Metabolic pathways visualisation (#731): context menu pathways condition weakening

client/client/app/components/ngbPathways/ngbCytoscapePathway/ngbCytoscapePathway.controller.js

@@ -235,6 +235,7 @@ export default class ngbCytoscapePathwayController {
                 const savedState = JSON.parse(localStorage.getItem(this.storageName) || '{}');
                 const savedLayout = savedState.layout ? savedState.layout[this.elements.id] : undefined;
                 let elements;
+                this.elements.nodes = this.saveDefaultPositions(this.elements.nodes, this.isCollage());
                 if (savedLayout) {
                     elements = {
                         nodes: this.wrapNodes(
@@ -246,7 +247,6 @@ export default class ngbCytoscapePathwayController {
                         edges: savedLayout.edges
                     };
                 } else {
-                    this.elements.nodes = this.saveDefaultPositions(this.elements.nodes, this.isCollage());
                     elements = {
                         nodes: this.wrapNodes(
                             this.getPlainNodes(this.positionedNodes(this.elements.nodes)),
@@ -307,14 +307,14 @@ export default class ngbCytoscapePathwayController {
                     zoomIn() {
                         const zoom = this.zoom() + this.ZOOM_STEP;
                         viewerContext.viewer.zoom(zoom);
-                        // viewerContext.centerCytoscape();
+                        viewerContext.centerCytoscape();
                         this.canZoomIn = zoom < viewerContext.viewer.maxZoom();
                         this.canZoomOut = zoom > viewerContext.viewer.minZoom();
                     },
                     zoomOut() {
                         const zoom = this.zoom() - this.ZOOM_STEP;
                         viewerContext.viewer.zoom(zoom);
-                        // viewerContext.centerCytoscape();
+                        viewerContext.centerCytoscape();
                         this.canZoomIn = zoom < viewerContext.viewer.maxZoom();
                         this.canZoomOut = zoom > viewerContext.viewer.minZoom();
                     },
@@ -327,6 +327,8 @@ export default class ngbCytoscapePathwayController {
                             viewerContext.viewer.layout(this.settings.loadedLayout).run();
                         });
                         viewerContext.saveLayout();
+                        this.actionsManager.canZoomIn = this.actionsManager.zoom() < viewerContext.viewer.maxZoom();
+                        this.actionsManager.canZoomOut = this.actionsManager.zoom() > viewerContext.viewer.minZoom();
                     },
                     canZoomIn: true,
                     canZoomOut: true,

client/client/app/components/ngbPathways/ngbInternalPathwaysResult/ngbInternalPathwaysResult.controller.js

@@ -134,6 +134,9 @@ export default class ngbInternalPathwaysResultController extends baseController
         if (this.ngbPathwaysService.currentInternalPathway) {
             this.annotationList = this.ngbPathwaysAnnotationService.getPathwayAnnotationList(this.ngbPathwaysService.currentInternalPathway.id);
             this.applyAnnotations();
+            if (this.annotationList && this.annotationList.length !== 0) {
+                this.annotationsPanelVisible = true;
+            }
         }
     }
 

client/client/app/components/ngbPathways/ngbPathwaysAnnotation/ngbPathwaysAnnotation.controller.js

@@ -151,10 +151,16 @@ export default class ngbPathwaysAnnotationController {
             };
             if (isHeatmapChange || !this.colorScheme) {
                 const colorSchemeParams = {colorFormat: ColorFormats.hex};
-                colorSchemeParams.minimum = this.annotation.config.minCellValue;
-                colorSchemeParams.maximum = this.annotation.config.maxCellValue;
+                if (this.annotation.config.minCellValue) {
+                    colorSchemeParams.minimum = this.annotation.config.minCellValue;
+                }
+                if (this.annotation.config.maxCellValue) {
+                    colorSchemeParams.maximum = this.annotation.config.maxCellValue;
+                }
                 this.colorScheme = options.colorScheme.copy(colorSchemeParams);
             }
+            this.annotation.config.minCellValue = this.colorScheme.minimum;
+            this.annotation.config.maxCellValue = this.colorScheme.maximum;
         });
         options.data.options = {id, projectId};
         this.annotation.name = this.annotation.name || this.heatmap.prettyName || this.heatmap.name;

client/client/app/components/ngbPathways/ngbPathwaysAnnotation/ngbPathwaysAnnotation.service.js

@@ -55,7 +55,9 @@ function parseConfigHeatmap(config, header) {
     return {
         labels,
         values: config.values,
-        heatmapId: config.heatmapId
+        heatmapId: config.heatmapId,
+        minCellValue: config.minCellValue,
+        maxCellValue: config.maxCellValue
     };
 }
 
@@ -191,7 +193,9 @@ export default class ngbPathwaysAnnotationService {
         for (const annotation of rawAnnotationList) {
             if (annotation.serializedColorScheme) {
                 annotation.colorScheme = ColorScheme.parse(annotation.serializedColorScheme).copy({
-                    colorFormat: ColorFormats.hex
+                    colorFormat: ColorFormats.hex,
+                    minimum: annotation.value.minCellValue,
+                    maximum: annotation.value.maxCellValue
                 });
                 delete annotation.serializedColorScheme;
             }

client/client/app/components/ngbPathways/ngbPathwaysAnnotation/ngbPathwaysAnnotation.tpl.html

@@ -10,7 +10,7 @@
         <md-input-container class="add-annotation-dlb-input">
             <md-checkbox aria-label="select heatmap" class="md-primary"
                          ng-change="$ctrl.onAnnotationTypeChange()"
-                         ng-false-value="undefined"
+                         ng-false-value="null"
                          ng-model="$ctrl.annotation.type"
                          ng-true-value="{{$ctrl.annotationTypeList.HEATMAP}}">
                 Select heatmap file
@@ -63,7 +63,7 @@
         <md-input-container class="add-annotation-dlb-input add-annotation-dlb-file-checkbox">
             <md-checkbox aria-label="upload TSV\CSV" class="md-primary"
                          ng-change="$ctrl.onAnnotationTypeChange()"
-                         ng-false-value="undefined"
+                         ng-false-value="null"
                          ng-model="$ctrl.annotation.type"
                          ng-true-value="{{$ctrl.annotationTypeList.CSV}}">
                 Upload TSV/CSV
@@ -108,7 +108,7 @@
         <md-input-container class="add-annotation-dlb-input">
             <md-checkbox aria-label="manual colors config" class="md-primary"
                          ng-change="$ctrl.onAnnotationTypeChange()"
-                         ng-false-value="undefined"
+                         ng-false-value="null"
                          ng-model="$ctrl.annotation.type"
                          ng-true-value="{{$ctrl.annotationTypeList.MANUAL}}">
                 Manual colors config

client/client/app/components/ngbPathways/ngbPathwaysAnnotationDlg/ngbPathwaysAnnotationAddDlg.controller.js

@@ -6,7 +6,10 @@ export default class ngbPathwaysAnnotationAddDlgController {
             this.annotation = {
                 ...annotation
             };
-            this.colorScheme = this.annotation.colorScheme.copy();
+            if (this.annotation.type === this.ngbPathwaysAnnotationService.annotationTypeList.HEATMAP
+                || this.annotation.type === this.ngbPathwaysAnnotationService.annotationTypeList.CSV) {
+                this.colorScheme = this.annotation.colorScheme.copy();
+            }
         } else {
             this.annotation = {
                 name: undefined,

client/client/app/components/ngbTracksView/ngbTrack/ngbTrack.events.js

@@ -217,9 +217,7 @@ export default class ngbTrackEvents {
                             : undefined,
                     });
                 }
-                if (data.feature.feature
-                    && data.feature.feature.toLowerCase() === 'gene'
-                    && data.feature.name) {
+                if (data.feature.feature && data.feature.name) {
                     const layoutChange = this.appLayout.Panels.pathways;
                     layoutChange.displayed = true;
                     menuData.push({
@@ -235,8 +233,8 @@ export default class ngbTrackEvents {
                                 name: 'read:show:pathways'
                             }],
                         title: 'Show pathways',
-                        disabled: (data.feature.feature || '').toLowerCase() !== 'gene' || !data.feature.name,
-                        warning: (data.feature.feature || '').toLowerCase() !== 'gene' || !data.feature.name
+                        disabled: !data.feature.name,
+                        warning: !data.feature.name
                             ? 'Feature type is not Gene or Name is missing'
                             : undefined,
                     });