diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/KeggAnnotator.java b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/KeggAnnotator.java
index 4f4238e70c7c1524f6df4c04a2cbfa040bbf533e..2097537be826e16e5138bbe13c2b96680a230580 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/KeggAnnotator.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/KeggAnnotator.java
@@ -78,7 +78,7 @@ public class KeggAnnotator extends ElementAnnotator implements IExternalService
String.class,
"Space-delimited list of organisms codes for which homologous genes"
+ " (GENE section in the KEGG enzyme record) should be imported."
- + " Currently ATH (Arabidopsis Thaliana) is supported.");
+ + " Currently only ATH (Arabidopsis Thaliana) is supported.");
this.addParameterDefinition(paramDef);
}
@@ -230,7 +230,6 @@ public class KeggAnnotator extends ElementAnnotator implements IExternalService
String[] tairCodes = m.group(1).trim().split(" ");
for (String tairCode: tairCodes) {
tairCode = tairCode.split("\\(")[0]; //some codes are in the form AT1G08510(FATB)
- logger.debug("Adding tair code " + tairCode);
result.add(createMiriamData(MiriamType.TAIR_LOCUS, tairCode));
}
}
diff --git a/frontend-js/src/main/js/gui/admin/ChooseAnnotatorsDialog.js b/frontend-js/src/main/js/gui/admin/ChooseAnnotatorsDialog.js
index 55befeaa794a10c67984438b52207ca09a55d247..9c4e8b9c567f247bcf94d679a51ea72c690ca701 100644
--- a/frontend-js/src/main/js/gui/admin/ChooseAnnotatorsDialog.js
+++ b/frontend-js/src/main/js/gui/admin/ChooseAnnotatorsDialog.js
@@ -56,7 +56,7 @@ ChooseAnnotatorsDialog.prototype.createGui = function () {
};
function onChangeParameterValue(element, user){
- var name = $(element).siblings(".minerva-annotator-param-name").text();
+ var name = $(element).siblings(".minerva-annotator-param-name")[0].childNodes[0].nodeValue;
var annotatorClassName = $(element).parent().parent().attr('name');
var data = new UserPreferences();
@@ -82,8 +82,7 @@ ChooseAnnotatorsDialog.prototype.setElementType = function (elementType) {
var element = $("[name='annotatorListBox']", self.getElement())[0];
var annotatorsParams = $(".minerva-annotators-params", self.getElement())[0];
Functions.removeChildren(element);
- Functions.removeChildren(annotatorsParams);
-
+
var selectElement = Functions.createElement({
type: "select",
className: "minerva-multi-select"
@@ -92,8 +91,6 @@ ChooseAnnotatorsDialog.prototype.setElementType = function (elementType) {
var annotators = configuration.getElementAnnotators(elementType);
var selectedAnnotators = user.getPreferences().getElementAnnotators(elementType.className);
- var existingAnnotatorsParameters = user.getPreferences().getAnnotatorsParameters();
-
for (var i = 0; i < annotators.length; i++) {
var annotator = annotators[i];
@@ -101,95 +98,110 @@ ChooseAnnotatorsDialog.prototype.setElementType = function (elementType) {
for (var j = 0; j < selectedAnnotators.length; j++) {
if (annotator.getName() === selectedAnnotators[j]) {
selected = true;
-
- var paramsDefs = annotator.getParametersDefinitions();
- if (paramsDefs.length > 0) {
+ }
+ }
+ var option = new Option();
+ option.value = annotator.getClassName();
+ option.attributes.selected = selected;
+ option.innerHTML = "<div>" + annotator.getName() + "</div>";
+ selectElement.appendChild(option);
+ };
+
+ function createAnnotatorsParams(){
+ var existingAnnotatorsParameters = user.getPreferences().getAnnotatorsParameters();
+
+ Functions.removeChildren(annotatorsParams);
+ for (var i = 0; i < annotators.length; i++) {
+ var annotator = annotators[i];
+ for (var j = 0; j < selectedAnnotators.length; j++) {
+ if (annotator.getName() === selectedAnnotators[j]) {
- annotatorsParams.appendChild(Functions.createElement({
- type: "div",
- className: "minerva-annotators-params-header",
- content: '<div>Available parameters</div>'
- }))
-
- var annotatorParams = Functions.createElement({
- type: "div",
- className: "minerva-annotator-params",
- name: annotator.getClassName()
- });
+ var paramsDefs = annotator.getParametersDefinitions();
+ if (paramsDefs.length > 0) {
+
+ annotatorsParams.appendChild(Functions.createElement({
+ type: "div",
+ className: "minerva-annotators-params-header",
+ content: '<div>Available parameters</div>'
+ }))
- annotatorParams.appendChild(Functions.createElement({
- type: "div",
- className: "minerva-annotator-params-header",
- content: annotator.getName()
- }));
-
- for (var k = 0; k < paramsDefs.length; k++) {
- var param = paramsDefs[k];
- var paramElement = Functions.createElement({
+ var annotatorParams = Functions.createElement({
type: "div",
- className: "minerva-annotator-param"
- });
-
- var paramName = Functions.createElement({
- type: "div",
- className: "minerva-annotator-param-name",
- content: param.name
- });
-
- var toolTip = Functions.createElement({
- type: "span",
- className: "annotator-tooltip",
- content: param.description
+ className: "minerva-annotator-params",
+ name: annotator.getClassName()
});
-
- paramName.appendChild(toolTip)
- paramElement.appendChild(paramName);
-
- var paramValue;
-
- var existingParamValue;
- if (existingAnnotatorsParameters[annotator.getClassName()]) {
- existingParamValue = existingAnnotatorsParameters[annotator.getClassName()][param.name]
- }
-
- if (param.type.indexOf("String") >= 0) {
- paramValue = Functions.createElement({
- type: "textarea",
- onchange: function(){return onChangeParameterValue(this, user);}
+
+ annotatorParams.appendChild(Functions.createElement({
+ type: "div",
+ className: "minerva-annotator-params-header",
+ content: annotator.getName()
+ }));
+
+ for (var k = 0; k < paramsDefs.length; k++) {
+ var param = paramsDefs[k];
+ var paramElement = Functions.createElement({
+ type: "div",
+ className: "minerva-annotator-param"
});
- if (existingParamValue) paramValue.value = existingParamValue;
- } else if (param.type.indexOf("Integer") >= 0) {
- paramValue = Functions.createElement({
- type: "input",
- inputType: "number",
- onchange: function(){return onChangeParameterValue(this, user);}
+
+ var paramName = Functions.createElement({
+ type: "div",
+ className: "minerva-annotator-param-name",
+ content: param.name
});
- if (existingParamValue) paramValue.value = existingParamValue;
- } else if (param.type.indexOf("Boolean") >= 0) {
- paramValue = Functions.createElement({
- type: "input",
- inputType: "checkbox",
- onchange: function(){return onChangeParameterValue(this, user);}
+
+ var toolTip = Functions.createElement({
+ type: "span",
+ className: "annotator-tooltip",
+ content: param.description
});
- paramValue.checked = (existingParamValue && existingParamValue === 'true');
- } else {
- throw new InvalidAlgorithmError("Unknown annotator parameter type");
- }
-
- paramElement.appendChild(paramValue);
- annotatorParams.appendChild(paramElement);
+
+ paramName.appendChild(toolTip)
+ paramElement.appendChild(paramName);
+
+ var paramValue;
+
+ var existingParamValue;
+ if (existingAnnotatorsParameters[annotator.getClassName()]) {
+ existingParamValue = existingAnnotatorsParameters[annotator.getClassName()][param.name]
+ }
+
+ if (param.type.indexOf("String") >= 0) {
+ paramValue = Functions.createElement({
+ type: "textarea",
+ onchange: function(){return onChangeParameterValue(this, user);}
+ });
+ if (existingParamValue) paramValue.value = existingParamValue;
+ } else if (param.type.indexOf("Integer") >= 0) {
+ paramValue = Functions.createElement({
+ type: "input",
+ inputType: "number",
+ onchange: function(){return onChangeParameterValue(this, user);}
+ });
+ if (existingParamValue) paramValue.value = existingParamValue;
+ } else if (param.type.indexOf("Boolean") >= 0) {
+ paramValue = Functions.createElement({
+ type: "input",
+ inputType: "checkbox",
+ onchange: function(){return onChangeParameterValue(this, user);}
+ });
+ paramValue.checked = (existingParamValue && existingParamValue === 'true');
+ } else {
+ throw new InvalidAlgorithmError("Unknown annotator parameter type");
+ }
+
+ paramElement.appendChild(paramValue);
+ annotatorParams.appendChild(paramElement);
+ }
+
+ annotatorsParams.appendChild(annotatorParams);
}
+ }
+ }
+ };
- annotatorsParams.appendChild(annotatorParams);
- }
- }
- }
- var option = new Option();
- option.value = annotator.getClassName();
- option.attributes.selected = selected;
- option.innerHTML = "<div>" + annotator.getName() + "</div>";
- selectElement.appendChild(option);
- };
+ }
+ createAnnotatorsParams();
element.appendChild(selectElement);
new DualListbox(selectElement, {
@@ -203,6 +215,8 @@ ChooseAnnotatorsDialog.prototype.setElementType = function (elementType) {
}
selectedAnnotators.push(annotator.getName());
+ createAnnotatorsParams();
+
var data = new UserPreferences();
var elementAnnotators = {};
@@ -223,6 +237,8 @@ ChooseAnnotatorsDialog.prototype.setElementType = function (elementType) {
selectedAnnotators.splice(index, 1);
}
+ createAnnotatorsParams();
+
var data = new UserPreferences();
var elementAnnotators = {};