
+ * @param params.parent
+ *
+ * @constructor
+ * @extends AbstractExportPanel
+ */
function ElementExportPanel(params) {
params.panelName = "elementExport";
AbstractExportPanel.call(this, params);
@@ -17,6 +28,10 @@ function ElementExportPanel(params) {
ElementExportPanel.prototype = Object.create(AbstractExportPanel.prototype);
ElementExportPanel.prototype.constructor = ElementExportPanel;
+/**
+ *
+ * @returns {Promise}
+ */
ElementExportPanel.prototype.init = function () {
var self = this;
var element = self.getElement();
@@ -43,6 +58,10 @@ ElementExportPanel.prototype.init = function () {
});
};
+/**
+ *
+ * @returns {Promise<string>}
+ */
ElementExportPanel.prototype.createResponseString = function () {
var self = this;
var types, miriamTypes;
@@ -102,6 +121,13 @@ ElementExportPanel.prototype.createResponseString = function () {
});
};
+/**
+ *
+ * @param {Alias} alias
+ * @param {Array} columns
+ * @param {MiriamType[]} miriamTypes
+ * @returns {string}
+ */
ElementExportPanel.prototype.createResponseRow = function (alias, columns, miriamTypes) {
var stringBuilder = [];
var i, value;
@@ -131,6 +157,10 @@ ElementExportPanel.prototype.createResponseRow = function (alias, columns, miria
return stringBuilder.join("\t");
};
+/**
+ *
+ * @returns {*[]}
+ */
ElementExportPanel.prototype.getAllColumns = function () {
return [{
"columnName": "id",
diff --git a/frontend-js/src/main/js/gui/export/GraphicsExportPanel.js b/frontend-js/src/main/js/gui/export/GraphicsExportPanel.js
index 9976880791..db001d2bb2 100644
--- a/frontend-js/src/main/js/gui/export/GraphicsExportPanel.js
+++ b/frontend-js/src/main/js/gui/export/GraphicsExportPanel.js
@@ -9,6 +9,17 @@ var GuiConnector = require('../../GuiConnector');
var logger = require('../../logger');
var xss = require('xss');
+/**
+ *
+ * @param {Configuration} [params.configuration]
+ * @param {HTMLElement} params.element
+ * @param {Project} params.project
+ * @param {string} [params.helpTip]
+ * @param params.parent
+ *
+ * @constructor
+ * @extends AbstractExportPanel
+ */
function GraphicsExportPanel(params) {
params.panelName = "graphicsExport";
AbstractExportPanel.call(this, params);
@@ -17,6 +28,10 @@ function GraphicsExportPanel(params) {
GraphicsExportPanel.prototype = Object.create(AbstractExportPanel.prototype);
GraphicsExportPanel.prototype.constructor = GraphicsExportPanel;
+/**
+ *
+ * @returns {Promise}
+ */
GraphicsExportPanel.prototype.init = function () {
var self = this;
var element = self.getElement();
@@ -31,6 +46,11 @@ GraphicsExportPanel.prototype.init = function () {
});
};
+/**
+ *
+ * @returns {HTMLElement}
+ * @private
+ */
GraphicsExportPanel.prototype._createSelectProjectDiv = function () {
var self = this;
var typeDiv = Functions.createElement({
@@ -68,6 +88,12 @@ GraphicsExportPanel.prototype._createSelectProjectDiv = function () {
return typeDiv;
};
+/**
+ *
+ * @param {ImageConverter[]} formats
+ * @returns {HTMLElement}
+ * @private
+ */
GraphicsExportPanel.prototype._createSelectGraphicsFormatDiv = function (formats) {
var typeDiv = Functions.createElement({
type: "div",
@@ -102,6 +128,10 @@ GraphicsExportPanel.prototype._createSelectGraphicsFormatDiv = function (formats
return typeDiv;
};
+/**
+ *
+ * @returns {string}
+ */
GraphicsExportPanel.prototype.getSubmapId = function () {
var self = this;
var div = $("div[name='modelSelectDiv']", $(self.getElement()))[0];
@@ -111,6 +141,11 @@ GraphicsExportPanel.prototype.getSubmapId = function () {
});
return id;
};
+
+/**
+ *
+ * @returns {string}
+ */
GraphicsExportPanel.prototype.getFormatHandler = function () {
var self = this;
var div = $("div[name='formatSelectDiv']", $(self.getElement()))[0];
@@ -121,6 +156,11 @@ GraphicsExportPanel.prototype.getFormatHandler = function () {
return format;
};
+/**
+ *
+ * @returns {HTMLElement}
+ * @private
+ */
GraphicsExportPanel.prototype._createDownloadButton = function () {
var self = this;
var downloadDiv = Functions.createElement({
diff --git a/frontend-js/src/main/js/gui/export/NetworkExportPanel.js b/frontend-js/src/main/js/gui/export/NetworkExportPanel.js
index 1543fafae7..dd90195a70 100644
--- a/frontend-js/src/main/js/gui/export/NetworkExportPanel.js
+++ b/frontend-js/src/main/js/gui/export/NetworkExportPanel.js
@@ -8,7 +8,17 @@ var Promise = require("bluebird");
var logger = require('../../logger');
var GuiMessageError = require('../GuiMessageError');
-
+/**
+ *
+ * @param {Configuration} [params.configuration]
+ * @param {HTMLElement} params.element
+ * @param {Project} params.project
+ * @param {string} [params.helpTip]
+ * @param params.parent
+ *
+ * @constructor
+ * @extends AbstractExportPanel
+ */
function NetworkExportPanel(params) {
params.panelName = "networkExport";
AbstractExportPanel.call(this, params);
@@ -17,6 +27,10 @@ function NetworkExportPanel(params) {
NetworkExportPanel.prototype = Object.create(AbstractExportPanel.prototype);
NetworkExportPanel.prototype.constructor = NetworkExportPanel;
+/**
+ *
+ * @returns {Promise}
+ */
NetworkExportPanel.prototype.init = function () {
var self = this;
@@ -42,9 +56,12 @@ NetworkExportPanel.prototype.init = function () {
}).then(function () {
$(window).trigger('resize');
});
-
};
+/**
+ *
+ * @returns {*[]}
+ */
NetworkExportPanel.prototype.getAllColumns = function () {
return [{
"columnName": "elements",
@@ -138,6 +155,12 @@ NetworkExportPanel.prototype.getAllColumns = function () {
}];
};
+/**
+ *
+ * @param {Reaction} reaction
+ * @param {Object<string,boolean>} elementIds
+ * @returns {boolean}
+ */
function matchReaction(reaction, elementIds) {
var count = 0;
reaction.getElements().forEach(function (element) {
@@ -148,6 +171,10 @@ function matchReaction(reaction, elementIds) {
return count > 1;
}
+/**
+ *
+ * @returns {Promise<string>}
+ */
NetworkExportPanel.prototype.createResponseString = function () {
var self = this;
var types, miriamTypes;
@@ -219,6 +246,14 @@ NetworkExportPanel.prototype.createResponseString = function () {
});
};
+/**
+ *
+ * @param {Reaction} reaction
+ * @param {Object} columns
+ * @param {MiriamType[]} miriamTypes
+ * @param {Object<string,boolean>} elementIds
+ * @returns {string}
+ */
NetworkExportPanel.prototype.createResponseRow = function (reaction, columns, miriamTypes, elementIds) {
var stringBuilder = [];
var i, value;
diff --git a/frontend-js/src/main/js/gui/leftPanel/AbstractDbPanel.js b/frontend-js/src/main/js/gui/leftPanel/AbstractDbPanel.js
index b6ead02a0d..75fab272c2 100644
--- a/frontend-js/src/main/js/gui/leftPanel/AbstractDbPanel.js
+++ b/frontend-js/src/main/js/gui/leftPanel/AbstractDbPanel.js
@@ -33,6 +33,10 @@ function AbstractDbPanel(params) {
AbstractDbPanel.prototype = Object.create(Panel.prototype);
AbstractDbPanel.prototype.constructor = AbstractDbPanel;
+/**
+ *
+ * @private
+ */
AbstractDbPanel.prototype._createEventHandlers = function () {
var self = this;
var searchButton = self.getControlElement(PanelControlElementType.SEARCH_BUTTON);
@@ -77,6 +81,11 @@ AbstractDbPanel.prototype._createEventHandlers = function () {
};
+/**
+ *
+ * @param {string} placeholder
+ * @private
+ */
AbstractDbPanel.prototype._initializeGui = function (placeholder) {
var searchQueryDiv = Functions.createElement({
type: "div",
@@ -170,6 +179,10 @@ AbstractDbPanel.prototype._initializeGui = function (placeholder) {
};
+/**
+ *
+ * @param {AbstractDbOverlay} overlayDb
+ */
AbstractDbPanel.prototype.setOverlayDb = function (overlayDb) {
if (overlayDb === undefined) {
throw new Error("Undefined overlayDb for panel: " + this.getPanelName());
@@ -185,6 +198,9 @@ AbstractDbPanel.prototype.getOverlayDb = function () {
return this._overlayDb;
};
+/**
+ *
+ */
AbstractDbPanel.prototype.clearResults = function () {
var navElement = this.getControlElement(PanelControlElementType.SEARCH_RESULTS_NAV_TAB);
while (navElement.firstChild) {
@@ -197,6 +213,10 @@ AbstractDbPanel.prototype.clearResults = function () {
}
};
+/**
+ *
+ * @returns {Promise}
+ */
AbstractDbPanel.prototype.refreshSearchResults = function () {
var self = this;
self.clearResults();
@@ -216,14 +236,26 @@ AbstractDbPanel.prototype.refreshSearchResults = function () {
});
};
+/**
+ *
+ */
AbstractDbPanel.prototype.getAutocomplete = function () {
logger.warn("Get autocomplete not implemented");
};
+/**
+ *
+ */
AbstractDbPanel.prototype.searchByQuery = function () {
throw new Error("searchByQuery is not implemented");
};
+/**
+ *
+ * @param {string} query
+ * @param {BioEntity[]} elements
+ * @returns {Promise}
+ */
AbstractDbPanel.prototype.addResultTab = function (query, elements) {
var self = this;
var name = JSON.parse(query).query;
@@ -288,10 +320,12 @@ AbstractDbPanel.prototype.addResultTab = function (query, elements) {
};
/**
+ * @param element
+ * @param {string} icon
*
* @returns {Promise<HTMLTableRowElement>}
*/
-AbstractDbPanel.prototype.createTableElement = function () {
+AbstractDbPanel.prototype.createTableElement = function (element, icon) {
throw new Error("Not implemented");
};
@@ -369,6 +403,10 @@ AbstractDbPanel.prototype.createTargetRow = function (target, icon) {
return Promise.resolve(result);
};
+/**
+ *
+ * @param {string[]} queries
+ */
AbstractDbPanel.prototype.computeAutocompleteDictionary = function (queries) {
var result = {};
diff --git a/frontend-js/src/main/js/gui/leftPanel/ChemicalPanel.js b/frontend-js/src/main/js/gui/leftPanel/ChemicalPanel.js
index 3a72aec79e..eb5decc273 100644
--- a/frontend-js/src/main/js/gui/leftPanel/ChemicalPanel.js
+++ b/frontend-js/src/main/js/gui/leftPanel/ChemicalPanel.js
@@ -35,6 +35,11 @@ function ChemicalPanel(params) {
ChemicalPanel.prototype = Object.create(AbstractDbPanel.prototype);
ChemicalPanel.prototype.constructor = ChemicalPanel;
+/**
+ *
+ * @param {Chemical} chemical
+ * @returns {HTMLDivElement}
+ */
ChemicalPanel.prototype.createPreamble = function (chemical) {
var self = this;
var guiUtils = self.getGuiUtils();
@@ -55,10 +60,20 @@ ChemicalPanel.prototype.createPreamble = function (chemical) {
return result;
};
+/**
+ *
+ * @param {Target} target
+ * @param {string} icon
+ * @returns {Promise<HTMLTableRowElement>}
+ */
ChemicalPanel.prototype.createTableElement = function (target, icon) {
return this.createTargetRow(target, icon);
};
+/**
+ *
+ * @returns {Promise}
+ */
ChemicalPanel.prototype.searchByQuery = function () {
var self = this;
var query = self.getControlElement(PanelControlElementType.SEARCH_INPUT).value;
@@ -66,6 +81,10 @@ ChemicalPanel.prototype.searchByQuery = function () {
return self.getOverlayDb().searchByQuery(query);
};
+/**
+ *
+ * @returns {Promise}
+ */
ChemicalPanel.prototype.init = function () {
var self = this;
return self.getToolTipForAnnotation(self.getProject().getDisease()).then(function (toolTip) {
@@ -77,10 +96,19 @@ ChemicalPanel.prototype.init = function () {
});
};
+/**
+ *
+ * @returns {Promise}
+ */
ChemicalPanel.prototype.destroy = function () {
return Promise.resolve();
};
+/**
+ *
+ * @param {string} query
+ * @returns {string[]}
+ */
ChemicalPanel.prototype.getAutocomplete = function (query) {
if (this._searchAutocomplete === undefined) {
this.refreshSearchAutocomplete();
@@ -90,6 +118,10 @@ ChemicalPanel.prototype.getAutocomplete = function (query) {
return this._searchAutocomplete[query];
};
+/**
+ *
+ * @returns {Promise}
+ */
ChemicalPanel.prototype.refreshSearchAutocomplete = function () {
var self = this;
self._searchAutocomplete = [];
@@ -99,6 +131,11 @@ ChemicalPanel.prototype.refreshSearchAutocomplete = function () {
});
};
+/**
+ *
+ * @param {Annotation} annotation
+ * @returns {string}
+ */
ChemicalPanel.prototype.getToolTipForAnnotation = function (annotation) {
var self = this;
var promise = Promise.resolve('disease');
diff --git a/frontend-js/src/main/js/gui/leftPanel/DrugPanel.js b/frontend-js/src/main/js/gui/leftPanel/DrugPanel.js
index d2b5c8447d..f20e2504dd 100644
--- a/frontend-js/src/main/js/gui/leftPanel/DrugPanel.js
+++ b/frontend-js/src/main/js/gui/leftPanel/DrugPanel.js
@@ -53,16 +53,30 @@ DrugPanel.prototype.createPreamble = function (drug) {
return result;
};
+/**
+ *
+ * @param {Target} target
+ * @param {string} icon
+ * @returns {Promise<HTMLTableRowElement>}
+ */
DrugPanel.prototype.createTableElement = function (target, icon) {
return this.createTargetRow(target, icon);
};
+/**
+ *
+ * @returns {Promise}
+ */
DrugPanel.prototype.searchByQuery = function () {
var self = this;
var query = self.getControlElement(PanelControlElementType.SEARCH_INPUT).value;
return self.getOverlayDb().searchByQuery(query);
};
+/**
+ *
+ * @returns {Promise}
+ */
DrugPanel.prototype.init = function () {
var query = ServerConnector.getSessionData().getDrugQuery();
if (query !== undefined) {
@@ -72,10 +86,19 @@ DrugPanel.prototype.init = function () {
}
};
+/**
+ *
+ * @returns {Promise}
+ */
DrugPanel.prototype.destroy = function () {
return Promise.resolve();
};
+/**
+ *
+ * @param {string} query
+ * @returns {string[]}
+ */
DrugPanel.prototype.getAutocomplete = function (query) {
if (this._searchAutocomplete === undefined) {
this.refreshSearchAutocomplete();
@@ -85,6 +108,10 @@ DrugPanel.prototype.getAutocomplete = function (query) {
return this._searchAutocomplete[query];
};
+/**
+ *
+ * @returns {Promise}
+ */
DrugPanel.prototype.refreshSearchAutocomplete = function () {
var self = this;
self._searchAutocomplete = [];
diff --git a/frontend-js/src/main/js/gui/leftPanel/GenericSearchPanel.js b/frontend-js/src/main/js/gui/leftPanel/GenericSearchPanel.js
index cb400d39b6..4bbc343c4f 100644
--- a/frontend-js/src/main/js/gui/leftPanel/GenericSearchPanel.js
+++ b/frontend-js/src/main/js/gui/leftPanel/GenericSearchPanel.js
@@ -15,6 +15,12 @@ var SearchBioEntityGroup = require('../../map/data/SearchBioEntityGroup');
var logger = require('../../logger');
var Functions = require('../../Functions');
+/**
+ *
+ * @param params
+ * @constructor
+ * @extends AbstractDbPanel
+ */
function GenericSearchPanel(params) {
params.panelName = "search";
params.helpTip = "<p>search tab allows to search for particular elements or interactions in the map</p>"
@@ -30,6 +36,9 @@ function GenericSearchPanel(params) {
GenericSearchPanel.prototype = Object.create(AbstractDbPanel.prototype);
GenericSearchPanel.prototype.constructor = GenericSearchPanel;
+/**
+ *
+ */
GenericSearchPanel.prototype.createSearchGui = function () {
var searchDiv = this.getControlElement(PanelControlElementType.SEARCH_DIV);
@@ -66,6 +75,10 @@ GenericSearchPanel.prototype.createTableElement = function (element, icon) {
}
};
+/**
+ *
+ * @returns {HTMLDivElement}
+ */
GenericSearchPanel.prototype.createPreamble = function () {
return document.createElement("div");
};
@@ -135,6 +148,10 @@ GenericSearchPanel.prototype.createSearchBioEntityGroupElement = function (group
};
+/**
+ *
+ * @returns {Promise}
+ */
GenericSearchPanel.prototype.searchByQuery = function () {
var self = this;
var query = this.getControlElement(PanelControlElementType.SEARCH_INPUT).value;
@@ -142,6 +159,11 @@ GenericSearchPanel.prototype.searchByQuery = function () {
return self.getOverlayDb().searchByQuery(query, perfect, true);
};
+/**
+ *
+ * @param {string} query
+ * @returns {string[]}
+ */
GenericSearchPanel.prototype.getAutocomplete = function (query) {
if (this._searchAutocomplete === undefined) {
this.refreshSearchAutocomplete();
@@ -151,6 +173,10 @@ GenericSearchPanel.prototype.getAutocomplete = function (query) {
return this._searchAutocomplete[query];
};
+/**
+ *
+ * @returns {Promise}
+ */
GenericSearchPanel.prototype.refreshSearchAutocomplete = function () {
var self = this;
self._searchAutocomplete = [];
@@ -160,6 +186,10 @@ GenericSearchPanel.prototype.refreshSearchAutocomplete = function () {
});
};
+/**
+ *
+ * @returns {Promise}
+ */
GenericSearchPanel.prototype.init = function () {
var query = ServerConnector.getSessionData().getSearchQuery();
if (query !== undefined) {
diff --git a/frontend-js/src/main/js/gui/leftPanel/LeftPanel.js b/frontend-js/src/main/js/gui/leftPanel/LeftPanel.js
index 0814cf115c..b5cbf2b550 100644
--- a/frontend-js/src/main/js/gui/leftPanel/LeftPanel.js
+++ b/frontend-js/src/main/js/gui/leftPanel/LeftPanel.js
@@ -42,6 +42,10 @@ function LeftPanel(params) {
LeftPanel.prototype = Object.create(AbstractGuiElement.prototype);
LeftPanel.prototype.constructor = LeftPanel;
+/**
+ *
+ * @private
+ */
LeftPanel.prototype._createPanelGui = function () {
var self = this;
var panels = self.getPanelsDefinition();
@@ -84,6 +88,10 @@ LeftPanel.prototype._createPanelGui = function () {
}
};
+/**
+ *
+ * @returns {*[]}
+ */
LeftPanel.prototype.getPanelsDefinition = function () {
return [{
name: "<div class='maintabdiv'><i class='fa fa-search maintab'></i><br>SEARCH</div>",
@@ -104,6 +112,10 @@ LeftPanel.prototype.getPanelsDefinition = function () {
}];
};
+/**
+ *
+ * @returns {Promise}
+ */
LeftPanel.prototype.init = function () {
var self = this;
@@ -132,6 +144,11 @@ LeftPanel.prototype.init = function () {
return Promise.all(promises);
};
+/**
+ *
+ * @param {BioEntity} element
+ * @returns {Promise}
+ */
LeftPanel.prototype.showElementDetails = function (element) {
var self = this;
var div = self.elementInfoDiv;
@@ -237,38 +254,73 @@ LeftPanel.prototype.getElementTitle = function (bioEntity) {
}
};
+/**
+ *
+ */
LeftPanel.prototype.hide = function () {
this.getElement().style.display = "none";
};
+
+/**
+ *
+ */
LeftPanel.prototype.show = function () {
this.getElement().style.display = "block";
};
+/**
+ *
+ * @param {Header} header
+ */
LeftPanel.prototype.setHeader = function (header) {
this._header = header;
};
+/**
+ *
+ * @returns {Header}
+ */
LeftPanel.prototype.getHeader = function () {
return this._header;
};
+/**
+ *
+ * @param {LoginDialog} loginDialog
+ */
LeftPanel.prototype.setLoginDialog = function (loginDialog) {
this._loginDialog = loginDialog;
};
+/**
+ *
+ * @returns {LoginDialog}
+ */
LeftPanel.prototype.getLoginDialog = function () {
return this._loginDialog;
};
+/**
+ *
+ * @param {PluginManager} pluginManager
+ */
LeftPanel.prototype.setPluginManager = function (pluginManager) {
this._pluginManager = pluginManager;
this.getHeader().setPluginManager(pluginManager);
};
+/**
+ *
+ * @returns {PluginManager}
+ */
LeftPanel.prototype.getPluginManager = function () {
return this._pluginManager;
};
+/**
+ *
+ * @returns {Promise}
+ */
LeftPanel.prototype.destroy = function () {
var self = this;
var promises = [];
@@ -294,10 +346,18 @@ LeftPanel.prototype.destroy = function () {
return Promise.all(promises);
};
+/**
+ *
+ * @param {boolean} value
+ */
LeftPanel.prototype.setGoogleLicenseConsentRequired = function (value) {
this._googleLicenseConsentRequired = value;
};
+/**
+ *
+ * @returns {boolean}
+ */
LeftPanel.prototype.isGoogleLicenseConsentRequired = function () {
return this._googleLicenseConsentRequired;
};
diff --git a/frontend-js/src/main/js/gui/leftPanel/MiRnaPanel.js b/frontend-js/src/main/js/gui/leftPanel/MiRnaPanel.js
index eb678ae5a4..e78e25bfc1 100644
--- a/frontend-js/src/main/js/gui/leftPanel/MiRnaPanel.js
+++ b/frontend-js/src/main/js/gui/leftPanel/MiRnaPanel.js
@@ -8,6 +8,12 @@ var logger = require('../../logger');
var AbstractDbPanel = require('./AbstractDbPanel');
var PanelControlElementType = require('../PanelControlElementType');
+/**
+ *
+ * @param params
+ * @constructor
+ * @extends AbstractDbPanel
+ */
function MiRnaPanel(params) {
params.panelName = "mirna";
params.helpTip = '<p>source: <a target="_mirtarbase" href="http://mirtarbase.mbc.nctu.edu.tw/">miRTarBase</a></p>'
@@ -20,6 +26,11 @@ function MiRnaPanel(params) {
MiRnaPanel.prototype = Object.create(AbstractDbPanel.prototype);
MiRnaPanel.prototype.constructor = MiRnaPanel;
+/**
+ *
+ * @param {MiRna} miRna
+ * @returns {HTMLDivElement}
+ */
MiRnaPanel.prototype.createPreamble = function(miRna) {
var self = this;
var guiUtils = self.getGuiUtils();
@@ -40,16 +51,30 @@ MiRnaPanel.prototype.createPreamble = function(miRna) {
return result;
};
+/**
+ *
+ * @param {Target} target
+ * @param {string} icon
+ * @returns {Promise<HTMLTableRowElement>}
+ */
MiRnaPanel.prototype.createTableElement = function(target, icon) {
return this.createTargetRow(target, icon);
};
+/**
+ *
+ * @returns {Promise}
+ */
MiRnaPanel.prototype.searchByQuery = function() {
var self = this;
var query = self.getControlElement(PanelControlElementType.SEARCH_INPUT).value;
return self.getOverlayDb().searchByQuery(query);
};
+/**
+ *
+ * @returns {Promise}
+ */
MiRnaPanel.prototype.init = function() {
var query = ServerConnector.getSessionData().getMiRnaQuery();
if (query !== undefined) {
@@ -59,10 +84,19 @@ MiRnaPanel.prototype.init = function() {
}
};
+/**
+ *
+ * @returns {Promise}
+ */
MiRnaPanel.prototype.destroy = function () {
return Promise.resolve();
};
+/**
+ *
+ * @param {string} query
+ * @returns {string[]}
+ */
MiRnaPanel.prototype.getAutocomplete = function (query) {
if (this._searchAutocomplete === undefined) {
this.refreshSearchAutocomplete();
@@ -72,6 +106,10 @@ MiRnaPanel.prototype.getAutocomplete = function (query) {
return this._searchAutocomplete[query];
};
+/**
+ *
+ * @returns {Promise}
+ */
MiRnaPanel.prototype.refreshSearchAutocomplete = function () {
var self = this;
self._searchAutocomplete = [];
diff --git a/frontend-js/src/main/js/gui/leftPanel/OverlayPanel.js b/frontend-js/src/main/js/gui/leftPanel/OverlayPanel.js
index 0a178c5e30..224549a89a 100644
--- a/frontend-js/src/main/js/gui/leftPanel/OverlayPanel.js
+++ b/frontend-js/src/main/js/gui/leftPanel/OverlayPanel.js
@@ -167,6 +167,9 @@ OverlayPanel.prototype._createOverlayPanelGui = function () {
this.setControlElement(PanelControlElementType.OVERLAY_ADD_OVERLAY_BUTTON, addOverlayButton);
};
+/**
+ *
+ */
OverlayPanel.prototype.clear = function () {
var table = this.getControlElement(PanelControlElementType.OVERLAY_GENERAL_OVERLAY_TABLE);
while (table.firstChild) {
@@ -543,7 +546,7 @@ OverlayPanel.prototype.getCustomOverlaysMessage = function () {
/**
*
- * @returns {PromiseLike}
+ * @returns {Promise}
*/
OverlayPanel.prototype.openAddOverlayDialog = function () {
var self = this;
@@ -659,6 +662,10 @@ OverlayPanel.prototype.destroy = function () {
}
};
+/**
+ *
+ * @param {boolean} value
+ */
OverlayPanel.prototype.setGoogleLicenseConsentRequired = function (value) {
var leftPanel = this.getParent();
if (leftPanel !== undefined) {
diff --git a/frontend-js/src/main/js/gui/leftPanel/ProjectInfoPanel.js b/frontend-js/src/main/js/gui/leftPanel/ProjectInfoPanel.js
index 004f351df9..de651e16a8 100644
--- a/frontend-js/src/main/js/gui/leftPanel/ProjectInfoPanel.js
+++ b/frontend-js/src/main/js/gui/leftPanel/ProjectInfoPanel.js
@@ -11,6 +11,18 @@ var PublicationListDialog = require('./PublicationListDialog');
var logger = require('../../logger');
var Functions = require('../../Functions');
+/**
+ *
+ * @param {Object} params
+ * @param {HTMLElement} params.element
+ * @param {CustomMap} params.customMap
+ * @param {Configuration} [params.configuration]
+ * @param {Project} [params.project]
+ * @param params.parent
+ *
+ * @constructor
+ * @extends Panel
+ */
function ProjectInfoPanel(params) {
params.panelName = "info";
params.scrollable = true;
@@ -33,6 +45,10 @@ function ProjectInfoPanel(params) {
ProjectInfoPanel.prototype = Object.create(Panel.prototype);
ProjectInfoPanel.prototype.constructor = ProjectInfoPanel;
+/**
+ *
+ * @private
+ */
ProjectInfoPanel.prototype._createInfoPanelGui = function () {
var self = this;
var guiUtils = self.getGuiUtils();
@@ -184,6 +200,10 @@ ProjectInfoPanel.prototype._createInfoPanelGui = function () {
};
+/**
+ *
+ * @private
+ */
ProjectInfoPanel.prototype._createInfoPanelLogic = function () {
var self = this;
@@ -198,6 +218,10 @@ ProjectInfoPanel.prototype._createInfoPanelLogic = function () {
};
};
+/**
+ *
+ * @returns {Promise}
+ */
ProjectInfoPanel.prototype.downloadSourceFile = function () {
var self = this;
return ServerConnector.getProjectSourceDownloadUrl().then(function (url) {
@@ -205,10 +229,18 @@ ProjectInfoPanel.prototype.downloadSourceFile = function () {
}).then(null, GuiConnector.alert);
};
+/**
+ *
+ * @returns {Promise}
+ */
ProjectInfoPanel.prototype.showPublicationListDialog = function () {
return this.publicationListDialog.show();
};
+/**
+ *
+ * @returns {Promise}
+ */
ProjectInfoPanel.prototype.refresh = function () {
var self = this;
@@ -228,6 +260,10 @@ ProjectInfoPanel.prototype.refresh = function () {
});
};
+/**
+ *
+ * @private
+ */
ProjectInfoPanel.prototype._createUserDataTab = function () {
var self = this;
var guiUtils = self.getGuiUtils();
@@ -335,7 +371,10 @@ ProjectInfoPanel.prototype._createUserDataTab = function () {
};
-
+/**
+ *
+ * @param {User} user
+ */
ProjectInfoPanel.prototype.showUserProfilePage = function (user) {
var self = this;
@@ -361,6 +400,10 @@ ProjectInfoPanel.prototype.showUserProfilePage = function (user) {
}
};
+/**
+ *
+ * @returns {Promise}
+ */
ProjectInfoPanel.prototype.init = function () {
var self = this;
var email, content;
@@ -376,6 +419,9 @@ ProjectInfoPanel.prototype.init = function () {
});
};
+/**
+ *
+ */
ProjectInfoPanel.prototype.destroy = function () {
return this.publicationListDialog.destroy();
};
diff --git a/frontend-js/src/main/js/gui/leftPanel/PublicationListDialog.js b/frontend-js/src/main/js/gui/leftPanel/PublicationListDialog.js
index 5f757ba484..9735174270 100644
--- a/frontend-js/src/main/js/gui/leftPanel/PublicationListDialog.js
+++ b/frontend-js/src/main/js/gui/leftPanel/PublicationListDialog.js
@@ -13,6 +13,17 @@ var Reaction = require('../../map/data/Reaction');
var Functions = require('../../Functions');
var logger = require('../../logger');
+/**
+ *
+ * @param {Object} params
+ * @param {HTMLElement} params.element
+ * @param {CustomMap} [params.customMap]
+ * @param {Configuration} params.configuration
+ * @param {Project} [params.project]
+ * @param {ServerConnector} [params.serverConnector]
+ * @constructor
+ * @extends AbstractGuiElement
+ */
function PublicationListDialog(params) {
AbstractGuiElement.call(this, params);
var self = this;
@@ -22,6 +33,9 @@ function PublicationListDialog(params) {
PublicationListDialog.prototype = Object.create(AbstractGuiElement.prototype);
PublicationListDialog.prototype.constructor = PublicationListDialog;
+/**
+ *
+ */
PublicationListDialog.prototype.createPublicationListDialogGui = function () {
var self = this;
var head = Functions.createElement({
@@ -51,6 +65,13 @@ PublicationListDialog.prototype.createPublicationListDialogGui = function () {
self.getElement().appendChild(tableElement);
};
+/**
+ *
+ * @param data
+ * @param {function} callback
+ * @returns {Promise}
+ * @private
+ */
PublicationListDialog.prototype._dataTableAjaxCall = function (data, callback) {
var self = this;
return ServerConnector.getPublications({
@@ -126,6 +147,10 @@ PublicationListDialog.prototype._dataTableAjaxCall = function (data, callback) {
});
};
+/**
+ *
+ * @returns {Promise}
+ */
PublicationListDialog.prototype.show = function () {
var self = this;
if (!$(self.getElement()).hasClass("ui-dialog-content")) {
@@ -158,6 +183,10 @@ PublicationListDialog.prototype.show = function () {
};
+/**
+ *
+ * @returns {*[]}
+ */
PublicationListDialog.prototype.getColumnsDefinition = function () {
return [{
name: "pubmedId"
@@ -180,6 +209,9 @@ PublicationListDialog.prototype.getColumnsDefinition = function () {
}];
};
+/**
+ *
+ */
PublicationListDialog.prototype.destroy = function () {
var self = this;
var div = self.getElement();
diff --git a/frontend-js/src/main/js/gui/leftPanel/SubmapPanel.js b/frontend-js/src/main/js/gui/leftPanel/SubmapPanel.js
index 2d08849eb5..d13f95c800 100644
--- a/frontend-js/src/main/js/gui/leftPanel/SubmapPanel.js
+++ b/frontend-js/src/main/js/gui/leftPanel/SubmapPanel.js
@@ -10,6 +10,18 @@ var PanelControlElementType = require('../PanelControlElementType');
var logger = require('../../logger');
var Functions = require('../../Functions');
+/**
+ *
+ * @param {Object} params
+ * @param {HTMLElement} params.element
+ * @param {CustomMap} params.customMap
+ * @param {Configuration} [params.configuration]
+ * @param {Project} [params.project]
+ * @param params.parent
+ *
+ * @constructor
+ * @extends Panel
+ */
function SubmapPanel(params) {
params.panelName = "submap";
params.scrollable = true;
@@ -24,6 +36,10 @@ function SubmapPanel(params) {
SubmapPanel.prototype = Object.create(Panel.prototype);
SubmapPanel.prototype.constructor = SubmapPanel;
+/**
+ *
+ * @private
+ */
SubmapPanel.prototype._createSubmapGui = function () {
var submapDiv = Functions.createElement({
type: "div",
@@ -35,6 +51,11 @@ SubmapPanel.prototype._createSubmapGui = function () {
};
+/**
+ *
+ * @param {MapModel} model
+ * @returns {HTMLTableRowElement}
+ */
SubmapPanel.prototype.createRow = function (model) {
var self = this;
var guiUtils = self.getGuiUtils();
@@ -62,6 +83,10 @@ SubmapPanel.prototype.createRow = function (model) {
return result;
};
+/**
+ *
+ * @returns {HTMLTableSectionElement}
+ */
SubmapPanel.prototype.createTableHeader = function () {
var result = document.createElement("thead");
@@ -81,6 +106,9 @@ SubmapPanel.prototype.createTableHeader = function () {
return result;
};
+/**
+ * @returns {Promise}
+ */
SubmapPanel.prototype.init = function () {
var self = this;
return new Promise(function (resolve) {
@@ -113,6 +141,12 @@ SubmapPanel.prototype.init = function () {
});
};
+/**
+ *
+ * @param {MapModel[]} models
+ * @param {string} type
+ * @returns {HTMLElement}
+ */
SubmapPanel.prototype.createTable = function (models, type) {
var self = this;
var result = Functions.createElement({
@@ -144,6 +178,10 @@ SubmapPanel.prototype.createTable = function (models, type) {
return result;
};
+/**
+ *
+ * @returns {Promise}
+ */
SubmapPanel.prototype.destroy = function () {
return Promise.resolve();
};
diff --git a/frontend-js/src/main/js/gui/topMenu/TopMenu.js b/frontend-js/src/main/js/gui/topMenu/TopMenu.js
index 44016f2259..33ffa629f1 100644
--- a/frontend-js/src/main/js/gui/topMenu/TopMenu.js
+++ b/frontend-js/src/main/js/gui/topMenu/TopMenu.js
@@ -12,6 +12,19 @@ var PanelControlElementType = require('../PanelControlElementType');
var Functions = require('../../Functions');
var logger = require('../../logger');
+/**
+ *
+ * @param {Object} params
+ * @param {HTMLElement} params.element
+ * @param {CustomMap} params.customMap
+ * @param {Configuration} params.configuration
+ * @param {Project} [params.project]
+ * @param {ServerConnector} [params.serverConnector]
+ *
+ * @constructor
+ *
+ * @extends AbstractGuiElement
+ */
function TopMenu(params) {
AbstractGuiElement.call(this, params);
var self = this;
@@ -22,6 +35,10 @@ function TopMenu(params) {
TopMenu.prototype = Object.create(AbstractGuiElement.prototype);
TopMenu.prototype.constructor = TopMenu;
+/**
+ *
+ * @private
+ */
TopMenu.prototype._createGui = function () {
var self = this;
@@ -140,6 +157,10 @@ TopMenu.prototype._createGui = function () {
};
+/**
+ *
+ * @returns {Promise}
+ */
TopMenu.prototype.init = function () {
var self = this;
self.getControlElement(PanelControlElementType.MENU_LEGEND_CHECKBOX).onclick = function () {
@@ -206,22 +227,42 @@ TopMenu.prototype.init = function () {
}
};
+/**
+ *
+ * @param {Legend} legend
+ */
TopMenu.prototype.setLegend = function (legend) {
this._legend = legend;
};
+/**
+ *
+ * @returns {Legend}
+ */
TopMenu.prototype.getLegend = function () {
return this._legend;
};
+/**
+ *
+ * @param {LeftPanel} leftPanel
+ */
TopMenu.prototype.setLeftPanel = function (leftPanel) {
this._leftPanel = leftPanel;
};
+/**
+ *
+ * @returns {LeftPanel}
+ */
TopMenu.prototype.getLeftPanel = function () {
return this._leftPanel;
};
+/**
+ *
+ * @returns {Promise}
+ */
TopMenu.prototype.destroy = function () {
var self = this;
if (self._overviewDialog !== undefined) {
@@ -230,6 +271,9 @@ TopMenu.prototype.destroy = function () {
return Promise.resolve();
};
+/**
+ *
+ */
TopMenu.prototype.toggleLegend = function () {
var self = this;
var legend = self.getLegend();
diff --git a/frontend-js/src/main/js/map/CustomMap.js b/frontend-js/src/main/js/map/CustomMap.js
index e68a051ec5..419f45e184 100644
--- a/frontend-js/src/main/js/map/CustomMap.js
+++ b/frontend-js/src/main/js/map/CustomMap.js
@@ -1270,6 +1270,9 @@ CustomMap.prototype.getSubmaps = function () {
return submaps;
};
+/**
+ *
+ */
CustomMap.prototype.destroy = function () {
var self = this;
AbstractCustomMap.prototype.destroy.call(self);
diff --git a/frontend-js/src/main/js/map/CustomMapOptions.js b/frontend-js/src/main/js/map/CustomMapOptions.js
index 900823b53a..b0ecfd6263 100644
--- a/frontend-js/src/main/js/map/CustomMapOptions.js
+++ b/frontend-js/src/main/js/map/CustomMapOptions.js
@@ -84,9 +84,18 @@ CustomMapOptions.prototype.setServerConnector = function (serverConnector) {
this._serverConnector = serverConnector;
};
+/**
+ *
+ * @returns {{url:string}[]}
+ */
CustomMapOptions.prototype.getPlugins = function () {
return this._plugins;
};
+
+/**
+ *
+ * @param {{url:string}[]} plugins
+ */
CustomMapOptions.prototype.setPlugins = function (plugins) {
if (plugins === undefined) {
plugins = [];
diff --git a/frontend-js/src/main/js/map/OverlayParser.js b/frontend-js/src/main/js/map/OverlayParser.js
index b785ca26b2..3a68e073e5 100644
--- a/frontend-js/src/main/js/map/OverlayParser.js
+++ b/frontend-js/src/main/js/map/OverlayParser.js
@@ -4,6 +4,10 @@ var logger = require('./../logger');
var DataOverlay = require('./data/DataOverlay');
var TextDecoder = require('text-encoding').TextDecoder;
+/**
+ *
+ * @constructor
+ */
function OverlayParser() {
}
diff --git a/frontend-js/src/main/js/map/Submap.js b/frontend-js/src/main/js/map/Submap.js
index 59ebc50730..37979fe92a 100644
--- a/frontend-js/src/main/js/map/Submap.js
+++ b/frontend-js/src/main/js/map/Submap.js
@@ -134,6 +134,9 @@ Submap.prototype.getProject = function () {
return this.getCustomMap().getProject();
};
+/**
+ *
+ */
Submap.prototype.destroy = function () {
var self = this;
AbstractCustomMap.prototype.destroy.call(self);
diff --git a/frontend-js/src/main/js/map/data/Annotator.js b/frontend-js/src/main/js/map/data/Annotator.js
index e5653d2b41..69a8c5c87d 100644
--- a/frontend-js/src/main/js/map/data/Annotator.js
+++ b/frontend-js/src/main/js/map/data/Annotator.js
@@ -6,6 +6,29 @@ var Article = require("./Article");
var logger = require('../../logger');
+/**
+ * @typedef {Object} AnnotatorOptions
+ * @property {string} className
+ * @property {string[]} elementClassNames
+ * @property {string} name
+ * @property {string} description
+ * @property {AnnotatorParameterDefinition[]} parametersDefinitions
+ * @property {string} url
+ */
+
+/**
+ * @typedef {Object} AnnotatorParameterDefinition
+ * @property {string} description
+ * @property {string} name
+ * @property {string} type
+ */
+
+/**
+ *
+ * @param {Annotator|AnnotatorOptions} javaObject
+ * @param {Configuration} configuration
+ * @constructor
+ */
function Annotator(javaObject, configuration) {
var self = this;
if (javaObject instanceof Annotator) {
@@ -25,46 +48,91 @@ function Annotator(javaObject, configuration) {
}
}
+/**
+ *
+ * @param {string} className
+ */
Annotator.prototype.setClassName = function (className) {
this._className = className;
};
+/**
+ *
+ * @returns {string}
+ */
Annotator.prototype.getClassName = function () {
return this._className;
};
+/**
+ *
+ * @param {string} name
+ */
Annotator.prototype.setName = function (name) {
this._name = name;
};
+/**
+ *
+ * @returns {string}
+ */
Annotator.prototype.getName = function () {
return this._name;
};
+/**
+ *
+ * @param {string} description
+ */
Annotator.prototype.setDescription = function (description) {
this._description = description;
};
+/**
+ *
+ * @returns {string}
+ */
Annotator.prototype.getDescription = function () {
return this._description;
};
+/**
+ *
+ * @param {string} url
+ */
Annotator.prototype.setUrl = function (url) {
this._url = url;
};
+/**
+ *
+ * @returns {string}
+ */
Annotator.prototype.getUrl = function () {
return this._url;
};
+/**
+ *
+ * @returns {AnnotatorParameterDefinition[]}
+ */
Annotator.prototype.getParametersDefinitions = function () {
return this._parametersDefinitions;
};
+/**
+ *
+ * @param {AnnotatorParameterDefinition[]} parametersDefinitions
+ */
Annotator.prototype.setParametersDefinitions = function (parametersDefinitions) {
this._parametersDefinitions = parametersDefinitions;
};
+/**
+ *
+ * @param {string[]} elementTypesClassNames
+ * @param {Configuration} configuration
+ */
Annotator.prototype.setElementTypes = function (elementTypesClassNames, configuration) {
this._elementTypes = [];
var typeByClassName = {};
@@ -90,6 +158,10 @@ Annotator.prototype.setElementTypes = function (elementTypesClassNames, configur
}
};
+/**
+ *
+ * @returns {BioEntityType[]}
+ */
Annotator.prototype.getElementTypes = function () {
return this._elementTypes;
};
diff --git a/frontend-js/src/main/js/map/data/DataOverlay.js b/frontend-js/src/main/js/map/data/DataOverlay.js
index 2e8b47eacd..16692fff0d 100644
--- a/frontend-js/src/main/js/map/data/DataOverlay.js
+++ b/frontend-js/src/main/js/map/data/DataOverlay.js
@@ -376,10 +376,18 @@ DataOverlay.prototype.setType = function (type) {
this._type = type;
};
+/**
+ *
+ * @param {boolean} value
+ */
DataOverlay.prototype.setGoogleLicenseConsent = function(value) {
this._googleLicenseConsent = value;
};
+/**
+ *
+ * @returns {boolean}
+ */
DataOverlay.prototype.isGoogleLicenseConsent = function() {
return this._googleLicenseConsent;
};
diff --git a/frontend-js/src/main/js/map/data/IdentifiedElement.js b/frontend-js/src/main/js/map/data/IdentifiedElement.js
index 855cdf88c3..c2bbe28b91 100644
--- a/frontend-js/src/main/js/map/data/IdentifiedElement.js
+++ b/frontend-js/src/main/js/map/data/IdentifiedElement.js
@@ -29,7 +29,7 @@ var logger = require('../../logger');
* objects are stored in {@link PointData}</li>
* </ul>
*
- * @param {BioEntity|LayoutAlias|LayoutReaction|PointData|IdentifiedElementInput} object
+ * @param {BioEntity|LayoutAlias|LayoutReaction|PointData|IdentifiedElement|IdentifiedElementInput} object
* @constructor
*/
function IdentifiedElement(object) {
@@ -193,40 +193,83 @@ IdentifiedElement.prototype.getColor = function () {
return this._visualizationdata._color;
};
+/**
+ *
+ * @param {string} color
+ */
IdentifiedElement.prototype.setColor = function (color) {
this._visualizationdata._color = color;
};
+/**
+ *
+ * @returns {number}
+ */
IdentifiedElement.prototype.getOpacity = function () {
return this._visualizationdata._opacity;
};
+/**
+ *
+ * @param {number} opacity
+ */
IdentifiedElement.prototype.setOpacity = function (opacity) {
this._visualizationdata._opacity = opacity;
};
+/**
+ *
+ * @returns {number}
+ */
IdentifiedElement.prototype.getLineWeight = function () {
return this._visualizationdata._lineWeight;
};
+/**
+ *
+ * @param {number} lineWeight
+ */
IdentifiedElement.prototype.setLineWeight = function (lineWeight) {
this._visualizationdata._lineWeight = lineWeight;
};
+
+/**
+ *
+ * @returns {number}
+ */
IdentifiedElement.prototype.getLineOpacity = function () {
return this._visualizationdata._lineOpacity;
};
+/**
+ *
+ * @param {number} lineOpacity
+ */
IdentifiedElement.prototype.setLineOpacity = function (lineOpacity) {
this._visualizationdata._lineOpacity = lineOpacity;
};
+
+/**
+ *
+ * @returns {string}
+ */
IdentifiedElement.prototype.getLineColor = function () {
return this._visualizationdata._lineColor;
};
+/**
+ *
+ * @param {string} lineColor
+ */
IdentifiedElement.prototype.setLineColor = function (lineColor) {
this._visualizationdata._lineColor = lineColor;
};
+/**
+ *
+ * @param {IdentifiedElement} argument
+ * @returns {boolean}
+ */
IdentifiedElement.prototype.equals = function (argument) {
if (argument instanceof IdentifiedElement) {
return (this.getType() === argument.getType() && //
diff --git a/frontend-js/src/main/js/map/data/KineticLaw.js b/frontend-js/src/main/js/map/data/KineticLaw.js
index 0fd2129d88..5dbb25721f 100644
--- a/frontend-js/src/main/js/map/data/KineticLaw.js
+++ b/frontend-js/src/main/js/map/data/KineticLaw.js
@@ -1,5 +1,18 @@
"use strict";
+/**
+ * @typedef {Object} KineticLawOptions
+ * @property {number[]} parameterIds
+ * @property {number[]} functionIds
+ * @property {string} definition
+ * @property {string} mathMlPresentation
+ */
+
+/**
+ *
+ * @param {KineticLawOptions} jsonObject
+ * @constructor
+ */
function KineticLaw(jsonObject) {
var self = this;
self.setParameterIds(jsonObject.parameterIds);
@@ -8,30 +21,66 @@ function KineticLaw(jsonObject) {
self.setMathMlPresentation(jsonObject.mathMlPresentation);
}
+/**
+ *
+ * @param {number[]} parameterIds
+ */
KineticLaw.prototype.setParameterIds = function (parameterIds) {
this._parameterIds = parameterIds;
};
+
+/**
+ *
+ * @returns {number[]}
+ */
KineticLaw.prototype.getParameterIds = function () {
return this._parameterIds;
};
+/**
+ *
+ * @param {number[]} functionIds
+ */
KineticLaw.prototype.setFunctionIds = function (functionIds) {
this._functionIds = functionIds;
};
+
+/**
+ *
+ * @returns {number[]}
+ */
KineticLaw.prototype.getFunctionIds = function () {
return this._functionIds;
};
+/**
+ *
+ * @param {string} definition
+ */
KineticLaw.prototype.setDefinition = function (definition) {
this._definition = definition;
};
+
+/**
+ *
+ * @returns {string}
+ */
KineticLaw.prototype.getDefinition = function () {
return this._definition;
};
+/**
+ *
+ * @param {string} mathMlPresentation
+ */
KineticLaw.prototype.setMathMlPresentation = function (mathMlPresentation) {
this._mathMlPresentation = mathMlPresentation;
};
+
+/**
+ *
+ * @returns {string}
+ */
KineticLaw.prototype.getMathMlPresentation = function () {
return this._mathMlPresentation;
};
diff --git a/frontend-js/src/main/js/map/data/LayoutAlias.js b/frontend-js/src/main/js/map/data/LayoutAlias.js
index e82336b0ce..a8dc512347 100644
--- a/frontend-js/src/main/js/map/data/LayoutAlias.js
+++ b/frontend-js/src/main/js/map/data/LayoutAlias.js
@@ -41,54 +41,106 @@ LayoutAlias.LIGHT = "LIGHT";
LayoutAlias.GENETIC_VARIANT = "GENETIC_VARIANT";
LayoutAlias.GENERIC = "GENERIC";
+/**
+ *
+ * @returns {number}
+ */
LayoutAlias.prototype.getId = function () {
return this.id;
};
+/**
+ *
+ * @param id
+ */
LayoutAlias.prototype.setId = function (id) {
this.id = parseInt(id);
};
+/**
+ *
+ * @returns {number}
+ */
LayoutAlias.prototype.getModelId = function () {
return this._modelId;
};
+/**
+ *
+ * @param modelId
+ */
LayoutAlias.prototype.setModelId = function (modelId) {
this._modelId = parseInt(modelId);
};
+/**
+ *
+ * @returns {number}
+ */
LayoutAlias.prototype.getValue = function () {
return this.value;
};
+/**
+ *
+ * @returns {string}
+ */
LayoutAlias.prototype.getColor = function () {
return this.color;
};
+/**
+ *
+ * @returns {string}
+ */
LayoutAlias.prototype.getType = function () {
return this._type;
};
+/**
+ *
+ * @returns {GeneVariant[]}
+ */
LayoutAlias.prototype.getGeneVariants = function () {
return this._geneVariants;
};
+/**
+ *
+ * @param {number} newValue
+ */
LayoutAlias.prototype.setValue = function (newValue) {
this.value = newValue;
};
+/**
+ *
+ * @param {string} newColor
+ */
LayoutAlias.prototype.setColor = function (newColor) {
this.color = newColor;
};
+/**
+ *
+ * @param {string} newType
+ */
LayoutAlias.prototype.setType = function (newType) {
this._type = newType;
};
+/**
+ *
+ * @param {GeneVariant[]} newGeneVariants
+ */
LayoutAlias.prototype.setGeneVariants = function (newGeneVariants) {
this._geneVariants = newGeneVariants;
};
+/**
+ *
+ * @param {LayoutAlias} alias
+ */
LayoutAlias.prototype.update = function (alias) {
if (!(alias instanceof LayoutAlias)) {
throw new Error("Unknown parameter type: " + alias);
@@ -101,14 +153,26 @@ LayoutAlias.prototype.update = function (alias) {
this.setDescription(alias.getDescription());
};
+/**
+ *
+ * @param {GeneVariant} geneVariant
+ */
LayoutAlias.prototype.addGeneVariant = function (geneVariant) {
this._geneVariants.push(geneVariant);
};
+/**
+ *
+ * @returns {string}
+ */
LayoutAlias.prototype.getDescription = function () {
return this._description;
};
+/**
+ *
+ * @param {string} description
+ */
LayoutAlias.prototype.setDescription = function (description) {
this._description = description;
};
diff --git a/frontend-js/src/main/js/map/data/LayoutReaction.js b/frontend-js/src/main/js/map/data/LayoutReaction.js
index 4c880969b5..f868ab6047 100644
--- a/frontend-js/src/main/js/map/data/LayoutReaction.js
+++ b/frontend-js/src/main/js/map/data/LayoutReaction.js
@@ -2,7 +2,7 @@
/**
* Class representing reaction visualized in a overlay.
- *
+ *
* @param javaObject
* object de-serialized from ajax query to the server side
*/
@@ -14,41 +14,83 @@ function LayoutReaction(javaObject) {
this.setReverse(javaObject.reverse);
}
-LayoutReaction.prototype.getId = function() {
+/**
+ *
+ * @returns {number }
+ */
+LayoutReaction.prototype.getId = function () {
return this.id;
};
-LayoutReaction.prototype.setId = function(id) {
+/**
+ *
+ * @param id
+ */
+LayoutReaction.prototype.setId = function (id) {
this.id = parseInt(id);
};
-LayoutReaction.prototype.getModelId = function() {
+/**
+ *
+ * @returns {number}
+ */
+LayoutReaction.prototype.getModelId = function () {
return this._modelId;
};
-LayoutReaction.prototype.setModelId = function(modelId) {
+/**
+ *
+ * @param modelId
+ */
+LayoutReaction.prototype.setModelId = function (modelId) {
this._modelId = parseInt(modelId);
};
-LayoutReaction.prototype.setWidth = function(width) {
+/**
+ *
+ * @param {number} width
+ */
+LayoutReaction.prototype.setWidth = function (width) {
this.width = width;
};
-LayoutReaction.prototype.setColor = function(color) {
+/**
+ *
+ * @param {string} color
+ */
+LayoutReaction.prototype.setColor = function (color) {
this.color = color;
};
-LayoutReaction.prototype.setReverse= function(reverse) {
+/**
+ *
+ * @param {boolean} reverse
+ */
+LayoutReaction.prototype.setReverse = function (reverse) {
this.reverse = reverse;
};
-LayoutReaction.prototype.getWidth = function() {
+/**
+ *
+ * @returns {number}
+ */
+LayoutReaction.prototype.getWidth = function () {
return this.width;
};
-LayoutReaction.prototype.getColor = function() {
+
+/**
+ *
+ * @returns {string}
+ */
+LayoutReaction.prototype.getColor = function () {
return this.color;
};
-LayoutReaction.prototype.getReverse = function() {
+
+/**
+ *
+ * @returns {boolean}
+ */
+LayoutReaction.prototype.getReverse = function () {
return this.reverse;
};
diff --git a/frontend-js/src/main/js/map/data/MapModel.js b/frontend-js/src/main/js/map/data/MapModel.js
index bbe8d32367..7e75d0e1d5 100644
--- a/frontend-js/src/main/js/map/data/MapModel.js
+++ b/frontend-js/src/main/js/map/data/MapModel.js
@@ -10,12 +10,25 @@ var PointData = require('./PointData');
var Point = require('../canvas/Point');
var Reaction = require('./Reaction');
-// This file describes javascript representation of Java Model class that
-// represents content of the map.
+/**
+ * @typedef {Object} MapModelOptions
+ * @property {number} idObject
+ * @property {string} name
+ * @property {number} tileSize
+ * @property {number} width
+ * @property {number} height
+ * @property {number} minZoom
+ * @property {number} maxZoom
+ * @property {string} submodelType
+ * @property {number} defaultCenterX
+ * @property {number} defaultCenterY
+ * @property {number} defaultZoomLevel
+ */
/**
- * Default constructor.
*
+ * @param {MapModel|MapModelOptions} configuration
+ * @constructor
*/
function MapModel(configuration) {
@@ -75,6 +88,13 @@ function MapModel(configuration) {
/**
* Return list of all aliases that were added to the model.
+ *
+ * @param {Object} params
+ * @param {string} params.type
+ * @param {number[]} params.includedCompartmentIds
+ * @param {number[]} params.excludedCompartmentIds
+ * @param {boolean} params.complete
+ * @returns {Promise}
*/
MapModel.prototype.getAliases = function (params) {
var self = this;
@@ -101,7 +121,7 @@ MapModel.prototype.getAliases = function (params) {
* @param {boolean} [complete]
* @param {number} id
* identifier of the {@link Alias}
- * @returns {PromiseLike<Alias>} by identifier
+ * @returns {Promise<Alias>} by identifier
*/
MapModel.prototype.getAliasById = function (id, complete) {
var self = this;
@@ -119,6 +139,13 @@ MapModel.prototype.getAliasById = function (id, complete) {
}
};
+/**
+ * Returns {@link Alias} by identifier.
+ *
+* @param {number} id
+ * identifier of the {@link Alias}
+ * @returns {Promise<Alias>} by identifier
+ */
MapModel.prototype.getCompleteAliasById = function (id) {
var self = this;
if (self._aliases[id] !== undefined && self._aliases[id].isComplete()) {
@@ -143,7 +170,7 @@ MapModel.prototype.getCompleteAliasById = function (id) {
* @param id
* identifier of the {@link Reaction}
* @param {boolean} [complete]
- * @returns {Promise<Reaction>| PromiseLike<Reaction>} by identifier
+ * @returns {Promise<Reaction>} by identifier
*/
MapModel.prototype.getReactionById = function (id, complete) {
var self = this;
@@ -161,6 +188,12 @@ MapModel.prototype.getReactionById = function (id, complete) {
}
};
+/**
+ * TODO this function probably doesn't work because elements are of class Alias
+ * @param {Reaction[]} reactions
+ * @returns {Array}
+ * @private
+ */
MapModel.prototype._getMissingReactionsElementIds = function (reactions) {
var self = this;
var result = [];
@@ -183,6 +216,11 @@ MapModel.prototype._getMissingReactionsElementIds = function (reactions) {
return result;
};
+/**
+ * TODO this reaction should be refactored because getMissingElements returns empty list
+ * @param {number} id
+ * @returns {Promise<Reaction>}
+ */
MapModel.prototype.getCompleteReactionById = function (id) {
var self = this;
if (self._reactions[id] instanceof Reaction && self._reactions[id].isComplete()) {
@@ -218,6 +256,11 @@ MapModel.prototype.getCompleteReactionById = function (id) {
}
};
+/**
+ *
+ * @param {{reactionIds:number[], aliasIds:number[]}} elements
+ * @returns {Promise}
+ */
MapModel.prototype.getMissingElements = function (elements) {
var self = this;
@@ -395,10 +438,18 @@ MapModel.prototype._pointToId = function (point) {
}
};
+/**
+ *
+ * @returns {number}
+ */
MapModel.prototype.getId = function () {
return this.id;
};
+/**
+ *
+ * @param id
+ */
MapModel.prototype.setId = function (id) {
this.id = parseInt(id);
};
@@ -411,6 +462,10 @@ MapModel.prototype.getWidth = function () {
return this._width;
};
+/**
+ *
+ * @param {number} width
+ */
MapModel.prototype.setWidth = function (width) {
this._width = width;
};
@@ -423,14 +478,26 @@ MapModel.prototype.getHeight = function () {
return this._height;
};
+/**
+ *
+ * @param {number} height
+ */
MapModel.prototype.setHeight = function (height) {
this._height = height;
};
+/**
+ *
+ * @returns {string}
+ */
MapModel.prototype.getName = function () {
return this._name;
};
+/**
+ *
+ * @param {string} name
+ */
MapModel.prototype.setName = function (name) {
this._name = name;
};
@@ -443,6 +510,10 @@ MapModel.prototype.getMinZoom = function () {
return this._minZoom;
};
+/**
+ *
+ * @param {number} minZoom
+ */
MapModel.prototype.setMinZoom = function (minZoom) {
this._minZoom = minZoom;
};
@@ -495,6 +566,10 @@ MapModel.prototype.getDefaultCenterY = function () {
return this._defaultCenterY;
};
+/**
+ *
+ * @param {number} defaultCenterY
+ */
MapModel.prototype.setDefaultCenterY = function (defaultCenterY) {
if (!isNaN(defaultCenterY)) {
this._defaultCenterY = defaultCenterY;
@@ -503,18 +578,34 @@ MapModel.prototype.setDefaultCenterY = function (defaultCenterY) {
}
};
+/**
+ *
+ * @returns {string}
+ */
MapModel.prototype.getSubmodelType = function () {
return this._submodelType;
};
+/**
+ *
+ * @param {string} submodelType
+ */
MapModel.prototype.setSubmodelType = function (submodelType) {
this._submodelType = submodelType;
};
+/**
+ *
+ * @returns {number}
+ */
MapModel.prototype.getMaxZoom = function () {
return this._maxZoom;
};
+/**
+ *
+ * @param {number} maxZoom
+ */
MapModel.prototype.setMaxZoom = function (maxZoom) {
this._maxZoom = maxZoom;
};
@@ -527,14 +618,28 @@ MapModel.prototype.getTileSize = function () {
return this._tileSize;
};
+/**
+ * TODO remove this - it's unused
+ * @returns {number}
+ */
MapModel.prototype.getPictureSize = function () {
return Math.max(this.getWidth(), this.getHeight());
};
+/**
+ *
+ * @param {number} tileSize
+ */
MapModel.prototype.setTileSize = function (tileSize) {
this._tileSize = tileSize;
};
+/**
+ *
+ * @param {IdentifiedElement} ie
+ * @param {boolean} complete
+ * @returns {Promise}
+ */
MapModel.prototype.getByIdentifiedElement = function (ie, complete) {
var self = this;
if (ie.getType() === "ALIAS") {
@@ -554,6 +659,12 @@ MapModel.prototype.getByIdentifiedElement = function (ie, complete) {
}
};
+/**
+ *
+ * @param {IdentifiedElement[]} identifiedElements
+ * @param {boolean} complete
+ * @returns {Promise}
+ */
MapModel.prototype.getByIdentifiedElements = function (identifiedElements, complete) {
var self = this;
var missingAliases = [];
@@ -583,9 +694,14 @@ MapModel.prototype.getByIdentifiedElements = function (identifiedElements, compl
}
return Promise.all(promises);
});
-
};
+/**
+ *
+ * @param {IdentifiedElement} ie
+ * @param {boolean} complete
+ * @returns {boolean}
+ */
MapModel.prototype.isAvailable = function (ie, complete) {
var element;
if (ie.getType() === "ALIAS") {
@@ -612,10 +728,22 @@ MapModel.prototype.isAvailable = function (ie, complete) {
}
};
+/**
+ *
+ * @param {Alias} element
+ * @param {boolean} complete
+ * @returns {Promise}
+ */
MapModel.prototype.getReactionsForElement = function (element, complete) {
return this.getReactionsForElements([element], complete);
};
+/**
+ *
+ * @param {Alias[]} elements
+ * @param {boolean} complete
+ * @returns {Promise}
+ */
MapModel.prototype.getReactionsForElements = function (elements, complete) {
var self = this;
var ids = [];
@@ -667,6 +795,10 @@ MapModel.prototype.getReactionsForElements = function (elements, complete) {
});
};
+/**
+ *
+ * @returns {Promise}
+ */
MapModel.prototype.getCompartments = function () {
var self = this;
@@ -688,16 +820,28 @@ MapModel.prototype.getCompartments = function () {
});
};
+/**
+ *
+ * @param {SbmlFunction} sbmlFunction
+ */
MapModel.prototype.addSbmlFunction = function (sbmlFunction) {
this._sbmlFunctions[sbmlFunction.getId()] = sbmlFunction;
};
+/**
+ *
+ * @param {SbmlParameter} sbmlParameter
+ */
MapModel.prototype.addSbmlParameter = function (sbmlParameter) {
this._sbmlParameters[sbmlParameter.getId()] = sbmlParameter;
};
-
+/**
+ *
+ * @param {number} id
+ * @returns {Promise}
+ */
MapModel.prototype.getSbmlFunctionById = function (id) {
var self = this;
if (self._sbmlFunctions[id] !== undefined) {
@@ -710,6 +854,11 @@ MapModel.prototype.getSbmlFunctionById = function (id) {
}
};
+/**
+ *
+ * @param {number} id
+ * @returns {Promise}
+ */
MapModel.prototype.getSbmlParameterById = function (id) {
var self = this;
if (self._sbmlParameters[id] !== undefined) {
diff --git a/frontend-js/src/main/js/map/data/Mesh.js b/frontend-js/src/main/js/map/data/Mesh.js
index 433f5ca992..e95d14c47b 100644
--- a/frontend-js/src/main/js/map/data/Mesh.js
+++ b/frontend-js/src/main/js/map/data/Mesh.js
@@ -1,5 +1,19 @@
"use strict";
+/**
+ * @typedef {Object} MeshOptions
+ * @property {string} name
+ * @property {string[]} synonyms
+ * @property {string} id
+ * @property {string} description
+ */
+
+
+/**
+ *
+ * @param {MeshOptions} jsonObject
+ * @constructor
+ */
function Mesh(jsonObject) {
var self = this;
self.setSynonyms(jsonObject.synonyms);
@@ -8,27 +22,66 @@ function Mesh(jsonObject) {
self.setDescription(jsonObject.description);
}
+/**
+ *
+ * @param {string[]} synonyms
+ */
Mesh.prototype.setSynonyms = function (synonyms) {
this._synonyms = synonyms;
};
+
+/**
+ *
+ * @returns {string[]}
+ */
Mesh.prototype.getSynonyms = function () {
return this._synonyms;
};
+
+/**
+ *
+ * @param {string} name
+ */
Mesh.prototype.setName = function (name) {
this._name = name;
};
+
+/**
+ *
+ * @returns {string}
+ */
Mesh.prototype.getName = function () {
return this._name;
};
+
+/**
+ *
+ * @param {string} id
+ */
Mesh.prototype.setId = function (id) {
this._id = id;
};
+
+/**
+ *
+ * @returns {string}
+ */
Mesh.prototype.getId = function () {
return this._id;
};
+
+/**
+ *
+ * @param {string} description
+ */
Mesh.prototype.setDescription = function (description) {
this._description = description;
};
+
+/**
+ *
+ * @returns {string}
+ */
Mesh.prototype.getDescription = function () {
return this._description;
};
diff --git a/frontend-js/src/main/js/map/data/MiRna.js b/frontend-js/src/main/js/map/data/MiRna.js
index a5b7996533..65f101f982 100644
--- a/frontend-js/src/main/js/map/data/MiRna.js
+++ b/frontend-js/src/main/js/map/data/MiRna.js
@@ -2,6 +2,12 @@
var TargettingStructure = require("./TargettingStructure");
+/**
+ *
+ * @param javaObject
+ * @constructor
+ * @extends TargettingStructure
+ */
function MiRna(javaObject) {
TargettingStructure.call(this, javaObject);
}
diff --git a/frontend-js/src/main/js/map/data/MiriamType.js b/frontend-js/src/main/js/map/data/MiriamType.js
index 80772a63e0..e97e5dc37a 100644
--- a/frontend-js/src/main/js/map/data/MiriamType.js
+++ b/frontend-js/src/main/js/map/data/MiriamType.js
@@ -1,7 +1,21 @@
"use strict";
var ObjectWithListeners = require('../../ObjectWithListeners');
+/**
+ * @typedef {Object} MiriamTypeOptions
+ * @property {string[]} uris
+ * @property {string} homepage
+ * @property {string} commonName
+ * @property {string} registryIdentifier
+ */
+
+/**
+ *
+ * @param {MiriamTypeOptions} data
+ * @param {string} name
+ * @constructor
+ */
function MiriamType(data, name) {
// call super constructor
ObjectWithListeners.call(this);
@@ -17,42 +31,82 @@ function MiriamType(data, name) {
MiriamType.prototype = Object.create(ObjectWithListeners.prototype);
MiriamType.prototype.constructor = MiriamType;
+/**
+ *
+ * @param {string[]} uris
+ */
MiriamType.prototype.setUris = function(uris) {
this._uris = uris;
};
+/**
+ *
+ * @returns {string[]}
+ */
MiriamType.prototype.getUris = function() {
return this._uris;
};
+/**
+ *
+ * @param {string} homepage
+ */
MiriamType.prototype.setHomepage = function(homepage) {
this._homepage = homepage;
};
+/**
+ *
+ * @returns {string}
+ */
MiriamType.prototype.getHomepage = function() {
return this._homepage;
};
+/**
+ *
+ * @param {string} name
+ */
MiriamType.prototype.setName = function(name) {
this._name = name;
};
+/**
+ *
+ * @returns {string}
+ */
MiriamType.prototype.getName = function() {
return this._name;
};
+/**
+ *
+ * @param {string} commonName
+ */
MiriamType.prototype.setCommonName = function(commonName) {
this._commonName = commonName;
};
+/**
+ *
+ * @returns {string}
+ */
MiriamType.prototype.getCommonName = function() {
return this._commonName;
};
+/**
+ *
+ * @param {string} registryIdentifier
+ */
MiriamType.prototype.setRegistryIdentifier = function(registryIdentifier) {
this._registryIdentifier = registryIdentifier;
};
+/**
+ *
+ * @returns {string}
+ */
MiriamType.prototype.getRegistryIdentifier = function() {
return this._registryIdentifier;
};
diff --git a/frontend-js/src/main/js/map/data/ModificationStateType.js b/frontend-js/src/main/js/map/data/ModificationStateType.js
index 3343d4de42..aa8f2b9520 100644
--- a/frontend-js/src/main/js/map/data/ModificationStateType.js
+++ b/frontend-js/src/main/js/map/data/ModificationStateType.js
@@ -2,6 +2,19 @@
var ObjectWithListeners = require('../../ObjectWithListeners');
+/**
+ * @typedef {Object} ModificationStateTypeOptions
+ * @property {string} abbreviation
+ * @property {string} commonName
+ */
+
+/**
+ *
+ * @param {ModificationStateTypeOptions} data
+ * @param {string} name
+ * @constructor
+ * @extends ObjectWithListeners
+ */
function ModificationStateType(data, name) {
// call super constructor
ObjectWithListeners.call(this);
@@ -15,27 +28,51 @@ function ModificationStateType(data, name) {
ModificationStateType.prototype = Object.create(ObjectWithListeners.prototype);
ModificationStateType.prototype.constructor = ModificationStateType;
-ModificationStateType.prototype.setName = function(name) {
+/**
+ *
+ * @param {string} name
+ */
+ModificationStateType.prototype.setName = function (name) {
this._name = name;
};
-ModificationStateType.prototype.getName = function() {
+/**
+ *
+ * @returns {string}
+ */
+ModificationStateType.prototype.getName = function () {
return this._name;
};
-ModificationStateType.prototype.setAbbreviation= function(abbreviation) {
+/**
+ *
+ * @param {string} abbreviation
+ */
+ModificationStateType.prototype.setAbbreviation = function (abbreviation) {
this._abbreviation = abbreviation;
};
-ModificationStateType.prototype.getAbbreviation = function() {
+/**
+ *
+ * @returns {string}
+ */
+ModificationStateType.prototype.getAbbreviation = function () {
return this._abbreviation;
};
-ModificationStateType.prototype.setCommonName = function(commonName) {
+/**
+ *
+ * @param {string} commonName
+ */
+ModificationStateType.prototype.setCommonName = function (commonName) {
this._commonName = commonName;
};
-ModificationStateType.prototype.getCommonName = function() {
+/**
+ *
+ * @returns {string}
+ */
+ModificationStateType.prototype.getCommonName = function () {
return this._commonName;
};
diff --git a/frontend-js/src/main/js/map/data/Modifier.js b/frontend-js/src/main/js/map/data/Modifier.js
index ea94bdd8b4..32aa7c212d 100644
--- a/frontend-js/src/main/js/map/data/Modifier.js
+++ b/frontend-js/src/main/js/map/data/Modifier.js
@@ -1,20 +1,49 @@
"use strict";
+/**
+ * @typedef {Object} ModifierOptions
+ * @property {number} aliasId
+ * @property {string} stoichiometry
+ */
+/**
+ *
+ * @param {ModifierOptions} javaObject
+ * @constructor
+ */
function Modifier(javaObject) {
this.setAlias(javaObject.aliasId);
this.setStoichiometry(javaObject.stoichiometry);
}
+/**
+ *
+ * @returns {number}
+ */
Modifier.prototype.getAlias = function () {
return this._alias;
};
+
+/**
+ *
+ * @param {number} alias
+ */
Modifier.prototype.setAlias = function (alias) {
this._alias = alias;
};
+
+/**
+ *
+ * @returns {string}
+ */
Modifier.prototype.getStoichiometry = function () {
return this._stoichiometry;
};
+
+/**
+ *
+ * @param {string} stoichiometry
+ */
Modifier.prototype.setStoichiometry = function (stoichiometry) {
this._stoichiometry = stoichiometry;
};
diff --git a/frontend-js/src/main/js/map/data/PointData.js b/frontend-js/src/main/js/map/data/PointData.js
index 0d23a5dd3c..8e1b4db620 100644
--- a/frontend-js/src/main/js/map/data/PointData.js
+++ b/frontend-js/src/main/js/map/data/PointData.js
@@ -49,6 +49,10 @@ PointData.prototype.getModelId = function() {
return this._modelId;
};
+/**
+ *
+ * @returns {boolean}
+ */
PointData.prototype.isComplete = function() {
return true;
};
diff --git a/frontend-js/src/main/js/map/data/PrivilegeType.js b/frontend-js/src/main/js/map/data/PrivilegeType.js
index be25207f9d..ddfb90ca88 100644
--- a/frontend-js/src/main/js/map/data/PrivilegeType.js
+++ b/frontend-js/src/main/js/map/data/PrivilegeType.js
@@ -2,6 +2,20 @@
var ObjectWithListeners = require('../../ObjectWithListeners');
+/**
+ * @typedef {Object} PrivilegeTypeOptions
+ * @property {string} commonName
+ * @property {string} objectType
+ * @property {string} valueType
+ */
+
+/**
+ *
+ * @param {PrivilegeTypeOptions} data
+ * @param {string} name
+ * @constructor
+ * @extends ObjectWithListeners
+ */
function PrivilegeType(data, name) {
// call super constructor
ObjectWithListeners.call(this);
@@ -21,32 +35,66 @@ PrivilegeType.MANAGE_GENOMES = 'MANAGE_GENOMES';
PrivilegeType.PROJECT_MANAGEMENT = 'PROJECT_MANAGEMENT';
PrivilegeType.USER_MANAGEMENT = 'USER_MANAGEMENT';
+/**
+ *
+ * @param {string} objectType
+ */
PrivilegeType.prototype.setObjectType = function (objectType) {
this._objectType = objectType;
};
+/**
+ *
+ * @returns {string}
+ */
PrivilegeType.prototype.getObjectType = function () {
return this._objectType;
};
+
+/**
+ *
+ * @param {string} valueType
+ */
PrivilegeType.prototype.setValueType = function (valueType) {
this._valueType = valueType;
};
+/**
+ *
+ * @returns {string}
+ */
PrivilegeType.prototype.getValueType = function () {
return this._valueType;
};
+
+/**
+ *
+ * @param {string} commonName
+ */
PrivilegeType.prototype.setCommonName = function (commonName) {
this._commonName = commonName;
};
+/**
+ *
+ * @returns {string}
+ */
PrivilegeType.prototype.getCommonName = function () {
return this._commonName;
};
+/**
+ *
+ * @param {string} name
+ */
PrivilegeType.prototype.setName = function (name) {
this._name = name;
};
+/**
+ *
+ * @returns {string}
+ */
PrivilegeType.prototype.getName = function () {
return this._name;
};
diff --git a/frontend-js/src/main/js/map/data/Product.js b/frontend-js/src/main/js/map/data/Product.js
index d14459e576..f223368acb 100644
--- a/frontend-js/src/main/js/map/data/Product.js
+++ b/frontend-js/src/main/js/map/data/Product.js
@@ -1,23 +1,45 @@
"use strict";
-
+/**
+ *
+ * @param {ModifierOptions} javaObject
+ * @constructor
+ */
function Product(javaObject) {
this.setAlias(javaObject.aliasId);
this.setStoichiometry(javaObject.stoichiometry);
}
+/**
+ *
+ * @returns {number}
+ */
Product.prototype.getAlias = function () {
return this._alias;
};
+
+/**
+ *
+ * @param {number} alias
+ */
Product.prototype.setAlias = function (alias) {
this._alias = alias;
};
+
+/**
+ *
+ * @returns {string}
+ */
Product.prototype.getStoichiometry = function () {
return this._stoichiometry;
};
+
+/**
+ *
+ * @param {string} stoichiometry
+ */
Product.prototype.setStoichiometry = function (stoichiometry) {
this._stoichiometry = stoichiometry;
};
-
module.exports = Product;
diff --git a/frontend-js/src/main/js/map/data/Project.js b/frontend-js/src/main/js/map/data/Project.js
index 0f9114d09d..82cab1d4c5 100644
--- a/frontend-js/src/main/js/map/data/Project.js
+++ b/frontend-js/src/main/js/map/data/Project.js
@@ -13,6 +13,15 @@ var Promise = require('bluebird');
// noinspection JSUnusedLocalSymbols
var logger = require('../../logger');
+/**
+ * @typedef {Object} OverviewImage
+ * @property {number} idObject
+ * @property {number} width
+ * @property {number} height
+ * @property {string} filename
+ */
+
+
/**
*
* @param {Project|string|Object} [data]
@@ -260,16 +269,34 @@ Project.prototype.addModel = function (model) {
this._models.push(model);
};
+/**
+ *
+ * @returns {OverviewImage[]}
+ */
Project.prototype.getOverviewImages = function () {
return this._overviewImages;
};
+
+/**
+ *
+ * @param {OverviewImage[]} overviewImages
+ */
Project.prototype.setOverviewImages = function (overviewImages) {
this._overviewImages = overviewImages;
};
+/**
+ *
+ * @returns {OverviewImage}
+ */
Project.prototype.getTopOverviewImage = function () {
return this._topOverviewImage;
};
+
+/**
+ *
+ * @param {OverviewImage} topOverviewImage
+ */
Project.prototype.setTopOverviewImage = function (topOverviewImage) {
this._topOverviewImage = topOverviewImage;
};
@@ -284,7 +311,7 @@ Project.prototype.getDisease = function () {
/**
*
- * @param {Object} disease
+ * @param {AnnotationOptions} disease
*/
Project.prototype.setDisease = function (disease) {
if (disease !== undefined && disease !== null) {
@@ -304,7 +331,7 @@ Project.prototype.getOrganism = function () {
/**
*
- * @param {Object} organism
+ * @param {AnnotationOptions} organism
*/
Project.prototype.setOrganism = function (organism) {
if (organism !== undefined && organism !== null) {
@@ -461,7 +488,7 @@ Project.prototype.getDataOverlays = function () {
*
* @param {number} overlayId
* overlay identifier
- * @returns {PromiseLike<DataOverlay>} for a given overlay identifier
+ * @returns {Promise<DataOverlay>} for a given overlay identifier
*/
Project.prototype.getDataOverlayById = function (overlayId) {
var self = this;
diff --git a/frontend-js/src/main/js/map/data/ProjectStatistics.js b/frontend-js/src/main/js/map/data/ProjectStatistics.js
index 5230dbdad6..a1bde29512 100644
--- a/frontend-js/src/main/js/map/data/ProjectStatistics.js
+++ b/frontend-js/src/main/js/map/data/ProjectStatistics.js
@@ -6,6 +6,13 @@ var ObjectWithListeners = require('../../ObjectWithListeners');
var logger = require('../../logger');
+/**
+ *
+ * @param data
+ * @param {Configuration} configuration
+ * @constructor
+ * @extends ObjectWithListeners
+ */
function ProjectStatistics(data, configuration) {
// call super constructor
ObjectWithListeners.call(this);
@@ -18,45 +25,73 @@ function ProjectStatistics(data, configuration) {
ProjectStatistics.prototype = Object.create(ObjectWithListeners.prototype);
ProjectStatistics.prototype.constructor = ProjectStatistics;
-ProjectStatistics.prototype.setReactionAnnotations = function(reactionAnnotations, configuration) {
+/**
+ *
+ * @param {Object<string, number>} reactionAnnotations
+ * @param {Configuration} configuration
+ */
+ProjectStatistics.prototype.setReactionAnnotations = function (reactionAnnotations, configuration) {
var self = this;
self._reactionAnnotations = [];
- for ( var key in reactionAnnotations) {
+ for (var key in reactionAnnotations) {
if (reactionAnnotations.hasOwnProperty(key)) {
var miriamType = configuration.getMiriamTypeByName(key);
self._reactionAnnotations.push({
- miriamType : miriamType,
- count : reactionAnnotations[key]
+ miriamType: miriamType,
+ count: reactionAnnotations[key]
});
}
}
};
-ProjectStatistics.prototype.setElementAnnotations = function(elementAnnotations, configuration) {
+/**
+ *
+ * @param {Object<string, number>} elementAnnotations
+ * @param {Configuration} configuration
+ */
+ProjectStatistics.prototype.setElementAnnotations = function (elementAnnotations, configuration) {
var self = this;
self._elementAnnotations = [];
- for ( var key in elementAnnotations) {
+ for (var key in elementAnnotations) {
if (elementAnnotations.hasOwnProperty(key)) {
var miriamType = configuration.getMiriamTypeByName(key);
self._elementAnnotations.push({
- miriamType : miriamType,
- count : elementAnnotations[key]
+ miriamType: miriamType,
+ count: elementAnnotations[key]
});
}
}
};
-ProjectStatistics.prototype.getElementAnnotations = function() {
+/**
+ *
+ * @returns {{miriamType:MiriamType, count:number}[]}
+ */
+ProjectStatistics.prototype.getElementAnnotations = function () {
return this._elementAnnotations;
};
-ProjectStatistics.prototype.getReactionAnnotations = function() {
+
+/**
+ *
+ * @returns {{miriamType:MiriamType, count:number}[]}
+ */
+ProjectStatistics.prototype.getReactionAnnotations = function () {
return this._reactionAnnotations;
};
-ProjectStatistics.prototype.setPublicationCount = function(count) {
+/**
+ *
+ * @param {number} count
+ */
+ProjectStatistics.prototype.setPublicationCount = function (count) {
this._publicationsCount = count;
};
-ProjectStatistics.prototype.getPublicationCount = function() {
+
+/**
+ *
+ * @returns {number}
+ */
+ProjectStatistics.prototype.getPublicationCount = function () {
return this._publicationsCount;
};
diff --git a/frontend-js/src/main/js/map/data/Reactant.js b/frontend-js/src/main/js/map/data/Reactant.js
index d6f65d3175..592de3d97b 100644
--- a/frontend-js/src/main/js/map/data/Reactant.js
+++ b/frontend-js/src/main/js/map/data/Reactant.js
@@ -3,28 +3,54 @@
var Alias = require("./Alias");
+/**
+ *
+ * @param {ModifierOptions} javaObject
+ * @constructor
+ */
function Reactant(javaObject) {
this.setAlias(javaObject.aliasId);
this.setStoichiometry(javaObject.stoichiometry);
}
+/**
+ *
+ * @returns {number}
+ */
Reactant.prototype.getAlias = function () {
return this._alias;
};
+/**
+ *
+ * @param {number} alias
+ */
Reactant.prototype.setAlias = function (alias) {
this._alias = alias;
};
-Reactant.prototype.isComplete = function (alias) {
+/**
+ * TODO check if this method is used
+ * @returns {boolean}
+ */
+Reactant.prototype.isComplete = function () {
return this.getAlias() instanceof Alias;
};
+
+/**
+ *
+ * @returns {string}
+ */
Reactant.prototype.getStoichiometry = function () {
return this._stoichiometry;
};
+
+/**
+ *
+ * @param {string} stoichiometry
+ */
Reactant.prototype.setStoichiometry = function (stoichiometry) {
this._stoichiometry = stoichiometry;
};
-
module.exports = Reactant;
diff --git a/frontend-js/src/main/js/map/data/Reaction.js b/frontend-js/src/main/js/map/data/Reaction.js
index 9e9efffa7d..e9f9daa203 100644
--- a/frontend-js/src/main/js/map/data/Reaction.js
+++ b/frontend-js/src/main/js/map/data/Reaction.js
@@ -17,6 +17,8 @@ var logger = require('../../logger');
*
* @param javaObject
* object de-serialized from ajax query to the server side
+ * @constructor
+ * @extends BioEntity
*/
function Reaction(javaObject) {
BioEntity.call(this, javaObject);
@@ -80,16 +82,34 @@ Reaction.prototype.getLines = function () {
return result;
};
+/**
+ *
+ * @returns {Object[]}
+ */
Reaction.prototype.getMidLines = function () {
return this.midLines;
};
+
+/**
+ *
+ * @returns {Object[]}
+ */
Reaction.prototype.getStartLines = function () {
return this.startLines;
};
+
+/**
+ *
+ * @returns {Object[]}
+ */
Reaction.prototype.getEndLines = function () {
return this.endLines;
};
+/**
+ *
+ * @param {Point| {x:number, y:number}} center
+ */
Reaction.prototype.setCenter = function (center) {
if (center === null || center === undefined) {
throw new Error("Setting undefined center: " + center);
@@ -97,6 +117,10 @@ Reaction.prototype.setCenter = function (center) {
this._center = new Point(center);
};
+/**
+ *
+ * @param javaObject
+ */
Reaction.prototype.update = function (javaObject) {
if (javaObject.reactionId === undefined) {
return;
@@ -147,6 +171,10 @@ Reaction.prototype.update = function (javaObject) {
this.setIsComplete(true);
};
+/**
+ *
+ * @returns {boolean}
+ */
Reaction.prototype.isComplete = function () {
var self = this;
var result = self._complete;
@@ -161,70 +189,138 @@ Reaction.prototype.isComplete = function () {
return result;
};
+/**
+ *
+ * @returns {string}
+ */
Reaction.prototype.getReactionId = function () {
return this._reactionId;
};
+/**
+ *
+ * @param {string} reactionId
+ */
Reaction.prototype.setReactionId = function (reactionId) {
this._reactionId = reactionId;
};
+/**
+ *
+ * @returns {string}
+ */
Reaction.prototype.getMechanicalConfidenceScore = function () {
return this._mechanicalConfidenceScore;
};
+/**
+ *
+ * @param {string} mechanicalConfidenceScore
+ */
Reaction.prototype.setMechanicalConfidenceScore = function (mechanicalConfidenceScore) {
this._mechanicalConfidenceScore = mechanicalConfidenceScore;
};
+/**
+ *
+ * @returns {string}
+ */
Reaction.prototype.getLowerBound = function () {
return this._lowerBound;
};
+/**
+ *
+ * @param {string} lowerBound
+ */
Reaction.prototype.setLowerBound = function (lowerBound) {
this._lowerBound = lowerBound;
};
+/**
+ *
+ * @returns {string}
+ */
Reaction.prototype.getUpperBound = function () {
return this._upperBound;
};
+/**
+ *
+ * @param {string} upperBound
+ */
Reaction.prototype.setUpperBound = function (upperBound) {
this._upperBound = upperBound;
};
+/**
+ *
+ * @param {string} geneProteinReaction
+ */
Reaction.prototype.setGeneProteinReaction = function (geneProteinReaction) {
this._geneProteinReaction = geneProteinReaction;
};
+/**
+ *
+ * @returns {string}
+ */
Reaction.prototype.getGeneProteinReaction = function () {
return this._geneProteinReaction;
};
+/**
+ *
+ * @param {string} subsystem
+ */
Reaction.prototype.setSubsystem = function (subsystem) {
this._subsystem = subsystem;
};
+/**
+ *
+ * @returns {string}
+ */
Reaction.prototype.getSubsystem = function () {
return this._subsystem;
};
+/**
+ *
+ * @returns {Reactant[]}
+ */
Reaction.prototype.getReactants = function () {
return this._reactants;
};
+/**
+ *
+ * @param {Reactant[]} reactants
+ */
Reaction.prototype.setReactants = function (reactants) {
this._reactants = reactants;
};
+/**
+ *
+ * @param {Product[]} products
+ */
Reaction.prototype.setProducts = function (products) {
this._products = products;
};
+/**
+ *
+ * @returns {Product[]}
+ */
Reaction.prototype.getProducts = function () {
return this._products;
};
+/**
+ *
+ * @returns {Alias[]}
+ */
Reaction.prototype.getElements = function () {
var result = [], i;
for (i = 0; i < this.getReactants().length; i++) {
@@ -239,17 +335,34 @@ Reaction.prototype.getElements = function () {
return result;
};
+/**
+ *
+ * @param {Modifier[]} modifiers
+ */
Reaction.prototype.setModifiers = function (modifiers) {
this._modifiers = modifiers;
};
+/**
+ *
+ * @returns {Modifier[]}
+ */
Reaction.prototype.getModifiers = function () {
return this._modifiers;
};
+/**
+ *
+ * @param {KineticLaw} kineticLaw
+ */
Reaction.prototype.setKineticLaw = function (kineticLaw) {
this._kineticLaw = kineticLaw;
};
+
+/**
+ *
+ * @returns {KineticLaw}
+ */
Reaction.prototype.getKineticLaw = function () {
return this._kineticLaw;
};
diff --git a/frontend-js/src/main/js/map/data/ReferenceGenome.js b/frontend-js/src/main/js/map/data/ReferenceGenome.js
index cc90df69f7..2b0d4d4c06 100644
--- a/frontend-js/src/main/js/map/data/ReferenceGenome.js
+++ b/frontend-js/src/main/js/map/data/ReferenceGenome.js
@@ -3,6 +3,23 @@
var Annotation = require('./Annotation');
var ReferenceGenomeGeneMapping = require('./ReferenceGenomeGeneMapping');
+/**
+ * @typedef {Object} ReferenceGenomeOptions
+ * @property {number} idObject
+ * @property {string} type
+ * @property {string} version
+ * @property {string} localUrl
+ * @property {string} sourceUrl
+ * @property {AnnotationOptions} organism
+ * @property {number} downloadProgress
+ * @property {GeneMappingOptions[]} geneMapping
+ */
+
+/**
+ *
+ * @param {ReferenceGenomeOptions} [javaObject]
+ * @constructor
+ */
function ReferenceGenome(javaObject) {
if (javaObject !== undefined && javaObject !== null) {
this.setId(javaObject.idObject);
diff --git a/frontend-js/src/main/js/map/data/ReferenceGenomeGeneMapping.js b/frontend-js/src/main/js/map/data/ReferenceGenomeGeneMapping.js
index d8e955bf20..1d5ec11c43 100644
--- a/frontend-js/src/main/js/map/data/ReferenceGenomeGeneMapping.js
+++ b/frontend-js/src/main/js/map/data/ReferenceGenomeGeneMapping.js
@@ -1,5 +1,20 @@
"use strict";
+
+/**
+ * @typedef {Object} GeneMappingOptions
+ * @property {number} idObject
+ * @property {number} downloadProgress
+ * @property {string} name
+ * @property {string} localUrl
+ * @property {string} sourceUrl
+ */
+
+/**
+ *
+ * @param {GeneMappingOptions} javaObject
+ * @constructor
+ */
function ReferenceGenomeGeneMapping(javaObject) {
this.setName(javaObject.name);
if (javaObject.localUrl !== undefined) {
diff --git a/frontend-js/src/main/js/map/data/SbmlFunction.js b/frontend-js/src/main/js/map/data/SbmlFunction.js
index 077b8a2377..d9a608aeb1 100644
--- a/frontend-js/src/main/js/map/data/SbmlFunction.js
+++ b/frontend-js/src/main/js/map/data/SbmlFunction.js
@@ -1,5 +1,17 @@
"use strict";
+/**
+ *
+ * @param {Object} jsonObject
+ * @param {string} jsonObject.functionId
+ * @param {boolean} jsonObject.global
+ * @param {string} jsonObject.name
+ * @param {number} jsonObject.id
+ * @param {string[]} jsonObject.arguments
+ * @param {string} jsonObject.definition
+ * @param {string} jsonObject.mathMlPresentation
+ * @constructor
+ */
function SbmlFunction(jsonObject) {
var self = this;
self.setFunctionId(jsonObject.functionId);
@@ -10,46 +22,100 @@ function SbmlFunction(jsonObject) {
self.setMathMlPresentation(jsonObject.mathMlPresentation);
}
+/**
+ *
+ * @param {string} functionId
+ */
SbmlFunction.prototype.setFunctionId = function (functionId) {
this._functionId = functionId;
};
+
+/**
+ *
+ * @returns {string}
+ */
SbmlFunction.prototype.getFunctionId = function () {
return this._functionId;
};
+/**
+ *
+ * @param {string} definition
+ */
SbmlFunction.prototype.setDefinition = function (definition) {
this._definition = definition;
};
+
+/**
+ *
+ * @returns {string}
+ */
SbmlFunction.prototype.getDefinition = function () {
return this._definition;
};
+/**
+ *
+ * @param {string} mathMlPresentation
+ */
SbmlFunction.prototype.setMathMlPresentation = function (mathMlPresentation) {
this._mathMlPresentation = mathMlPresentation;
};
+
+/**
+ *
+ * @returns {string}
+ */
SbmlFunction.prototype.getMathMlPresentation = function () {
return this._mathMlPresentation;
};
+/**
+ *
+ * @param {string} name
+ */
SbmlFunction.prototype.setName = function (name) {
this._name = name;
};
+
+/**
+ *
+ * @returns {string}
+ */
SbmlFunction.prototype.getName = function () {
return this._name;
};
+
+/**
+ *
+ * @param {string[]} args
+ */
SbmlFunction.prototype.setArguments = function (args) {
this._arguments = args;
};
+
+/**
+ *
+ * @returns {string[]}
+ */
SbmlFunction.prototype.getArguments = function () {
return this._arguments;
};
+/**
+ *
+ * @param {number} id
+ */
SbmlFunction.prototype.setId = function (id) {
this._id = id;
};
+
+/**
+ *
+ * @returns {number}
+ */
SbmlFunction.prototype.getId = function () {
return this._id;
};
-
module.exports = SbmlFunction;
diff --git a/frontend-js/src/main/js/map/data/SbmlParameter.js b/frontend-js/src/main/js/map/data/SbmlParameter.js
index 3bf2430104..723a82f403 100644
--- a/frontend-js/src/main/js/map/data/SbmlParameter.js
+++ b/frontend-js/src/main/js/map/data/SbmlParameter.js
@@ -1,5 +1,16 @@
"use strict";
+/**
+ *
+ * @param {Object} jsonObject
+ * @param {string} jsonObject.parameterId
+ * @param {number} jsonObject.value
+ * @param {boolean} jsonObject.global
+ * @param {string} jsonObject.name
+ * @param {number} jsonObject.id
+ * @param {number} jsonObject.unitsId
+ * @constructor
+ */
function SbmlParameter(jsonObject) {
var self = this;
self.setParameterId(jsonObject.parameterId);
@@ -10,44 +21,98 @@ function SbmlParameter(jsonObject) {
self.setUnitsId(jsonObject.unitsId);
}
+/**
+ *
+ * @param {string} parameterId
+ */
SbmlParameter.prototype.setParameterId = function (parameterId) {
this._parameterId = parameterId;
};
+
+/**
+ *
+ * @returns {string}
+ */
SbmlParameter.prototype.getParameterId = function () {
return this._parameterId;
};
+/**
+ *
+ * @param {number} unitsId
+ */
SbmlParameter.prototype.setUnitsId = function (unitsId) {
this._unitsId = unitsId;
};
+
+/**
+ *
+ * @returns {number}
+ */
SbmlParameter.prototype.getUnitsId = function () {
return this._unitsId;
};
+/**
+ *
+ * @param {string} value
+ */
SbmlParameter.prototype.setValue = function (value) {
this._value = value;
};
+
+/**
+ *
+ * @returns {string}
+ */
SbmlParameter.prototype.getValue = function () {
return this._value;
};
+/**
+ *
+ * @param {boolean} global
+ */
SbmlParameter.prototype.setGlobal = function (global) {
this._global = global;
};
+
+/**
+ *
+ * @returns {boolean}
+ */
SbmlParameter.prototype.getGlobal = function () {
return this._global;
};
+/**
+ *
+ * @param {string} name
+ */
SbmlParameter.prototype.setName = function (name) {
this._name = name;
};
+
+/**
+ *
+ * @returns {string}
+ */
SbmlParameter.prototype.getName = function () {
return this._name;
};
+/**
+ *
+ * @param {number} id
+ */
SbmlParameter.prototype.setId = function (id) {
this._id = id;
};
+
+/**
+ *
+ * @returns {number}
+ */
SbmlParameter.prototype.getId = function () {
return this._id;
};
diff --git a/frontend-js/src/main/js/map/data/SearchBioEntityGroup.js b/frontend-js/src/main/js/map/data/SearchBioEntityGroup.js
index a7ce5c1c9c..19b4cbe840 100644
--- a/frontend-js/src/main/js/map/data/SearchBioEntityGroup.js
+++ b/frontend-js/src/main/js/map/data/SearchBioEntityGroup.js
@@ -10,8 +10,9 @@ var logger = require('../../logger');
/**
* Class representing merged search bioEntities.
*
- * @param bioEntity
+ * @param {BioEntity} bioEntity
* initial bioEntity from which group is created
+ * @constructor
*/
function SearchBioEntityGroup(bioEntity) {
if (!(bioEntity instanceof BioEntity)) {
@@ -20,6 +21,11 @@ function SearchBioEntityGroup(bioEntity) {
this._bioEntites = [bioEntity];
}
+/**
+ *
+ * @param {BioEntity} newBioEntity
+ * @returns {boolean}
+ */
SearchBioEntityGroup.prototype.bioEntityMatch = function (newBioEntity) {
var result = true;
var self = this;
@@ -33,14 +39,28 @@ SearchBioEntityGroup.prototype.bioEntityMatch = function (newBioEntity) {
return result;
};
+/**
+ *
+ * @param {BioEntity} newBioEntity
+ */
SearchBioEntityGroup.prototype.addBioEntity = function (newBioEntity) {
this._bioEntites.push(newBioEntity);
};
+/**
+ *
+ * @returns {BioEntity[]}
+ */
SearchBioEntityGroup.prototype.getBioEntities = function () {
return this._bioEntites;
};
+/**
+ *
+ * @param {BioEntity} bioEntity1
+ * @param {BioEntity} bioEntity2
+ * @returns {number}
+ */
SearchBioEntityGroup.prototype.bioEntityComparator = function (bioEntity1, bioEntity2) {
if (bioEntity1 instanceof Alias && bioEntity2 instanceof Alias) {
if (bioEntity1.getName() !== bioEntity2.getName()) {
@@ -92,92 +112,196 @@ SearchBioEntityGroup.prototype.bioEntityComparator = function (bioEntity1, bioEn
return -9;
};
+/**
+ *
+ * @param {string} icon
+ */
SearchBioEntityGroup.prototype.setIcon = function (icon) {
this._icon = icon;
};
+/**
+ *
+ * @returns {string}
+ */
SearchBioEntityGroup.prototype.getIcon = function () {
return this._icon;
};
//aggregated data
+/**
+ *
+ * @returns {string}
+ */
SearchBioEntityGroup.prototype.getType = function () {
return this._bioEntites[0].getType();
};
+/**
+ *
+ * @returns {string}
+ */
SearchBioEntityGroup.prototype.getName = function () {
return this._bioEntites[0].getName();
};
+/**
+ *
+ * @returns {number}
+ */
SearchBioEntityGroup.prototype.getModelId = function () {
return this._bioEntites[0].getModelId();
};
+/**
+ *
+ * @returns {number}
+ */
SearchBioEntityGroup.prototype.getCompartmentId = function () {
return this._bioEntites[0].getCompartmentId();
};
+/**
+ *
+ * @returns {Reactant[]}
+ */
SearchBioEntityGroup.prototype.getReactants = function () {
return this._bioEntites[0].getReactants();
};
+
+/**
+ *
+ * @returns {Product[]}
+ */
SearchBioEntityGroup.prototype.getProducts = function () {
return this._bioEntites[0].getProducts();
};
+
+/**
+ *
+ * @returns {Modifier[]}
+ */
SearchBioEntityGroup.prototype.getModifiers = function () {
return this._bioEntites[0].getModifiers();
};
+/**
+ * @returns {string}
+ */
SearchBioEntityGroup.prototype.getFullName = function () {
return this.getMergedParameterByFunction("getFullName");
};
+/**
+ * @returns {string}
+ */
SearchBioEntityGroup.prototype.getReactionId = function () {
return this.getMergedParameterByFunction("getReactionId");
};
+
+/**
+ * @returns {number}
+ */
SearchBioEntityGroup.prototype.getLinkedSubmodelId = function () {
return this.getMergedParameterByFunction("getLinkedSubmodelId");
};
+
+/**
+ * @returns {string}
+ */
SearchBioEntityGroup.prototype.getSymbol = function () {
return this.getMergedParameterByFunction("getSymbol");
};
+
+/**
+ * @returns {string}
+ */
SearchBioEntityGroup.prototype.getAbbreviation = function () {
return this.getMergedParameterByFunction("getAbbreviation");
};
+
+/**
+ * @returns {string}
+ */
SearchBioEntityGroup.prototype.getFormula = function () {
return this.getMergedParameterByFunction("getFormula");
};
+
+/**
+ * @returns {string}
+ */
SearchBioEntityGroup.prototype.getMechanicalConfidenceScore = function () {
return this.getMergedParameterByFunction("getMechanicalConfidenceScore");
};
+
+/**
+ * @returns {string}
+ */
SearchBioEntityGroup.prototype.getLowerBound = function () {
return this.getMergedParameterByFunction("getLowerBound");
};
+
+/**
+ * @returns {string}
+ */
SearchBioEntityGroup.prototype.getUpperBound = function () {
return this.getMergedParameterByFunction("getUpperBound");
};
+
+/**
+ * @returns {string}
+ */
SearchBioEntityGroup.prototype.getGeneProteinReaction = function () {
return this.getMergedParameterByFunction("getGeneProteinReaction");
};
+
+/**
+ * @returns {string}
+ */
SearchBioEntityGroup.prototype.getSubsystem = function () {
return this.getMergedParameterByFunction("getSubsystem");
};
+
+/**
+ * @returns {string}
+ */
SearchBioEntityGroup.prototype.getDescription = function () {
return this.getMergedParameterByFunction("getDescription");
};
+
+/**
+ * @returns {number}
+ */
SearchBioEntityGroup.prototype.getCharge = function () {
return this.getMergedParameterByFunction("getCharge");
};
+
+/**
+ * @returns {string[]}
+ */
SearchBioEntityGroup.prototype.getSynonyms = function () {
return this.getIntersectionListByFunction("getSynonyms");
};
+
+/**
+ * @returns {string[]}
+ */
SearchBioEntityGroup.prototype.getFormerSymbols = function () {
return this.getIntersectionListByFunction("getFormerSymbols");
};
+/**
+ * @returns {Annotation[]}
+ */
SearchBioEntityGroup.prototype.getReferences = function () {
return this.getIntersectionListByFunction("getReferences");
};
+/**
+ *
+ * @param {string} param
+ * @returns {Object}
+ */
SearchBioEntityGroup.prototype.getOther = function (param) {
if (param === "modifications") {
return this.getIntersectionListByFunction(function (alias) {
@@ -188,6 +312,11 @@ SearchBioEntityGroup.prototype.getOther = function (param) {
}
};
+/**
+ *
+ * @param {string} functionName
+ * @returns {*}
+ */
SearchBioEntityGroup.prototype.getMergedParameterByFunction = function (functionName) {
var bioEntities = this.getBioEntities();
var result = bioEntities[0][functionName]();
@@ -200,6 +329,11 @@ SearchBioEntityGroup.prototype.getMergedParameterByFunction = function (function
return result;
};
+/**
+ *
+ * @param {string} functionName
+ * @returns {Array}
+ */
SearchBioEntityGroup.prototype.getIntersectionListByFunction = function (functionName) {
var bioEntities = this.getBioEntities();
var result;
diff --git a/frontend-js/src/main/js/map/data/Target.js b/frontend-js/src/main/js/map/data/Target.js
index 08e5f71303..e4fe0010c5 100644
--- a/frontend-js/src/main/js/map/data/Target.js
+++ b/frontend-js/src/main/js/map/data/Target.js
@@ -7,6 +7,19 @@ var IdentifiedElement = require('./IdentifiedElement');
var logger = require('../../logger');
+/**
+ * @typedef {Object} TargetOptions
+ * @property {string} name
+ * @property {IdentifiedElementInput[]} targetElements
+ * @property {AnnotationOptions[]} targetParticipants
+ * @property {AnnotationOptions[]} references
+ */
+
+/**
+ *
+ * @param {TargetOptions} javaObject
+ * @constructor
+ */
function Target(javaObject) {
this.setName(javaObject.name);
this.setTargetElements(javaObject.targetElements);
@@ -14,7 +27,11 @@ function Target(javaObject) {
this.setReferences(javaObject.references);
}
-Target.prototype.setTargetElements = function(targetElements) {
+/**
+ *
+ * @param {IdentifiedElementInput[]} targetElements
+ */
+Target.prototype.setTargetElements = function (targetElements) {
this._targetElements = [];
for (var i = 0; i < targetElements.length; i++) {
this._targetElements.push(new IdentifiedElement(targetElements[i]));
@@ -22,45 +39,81 @@ Target.prototype.setTargetElements = function(targetElements) {
this.setIsVisible(this._targetElements.length > 0);
};
-Target.prototype.getTargetElements = function() {
+/**
+ *
+ * @returns {IdentifiedElement[]}
+ */
+Target.prototype.getTargetElements = function () {
return this._targetElements;
};
-Target.prototype.setTargetParticipants = function(targetParticipants) {
+/**
+ *
+ * @param {AnnotationOptions[]} targetParticipants
+ */
+Target.prototype.setTargetParticipants = function (targetParticipants) {
this._targetParticipants = [];
for (var i = 0; i < targetParticipants.length; i++) {
this._targetParticipants.push(new Annotation(targetParticipants[i]));
}
};
-Target.prototype.getTargetParticipants = function() {
+/**
+ *
+ * @returns {AnnotationOptions[]}
+ */
+Target.prototype.getTargetParticipants = function () {
return this._targetParticipants;
};
-Target.prototype.setName = function(name) {
+/**
+ *
+ * @param {string} name
+ */
+Target.prototype.setName = function (name) {
this._name = name;
};
-Target.prototype.getName = function() {
+/**
+ *
+ * @returns {string}
+ */
+Target.prototype.getName = function () {
return this._name;
};
-Target.prototype.setIsVisible = function(visible) {
+/**
+ *
+ * @param {boolean} visible
+ */
+Target.prototype.setIsVisible = function (visible) {
this._isVisible = visible;
};
-Target.prototype.isVisible = function() {
+/**
+ *
+ * @returns {boolean}
+ */
+Target.prototype.isVisible = function () {
return this._isVisible;
};
-Target.prototype.setReferences = function(references) {
+/**
+ *
+ * @param {AnnotationOptions[]} references
+ */
+Target.prototype.setReferences = function (references) {
this._references = [];
for (var i = 0; i < references.length; i++) {
this._references.push(new Annotation(references[i]));
}
};
-Target.prototype.getReferences = function() {
+/**
+ *
+ * @returns {Annotation[]}
+ */
+Target.prototype.getReferences = function () {
return this._references;
};
diff --git a/frontend-js/src/main/js/map/data/TargettingStructure.js b/frontend-js/src/main/js/map/data/TargettingStructure.js
index b35a23713c..6bb252a337 100644
--- a/frontend-js/src/main/js/map/data/TargettingStructure.js
+++ b/frontend-js/src/main/js/map/data/TargettingStructure.js
@@ -6,6 +6,14 @@ var Target = require("./Target");
var logger = require('../../logger');
+/**
+ *
+ * @param {Object} [javaObject]
+ * @param {string} javaObject.name
+ * @param {number} javaObject.id
+ * @param {TargetOptions[]} javaObject.targets
+ * @constructor
+ */
function TargettingStructure(javaObject) {
if (javaObject !== undefined) {
this.setName(javaObject.name);
@@ -14,22 +22,42 @@ function TargettingStructure(javaObject) {
}
}
+/**
+ *
+ * @param {string} name
+ */
TargettingStructure.prototype.setName = function(name) {
this._name = name;
};
+/**
+ *
+ * @returns {string}
+ */
TargettingStructure.prototype.getName = function() {
return this._name;
};
+/**
+ *
+ * @param {number} id
+ */
TargettingStructure.prototype.setId = function(id) {
this._id = id;
};
+/**
+ *
+ * @returns {number}
+ */
TargettingStructure.prototype.getId = function() {
return this._id;
};
+/**
+ *
+ * @param {TargetOptions[]} targets
+ */
TargettingStructure.prototype.setTargets = function(targets) {
this._targets = [];
for (var i = 0; i < targets.length; i++) {
@@ -37,10 +65,19 @@ TargettingStructure.prototype.setTargets = function(targets) {
}
};
+/**
+ *
+ * @returns {Target[]}
+ */
TargettingStructure.prototype.getTargets = function() {
return this._targets;
};
+/**
+ *
+ * @param {IdentifiedElement[]} targetIdentifiedElement
+ * @returns {Target[]}
+ */
TargettingStructure.prototype.getTargetsForIdentifiedElement = function(targetIdentifiedElement) {
var result = [];
this.getTargets().forEach(function(target) {
diff --git a/frontend-js/src/main/js/map/data/UserPreferences.js b/frontend-js/src/main/js/map/data/UserPreferences.js
index 6d2fa23a5c..634c42897d 100644
--- a/frontend-js/src/main/js/map/data/UserPreferences.js
+++ b/frontend-js/src/main/js/map/data/UserPreferences.js
@@ -5,6 +5,11 @@
// noinspection JSUnusedLocalSymbols
var logger = require('../../logger');
+/**
+ *
+ * @param [javaObject]
+ * @constructor
+ */
function UserPreferences(javaObject) {
if (javaObject !== undefined) {
this.setProjectUpload(javaObject["project-upload"]);
@@ -23,6 +28,10 @@ function UserPreferences(javaObject) {
}
}
+/**
+ *
+ * @param {UserPreferences} userPreferences
+ */
UserPreferences.prototype.update = function (userPreferences) {
var updateDict = function (originalDict, newDict) {
for (var key in newDict) {
@@ -40,6 +49,16 @@ UserPreferences.prototype.update = function (userPreferences) {
updateDict(this._guiPreferences, userPreferences.getGuiPreferences());
};
+/**
+ *
+ * @param {Object} projectUpload
+ * @param {boolean} projectUpload.auto-resize
+ * @param {boolean} projectUpload.validate-miriam
+ * @param {boolean} projectUpload.validate-miriam
+ * @param {boolean} projectUpload.cache-data
+ * @param {boolean} projectUpload.semantic-zooming
+ * @param {boolean} projectUpload.sbgn
+ */
UserPreferences.prototype.setProjectUpload = function (projectUpload) {
this._projectUpload = {
autoResize: projectUpload["auto-resize"],
diff --git a/frontend-js/src/main/js/map/marker/AliasMarker.js b/frontend-js/src/main/js/map/marker/AliasMarker.js
index 9418c84a78..f1f7578e91 100644
--- a/frontend-js/src/main/js/map/marker/AliasMarker.js
+++ b/frontend-js/src/main/js/map/marker/AliasMarker.js
@@ -52,6 +52,10 @@ AliasMarker.prototype.getCoordinates = function () {
return new Point(alias.getX() + alias.getWidth() / 2, alias.getY() + alias.getHeight() / 2);
};
+/**
+ * TODO sel._init should be called as overriden method (withouth '_')
+ * @returns {Promise<any>}
+ */
AliasMarker.prototype.init = function () {
var self = this;
var model = self.getCustomMap().getModel();
diff --git a/frontend-js/src/main/js/map/overlay/AbstractDbOverlay.js b/frontend-js/src/main/js/map/overlay/AbstractDbOverlay.js
index aedfaaa67d..5f008db463 100644
--- a/frontend-js/src/main/js/map/overlay/AbstractDbOverlay.js
+++ b/frontend-js/src/main/js/map/overlay/AbstractDbOverlay.js
@@ -9,10 +9,22 @@ var Promise = require("bluebird");
var IdentifiedElement = require('../data/IdentifiedElement');
var ObjectWithListeners = require('../../ObjectWithListeners');
-var Point= require('../canvas/Point');
+var Point = require('../canvas/Point');
var ServerConnector = require('../../ServerConnector');
+/**
+ *
+ * @param {Object} params
+ * @param {CustomMap} params.map
+ * @param {string} params.name
+ * @param {boolean} params.allowGeneralSearch
+ * @param {boolean} params.allowSearchById
+ * @param {string} params.iconType
+ * @param {number} params.iconColorStart
+ * @constructor
+ * @extends ObjectWithListeners
+ */
function AbstractDbOverlay(params) {
// call super constructor
ObjectWithListeners.call(this);
@@ -55,6 +67,14 @@ AbstractDbOverlay.QueryType = {
SEARCH_BY_QUERY: "SEARCH_BY_QUERY"
};
+/**
+ * TODO parameters to this function should be changed into a dict
+ * @param {string} type
+ * @param arg0
+ * @param [arg1]
+ * @param [arg2]
+ * @returns {string}
+ */
AbstractDbOverlay.prototype.encodeQuery = function (type, arg0, arg1, arg2) {
if (type === AbstractDbOverlay.QueryType.SEARCH_BY_COORDINATES) {
var modelId = arg0;
@@ -88,10 +108,22 @@ AbstractDbOverlay.prototype.encodeQuery = function (type, arg0, arg1, arg2) {
}
};
+/**
+ *
+ * @param {string} query
+ * @returns {any}
+ */
AbstractDbOverlay.prototype.decodeQuery = function (query) {
return JSON.parse(query);
};
+/**
+ *
+ * @param {string} originalQuery
+ * @param {boolean} [perfect]
+ * @param {boolean} [fitBounds]
+ * @returns {Promise}
+ */
AbstractDbOverlay.prototype.searchByQuery = function (originalQuery, perfect, fitBounds) {
var self = this;
var query = self.encodeQuery(AbstractDbOverlay.QueryType.SEARCH_BY_QUERY, originalQuery, perfect);
@@ -145,14 +177,28 @@ AbstractDbOverlay.prototype.searchByQuery = function (originalQuery, perfect, fi
}
;
+/**
+ *
+ * @param {string[]} queries
+ */
AbstractDbOverlay.prototype.setQueries = function (queries) {
this._queries = queries;
};
+/**
+ *
+ * @returns {string[]}
+ */
AbstractDbOverlay.prototype.getQueries = function () {
return this._queries;
};
+/**
+ *
+ * @param {TargettingStructure} targetingElement
+ * @param {number} colourId
+ * @returns {IdentifiedElement[]}
+ */
AbstractDbOverlay.prototype.createIdentifiedElementsForTargetingClass = function (targetingElement, colourId) {
var self = this;
var result = [];
@@ -179,7 +225,7 @@ AbstractDbOverlay.prototype.createIdentifiedElementsForTargetingClass = function
};
/**
- * @returns {PromiseLike}
+ * @returns {Promise}
*/
AbstractDbOverlay.prototype.refresh = function () {
throw new Error("Refreshing shouldn't be called");
@@ -194,6 +240,12 @@ AbstractDbOverlay.prototype.searchByTarget = function (element) {
throw new Error("Not implemented");
};
+/**
+ *
+ * @param {string} originalQuery
+ * @param {boolean} fitBounds
+ * @returns {*}
+ */
AbstractDbOverlay.prototype.searchByEncodedQuery = function (originalQuery, fitBounds) {
var query = this.decodeQuery(originalQuery);
query.fitBounds = fitBounds;
@@ -215,6 +267,10 @@ AbstractDbOverlay.prototype.searchByEncodedQuery = function (originalQuery, fitB
}
};
+/**
+ *
+ * @returns {Promise<any>}
+ */
AbstractDbOverlay.prototype.clear = function () {
var self = this;
return self.searchByQuery("").then(function () {
@@ -224,6 +280,8 @@ AbstractDbOverlay.prototype.clear = function () {
/**
* Returns true if overlay allows to get general data for element.
+ *
+ * @returns {boolean}
*/
AbstractDbOverlay.prototype.allowGeneralSearch = function () {
return this._allowGeneralSearch;
@@ -231,27 +289,48 @@ AbstractDbOverlay.prototype.allowGeneralSearch = function () {
/**
* Returns true if overlay allows to get data for element by search id.
+ * @returns {boolean}
*/
AbstractDbOverlay.prototype.allowSearchById = function () {
return this._allowSearchById;
};
+/**
+ *
+ * @param {CustomMap} map
+ */
AbstractDbOverlay.prototype.setMap = function (map) {
this._map = map;
};
+/**
+ *
+ * @returns {CustomMap}
+ */
AbstractDbOverlay.prototype.getMap = function () {
return this._map;
};
+/**
+ *
+ * @param {string} name
+ */
AbstractDbOverlay.prototype.setName = function (name) {
this.name = name;
};
+/**
+ *
+ * @returns {string}
+ */
AbstractDbOverlay.prototype.getName = function () {
return this.name;
};
+/**
+ *
+ * @param {boolean} allowSearchById
+ */
AbstractDbOverlay.prototype.setAllowSearchById = function (allowSearchById) {
// configure if the overlay can contain detailed data about elements that
// should be visualized in detailed mode of the Info Window
@@ -264,6 +343,10 @@ AbstractDbOverlay.prototype.setAllowSearchById = function (allowSearchById) {
}
};
+/**
+ *
+ * @param {boolean} allowGeneralSearch
+ */
AbstractDbOverlay.prototype.setAllowGeneralSearch = function (allowGeneralSearch) {
if (typeof allowGeneralSearch === "boolean") {
this._allowGeneralSearch = allowGeneralSearch;
@@ -274,21 +357,41 @@ AbstractDbOverlay.prototype.setAllowGeneralSearch = function (allowGeneralSearch
}
};
+/**
+ *
+ * @param {string} iconType
+ */
AbstractDbOverlay.prototype.setIconType = function (iconType) {
this._iconType = iconType;
};
+
+/**
+ *
+ * @param {number} iconStart
+ */
AbstractDbOverlay.prototype.setIconStart = function (iconStart) {
this._iconStart = iconStart;
};
AbstractDbOverlay.IconColors = ["red", "blue", "green", "purple", "yellow", "pink", "paleblue", "brown", "orange"];
+/**
+ *
+ * @param {number} colorId
+ * @returns {string}
+ */
AbstractDbOverlay.prototype.getColor = function (colorId) {
var id = colorId + this._iconStart;
id %= AbstractDbOverlay.IconColors.length;
return AbstractDbOverlay.IconColors[id];
};
+/**
+ *
+ * @param {number} colorId
+ * @param {number} id
+ * @returns {string}
+ */
AbstractDbOverlay.prototype.getIcon = function (colorId, id) {
var suffix = "_" + id;
if (id >= 100 || id === undefined) {
@@ -298,6 +401,12 @@ AbstractDbOverlay.prototype.getIcon = function (colorId, id) {
return "marker/" + this._iconType + "/" + this._iconType + "_" + color + suffix + ".png";
};
+/**
+ *
+ * @param {string} query
+ * @param {boolean} [useFullName]
+ * @returns {string[]}
+ */
AbstractDbOverlay.prototype.splitQuery = function (query, useFullName) {
var result = [];
if (query.indexOf(";") >= 0) {
diff --git a/frontend-js/src/main/js/map/overlay/AbstractTargettingDbOverlay.js b/frontend-js/src/main/js/map/overlay/AbstractTargettingDbOverlay.js
index c357e9cabd..0c14150f97 100644
--- a/frontend-js/src/main/js/map/overlay/AbstractTargettingDbOverlay.js
+++ b/frontend-js/src/main/js/map/overlay/AbstractTargettingDbOverlay.js
@@ -9,6 +9,18 @@ var Promise = require("bluebird");
var IdentifiedElement = require('../data/IdentifiedElement');
var AbstractDbOverlay = require('./AbstractDbOverlay');
+/**
+ *
+ * @param {Object} params
+ * @param {CustomMap} params.map
+ * @param {string} params.name
+ * @param {boolean} params.allowGeneralSearch
+ * @param {boolean} params.allowSearchById
+ * @param {string} params.iconType
+ * @param {number} params.iconColorStart
+ * @constructor
+ * @extends AbstractDbOverlay
+ */
function AbstractTargettingDbOverlay(params) {
// call super constructor
AbstractDbOverlay.call(this, params);
@@ -17,6 +29,11 @@ function AbstractTargettingDbOverlay(params) {
AbstractTargettingDbOverlay.prototype = Object.create(AbstractDbOverlay.prototype);
AbstractTargettingDbOverlay.prototype.constructor = AbstractTargettingDbOverlay;
+/**
+ *
+ * @param {string} query
+ * @returns {Promise}
+ */
AbstractTargettingDbOverlay.prototype.getElementsByQuery = function (query) {
var self = this;
return new Promise(function (resolve) {
@@ -58,6 +75,11 @@ AbstractTargettingDbOverlay.prototype.getElementsByQuery = function (query) {
});
};
+/**
+ *
+ * @param {string} originalQuery
+ * @returns {Promise}
+ */
AbstractTargettingDbOverlay.prototype.searchBySingleQuery = function (originalQuery) {
var self = this;
var query = self.encodeQuery(AbstractDbOverlay.QueryType.SEARCH_BY_QUERY, originalQuery);
@@ -86,6 +108,9 @@ AbstractTargettingDbOverlay.prototype.searchBySingleQuery = function (originalQu
}
};
+/**
+ * @returns {Promise}
+ */
AbstractTargettingDbOverlay.prototype.getIdentifiedElements = function () {
var self = this;
@@ -120,6 +145,11 @@ AbstractTargettingDbOverlay.prototype.searchByTarget = function (element) {
return this.searchNamesByTarget(element);
};
+/**
+ *
+ * @param {IdentifiedElement} element
+ * @returns {string[]}
+ */
AbstractTargettingDbOverlay.prototype.searchNamesByTarget = function (element) {
var self = this;
var query = self.encodeQuery(AbstractDbOverlay.QueryType.SEARCH_BY_TARGET, element);
@@ -136,7 +166,12 @@ AbstractTargettingDbOverlay.prototype.searchNamesByTarget = function (element) {
}
};
-
+/**
+ *
+ * @param {IdentifiedElement} element
+ * @param {boolean} general
+ * @returns {Promise}
+ */
AbstractTargettingDbOverlay.prototype.getDetailDataByIdentifiedElement = function (element, general) {
var self = this;
if (general) {
diff --git a/frontend-js/src/main/js/map/overlay/ChemicalDbOverlay.js b/frontend-js/src/main/js/map/overlay/ChemicalDbOverlay.js
index e77a989410..f55c4b3a56 100644
--- a/frontend-js/src/main/js/map/overlay/ChemicalDbOverlay.js
+++ b/frontend-js/src/main/js/map/overlay/ChemicalDbOverlay.js
@@ -8,6 +8,12 @@ var AbstractTargettingDbOverlay = require('./AbstractTargettingDbOverlay');
var ServerConnector = require('../../ServerConnector');
+/**
+ *
+ * @param params
+ * @constructor
+ * @extends AbstractTargettingDbOverlay
+ */
function ChemicalDbOverlay(params) {
params.iconType= "ball";
params.iconColorStart = 1;
@@ -19,10 +25,20 @@ function ChemicalDbOverlay(params) {
ChemicalDbOverlay.prototype = Object.create(AbstractTargettingDbOverlay.prototype);
ChemicalDbOverlay.prototype.constructor = ChemicalDbOverlay;
+/**
+ *
+ * @param {IdentifiedElement} param
+ * @returns {Promise<string[]>}
+ */
ChemicalDbOverlay.prototype.getNamesByTargetFromServer = function(param) {
return ServerConnector.getChemicalNamesByTarget(param);
};
+/**
+ *
+ * @param {string} param.query
+ * @returns {Promise<Chemical[]>}
+ */
ChemicalDbOverlay.prototype.getElementsByQueryFromServer = function(param) {
return ServerConnector.getChemicalsByQuery(param);
};
diff --git a/frontend-js/src/main/js/map/overlay/CommentDbOverlay.js b/frontend-js/src/main/js/map/overlay/CommentDbOverlay.js
index da24726b03..b4a629cb36 100644
--- a/frontend-js/src/main/js/map/overlay/CommentDbOverlay.js
+++ b/frontend-js/src/main/js/map/overlay/CommentDbOverlay.js
@@ -9,6 +9,12 @@ var ServerConnector = require('../../ServerConnector');
var logger = require('../../logger');
+/**
+ *
+ * @param params
+ * @constructor
+ * @extends AbstractDbOverlay
+ */
function CommentDbOverlay(params) {
// call super constructor
AbstractDbOverlay.call(this, params);
@@ -21,32 +27,50 @@ function CommentDbOverlay(params) {
CommentDbOverlay.prototype = Object.create(AbstractDbOverlay.prototype);
CommentDbOverlay.prototype.constructor = CommentDbOverlay;
-CommentDbOverlay.prototype.refresh = function() {
+/**
+ *
+ * @returns {Promise}
+ */
+CommentDbOverlay.prototype.refresh = function () {
var self = this;
- return ServerConnector.getLightComments({}).then(function(comments) {
+ return ServerConnector.getLightComments({}).then(function (comments) {
self._elements = comments;
return self.callListeners('onRefresh');
- }).then(function() {
+ }).then(function () {
return self._elements;
});
};
-CommentDbOverlay.prototype.addComment = function(newComment) {
+/**
+ *
+ * @param {Comment} newComment
+ * @returns {PromiseLike}
+ */
+CommentDbOverlay.prototype.addComment = function (newComment) {
var self = this;
self._elements.push(newComment);
- return self.callListeners('onRefresh').then(function() {
+ return self.callListeners('onRefresh').then(function () {
return self._elements;
});
};
-CommentDbOverlay.prototype.clear = function() {
+/**
+ *
+ * @returns {PromiseLike}
+ */
+CommentDbOverlay.prototype.clear = function () {
var self = this;
self._elements = [];
self._detailDataByIdentifiedElement = [];
return self.callListeners('onClear');
};
-CommentDbOverlay.prototype.getDetailDataByIdentifiedElement = function(element) {
+/**
+ *
+ * @param {IdentifiedElement} element
+ * @returns {Promise}
+ */
+CommentDbOverlay.prototype.getDetailDataByIdentifiedElement = function (element) {
var self = this;
var elementKey = element.getId() + "," + element.getType() + "," + element.getModelId();
if (this._detailDataByIdentifiedElement[elementKey] !== undefined) {
@@ -57,19 +81,23 @@ CommentDbOverlay.prototype.getDetailDataByIdentifiedElement = function(element)
coordinates = element.getPoint().x.toFixed(2) + "," + element.getPoint().y.toFixed(2);
}
return ServerConnector.getComments({
- elementId : element.getId(),
- elementType : element.getType(),
- coordinates : coordinates
- }).then(function(comments) {
+ elementId: element.getId(),
+ elementType: element.getType(),
+ coordinates: coordinates
+ }).then(function (comments) {
self._detailDataByIdentifiedElement[elementKey] = comments;
return comments;
});
}
};
-CommentDbOverlay.prototype.getIdentifiedElements = function() {
+/**
+ * TODO this method can be simplified (instead of new Promise, Promise.resolve should be used)
+ * @returns {Promise}
+ */
+CommentDbOverlay.prototype.getIdentifiedElements = function () {
var self = this;
- return new Promise(function(resolve) {
+ return new Promise(function (resolve) {
var result = [];
for (var i = 0; i < self._elements.length; i++) {
// we return only elements that are pinned to the map and weren't removed
diff --git a/frontend-js/src/main/js/map/overlay/DbOverlayCollection.js b/frontend-js/src/main/js/map/overlay/DbOverlayCollection.js
index 97eb7f90aa..5086ef0ea6 100644
--- a/frontend-js/src/main/js/map/overlay/DbOverlayCollection.js
+++ b/frontend-js/src/main/js/map/overlay/DbOverlayCollection.js
@@ -11,6 +11,12 @@ var DrugDbOverlay = require('./DrugDbOverlay');
var MiRnaDbOverlay = require('./MiRnaDbOverlay');
var SearchDbOverlay = require('./SearchDbOverlay');
+/**
+ *
+ * @param {CustomMap} params.map
+ * @constructor
+ * @extends ObjectWithListeners
+ */
function DbOverlayCollection(params) {
// call super constructor
ObjectWithListeners.call(this);
diff --git a/frontend-js/src/main/js/map/overlay/DrugDbOverlay.js b/frontend-js/src/main/js/map/overlay/DrugDbOverlay.js
index 23582176ed..91466b2d22 100644
--- a/frontend-js/src/main/js/map/overlay/DrugDbOverlay.js
+++ b/frontend-js/src/main/js/map/overlay/DrugDbOverlay.js
@@ -8,6 +8,12 @@ var AbstractTargettingDbOverlay = require('./AbstractTargettingDbOverlay');
var ServerConnector = require('../../ServerConnector');
+/**
+ *
+ * @param params
+ * @constructor
+ * @extends AbstractTargettingDbOverlay
+ */
function DrugDbOverlay(params) {
params.iconType= "drug";
params.iconColorStart = 5;
@@ -18,10 +24,20 @@ function DrugDbOverlay(params) {
DrugDbOverlay.prototype = Object.create(AbstractTargettingDbOverlay.prototype);
DrugDbOverlay.prototype.constructor = DrugDbOverlay;
+/**
+ *
+ * @param {IdentifiedElement} param
+ * @returns {Promise<string[]>}
+ */
DrugDbOverlay.prototype.getNamesByTargetFromServer = function(param) {
return ServerConnector.getDrugNamesByTarget(param);
};
+/**
+ *
+ * @param {string} param.query
+ * @returns {Promise<Drug[]>}
+ */
DrugDbOverlay.prototype.getElementsByQueryFromServer = function(param) {
return ServerConnector.getDrugsByQuery(param);
};
diff --git a/frontend-js/src/main/js/map/overlay/MiRnaDbOverlay.js b/frontend-js/src/main/js/map/overlay/MiRnaDbOverlay.js
index 8526cf7c80..4ffb143102 100644
--- a/frontend-js/src/main/js/map/overlay/MiRnaDbOverlay.js
+++ b/frontend-js/src/main/js/map/overlay/MiRnaDbOverlay.js
@@ -8,6 +8,12 @@ var AbstractTargettingDbOverlay = require('./AbstractTargettingDbOverlay');
var ServerConnector = require('../../ServerConnector');
+/**
+ *
+ * @param params
+ * @constructor
+ * @extends AbstractTargettingDbOverlay
+ */
function MiRnaDbOverlay(params) {
params.iconType= "target";
params.iconColorStart = 2;
@@ -19,10 +25,20 @@ function MiRnaDbOverlay(params) {
MiRnaDbOverlay.prototype = Object.create(AbstractTargettingDbOverlay.prototype);
MiRnaDbOverlay.prototype.constructor = MiRnaDbOverlay;
+/**
+ *
+ * @param {IdentifiedElement} param
+ * @returns {Promise<string[]>}
+ */
MiRnaDbOverlay.prototype.getNamesByTargetFromServer = function(param) {
return ServerConnector.getMiRnaNamesByTarget(param);
};
+/**
+ *
+ * @param {string} param.query
+ * @returns {Promise<Drug[]>}
+ */
MiRnaDbOverlay.prototype.getElementsByQueryFromServer = function(param) {
return ServerConnector.getMiRnasByQuery(param);
};
diff --git a/frontend-js/src/main/js/map/overlay/SearchDbOverlay.js b/frontend-js/src/main/js/map/overlay/SearchDbOverlay.js
index 4720bfcac3..f92ba6c440 100644
--- a/frontend-js/src/main/js/map/overlay/SearchDbOverlay.js
+++ b/frontend-js/src/main/js/map/overlay/SearchDbOverlay.js
@@ -33,6 +33,11 @@ function SearchDbOverlay(params) {
SearchDbOverlay.prototype = Object.create(AbstractDbOverlay.prototype);
SearchDbOverlay.prototype.constructor = SearchDbOverlay;
+/**
+ *
+ * @param {string} query
+ * @returns {Promise}
+ */
SearchDbOverlay.prototype.getElementsByQuery = function (query) {
var self = this;
var i;
@@ -86,6 +91,14 @@ SearchDbOverlay.prototype.getElementsByQuery = function (query) {
});
};
+/**
+ *
+ * @param {IdentifiedElement} identifiedElement
+ * @param {number} zoomLevel
+ * @param {Point}coordinates
+ * @returns {Promise}
+ * @private
+ */
SearchDbOverlay.prototype._getFirstVisibleParentOrObject = function (identifiedElement, zoomLevel, coordinates) {
if (identifiedElement === undefined) {
return Promise.resolve();
@@ -125,6 +138,15 @@ SearchDbOverlay.prototype._getFirstVisibleParentOrObject = function (identifiedE
}
});
};
+
+/**
+ *
+ * @param {Object} params
+ * @param {number} params.modelId
+ * @param {Point} params.coordinates
+ * @param {number} params.zoom
+ * @returns {Promise}
+ */
SearchDbOverlay.prototype.searchByCoordinates = function (params) {
var modelId = params.modelId;
var coordinates = params.coordinates;
@@ -241,6 +263,12 @@ SearchDbOverlay.prototype.searchByCoordinates = function (params) {
}
};
+/**
+ *
+ * @param {string} originalQuery
+ * @param {boolean} [perfect]
+ * @returns {Promise}
+ */
SearchDbOverlay.prototype.searchBySingleQuery = function (originalQuery, perfect) {
var self = this;
var query = self.encodeQuery(AbstractDbOverlay.QueryType.SEARCH_BY_QUERY, originalQuery, perfect);
@@ -289,7 +317,10 @@ SearchDbOverlay.prototype.searchByTarget = function (element) {
});
};
-
+/**
+ *
+ * @returns {Promise}
+ */
SearchDbOverlay.prototype.getIdentifiedElements = function () {
var self = this;
var queries = self.getQueries();
diff --git a/frontend-js/src/main/js/map/overlay/UserDbOverlay.js b/frontend-js/src/main/js/map/overlay/UserDbOverlay.js
index eac4eea005..12e72ca113 100644
--- a/frontend-js/src/main/js/map/overlay/UserDbOverlay.js
+++ b/frontend-js/src/main/js/map/overlay/UserDbOverlay.js
@@ -11,6 +11,12 @@ var InvalidArgumentError = require('../../InvalidArgumentError');
var Promise = require("bluebird");
+/**
+ *
+ * @param params
+ * @constructor
+ * @extends AbstractDbOverlay
+ */
function UserDbOverlay(params) {
params.iconType = "marker";
params.iconColorStart = 1;
@@ -32,6 +38,11 @@ function UserDbOverlay(params) {
UserDbOverlay.prototype = Object.create(AbstractDbOverlay.prototype);
UserDbOverlay.prototype.constructor = UserDbOverlay;
+/**
+ *
+ * @param {IdentifiedElement} element
+ * @returns {Promise}
+ */
UserDbOverlay.prototype.getDetailDataByIdentifiedElement = function (element) {
if (element.getType() === "POINT") {
return Promise.resolve(null);
@@ -40,6 +51,14 @@ UserDbOverlay.prototype.getDetailDataByIdentifiedElement = function (element) {
return model.getByIdentifiedElement(element, true);
};
+/**
+ *
+ * @param {PluginElementParam[]} params
+ * @param {{ALIAS:Array, REACTION:Array, POINT:Array}} sourceArray
+ * @param {boolean} mustBeUndefined
+ * @returns {Promise}
+ * @private
+ */
UserDbOverlay.prototype._createIdentifiedElements = function (params, sourceArray, mustBeUndefined) {
var self = this;
var result = [];
@@ -81,6 +100,11 @@ UserDbOverlay.prototype._createIdentifiedElements = function (params, sourceArra
});
};
+/**
+ *
+ * @param {PluginElementParam[]|PluginElementParam} params
+ * @returns {Promise<any>}
+ */
UserDbOverlay.prototype.addMarker = function (params) {
var self = this;
self.disableAddRemoveElements();
@@ -106,6 +130,11 @@ UserDbOverlay.prototype.addMarker = function (params) {
});
};
+/**
+ *
+ * @param {PluginElementParam[]|PluginElementParam} params
+ * @returns {Promise<any>}
+ */
UserDbOverlay.prototype.addSurface = function (params) {
var self = this;
self.disableAddRemoveElements();
@@ -132,6 +161,11 @@ UserDbOverlay.prototype.addSurface = function (params) {
});
};
+/**
+ *
+ * @param {PluginElementParam[]|PluginElementParam} params
+ * @returns {Promise<any>}
+ */
UserDbOverlay.prototype.removeMarker = function (params) {
var self = this;
self.disableAddRemoveElements();
@@ -159,6 +193,11 @@ UserDbOverlay.prototype.removeMarker = function (params) {
});
};
+/**
+ *
+ * @param {PluginElementParam[]|PluginElementParam} params
+ * @returns {Promise<any>}
+ */
UserDbOverlay.prototype.removeSurface = function (params) {
var self = this;
self.disableAddRemoveElements();
@@ -185,6 +224,9 @@ UserDbOverlay.prototype.removeSurface = function (params) {
});
};
+/**
+ *
+ */
UserDbOverlay.prototype.disableAddRemoveElements = function () {
if (this._addRemoveElementsDisabled) {
throw new Error("wait until previous Promise for showBioEntity/hideBioEntity is resolved");
@@ -192,6 +234,10 @@ UserDbOverlay.prototype.disableAddRemoveElements = function () {
this._addRemoveElementsDisabled = true;
}
};
+
+/**
+ *
+ */
UserDbOverlay.prototype.enableAddRemoveElements = function () {
if (this._addRemoveElementsDisabled) {
this._addRemoveElementsDisabled = false;
@@ -200,6 +246,10 @@ UserDbOverlay.prototype.enableAddRemoveElements = function () {
}
};
+/**
+ *
+ * @returns {Promise}
+ */
UserDbOverlay.prototype.getIdentifiedElements = function () {
var result = [];
var markerType, key, markers;
@@ -232,6 +282,10 @@ UserDbOverlay.prototype.getIdentifiedElements = function () {
return Promise.resolve(result);
};
+/**
+ *
+ * @returns {PromiseLike}
+ */
UserDbOverlay.prototype.clear = function () {
var self = this;
self._markerIdentifiedElements = {
diff --git a/frontend-js/src/main/js/map/structure/MolArt.js b/frontend-js/src/main/js/map/structure/MolArt.js
index e68165aab7..3b9be31754 100644
--- a/frontend-js/src/main/js/map/structure/MolArt.js
+++ b/frontend-js/src/main/js/map/structure/MolArt.js
@@ -1,7 +1,12 @@
var Functions = require('../../Functions');
var SubMenu = require('../../gui/SubMenu');
-
+/**
+ *
+ * @param {HTMLElement} containerParentElement
+ * @param {CustomMap} customMap
+ * @constructor
+ */
function MolArt(containerParentElement, customMap) {
var molartDiv = Functions.createElement({
@@ -15,18 +20,34 @@ function MolArt(containerParentElement, customMap) {
this._customMap = customMap;
}
+/**
+ *
+ * @param {HTMLElement} containerElement
+ */
MolArt.prototype.setContainerElement = function (containerElement) {
this._containerElement = containerElement;
};
+/**
+ *
+ * @returns {HTMLElement}
+ */
MolArt.prototype.getContainerElement = function () {
return this._containerElement;
};
+/**
+ *
+ * @param {ContextMenu} menu
+ */
function removeFromContextMenu(menu) {
$(menu.getElement()).find('li:contains("MolArt")').remove();
}
+/**
+ *
+ * @param {string[]} uniprotIds
+ */
MolArt.prototype.activateInContextMenu = function (uniprotIds) {
var self = this;
@@ -47,6 +68,9 @@ MolArt.prototype.activateInContextMenu = function (uniprotIds) {
};
+/**
+ *
+ */
MolArt.prototype.deactivateInContextMenu = function () {
var menu = this._customMap.getContextMenu();
removeFromContextMenu(menu);
@@ -54,6 +78,10 @@ MolArt.prototype.deactivateInContextMenu = function () {
}, true);
};
+/**
+ *
+ * @private
+ */
MolArt.prototype._deactivate = function () {
var container = this.getContainerElement();
container.style.display = 'none';
@@ -62,6 +90,11 @@ MolArt.prototype._deactivate = function () {
this.molArt = undefined;
};
+/**
+ *
+ * @param {string} uniprotId
+ * @private
+ */
MolArt.prototype._activate = function (uniprotId) {
var self = this;
diff --git a/frontend-js/src/main/js/map/surface/AliasSurface.js b/frontend-js/src/main/js/map/surface/AliasSurface.js
index b80391ef41..48fb6e6117 100644
--- a/frontend-js/src/main/js/map/surface/AliasSurface.js
+++ b/frontend-js/src/main/js/map/surface/AliasSurface.js
@@ -178,6 +178,11 @@ AliasSurface.prototype.setBoundsForAlias = function (startX, endX) {
this.getMapCanvasObjects()[0].setBounds(bounds);
};
+/**
+ *
+ * @returns {Promise}
+ * @private
+ */
AliasSurface.prototype._computeColors = function () {
var self = this;
var overlayData = self.getOverlayData();
diff --git a/frontend-js/src/main/js/map/window/AliasInfoWindow.js b/frontend-js/src/main/js/map/window/AliasInfoWindow.js
index f80f8bfc7e..7284a9b3fc 100644
--- a/frontend-js/src/main/js/map/window/AliasInfoWindow.js
+++ b/frontend-js/src/main/js/map/window/AliasInfoWindow.js
@@ -530,6 +530,9 @@ AliasInfoWindow.prototype.getAlias = function () {
return this.alias;
};
+/**
+ *
+ */
AliasInfoWindow.prototype.destroy = function () {
if (this.pileup !== undefined) {
this.pileup.destroy();
diff --git a/frontend-js/src/main/js/minerva.js b/frontend-js/src/main/js/minerva.js
index 1127f3d3f6..3d524d5e6d 100644
--- a/frontend-js/src/main/js/minerva.js
+++ b/frontend-js/src/main/js/minerva.js
@@ -32,6 +32,10 @@ var logger = require('./logger');
var customMap, leftPanel, topMenu, legend, mapContextMenu, selectionContextMenu;
+/**
+ *
+ * @param {CustomMapOptions} params
+ */
function processUrlGetParams(params) {
var project = params.getProject();
var sessionData = ServerConnector.getSessionData(project);
@@ -122,6 +126,10 @@ function requestConsent(user, termsOfUseUrl) {
$(dialog).dialog("open");
}
+/**
+ *
+ * @returns {Promise}
+ */
function insertGoogleAnalyticsCode() {
return ServerConnector.getConfigurationParam(ConfigurationType.GOOGLE_ANALYTICS_IDENTIFIER).then(function (identifier) {
if (identifier === "" || identifier === undefined || identifier === null) {
@@ -145,6 +153,10 @@ function insertGoogleAnalyticsCode() {
});
}
+/**
+ *
+ * @param {HTMLElement} element
+ */
function createDivStructure(element) {
var tableDiv = functions.createElement({
type: "div",
@@ -211,7 +223,10 @@ function createDivStructure(element) {
element.appendChild(selectionContextMenu);
}
-
+/**
+ *
+ * @param {CustomMapOptions} params
+ */
function initGlobals(params) {
if (global.ServerConnector === undefined) {
global.ServerConnector = ServerConnector;
@@ -230,6 +245,9 @@ function initGlobals(params) {
}
+/**
+ *
+ */
function verifyBrowser() {
var browser = functions.browser;
@@ -247,6 +265,11 @@ function verifyBrowser() {
}
}
+/**
+ *
+ * @param {CustomMapOptions} params
+ * @returns {Promise<Project>}
+ */
function getProject(params) {
if (params.getProject() !== undefined) {
return Promise.resolve(params.getProject());
@@ -255,6 +278,11 @@ function getProject(params) {
}
}
+/**
+ *
+ * @param params
+ * @returns {*}
+ */
function modifyParamsForTouchTable(params) {
if (params.bigLogo === undefined) {
// noinspection UnnecessaryLocalVariableJS
@@ -264,6 +292,11 @@ function modifyParamsForTouchTable(params) {
return params;
}
+/**
+ *
+ * @param {CustomMap} customMap
+ * @param {PluginManager} pluginManager
+ */
function assignSplitBarHandler(customMap, pluginManager) {
var splitBar = $('.minerva-plugin-split-bar');
var rightPanelDiv = $('.minerva-plugin');
@@ -284,6 +317,11 @@ function assignSplitBarHandler(customMap, pluginManager) {
});
}
+/**
+ *
+ * @param {CustomMapOptions|*} params
+ * @returns {Promise}
+ */
function create(params) {
params = modifyParamsForTouchTable(params);
if (!(params instanceof CustomMapOptions)) {
@@ -440,6 +478,10 @@ function create(params) {
}
+/**
+ *
+ * @returns {Promise}
+ */
function createFooter() {
var logoLink, logoText, logoImg;
return ServerConnector.getConfigurationParam(ConfigurationType.LOGO_LINK).then(function (result) {
@@ -472,6 +514,10 @@ function createFooter() {
})
}
+/**
+ *
+ * @returns {HTMLElement}
+ */
function createLoginDiv() {
var loggedIn = false;
@@ -568,7 +614,11 @@ function createLoginDiv() {
return result;
}
-
+/**
+ *
+ * @param {CustomMapOptions|*} params
+ * @returns {Promise}
+ */
function createLogin(params) {
params = modifyParamsForTouchTable(params);
if (!(params instanceof CustomMapOptions)) {
@@ -588,6 +638,11 @@ function createLogin(params) {
})
}
+/**
+ *
+ * @param {CustomMapOptions|*} params
+ * @returns {Promise}
+ */
function createExport(params) {
params = modifyParamsForTouchTable(params);
if (!(params instanceof CustomMapOptions)) {
@@ -612,6 +667,11 @@ function createExport(params) {
});
}
+/**
+ *
+ * @param {CustomMapOptions|*} params
+ * @returns {Promise}
+ */
function createAdmin(params) {
params = modifyParamsForTouchTable(params);
if (!(params instanceof CustomMapOptions)) {
diff --git a/frontend-js/src/main/js/plugin/MinervaPluginProxy.js b/frontend-js/src/main/js/plugin/MinervaPluginProxy.js
index 4116d900b1..594cd2fb94 100644
--- a/frontend-js/src/main/js/plugin/MinervaPluginProxy.js
+++ b/frontend-js/src/main/js/plugin/MinervaPluginProxy.js
@@ -12,6 +12,24 @@ var logger = require('../logger');
var Promise = require("bluebird");
+/**
+ * @typedef {Object} PluginElementParam
+ * @property {IdentifiedElement} element
+ * @property {string} [icon]
+ * @property {Object} [options]
+ * @property {string} options.color
+ * @property {number} options.opacity
+ * @property {string} options.lineColor
+ * @property {number} options.lineWeight
+ * @property {number} options.lineOpacity
+ */
+
+/**
+ *
+ * @param {CustomMap} customMap
+ * @param {string} dbOverlayName
+ * @returns {AbstractDbOverlay}
+ */
function getOverlayByName(customMap, dbOverlayName) {
var dbOverlay = customMap.getOverlayByName(dbOverlayName);
if (dbOverlay === null) {
@@ -28,6 +46,12 @@ function getOverlayByName(customMap, dbOverlayName) {
}
}
+/**
+ *
+ * @param {CustomMap} customMap
+ * @param {IdentifiedElement[]} identifiedElements
+ * @returns {Promise}
+ */
function getFullElements(customMap, identifiedElements) {
var result = [];
return Promise.each(
@@ -48,6 +72,12 @@ function getFullElements(customMap, identifiedElements) {
});
}
+/**
+ *
+ * @param {IdentifiedElement[]} elementIdentifiers
+ * @param {CustomMap} customMap
+ * @returns {Promise}
+ */
function getElements(elementIdentifiers, customMap) {
var identifiedElements = [];
@@ -83,6 +113,12 @@ function getElements(elementIdentifiers, customMap) {
}
+/**
+ *
+ * @param {Object} options
+ * @param {CustomMap} options.map
+ * @returns {{getBioEntityById: function(*=): Promise<any>, getAllBioEntities: function(): *, getReactionsWithElement: function(*=): *, getProjectId: function(): string, getName: function(): string, getVersion: function(): string, getDisease: getDisease, getOrganism: getOrganism, getModels: function(): *[]}}
+ */
function createProjectData(options) {
var map = options.map;
return {
@@ -173,6 +209,12 @@ function createProjectData(options) {
};
}
+/**
+ *
+ * @param {IdentifiedElement[]} elementIdentifiers
+ * @param {CustomMap} customMap
+ * @returns {Promise}
+ */
function getReactionsForElements(elementIdentifiers, customMap) {
var elementsByModelId = [];
for (var i = 0; i < elementIdentifiers.length; i++) {
@@ -202,7 +244,14 @@ function getReactionsForElements(elementIdentifiers, customMap) {
});
}
-
+/**
+ *
+ * @param {Object} options
+ * @param {Object} options.params
+ * @param {string} [options.filteredType]
+ * @param {boolean} [options.isDefault]
+ * @returns {Array}
+ */
function createMarkerElements(options) {
var params = options.params;
var filteredType = options.filteredType;
@@ -230,6 +279,14 @@ function createMarkerElements(options) {
return markerElements;
}
+/**
+ *
+ * @param {Object} options
+ * @param {CustomMap} options.map
+ * @param {Plugin} options.plugin
+ * @param {string} options.pluginId
+ * @returns {{getVisibleDataOverlays: function(): (Promise<DataOverlay[]>|*), addListener: addListener, removeListener: removeListener, removeAllListeners: function(): Array, getHighlightedBioEntities: function(*=): *, showBioEntity: function(*=): *, hideBioEntity: function(*=): Promise<T>, setCenter: function(*): PromiseLike, getCenter: function(*): Point, getBounds: function(*): Bounds, fitBounds: function(*): void, setZoom: function(*): *, getZoom: function(*): number, openMap: function(*): PromiseLike}}
+ */
function createProjectMap(options) {
var map = options.map;
var pluginId = options.pluginId;
@@ -445,6 +502,14 @@ function createProjectMap(options) {
}
}
+/**
+ *
+ * @param {Object} options
+ * @param {CustomMap} options.map
+ * @param {Plugin} options.plugin
+ * @param {string} options.pluginId
+ * @returns {{data: {getBioEntityById: function(*=): Promise<any>, getAllBioEntities: function(): *, getReactionsWithElement: function(*=): *, getProjectId: function(): string, getName: function(): string, getVersion: function(): string, getDisease: getDisease, getOrganism: getOrganism, getModels: function(): *[]}, map: {getVisibleDataOverlays: function(): (Promise<DataOverlay[]>|*), addListener: addListener, removeListener: removeListener, removeAllListeners: function(): Array, getHighlightedBioEntities: function(*=): *, showBioEntity: function(*=): *, hideBioEntity: function(*=): Promise<T>, setCenter: function(*): PromiseLike, getCenter: function(*): Point, getBounds: function(*): Bounds, fitBounds: function(*): void, setZoom: function(*): *, getZoom: function(*): number, openMap: function(*): PromiseLike}}}
+ */
function createProject(options) {
return {
data: createProjectData(options),
@@ -452,6 +517,12 @@ function createProject(options) {
};
}
+/**
+ *
+ * @param {Object} options
+ * @param {Configuration} options.configuration
+ * @returns {{options: ConfigurationOption[], overlayTypes: string[], imageConverters: *, modelConverters: *, elementTypes: *, reactionTypes: *, miriamTypes: MiriamType, mapTypes: *, modificationStateTypes: *, privilegeTypes: PrivilegeType[], annotators: *}}
+ */
function createConfiguration(options) {
var configuration = new Configuration(options.configuration);
return {
@@ -469,6 +540,12 @@ function createConfiguration(options) {
};
}
+/**
+ *
+ * @param {Object} options
+ * @param {string} options.hash
+ * @returns {{setGlobalParam: function(*=, *=): *, getGlobalParam: function(*=): *, setUserParam: function(*=, *=): *, getUserParam: function(*=): *}}
+ */
function createPluginData(options) {
return {
setGlobalParam: function (key, value) {
@@ -486,7 +563,18 @@ function createPluginData(options) {
};
}
-
+/**
+ *
+ * @param {Object} options
+ * @param {CustomMap} options.map
+ * @param {Plugin} options.plugin
+ * @param {string} options.pluginId
+ * @param {string} options.hash
+ * @param {HTMLElement} options.element
+ * @param {Configuration} options.configuration
+ * @returns {{pluginId: string|string, element: *, project: {data: {getBioEntityById: function(*=): Promise<any>, getAllBioEntities: function(): *, getReactionsWithElement: function(*=): *, getProjectId: function(): string, getName: function(): string, getVersion: function(): string, getDisease: getDisease, getOrganism: getOrganism, getModels: function(): *[]}, map: {getVisibleDataOverlays: function(): (Promise<DataOverlay[]>|*), addListener: addListener, removeListener: removeListener, removeAllListeners: function(): Array, getHighlightedBioEntities: function(*=): *, showBioEntity: function(*=): *, hideBioEntity: function(*=): Promise<T>, setCenter: function(*): PromiseLike, getCenter: function(*): Point, getBounds: function(*): Bounds, fitBounds: function(*): void, setZoom: function(*): *, getZoom: function(*): number, openMap: function(*): PromiseLike}}, configuration: {options: ConfigurationOption[], overlayTypes: string[], imageConverters: *, modelConverters: *, elementTypes: *, reactionTypes: *, miriamTypes: MiriamType, mapTypes: *, modificationStateTypes: *, privilegeTypes: PrivilegeType[], annotators: *}, pluginData: {setGlobalParam: function(*=, *=): *, getGlobalParam: function(*=): *, setUserParam: function(*=, *=): *, getUserParam: function(*=): *}}}
+ * @constructor
+ */
function MinervaPluginProxy(options) {
return {
pluginId: options.pluginId,
diff --git a/frontend-js/src/main/js/plugin/Plugin.js b/frontend-js/src/main/js/plugin/Plugin.js
index 215a4a3cab..153e3e2d5c 100644
--- a/frontend-js/src/main/js/plugin/Plugin.js
+++ b/frontend-js/src/main/js/plugin/Plugin.js
@@ -34,31 +34,66 @@ function Plugin(options) {
Plugin.prototype = Object.create(ObjectWithListeners.prototype);
Plugin.prototype.constructor = ObjectWithListeners;
+/**
+ *
+ * @param {PluginOptions} options
+ */
Plugin.prototype.setOptions = function (options) {
this._options = options;
};
+/**
+ *
+ * @returns {PluginOptions}
+ */
Plugin.prototype.getOptions = function () {
return this._options;
};
+/**
+ *
+ * @param loadedPluginData
+ */
Plugin.prototype.setLoadedPluginData = function (loadedPluginData) {
this._loadedPluginData = loadedPluginData;
};
+
+/**
+ *
+ * @returns {*}
+ */
Plugin.prototype.getLoadedPluginData = function () {
return this._loadedPluginData;
};
+/**
+ *
+ * @param minervaPluginProxy
+ */
Plugin.prototype.setMinervaPluginProxy = function (minervaPluginProxy) {
this._minervaPluginProxy = minervaPluginProxy;
};
+
+/**
+ *
+ * @returns {*}
+ */
Plugin.prototype.getMinervaPluginProxy = function () {
return this._minervaPluginProxy;
};
+
+/**
+ *
+ * @returns {string}
+ */
Plugin.prototype.getPluginId = function () {
return this.getMinervaPluginProxy().pluginId;
};
+/**
+ *
+ * @returns {Promise}
+ */
Plugin.prototype.load = function () {
var self = this;
var options = self.getOptions();
@@ -121,6 +156,10 @@ Plugin.prototype.load = function () {
};
+/**
+ *
+ * @returns {number}
+ */
Plugin.prototype.getMinWidth = function () {
var value;
var data = this.getLoadedPluginData();
@@ -134,6 +173,10 @@ Plugin.prototype.getMinWidth = function () {
return value;
};
+/**
+ *
+ * @returns {Promise}
+ */
Plugin.prototype.unload = function () {
var self = this;
return Promise.resolve().then(function () {
@@ -149,6 +192,10 @@ Plugin.prototype.unload = function () {
});
};
+/**
+ *
+ * @returns {string}
+ */
Plugin.prototype.getName = function () {
if (this.getLoadedPluginData() === undefined) {
return "";
@@ -156,6 +203,10 @@ Plugin.prototype.getName = function () {
return this.getLoadedPluginData().getName();
};
+/**
+ *
+ * @returns {string}
+ */
Plugin.prototype.getVersion = function () {
if (this.getLoadedPluginData() === undefined) {
return "";
@@ -163,10 +214,18 @@ Plugin.prototype.getVersion = function () {
return this.getLoadedPluginData().getVersion();
};
+/**
+ *
+ * @returns {Promise}
+ */
Plugin.prototype.destroy = function () {
return Promise.resolve();
};
+/**
+ *
+ * @param {string} hash
+ */
Plugin.prototype.setHash = function (hash) {
this.getMinervaPluginProxy().hash = hash;
};
diff --git a/frontend-js/src/main/js/plugin/PluginManager.js b/frontend-js/src/main/js/plugin/PluginManager.js
index fad5ab69e5..de602f3259 100644
--- a/frontend-js/src/main/js/plugin/PluginManager.js
+++ b/frontend-js/src/main/js/plugin/PluginManager.js
@@ -128,6 +128,10 @@ PluginManager.prototype.isValidUrl = function (url) {
return isUrl(url);
};
+/**
+ *
+ * @returns {Promise}
+ */
PluginManager.prototype.adjustMinWidth = function () {
var self = this;
var oldVal = self.getElement().style.minWidth;
@@ -149,6 +153,11 @@ PluginManager.prototype.adjustMinWidth = function () {
}
};
+/**
+ *
+ * @param {Plugin} plugin
+ * @returns {Promise}
+ */
PluginManager.prototype.removePlugin = function (plugin) {
var self = this;
var found = false;
@@ -167,6 +176,10 @@ PluginManager.prototype.removePlugin = function (plugin) {
});
};
+/**
+ *
+ * @returns {Promise}
+ */
PluginManager.prototype.destroy = function () {
var self = this;
var promises = [];
--
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