diff --git a/frontend-js/src/main/js/map/data/IdentifiedElement.js b/frontend-js/src/main/js/map/data/IdentifiedElement.js
index 727425d6611892b1f64a0fee59f72e9d816bb65a..4b7f15df7b1ab78be0e9f2d8dea825201339fbf9 100644
--- a/frontend-js/src/main/js/map/data/IdentifiedElement.js
+++ b/frontend-js/src/main/js/map/data/IdentifiedElement.js
@@ -82,11 +82,11 @@ function IdentifiedElement(javaObject) {
/**
* Returns point where it should be visualized when the type of object is
* "POINT".
- *
+ *
* @returns {@linke google.maps.Point} where it should be visualized when the
* type of object is "POINT".
*/
-IdentifiedElement.prototype.getPoint = function () {
+IdentifiedElement.prototype.getPoint = function() {
if (this._point === undefined || this._point === null) {
logger.warn("No point associated with IdentifiedElement");
return null;
@@ -97,10 +97,10 @@ IdentifiedElement.prototype.getPoint = function () {
/**
* Returns element identifier.
- *
+ *
* @returns element identifier
*/
-IdentifiedElement.prototype.getId = function () {
+IdentifiedElement.prototype.getId = function() {
return this.id;
};
@@ -113,7 +113,7 @@ IdentifiedElement.prototype.setId = function (id) {
this.id = id;
};
-IdentifiedElement.prototype.setModelId = function (modelId) {
+IdentifiedElement.prototype.setModelId = function(modelId) {
if (modelId === undefined || modelId === null) {
throw new Error("ModelId is invalid");
}
@@ -122,10 +122,10 @@ IdentifiedElement.prototype.setModelId = function (modelId) {
/**
* Returns model identifier where element is placed.
- *
+ *
* @returns model identifier
*/
-IdentifiedElement.prototype.getModelId = function () {
+IdentifiedElement.prototype.getModelId = function() {
return this.modelId;
};
@@ -137,14 +137,14 @@ IdentifiedElement.prototype.getModelId = function () {
* <li>"POINT" - for any point on the map, the data connected to this kind of
* objects are stored in {@link PointData}</li>
* </ul>
- *
+ *
* @returns type of the element
*/
-IdentifiedElement.prototype.getType = function () {
+IdentifiedElement.prototype.getType = function() {
return this.type;
};
-IdentifiedElement.prototype.setType = function (type) {
+IdentifiedElement.prototype.setType = function(type) {
if (type === undefined || type === null) {
throw new Error("Type not defined");
}
diff --git a/frontend-js/src/main/js/map/window/AbstractInfoWindow.js b/frontend-js/src/main/js/map/window/AbstractInfoWindow.js
index a9cb40dcbc89770769cb33d22c85d72ab60126e8..23ddf813c44a5fc24a5bcb90c43865617fbb07da 100644
--- a/frontend-js/src/main/js/map/window/AbstractInfoWindow.js
+++ b/frontend-js/src/main/js/map/window/AbstractInfoWindow.js
@@ -14,7 +14,7 @@ var TargettingStructure = require('../data/TargettingStructure');
/**
* Class representing any info window in our map.
- *
+ *
* @param abstractMarker
* {@link AbstractMarker} to which this window is pointing, can be null
*/
@@ -22,6 +22,8 @@ function AbstractInfoWindow(params) {
// call super constructor
ObjectWithListeners.call(this);
+ this.setIdentifiedElement(params.identifiedElement);
+
this.setCustomMap(params.map);
this.setGoogleMarker(params.marker);
@@ -32,15 +34,15 @@ function AbstractInfoWindow(params) {
this.registerPropertyType("overlayFullView");
// listener called when user want to see all data about specific data overlay
- var onOverlayFullViewChanged = function(e) {
+ var onOverlayFullViewChanged = function (e) {
var self = e.object;
// first change the content of the element
- return self.update().then(function() {
+ return self.update().then(function () {
if (e.newVal) {
var element = new IdentifiedElement({
- objectId : self.getElementId(),
- modelId : self.getCustomMap().getId(),
- type : self.getElementType()
+ objectId: self.getElementId(),
+ modelId: self.getCustomMap().getId(),
+ type: self.getElementType()
});
var topMap = self.getCustomMap().getTopMap();
return topMap.retrieveOverlayDetailDataForElement(element, self.getOverlayFullViewArray());
@@ -72,12 +74,12 @@ AbstractInfoWindow.prototype.constructor = AbstractInfoWindow;
/**
* Returns <code>true</code> if overlay should visualize all possible values.
- *
+ *
* @param overlayName
* name of the overlay
- * @returns <code>true</code> if overlay should visualize all possible values
+ * @returns boolean, <code>true</code> if overlay should visualize all possible values
*/
-AbstractInfoWindow.prototype.isOverlayFullView = function(overlayName) {
+AbstractInfoWindow.prototype.isOverlayFullView = function (overlayName) {
if (this._overlayFullView[overlayName] === undefined) {
this._overlayFullView[overlayName] = false;
}
@@ -87,15 +89,15 @@ AbstractInfoWindow.prototype.isOverlayFullView = function(overlayName) {
/**
* Returns associative array with information if specific overlay should present
* all possible results or only specified by the data searched by user.
- *
+ *
* @returns {Array} with information if specific overlay should present all
* possible results or only specified by the data searched by user
*/
-AbstractInfoWindow.prototype.getOverlayFullViewArray = function() {
+AbstractInfoWindow.prototype.getOverlayFullViewArray = function () {
return this._overlayFullView;
};
-AbstractInfoWindow.prototype.setOverlayFullView = function(overlayName, value) {
+AbstractInfoWindow.prototype.setOverlayFullView = function (overlayName, value) {
var oldVal = this._overlayFullView[overlayName];
this._overlayFullView[overlayName] = value;
return this.firePropertyChangeListener("overlayFullView", overlayName + "," + oldVal, value);
@@ -103,11 +105,11 @@ AbstractInfoWindow.prototype.setOverlayFullView = function(overlayName, value) {
/**
* This method checks if {@link AbstractInfoWindow} is opened.
- *
+ *
* @returns {Boolean} <code>true</code> if window is opened,
* <code>false</code> otherwise
*/
-AbstractInfoWindow.prototype.isOpened = function() {
+AbstractInfoWindow.prototype.isOpened = function () {
if (this.googleInfowindow === undefined) {
return false;
}
@@ -122,7 +124,7 @@ AbstractInfoWindow.prototype.isOpened = function() {
/**
* Opens Info Window.
*/
-AbstractInfoWindow.prototype.open = function(newMarker) {
+AbstractInfoWindow.prototype.open = function (newMarker) {
var self = this;
if (self.googleInfowindow === null) {
logger.warn("Cannot open window.");
@@ -133,18 +135,18 @@ AbstractInfoWindow.prototype.open = function(newMarker) {
}
self.googleInfowindow.open(self.getCustomMap().getGoogleMap(), self.getGoogleMarker());
- return self.update().then(function() {
+ return self.update().then(function () {
return self.callListeners("onShow");
});
};
/**
* Sets new content of the info window.
- *
+ *
* @param content
* new content of the window
*/
-AbstractInfoWindow.prototype.setContent = function(content) {
+AbstractInfoWindow.prototype.setContent = function (content) {
this._content = content;
if (this.googleInfowindow !== undefined) {
this.googleInfowindow.setContent(content);
@@ -153,46 +155,46 @@ AbstractInfoWindow.prototype.setContent = function(content) {
/**
* Returns content visualized in the info window.
- *
+ *
* @returns {String} content visualized in the info window
*/
-AbstractInfoWindow.prototype.getContent = function() {
+AbstractInfoWindow.prototype.getContent = function () {
return this._content;
};
/**
* Creates div for an overlay data.
- *
+ *
* @param overlay
* corresponding {@link OverlayCollection}
* @param data
* data taken from overlay
* @returns string representing div for given overlay data
*/
-AbstractInfoWindow.prototype.createOverlayInfoDiv = function(overlay, data) {
+AbstractInfoWindow.prototype.createOverlayInfoDiv = function (overlay, data) {
var alias = this.alias;
if (alias !== undefined) {
if (alias.getType() !== undefined) {
if (overlay.name === "drug") {
if (alias.getType().toUpperCase() === "RNA" || //
- alias.getType().toUpperCase() === "PROTEIN" || //
- alias.getType().toUpperCase() === "GENE") {
+ alias.getType().toUpperCase() === "PROTEIN" || //
+ alias.getType().toUpperCase() === "GENE") {
return this._createDrugInfoDiv(overlay, data);
} else {
return null;
}
} else if (overlay.name === "chemical") {
if (this.alias.getType().toUpperCase() === "RNA" || //
- alias.getType().toUpperCase() === "PROTEIN" || //
- alias.getType().toUpperCase() === "GENE") {
+ alias.getType().toUpperCase() === "PROTEIN" || //
+ alias.getType().toUpperCase() === "GENE") {
return this._createChemicalInfoDiv(overlay, data);
} else {
return null;
}
} else if (overlay.name === "mirna") {
if (alias.getType().toUpperCase() === "RNA" || //
- alias.getType().toUpperCase() === "PROTEIN" || //
- alias.getType().toUpperCase() === "GENE") {
+ alias.getType().toUpperCase() === "PROTEIN" || //
+ alias.getType().toUpperCase() === "GENE") {
return this._createMiRnaInfoDiv(overlay, data);
} else {
return null;
@@ -220,27 +222,27 @@ AbstractInfoWindow.prototype.createOverlayInfoDiv = function(overlay, data) {
/**
* Creates and returns div for drug overlay information.
- *
+ *
* @param data
* data taken from drug iverlay
* @returns {String} with a div for drug overlay information
*/
-AbstractInfoWindow.prototype._createDrugInfoDiv = function(overlay, data) {
+AbstractInfoWindow.prototype._createDrugInfoDiv = function (overlay, data) {
return this._createTargetInfoDiv({
- overlay : overlay,
- data : data,
- name : "Interacting drugs"
+ overlay: overlay,
+ data: data,
+ name: "Interacting drugs"
});
};
/**
* Creates and returns div for comment overlay information.
- *
+ *
* @param data
* data taken from comment iverlay
* @returns {String} with a div for comment overlay information
*/
-AbstractInfoWindow.prototype._createCommentInfoDiv = function(overlay, data) {
+AbstractInfoWindow.prototype._createCommentInfoDiv = function (overlay, data) {
if (data.length === 0 || data[0] === undefined) {
return null;
}
@@ -272,7 +274,7 @@ AbstractInfoWindow.prototype._createCommentInfoDiv = function(overlay, data) {
/**
* Creates and returns div for unknown overlay.
- *
+ *
* @param overlay
* some {@link OverlayCollection}
* @param data
@@ -280,7 +282,7 @@ AbstractInfoWindow.prototype._createCommentInfoDiv = function(overlay, data) {
* @returns Dom element with a div for overlay information
*/
-AbstractInfoWindow.prototype._createDefaultInfoDiv = function(overlay, data) {
+AbstractInfoWindow.prototype._createDefaultInfoDiv = function (overlay, data) {
var divElement = document.createElement("div");
var count = 0;
@@ -288,7 +290,7 @@ AbstractInfoWindow.prototype._createDefaultInfoDiv = function(overlay, data) {
var title = document.createTextNode(overlay.getName());
titleElement.appendChild(title);
divElement.appendChild(titleElement);
- for ( var searchId in data) {
+ for (var searchId in data) {
if (data.hasOwnProperty(searchId) && data[searchId] !== undefined && data[searchId] !== null) {
count++;
var resultTitleElement = document.createElement("h4");
@@ -314,27 +316,27 @@ AbstractInfoWindow.prototype._createDefaultInfoDiv = function(overlay, data) {
/**
* Returns google.maps.Marker object where this info window is attached.
- *
+ *
* @returns google.maps.Marker object where this info window is attached
*/
-AbstractInfoWindow.prototype.getGoogleMarker = function() {
+AbstractInfoWindow.prototype.getGoogleMarker = function () {
return this._marker;
};
-AbstractInfoWindow.prototype.setGoogleMarker = function(marker) {
+AbstractInfoWindow.prototype.setGoogleMarker = function (marker) {
this._marker = marker;
};
/**
* Returns {@link AbstractCustomMap} where this window is presented.
- *
+ *
* @returns {@link AbstractCustomMap} where this window is presented
*/
-AbstractInfoWindow.prototype.getCustomMap = function() {
+AbstractInfoWindow.prototype.getCustomMap = function () {
return this.customMap;
};
-AbstractInfoWindow.prototype.setCustomMap = function(map) {
+AbstractInfoWindow.prototype.setCustomMap = function (map) {
if (map === undefined) {
throw new Error("Map must be defined");
}
@@ -344,11 +346,11 @@ AbstractInfoWindow.prototype.setCustomMap = function(map) {
/**
* Returns html DOM object with content that should presented when waiting for
* some data from server.
- *
+ *
* @returns {String} html with content that should presented when waiting for
* some data from server
*/
-AbstractInfoWindow.prototype.createWaitingContentDiv = function() {
+AbstractInfoWindow.prototype.createWaitingContentDiv = function () {
var result = document.createElement("div");
var img = document.createElement("img");
img.src = GuiConnector.getImgPrefix() + GuiConnector.getLoadingImg();
@@ -362,7 +364,7 @@ AbstractInfoWindow.prototype.createWaitingContentDiv = function() {
/**
* This is a generic method that updates content of the window.
*/
-AbstractInfoWindow.prototype._updateContent = function() {
+AbstractInfoWindow.prototype._updateContent = function () {
var contentDiv = null;
var self = this;
@@ -371,10 +373,10 @@ AbstractInfoWindow.prototype._updateContent = function() {
} else {
self.setContent(self.createWaitingContentDiv());
- return self.createContentDiv().then(function(content) {
+ return self.createContentDiv().then(function (content) {
contentDiv = content;
return self.createOverlaysDiv();
- }).then(function(overlaysDiv) {
+ }).then(function (overlaysDiv) {
if (overlaysDiv !== undefined && overlaysDiv !== null) {
contentDiv.appendChild(overlaysDiv);
}
@@ -389,14 +391,14 @@ AbstractInfoWindow.prototype._updateContent = function() {
/**
* Creates and returns div with overlays content.
- *
+ *
* @returns {String} with html representing data taken from
* {@link OverlayCollection} for this window
*/
-AbstractInfoWindow.prototype.createOverlaysDiv = function() {
+AbstractInfoWindow.prototype.createOverlaysDiv = function () {
var self = this;
var result = document.createElement("div");
- return this.getOverlaysData(self.getOverlayFullViewArray()).then(function(overlayData) {
+ return this.getOverlaysData(self.getOverlayFullViewArray()).then(function (overlayData) {
for (var i = 0; i < overlayData.length; i++) {
var overlay = overlayData[i].overlay;
var data = overlayData[i].data;
@@ -412,11 +414,11 @@ AbstractInfoWindow.prototype.createOverlaysDiv = function() {
/**
* Abstract method (to be implemented by subclasses) for updating content.
*/
-AbstractInfoWindow.prototype.update = function() {
+AbstractInfoWindow.prototype.update = function () {
return this._updateContent();
};
-AbstractInfoWindow.prototype._createTargetInfoDiv = function(params) {
+AbstractInfoWindow.prototype._createTargetInfoDiv = function (params) {
var overlay = params.overlay;
var data = params.data;
var name = params.name;
@@ -437,7 +439,7 @@ AbstractInfoWindow.prototype._createTargetInfoDiv = function(params) {
checkbox.id = "checkbox-" + name + "-" + this.getElementType() + "-" + this.getElementId();
checkbox.type = "checkbox";
checkbox.checked = self.isOverlayFullView(overlay.getName());
- var checkboxClickedFunction = function() {
+ var checkboxClickedFunction = function () {
return self.setOverlayFullView(overlay.getName(), this.checked).then(null, GuiConnector.alert);
};
checkbox.onclick = checkboxClickedFunction;
@@ -451,7 +453,7 @@ AbstractInfoWindow.prototype._createTargetInfoDiv = function(params) {
result.appendChild(checkboxDiv);
}
count = 0;
- for ( var dataId in data) {
+ for (var dataId in data) {
if (data.hasOwnProperty(dataId)) {
count++;
}
@@ -468,7 +470,7 @@ AbstractInfoWindow.prototype._createTargetInfoDiv = function(params) {
return result;
};
-AbstractInfoWindow.prototype._createTableForTargetDiv = function(data, overlay) {
+AbstractInfoWindow.prototype._createTableForTargetDiv = function (data, overlay) {
var self = this;
var table = document.createElement("table");
table.className = "minerva-window-drug-table";
@@ -484,13 +486,13 @@ AbstractInfoWindow.prototype._createTableForTargetDiv = function(data, overlay)
table.appendChild(header);
var row;
- var onclick = function() {
+ var onclick = function () {
// ';' enforces single query (in case there are ',' characters in the name)
return overlay.searchByQuery(this.innerHTML + ";");
};
var count = 0;
- for ( var searchId in data) {
+ for (var searchId in data) {
if (data.hasOwnProperty(searchId)) {
row = document.createElement("tr");
@@ -509,20 +511,20 @@ AbstractInfoWindow.prototype._createTableForTargetDiv = function(data, overlay)
}
}
var link = Functions.createElement({
- type : "a",
- onclick : onclick,
- href : "#",
- content : nameContent,
+ type: "a",
+ onclick: onclick,
+ href: "#",
+ content: nameContent,
});
var nameTd = Functions.createElement({
- type : "td",
+ type: "td",
});
nameTd.appendChild(link);
row.appendChild(nameTd);
var referencesCell = Functions.createElement({
- type : "td",
+ type: "td",
});
referencesCell.appendChild(self.getGuiUtils().createAnnotationList(annotations));
@@ -553,73 +555,74 @@ AbstractInfoWindow.prototype._createTableForTargetDiv = function(data, overlay)
return table;
};
-AbstractInfoWindow.prototype.init = function() {
+AbstractInfoWindow.prototype.init = function () {
var self = this;
- return ServerConnector.getConfiguration().then(function(configuration) {
+ return ServerConnector.getConfiguration().then(function (configuration) {
self.getGuiUtils().setConfiguration(configuration);
self.getGuiUtils().setMap(self.getCustomMap());
});
};
-AbstractInfoWindow.prototype.setGuiUtils = function(guiUtils) {
+AbstractInfoWindow.prototype.setGuiUtils = function (guiUtils) {
this._guiUtils = guiUtils;
};
-AbstractInfoWindow.prototype.getGuiUtils = function() {
+AbstractInfoWindow.prototype.getGuiUtils = function () {
return this._guiUtils;
};
/**
* Creates and returns DOM div for chemical overlay information.
- *
+ *
* @param data
* data taken from chemical overlay
* @returns DOM element with a div for comment overlay information
*/
-AbstractInfoWindow.prototype._createChemicalInfoDiv = function(overlay, data) {
+AbstractInfoWindow.prototype._createChemicalInfoDiv = function (overlay, data) {
return this._createTargetInfoDiv({
- overlay : overlay,
- data : data,
- name : "Interacting chemicals",
+ overlay: overlay,
+ data: data,
+ name: "Interacting chemicals",
});
};
/**
* Creates and returns DOM div for mi rna overlay information.
- *
+ *
* @param data
* data taken from mi rna overlay
* @returns DOM element with a div for comment overlay information
*/
-AbstractInfoWindow.prototype._createMiRnaInfoDiv = function(overlay, data) {
+AbstractInfoWindow.prototype._createMiRnaInfoDiv = function (overlay, data) {
return this._createTargetInfoDiv({
- overlay : overlay,
- data : data,
- name : "Interacting Micro RNAs"
+ overlay: overlay,
+ data: data,
+ name: "Interacting Micro RNAs"
});
};
-/**
- * Abstract method returning identifier of the object for which this window was
- * created.
- */
-AbstractInfoWindow.prototype.getElementId = function() {
- throw new Error("Not implemented");
+AbstractInfoWindow.prototype.setIdentifiedElement = function (identifiedElement) {
+ if (identifiedElement === undefined) {
+ throw new Error("identifiedElement cannot be undefined");
+ }
+ this._identifiedElement = identifiedElement;
+};
+
+AbstractInfoWindow.prototype.getIdentifiedElement = function () {
+ return this._identifiedElement;
};
+
/**
- * Abstract method returning type of the object for which this window was
- * created.
+ * Method returning identifier of the object for which this window was created.
*/
-AbstractInfoWindow.prototype.getElementType = function() {
- throw new Error("Not implemented");
+AbstractInfoWindow.prototype.getElementId = function () {
+ return this.getIdentifiedElement().getId();
};
-AbstractInfoWindow.prototype.getIdentifiedElement = function() {
- var self = this;
- return new IdentifiedElement({
- id : self.getElementId(),
- type : self.getElementType(),
- modelId : self.getCustomMap().getId()
- });
+/**
+ * Method returning type of the object for which this window was created.
+ */
+AbstractInfoWindow.prototype.getElementType = function () {
+ return this.getIdentifiedElement().getType();
};
module.exports = AbstractInfoWindow;
diff --git a/frontend-js/src/main/js/map/window/AliasInfoWindow.js b/frontend-js/src/main/js/map/window/AliasInfoWindow.js
index 4fb18d9a557c48e5e46b237784ba0c8c480eea53..7edbbd32bd8b25d20a6865be01c67e4a975a03e3 100644
--- a/frontend-js/src/main/js/map/window/AliasInfoWindow.js
+++ b/frontend-js/src/main/js/map/window/AliasInfoWindow.js
@@ -5,7 +5,9 @@ var functions = require('../../Functions');
var AbstractInfoWindow = require('./AbstractInfoWindow');
var Alias = require('../data/Alias');
+var IdentifiedElement = require('../data/IdentifiedElement');
var LayoutAlias = require('../data/LayoutAlias');
+
var pileup = require('pileup');
var Promise = require("bluebird");
@@ -14,6 +16,9 @@ var Promise = require("bluebird");
* Class representing info window that should be opened when clicking on alias.
*/
function AliasInfoWindow(params) {
+ if (params.identifiedElement === undefined) {
+ params.identifiedElement = new IdentifiedElement(params.alias);
+ }
// call super constructor
AbstractInfoWindow.call(this, params);
@@ -24,8 +29,8 @@ function AliasInfoWindow(params) {
var point = new google.maps.Point(alias.x + alias.width / 2, alias.y + alias.height / 2);
var latLng = this.customMap.fromPointToLatLng(point);
this.googleInfowindow = new google.maps.InfoWindow({
- content : this.content,
- position : latLng
+ content: this.content,
+ position: latLng
});
}
@@ -37,26 +42,26 @@ AliasInfoWindow.prototype.constructor = AliasInfoWindow;
* Updates content of info window. The content will be automatically obtained
* from {@link CustomMap} instance. The only optional parameter is {@link Alias}
* data.
- *
+ *
* @param newAlias
* optional {@link Alias} data for which this {@link AliasInfoWindow}
* was created
*/
-AliasInfoWindow.prototype.update = function(newAlias) {
+AliasInfoWindow.prototype.update = function (newAlias) {
if (this.alias === undefined && newAlias !== undefined) {
this.alias = newAlias;
}
return this._updateContent();
};
-AliasInfoWindow.prototype.init = function() {
+AliasInfoWindow.prototype.init = function () {
var self = this;
var alias = self.getAlias();
- return AbstractInfoWindow.prototype.init.call(self).then(function() {
+ return AbstractInfoWindow.prototype.init.call(self).then(function () {
return self.getCustomMap().getModel().getAliasById(alias.getId(), true);
- }).then(function(alias) {
+ }).then(function (alias) {
return self.update(alias);
- }).then(function(){
+ }).then(function () {
return self.open();
});
};
@@ -64,15 +69,15 @@ AliasInfoWindow.prototype.init = function() {
/**
* Creates and returns chart representing data related to alias on different
* layouts.
- *
+ *
* @returns {String} html string representing chart with data related to alias
* on different layouts
*/
-AliasInfoWindow.prototype.createChartDiv = function() {
+AliasInfoWindow.prototype.createChartDiv = function () {
var result = document.createElement("div");
var rows = [];
var self = this;
- return Promise.each(self.layoutAliases, function(data, i) {
+ return Promise.each(self.layoutAliases, function (data, i) {
var rowDiv = document.createElement("div");
if (i % 2 === 0) {
rowDiv.className = "mapChartRowEvenDiv";
@@ -87,7 +92,7 @@ AliasInfoWindow.prototype.createChartDiv = function() {
rows[i] = rowDiv;
if (data !== undefined && data !== null) {
- return functions.overlayToColor(data).then(function(color) {
+ return functions.overlayToColor(data).then(function (color) {
var value = parseFloat(data.value);
var description = data.description;
if (description === null || description === undefined || description === "") {
@@ -157,7 +162,7 @@ AliasInfoWindow.prototype.createChartDiv = function() {
rowDiv.appendChild(emptyDiv);
return Promise.resolve();
}
- }).then(function() {
+ }).then(function () {
for (var i = 0; i < rows.length; i++) {
result.appendChild(rows[i]);
}
@@ -167,10 +172,10 @@ AliasInfoWindow.prototype.createChartDiv = function() {
/**
* Methods that creates and return DOM object with the content of the window.
- *
+ *
* @returns DOM object representing html code for content of the info window
*/
-AliasInfoWindow.prototype.createContentDiv = function() {
+AliasInfoWindow.prototype.createContentDiv = function () {
var self = this;
var alias = self.getAlias();
if (alias.isComplete()) {
@@ -183,19 +188,19 @@ AliasInfoWindow.prototype.createContentDiv = function() {
result.appendChild(layoutsDiv);
- return self.getCustomMap().getAliasVisibleLayoutsData(alias.getId()).then(function(layoutAliases) {
+ return self.getCustomMap().getAliasVisibleLayoutsData(alias.getId()).then(function (layoutAliases) {
self.layoutAliases = layoutAliases;
return self.getCustomMap().getTopMap().getVisibleDataOverlays();
- }).then(function(dataOverlays) {
+ }).then(function (dataOverlays) {
self.layoutNames = [];
for (var i = 0; i < dataOverlays.length; i++) {
self.layoutNames.push(dataOverlays[i].getName());
}
return self.createChartDiv();
- }).then(function(chartDiv) {
+ }).then(function (chartDiv) {
layoutsDiv.appendChild(chartDiv);
return self.createGenomicDiv();
- }).then(function(genomicDiv) {
+ }).then(function (genomicDiv) {
layoutsDiv.appendChild(genomicDiv);
return result;
});
@@ -206,32 +211,14 @@ AliasInfoWindow.prototype.createContentDiv = function() {
/**
* Returns array with data taken from all known {@link OverlayCollection}.
- *
+ *
* @returns array with data from {@link OverlayCollection}
*/
-AliasInfoWindow.prototype.getOverlaysData = function(general) {
+AliasInfoWindow.prototype.getOverlaysData = function (general) {
return this.getCustomMap().getTopMap().getOverlayDataForAlias(this.getAlias(), general);
};
-/**
- * Method returning identifier of the object for which this window was created.
- */
-AliasInfoWindow.prototype.getElementId = function() {
- if (this.alias !== undefined) {
- return this.alias.getId();
- } else {
- return null;
- }
-};
-
-/**
- * Method returning type of the object for which this window was created.
- */
-AliasInfoWindow.prototype.getElementType = function() {
- return "ALIAS";
-};
-
-AliasInfoWindow.prototype.createGenomicDiv = function() {
+AliasInfoWindow.prototype.createGenomicDiv = function () {
var self = this;
var result = document.createElement("div");
@@ -248,71 +235,71 @@ AliasInfoWindow.prototype.createGenomicDiv = function() {
var genomes = [];
var genomeUrls = [];
- var pileupSource = [ {
- viz : pileup.viz.scale(),
- name : 'Scale'
+ var pileupSource = [{
+ viz: pileup.viz.scale(),
+ name: 'Scale'
}, {
- viz : pileup.viz.location(),
- name : 'Location'
- } ];
+ viz: pileup.viz.location(),
+ name: 'Location'
+ }];
var pileupRange = {
- contig : 'chr1',
- start : 3000000000,
- stop : 0
+ contig: 'chr1',
+ start: 3000000000,
+ stop: 0
};
var globalGeneVariants = [];
return Promise.each(
- self.layoutAliases,
- function(data) {
- if (data !== null && data !== undefined && data.getType() === LayoutAlias.GENETIC_VARIANT) {
- geneticInformation = true;
- return Promise.each(data.getGeneVariants(), function(variant) {
- return self.getCustomMap().getReferenceGenome(variant.getReferenceGenomeType(),
- variant.getReferenceGenomeVersion()).then(
- function(genome) {
- if (genome.getUrl() !== null && genome.getUrl() !== undefined) {
- if (genomes[genome.getUrl()] === undefined) {
- genomes[genome.getUrl()] = genome;
- genomeUrls.push(genome.getUrl());
- }
- } else {
- logger.warn("Genome for " + variant.getReferenceGenomeType() + ","
- + variant.getReferenceGenomeVersion() + " not loaded");
- }
- },
- function() {
- logger.warn("Genome for " + variant.getReferenceGenomeType() + ","
- + variant.getReferenceGenomeVersion() + " not loaded");
-
- });
- });
+ self.layoutAliases,
+ function (data) {
+ if (data !== null && data !== undefined && data.getType() === LayoutAlias.GENETIC_VARIANT) {
+ geneticInformation = true;
+ return Promise.each(data.getGeneVariants(), function (variant) {
+ return self.getCustomMap().getReferenceGenome(variant.getReferenceGenomeType(),
+ variant.getReferenceGenomeVersion()).then(
+ function (genome) {
+ if (genome.getUrl() !== null && genome.getUrl() !== undefined) {
+ if (genomes[genome.getUrl()] === undefined) {
+ genomes[genome.getUrl()] = genome;
+ genomeUrls.push(genome.getUrl());
+ }
+ } else {
+ logger.warn("Genome for " + variant.getReferenceGenomeType() + ","
+ + variant.getReferenceGenomeVersion() + " not loaded");
+ }
+ },
+ function () {
+ logger.warn("Genome for " + variant.getReferenceGenomeType() + ","
+ + variant.getReferenceGenomeVersion() + " not loaded");
- }
- }).then(function() {
+ });
+ });
+
+ }
+ }).then(function () {
for (var i = 0; i < genomeUrls.length; i++) {
var genome = genomes[genomeUrls[i]];
pileupSource.splice(0, 0, {
- viz : pileup.viz.genome(),
- isReference : pileupSource.length === 2,
- data : pileup.formats.twoBit({
- url : genome.getUrl()
+ viz: pileup.viz.genome(),
+ isReference: pileupSource.length === 2,
+ data: pileup.formats.twoBit({
+ url: genome.getUrl()
}),
- name : 'Reference ' + genome.getVersion()
+ name: 'Reference ' + genome.getVersion()
});
for (var k = 0; k < genome.getGeneMappings().length; k++) {
var mapping = genome.getGeneMappings()[k];
pileupSource.push({
- viz : pileup.viz.genes(),
- data : pileup.formats.bigBed({
- url : mapping.getUrl()
+ viz: pileup.viz.genes(),
+ data: pileup.formats.bigBed({
+ url: mapping.getUrl()
}),
- name : 'Genes ' + mapping.getName()
+ name: 'Genes ' + mapping.getName()
});
}
}
- return Promise.each(self.layoutAliases, function(data, i) {
+ return Promise.each(self.layoutAliases, function (data, i) {
globalGeneVariants[i] = [];
if (data !== null && data !== undefined && data.getType() === LayoutAlias.GENETIC_VARIANT) {
var geneVariants = data.getGeneVariants();
@@ -328,7 +315,7 @@ AliasInfoWindow.prototype.createGenomicDiv = function() {
}
}
});
- }).then(function() {
+ }).then(function () {
if (geneticInformation) {
if (genomeUrls.length === 0) {
contentElement.innerHTML = "No reference genome data available on minerva platform";
@@ -337,13 +324,13 @@ AliasInfoWindow.prototype.createGenomicDiv = function() {
if (globalGeneVariants[iter].length > 0) {
var vcfContent = self.createVcfString(globalGeneVariants[iter]);
pileupSource.push({
- viz : pileup.viz.variants(),
- data : pileup.formats.vcf({
- content : vcfContent
+ viz: pileup.viz.variants(),
+ data: pileup.formats.vcf({
+ content: vcfContent
}),
- name : self.layoutNames[iter] + ' - Variants',
- options : {
- variantHeightByFrequency : true
+ name: self.layoutNames[iter] + ' - Variants',
+ options: {
+ variantHeightByFrequency: true
},
});
}
@@ -360,8 +347,8 @@ AliasInfoWindow.prototype.createGenomicDiv = function() {
logger.debug("Pileup destroyed");
}
self.pileup = pileup.create(contentElement, {
- range : pileupRange,
- tracks : pileupSource
+ range: pileupRange,
+ tracks: pileupSource
});
}
@@ -372,7 +359,7 @@ AliasInfoWindow.prototype.createGenomicDiv = function() {
});
};
-AliasInfoWindow.prototype.createVcfString = function(geneVariants) {
+AliasInfoWindow.prototype.createVcfString = function (geneVariants) {
var result = "";
result += "##fileformat=VCFv4.0\n";
result += "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\n";
@@ -387,29 +374,29 @@ AliasInfoWindow.prototype.createVcfString = function(geneVariants) {
variantId = variant.getVariantIdentifier();
}
result += variant.getContig() + "\t" + //
- variant.getPosition() + "\t" + //
- variantId + "\t" + //
- variant.getOriginalDna() + "\t" + //
- variant.getModifiedDna() + "\t" + //
- "100.0\t" + //
- "PASS\t" + //
- additionalInfo + "\n";
+ variant.getPosition() + "\t" + //
+ variantId + "\t" + //
+ variant.getOriginalDna() + "\t" + //
+ variant.getModifiedDna() + "\t" + //
+ "100.0\t" + //
+ "PASS\t" + //
+ additionalInfo + "\n";
}
return result;
};
-AliasInfoWindow.prototype.setAlias = function(alias) {
+AliasInfoWindow.prototype.setAlias = function (alias) {
if (alias === undefined || alias === null || (!(alias instanceof Alias))) {
throw new Error("invalid alias");
}
this.alias = alias;
};
-AliasInfoWindow.prototype.getAlias = function() {
+AliasInfoWindow.prototype.getAlias = function () {
return this.alias;
};
-AliasInfoWindow.prototype.destroy = function() {
+AliasInfoWindow.prototype.destroy = function () {
if (this.pileup !== undefined) {
this.pileup.destroy();
}
diff --git a/frontend-js/src/main/js/map/window/PointInfoWindow.js b/frontend-js/src/main/js/map/window/PointInfoWindow.js
index 7a32e32dd25bd592f7016d7f0142b20f1bc43151..c850896c7ab42a313eae7b6a9a593762edcc0d30 100644
--- a/frontend-js/src/main/js/map/window/PointInfoWindow.js
+++ b/frontend-js/src/main/js/map/window/PointInfoWindow.js
@@ -3,8 +3,12 @@
var Promise = require("bluebird");
var AbstractInfoWindow = require('./AbstractInfoWindow');
+var IdentifiedElement = require('../data/IdentifiedElement');
function PointInfoWindow(params) {
+ if (params.identifiedElement === undefined) {
+ params.identifiedElement = new IdentifiedElement(params.point);
+ }
// call super constructor
AbstractInfoWindow.call(this, params);
@@ -13,8 +17,8 @@ function PointInfoWindow(params) {
var point = this.pointData.getPoint();
var latLng = this.getCustomMap().fromPointToLatLng(point);
this.googleInfowindow = new google.maps.InfoWindow({
- content : this.content,
- position : latLng
+ content: this.content,
+ position: latLng
});
this.googleInfowindow.open(this.getCustomMap().getGoogleMap(), this.getGoogleMarker());
this.update();
@@ -23,7 +27,7 @@ function PointInfoWindow(params) {
PointInfoWindow.prototype = Object.create(AbstractInfoWindow.prototype);
PointInfoWindow.prototype.constructor = PointInfoWindow;
-PointInfoWindow.prototype.createContentDiv = function() {
+PointInfoWindow.prototype.createContentDiv = function () {
var result = document.createElement("div");
var title = document.createElement("h3");
title.innerHTML = "Point: " + this.pointData.getPoint();
@@ -32,26 +36,9 @@ PointInfoWindow.prototype.createContentDiv = function() {
return Promise.resolve(result);
};
-PointInfoWindow.prototype.getOverlaysData = function(general) {
+PointInfoWindow.prototype.getOverlaysData = function (general) {
return this.getCustomMap().getTopMap().getOverlayDataForPoint(this.pointData, general);
};
-/**
- * Method returning identifier of the object for which this window was created.
- */
-PointInfoWindow.prototype.getElementId = function() {
- if (this.pointData !== undefined) {
- return this.pointData.getId();
- } else {
- return null;
- }
-};
-
-/**
- * Method returning type of the object for which this window was created.
- */
-PointInfoWindow.prototype.getElementType = function() {
- return "POINT";
-};
module.exports = PointInfoWindow;
diff --git a/frontend-js/src/main/js/map/window/ReactionInfoWindow.js b/frontend-js/src/main/js/map/window/ReactionInfoWindow.js
index 1df46abffa587dc974b5a8ee2a5172b13762bc78..4ff09bae2ecad8450637938c3726dd6d6c97d9b4 100644
--- a/frontend-js/src/main/js/map/window/ReactionInfoWindow.js
+++ b/frontend-js/src/main/js/map/window/ReactionInfoWindow.js
@@ -3,6 +3,7 @@
var Promise = require("bluebird");
var AbstractInfoWindow = require('./AbstractInfoWindow');
+var IdentifiedElement = require('../data/IdentifiedElement');
var Reaction = require('../data/Reaction');
/**
@@ -10,6 +11,9 @@ var Reaction = require('../data/Reaction');
* reaction.
*/
function ReactionInfoWindow(params) {
+ if (params.identifiedElement === undefined) {
+ params.identifiedElement = new IdentifiedElement(params.reaction);
+ }
// call super constructor
AbstractInfoWindow.call(this, params);