Fix mapping reload

app/view/button/buttonImportMapping/ButtonImportMappingController.js

@@ -22,7 +22,7 @@ Ext.define('metExploreViz.view.button.buttonImportMapping.ButtonImportMappingCon
 
 		view.on({
 			reloadMapping:function(){
-				view.reset();
+				me.resetCondition();
 			},
 			jsonmapping : function(mappingJSON){
 				me.addConditions(mappingJSON);
@@ -110,11 +110,23 @@ Ext.define('metExploreViz.view.button.buttonImportMapping.ButtonImportMappingCon
 		}
 		else
 			newConditions.push(mapping.getName());
-		
+
 		newConditions
 			.filter(function(cond){
 				return !(cond.includes("PathwayEnrichment") || cond.includes("PathwayCoverage"))
 			})
-			.forEach(function (value) { conditionStore.add({name: value, type: 'int', biologicalType: biologicalType}); });
+			.forEach(function (value) {
+				if(conditionStore.find("name", value)===-1)
+					conditionStore.add({name: value, type: 'int', biologicalType: biologicalType});
+			});
+	},
+
+	/*****************************************************
+	 * Fill condition store store
+	 * @param mapping : Mapping object
+	 */
+	resetCondition : function() {
+		var conditionStore = Ext.getStore("conditionStore");
+		conditionStore.loadData([], false);
 	}
 });

app/view/form/aStyleForm/AStyleFormController.js

@@ -463,7 +463,6 @@ Ext.define('metExploreViz.view.form.aStyleForm.AStyleFormController', {
 						metExploreD3.GraphStyleEdition.setCollectionStyle(view.target, view.attrType, view.attrName, view.biologicalType, val);
 						styleToUse[view.access] = val;
 						view.default = val;
-						console.log(styleToUse);
 					});
 				},
 				scope : me
@@ -523,8 +522,6 @@ Ext.define('metExploreViz.view.form.aStyleForm.AStyleFormController', {
 					metExploreD3.GraphStyleEdition.setCollectionStyle(view.target, view.attrType, view.attrName, view.biologicalType, color);
 
 					styleToUse[view.access]=color;
-
-					console.log(styleToUse);
 				});
 
 			colorButtonBypass.on({

app/view/form/allStylesForm/AllStylesFormController.js

@@ -15,6 +15,11 @@ Ext.define('metExploreViz.view.form.allStylesForm.AllStylesFormController', {
             viewModel   = me.getViewModel(),
             view      	= me.getView();
 
+        view.on({
+            refreshAllStyles : this.reloadAllScales,
+            scope:me
+        });
+
          view.query("allStylesByTypeForm").forEach(function (allStylesByTypeForm) {
             allStylesByTypeForm.lookupReference('saveAllScales')
                 .on({
@@ -167,7 +172,6 @@ Ext.define('metExploreViz.view.form.allStylesForm.AllStylesFormController', {
                     }
                 }
 
-                console.log('--------------------------------------------------');
             });
 
             view.query("allStylesByTypeForm")
@@ -182,5 +186,65 @@ Ext.define('metExploreViz.view.form.allStylesForm.AllStylesFormController', {
         });
 
 
+    },
+    reloadAllScales:function () {
+        var me 		= this,
+            viewModel   = me.getViewModel(),
+            view      	= me.getView();
+        var allScales = [];
+        view.query("allStylesByTypeForm").forEach(function (allStylesByTypeForm) {
+            var partOfAllScales = allStylesByTypeForm.query("aStyleForm")
+                .forEach(function (scale) {
+                    var form = Ext.getCmp(scale.biologicalType+"StyleForm");
+                    if(form){
+                        var theStyleForm = form.query("aStyleForm").find(function (aStyleForm) { return aStyleForm.title===scale.title;});
+                        if(theStyleForm){
+
+                            var selectConditionForm = theStyleForm.lookupReference('selectConditionForm');
+                            var selectCondition = selectConditionForm.lookupReference('selectCondition');
+                            var selectConditionType = selectConditionForm.lookupReference('selectConditionType');
+
+                            var dataType = selectConditionType.getValue();
+                            var selectedCondition = selectCondition.getValue();
+
+                            if (scale.scaleRange){
+                                if(dataType==="Continuous" && selectedCondition!==null){
+                                    selectConditionForm.getController().map(true, true, theStyleForm);
+                                }
+                            }
+
+                            if (scale.valueDiscreteMappings){
+                                if(dataType==="Discrete" && selectedCondition!==null){
+                                    selectConditionForm.getController().map(true, true, theStyleForm);
+                                }
+                            }
+
+                            if (scale.valueAsSelectionMappings){
+                               if(dataType==="As selection" && selectedCondition!==null){
+                                    selectConditionForm.getController().map(true, true, theStyleForm);
+                                }
+                            }
+
+                            if (scale.valueAliasMappings){
+                                if(dataType==="Alias" && selectedCondition!==null){
+                                    selectConditionForm.getController().map(true, true, theStyleForm);
+                                }
+                            }
+                        }
+                    }
+                });
+        });
+
+        /*
+        view.query("allStylesByTypeForm")
+            .forEach(function (allStylesByTypeForm) {
+                allStylesByTypeForm.query("aStyleForm")
+                    .forEach(function (aStyleForm) {
+                        if (aStyleForm.scaleRange)
+                            aStyleForm.getController().updateContinuousCaption();
+
+                    })
+            });
+        */
     }
 });
\ No newline at end of file

app/view/form/captionForm/CaptionFormController.js

@@ -478,13 +478,11 @@ Ext.define('metExploreViz.view.form.captionForm.CaptionFormController', {
                                                         }
 
                                                         var anim = session.isAnimated("viz");
-                                                        if (anim == 'true') {
+                                                        if (anim) {
                                                             var session = _metExploreViz.getSessionById('viz');
                                                             var force = session.getForce();
 
-                                                            if (metExploreD3.GraphNetwork.animation) {
-                                                                force.alpha(1).restart();
-                                                            }
+                                                            force.alpha(force.alpha()).restart();
                                                         }
                                                     }
                                                     catch (e) {
@@ -493,13 +491,11 @@ Ext.define('metExploreViz.view.form.captionForm.CaptionFormController', {
                                                         metExploreD3.hideMask(myMask);
 
                                                         var anim=session.isAnimated("viz");
-                                                        if (anim=='true') {
+                                                        if (anim=== true) {
                                                             var session = _metExploreViz.getSessionById('viz');
                                                             var force = session.getForce();
 
-                                                            if (metExploreD3.GraphNetwork.animation) {
-                                                                force.alpha(1).restart();
-                                                            }
+                                                            force.alpha(force.alpha()).restart();
                                                         }
                                                         throw e;
                                                     }

app/view/form/continuousNumberMappingEditor/ContinuousNumberMappingEditorController.js

@@ -51,10 +51,6 @@ Ext.define('metExploreViz.view.form.continuousNumberMappingEditor.ContinuousNumb
 
 		view.lookupReference('textfieldValue').on({
 			focusleave : function(that){
-				console.log(me);
-				console.log(view);
-
-
 				var value =parseFloat(that.getRawValue());
 
 				if(value==="< min" || value==="> max")

app/view/form/selectConditionForm/SelectConditionFormController.js

@@ -544,7 +544,8 @@ Ext.define('metExploreViz.view.form.selectConditionForm.SelectConditionFormContr
      * @param fluxType : string, one or two arrows for fluxes
      */
     graphMapping : function(dataType, conditionName, parentAStyleForm) {
-        var session = _metExploreViz.getSessionById('viz');
+
+		var session = _metExploreViz.getSessionById('viz');
 
         if(dataType==="Continuous"){
             metExploreD3.GraphMapping.graphMappingContinuousData(conditionName, parentAStyleForm);
@@ -566,6 +567,8 @@ Ext.define('metExploreViz.view.form.selectConditionForm.SelectConditionFormContr
             metExploreD3.GraphMapping.graphMappingDiscreteData(conditionName, parentAStyleForm);
         }
 
+
+
         if(dataType==="As selection"){
             session.setMappingDataType(dataType);
             metExploreD3.GraphMapping.graphMappingAsSelectionData(conditionName, parentAStyleForm);
@@ -597,7 +600,8 @@ Ext.define('metExploreViz.view.form.selectConditionForm.SelectConditionFormContr
         var aStyleFormParent = me.getAStyleFormParent();
         if(type!=="suggestion"){
             networkVizSession.setMapped(selectedCondition);
-            colorStore = aStyleFormParent.getController().getValueMappingsSet(networkVizSession.getMappingDataType());
+
+            colorStore = aStyleFormParent.getController().getValueMappingsSet(dataType);
 
         }
         else {

app/view/form/selectMapping/SelectMappingController.js

@@ -16,6 +16,9 @@ Ext.define('metExploreViz.view.form.selectMapping.SelectMappingController', {
 		view      	= me.getView();
 
 		view.on({
+			reloadMapping:function(){
+				me.resetMapping();
+			},
 			jsonmapping : function(mappingJSON){
 				me.initMapping(mappingJSON);
 			},
@@ -23,6 +26,15 @@ Ext.define('metExploreViz.view.form.selectMapping.SelectMappingController', {
 		});
 	},
 
+	/*****************************************************
+	 * Fill condition store store
+	 * @param mapping : Mapping object
+	 */
+	resetMapping : function() {
+		var store = Ext.getStore("mappingStore");
+		store.loadData([], false);
+	},
+
 	initMapping:function(mappingJSON){
 		var me 		= this,
 			view      	= me.getView();
@@ -36,7 +48,8 @@ Ext.define('metExploreViz.view.form.selectMapping.SelectMappingController', {
 
 				var store = Ext.getStore("mappingStore");
 
-				store.add({name: mappingJSON.getName()});
+				if(store.find("name", mappingJSON.getName())===-1)
+					store.add({name: mappingJSON.getName()});
 				//
 	            // //take an array to store the object that we will get from the ajax response
 				// var records = [];

app/view/form/selectMappingForExtraction/SelectMappingForExtractionController.js

@@ -19,7 +19,6 @@ Ext.define('metExploreViz.view.form.selectMappingForExtraction.SelectMappingForE
 			show : function(that){
 				var store = Ext.getStore("mappingStore");
 				store.filter(function (mapping) {
-					console.log(mapping.get("name"));
 					return mapping.get("name")!=="None";
 				})
 			},

resources/lib/functions/GraphFunction.js

@@ -1390,7 +1390,7 @@ metExploreD3.GraphFunction = {
 					{
 						if(force!=undefined)
 						{
-							if(session.isAnimated("viz")== true)
+							if(session.isAnimated("viz"))
 								force.alpha(1).restart();
 						}
 					}

resources/lib/functions/GraphMapping.js

@@ -174,12 +174,10 @@ metExploreD3.GraphMapping = {
 					metExploreD3.hideMask(myMask);
 
 					var anim = session.isAnimated("viz");
-					if (anim == 'true') {
+					if (anim) {
 						var force = session.getForce();
 
-						if (metExploreD3.GraphNetwork.animation) {
-							force.alpha(1).restart();
-						}
+						force.alpha(force.alpha()).restart();
 					}
 				}
 				catch (e) {
@@ -187,13 +185,11 @@ metExploreD3.GraphMapping = {
 					e.functionUsed="mapNodeDataFile";
 					metExploreD3.hideMask(myMask);
 					var anim=session.isAnimated("viz");
-					if (anim=='true') {
+					if (anim) {
 						var session = _metExploreViz.getSessionById('viz');
 						var force = session.getForce();
 
-						if (metExploreD3.GraphNetwork.animation) {
-							force.alpha(1).restart();
-						}
+						force.alpha(force.alpha()).restart();
 					}
 					throw e;
 				}
@@ -222,7 +218,7 @@ metExploreD3.GraphMapping = {
 					});
 					var nodes = d3.select("#viz").select("#D3viz").select("#graphComponent").selectAll("g.node");
 					var node = undefined;
-
+					var links = undefined;
 					switch (mapping.getTargetLabel()) {
 						case "reactionDBIdentifier":
 							for (var i = conditions.length - 1; i >= 0; i--) {
@@ -253,7 +249,6 @@ metExploreD3.GraphMapping = {
 										var mapNode = new MappingData(node, mapping.getName(), conditions[i], line[i + 1]);
 										node.addMappingData(mapNode);
 
-
 										links = networkData.getLinkByDBIdReaction(node.getDbIdentifier());
 										links.forEach(function (link) {
 											link.addMappingData(mapNode);
@@ -302,12 +297,10 @@ metExploreD3.GraphMapping = {
 					metExploreD3.hideMask(myMask);
 
 					var anim = session.isAnimated("viz");
-					if (anim == 'true') {
+					if (anim) {
 						var force = session.getForce();
 
-						if (metExploreD3.GraphNetwork.animation) {
-							force.alpha(1).restart();
-						}
+						force.alpha(force.alpha()).restart();
 					}
 				}
 				catch (e) {
@@ -316,13 +309,11 @@ metExploreD3.GraphMapping = {
 					metExploreD3.hideMask(myMask);
 
 					var anim=session.isAnimated("viz");
-					if (anim=='true') {
+					if (anim) {
 						var session = _metExploreViz.getSessionById('viz');
 						var force = session.getForce();
 
-						if (metExploreD3.GraphNetwork.animation) {
-							force.alpha(1).restart();
-						}
+						force.alpha(force.alpha()).restart();
 					}
 					throw e;
 				}
@@ -672,13 +663,11 @@ metExploreD3.GraphMapping = {
 
 
 							var anim = session.isAnimated("viz");
-							if (anim == 'true') {
+							if (anim) {
 								var session = _metExploreViz.getSessionById('viz');
 								var force = session.getForce();
 
-								if (metExploreD3.GraphNetwork.animation) {
-									force.alpha(1).restart();
-								}
+								force.alpha(force.alpha()).restart();
 							}
 						}
 						catch (e) {
@@ -687,13 +676,11 @@ metExploreD3.GraphMapping = {
 							metExploreD3.hideMask(myMask);
 
 							var anim=session.isAnimated("viz");
-							if (anim=='true') {
+							if (anim) {
 								var session = _metExploreViz.getSessionById('viz');
 								var force = session.getForce();
 
-								if (metExploreD3.GraphNetwork.animation) {
-									force.alpha(1).restart();
-								}
+								force.alpha(force.alpha()).restart();
 							}
 							throw e;
 						}
@@ -810,17 +797,23 @@ metExploreD3.GraphMapping = {
 						return c !== "PathwayCoverage" && c !== "PathwayEnrichment"
 					});
 					var node = undefined;
+					var links = undefined;
 					switch (mapping.getTargetLabel()) {
 						case "reactionDBIdentifier":
 							mapping.getData().forEach(function (map) {
 								if (typeof map.getNode() == "object")
-									var node = networkData.getNodeByDbIdentifier(map.getNode().getDbIdentifier());
+									node = networkData.getNodeByDbIdentifier(map.getNode().getDbIdentifier());
 								else
-									var node = networkData.getNodeByDbIdentifier(map.getNode());
+									node = networkData.getNodeByDbIdentifier(map.getNode());
 
 								if (node != undefined) {
 									var mapNode = new MappingData(node, mapping.getName(), map.getConditionName(), map.getMapValue());
 									node.addMappingData(mapNode);
+
+									links = networkData.getLinkByDBIdReaction(node.getDbIdentifier());
+									links.forEach(function (link) {
+										link.addMappingData(mapNode);
+									})
 								}
 							});
 							break;
@@ -835,6 +828,11 @@ metExploreD3.GraphMapping = {
 								if (node != undefined) {
 									var mapNode = new MappingData(node, mapping.getName(), map.getConditionName(), map.getMapValue());
 									node.addMappingData(mapNode);
+
+									links = networkData.getLinkByDBIdReaction(node.getDbIdentifier());
+									links.forEach(function (link) {
+										link.addMappingData(mapNode);
+									})
 								}
 							});
 							break;
@@ -876,12 +874,10 @@ metExploreD3.GraphMapping = {
 					metExploreD3.hideMask(myMask);
 
 					var anim = session.isAnimated("viz");
-					if (anim == 'true') {
+					if (anim) {
 						var force = session.getForce();
 
-						if (metExploreD3.GraphNetwork.animation) {
-							force.alpha(1).restart();
-						}
+						force.alpha(force.alpha()).restart();
 					}
 				}
 				catch (e) {
@@ -889,13 +885,11 @@ metExploreD3.GraphMapping = {
 					metExploreD3.hideMask(myMask);
 
 					var anim=session.isAnimated("viz");
-					if (anim=='true') {
+					if (anim) {
 						var session = _metExploreViz.getSessionById('viz');
 						var force = session.getForce();
 
-						if (metExploreD3.GraphNetwork.animation) {
-							force.alpha(1).restart();
-						}
+						force.alpha(force.alpha()).restart();
 					}
 					throw e;
 				}
@@ -995,7 +989,7 @@ metExploreD3.GraphMapping = {
 									aStyleFormParent.getController().addValueMapping("Discrete", values[i], aStyleFormParent.default);
 								}
 
-								var valueMapping = aStyleFormParent.getController().getValueMappingsSet(session.getMappingDataType());
+								var valueMapping = aStyleFormParent.getController().getValueMappingsSet("Discrete");
 								valueMapping.forEach(function(valMapping){
 									metExploreD3.GraphStyleEdition.setCollectionStyleDiscreteMapping(aStyleFormParent.target, aStyleFormParent.attrType, aStyleFormParent.attrName, aStyleFormParent.biologicalType, conditionName, mappingName, valMapping.getName(), valMapping.getValue())
 								});
@@ -1016,7 +1010,7 @@ metExploreD3.GraphMapping = {
 									aStyleFormParent.getController().addValueMapping("Discrete", values[i], color);
 									// metExploreD3.GraphMapping.fixMappingColorOnNodeData(color, values[i], conditionName, mappingName);
 								}
-								var colorStore = aStyleFormParent.getController().getValueMappingsSet(session.getMappingDataType());
+								var colorStore = aStyleFormParent.getController().getValueMappingsSet("Discrete");
 								colorStore.forEach(function(color){
 									metExploreD3.GraphStyleEdition.setCollectionStyleDiscreteMapping(aStyleFormParent.target, aStyleFormParent.attrType, aStyleFormParent.attrName, aStyleFormParent.biologicalType, conditionName, mappingName, color.getName(), color.getValue())
 								});
@@ -1037,13 +1031,13 @@ metExploreD3.GraphMapping = {
 								metExploreD3.displayMessage("Warning", 'No mapped node on network.');
 
 							var anim = session.isAnimated("viz");
-							if (anim == 'true') {
+
+							if (anim) {
+
 								var session = _metExploreViz.getSessionById('viz');
 								var force = session.getForce();
 
-								if (metExploreD3.GraphNetwork.animation) {
-									force.alpha(1).restart();
-								}
+								force.alpha(force.alpha()).restart();
 							}
 						}
 						catch (e) {
@@ -1051,13 +1045,11 @@ metExploreD3.GraphMapping = {
 							metExploreD3.hideMask(myMask);
 
 							var anim=session.isAnimated("viz");
-							if (anim=='true') {
+							if (anim) {
 								var session = _metExploreViz.getSessionById('viz');
 								var force = session.getForce();
 
-								if (metExploreD3.GraphNetwork.animation) {
-									force.alpha(1).restart();
-								}
+								force.alpha(force.alpha()).restart();
 							}
 							throw e;
 						}
@@ -1102,16 +1094,29 @@ metExploreD3.GraphMapping = {
 
 							if(aStyleFormParent.styleType==="float"  || aStyleFormParent.styleType==="int" ) {
 
-								var medium = (aStyleFormParent.min + aStyleFormParent.max)/2;
-								aStyleFormParent.getController().addValueMapping("As selection", "Identified", medium);
+								if(aStyleFormParent.getController().getValueMappingsSet("As selection").length===0) {
+									var medium = (aStyleFormParent.min + aStyleFormParent.max) / 2;
+									aStyleFormParent.getController().addValueMapping("As selection", "Identified", medium);
+								}
+								else
+								{
+									var medium = aStyleFormParent.getController().getValueMappingsSet("As selection")[0].getValue();
+								}
+
 								metExploreD3.GraphStyleEdition.setCollectionStyleAsSelectionMapping(aStyleFormParent.target, aStyleFormParent.attrType, aStyleFormParent.attrName, aStyleFormParent.biologicalType, conditionName, mappingName, "Identified", medium)
 
 							}
 							if(aStyleFormParent.styleType==="color" ) {
+								if(aStyleFormParent.getController().getValueMappingsSet("As selection").length===0){
+									var color = aStyleFormParent.max;
 
-								var color = aStyleFormParent.max;
+									aStyleFormParent.getController().addValueMapping("As selection", "Identified", color);
+								}
+								else
+								{
+									var color = aStyleFormParent.getController().getValueMappingsSet("As selection")[0].getValue();
+								}
 
-								aStyleFormParent.getController().addValueMapping("As selection", "Identified", color);
 								metExploreD3.GraphStyleEdition.setCollectionStyleAsSelectionMapping(aStyleFormParent.target, aStyleFormParent.attrType, aStyleFormParent.attrName, aStyleFormParent.biologicalType, conditionName, mappingName, "Identified", color)
 							}
 
@@ -1130,13 +1135,12 @@ metExploreD3.GraphMapping = {
 								metExploreD3.displayMessage("Warning", 'No mapped node on network.');
 
 							var anim = session.isAnimated("viz");
-							if (anim == 'true') {
+
+							if (anim) {
 								var session = _metExploreViz.getSessionById('viz');
 								var force = session.getForce();
 
-								if (metExploreD3.GraphNetwork.animation) {
-									force.alpha(1).restart();
-								}
+								force.alpha(force.alpha()).restart();
 							}
 						}
 						catch (e) {
@@ -1144,13 +1148,11 @@ metExploreD3.GraphMapping = {
 							metExploreD3.hideMask(myMask);
 
 							var anim=session.isAnimated("viz");
-							if (anim=='true') {
+							if (anim) {
 								var session = _metExploreViz.getSessionById('viz');
 								var force = session.getForce();
 
-								if (metExploreD3.GraphNetwork.animation) {
-									force.alpha(1).restart();
-								}
+								force.alpha(force.alpha()).restart();
 							}
 							throw e;
 						}
@@ -1338,10 +1340,12 @@ metExploreD3.GraphMapping = {
 					function() {
 
 						try {
+							var session = _metExploreViz.getSessionById('viz');
+							var force = session.getForce();
+							force.stop();
 
 							var generalStyle = _metExploreViz.getGeneralStyle();
 							var vis = d3.select("#viz").select("#D3viz");
-							var session = _metExploreViz.getSessionById('viz');
 							var nodes = _metExploreViz.getSessionById('viz').getD3Data().getNodes();
 							var conditions = mapping.getConditions().filter(function (c) { return c!=="PathwayCoverage" && c!=="PathwayEnrichment" });
 
@@ -1458,13 +1462,12 @@ metExploreD3.GraphMapping = {
 							}
 
 							var anim=session.isAnimated("viz");
-							if (anim=='true') {
+							if (anim) {
 								var session = _metExploreViz.getSessionById('viz');
 								var force = session.getForce();
 
-								if (metExploreD3.GraphNetwork.animation) {
-									force.alpha(1).restart();
-								}
+								force.alpha(force.alpha()).restart();
+
 							}
 						}