Metabolic pathways visualisation (#731):

- #issuecomment-1080851310; - #issuecomment-1081402608; - #issuecomment-1081405879;
epam · Mar 29, 2022 · 9ae2bd0 · 9ae2bd0
1 parent 3184d50
commit 9ae2bd0
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Showing 4 changed files with 15 additions and 7 deletions.
diff --git a/...t/client/app/components/ngbPathways/ngbCytoscapePathway/ngbCytoscapePathway.controller.js b/...t/client/app/components/ngbPathways/ngbCytoscapePathway/ngbCytoscapePathway.controller.js
@@ -244,6 +244,7 @@ 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(
@@ -255,7 +256,6 @@ 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)),
@@ -316,14 +316,14 @@ 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();
                     },
@@ -336,6 +336,8 @@ 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,

diff --git a/.../components/ngbPathways/ngbInternalPathwaysResult/ngbInternalPathwaysResult.controller.js b/.../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;
+            }
         }
     }
 

diff --git a/...nt/client/app/components/ngbPathways/ngbPathwaysAnnotation/ngbPathwaysAnnotation.tpl.html b/...nt/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="{{$ctrl.annotationTypeList.HEATMAP}}">
                 Select heatmap file
@@ -119,7 +119,7 @@
         <md-input-container class="add-annotation-dlb-input add-annotation-dlb-file-checkbox">
             <md-checkbox aria-label="upload TSV\CSV" class="md-primary"
                          ng-change="$ctrl.onAnnotationTypeChange()"
-                         ng-false-value="undefined"
+                         ng-false-value="null"
                          ng-model="$ctrl.annotation.type"
                          ng-true-value="{{$ctrl.annotationTypeList.CSV}}">
                 Upload TSV/CSV
@@ -164,7 +164,7 @@
         <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

diff --git a/...components/ngbPathways/ngbPathwaysAnnotationDlg/ngbPathwaysAnnotationAddDlg.controller.js b/...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,