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Merge pull request #714 from umut-er/unstable
Highlight query seed genes / paths #389
2 parents 7abcfd5 + fd17962 commit 2a0c4a2

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‎app/js/backbone-views.js

Lines changed: 157 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -2183,6 +2183,23 @@ var NeighborhoodQueryView = Backbone.View.extend({
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currentGeneralProperties.inferNestingOnLoad =
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currentInferNestingOnLoad;
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chiseInstance.endSpinner("neighborhood-spinner");
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// Highlighting feature
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eles = cy.collection();
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geneSymbolsArray.forEach(function (gene) {
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eles.merge(cy.nodes().filter(function (ele) {
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if(ele.data('label') && ele.data('label').toLowerCase().indexOf(gene.toLowerCase()) >= 0){
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return true;
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}
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return false;
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}))
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})
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var x = cy.elements().kNeighborhood(eles, self.currentQueryParameters.lengthLimit, 'BOTHSTREAM');
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cy.viewUtilities('get').highlight(x.neighborNodes, 2);
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cy.viewUtilities('get').highlight(x.neighborEdges, 2);
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cy.viewUtilities('get').highlight(eles, 0);
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// Highlighting feature end
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$(document).trigger("sbgnvizLoadFileEnd", [filename, cy]);
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} else {
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new PromptEmptyQueryResultView({
@@ -2251,6 +2268,23 @@ var NeighborhoodQueryView = Backbone.View.extend({
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currentGeneralProperties.inferNestingOnLoad =
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currentInferNestingOnLoad;
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chiseInstance.endSpinner("neighborhood-spinner");
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// Highlighting feature
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eles = cy.collection();
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geneSymbolsArray.forEach(function (gene) {
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eles.merge(cy.nodes().filter(function (ele) {
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if(ele.data('label') && ele.data('label').toLowerCase().indexOf(gene.toLowerCase()) >= 0){
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return true;
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}
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return false;
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}))
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})
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var x = cy.elements().kNeighborhood(eles, self.currentQueryParameters.lengthLimit, 'BOTHSTREAM');
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cy.viewUtilities('get').highlight(x.neighborNodes, 2);
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cy.viewUtilities('get').highlight(x.neighborEdges, 2);
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cy.viewUtilities('get').highlight(eles, 0);
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// Highlighting feature end
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$(document).trigger("sbgnvizLoadFileEnd", [filename, cy]);
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} else if (data.error) {
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let { code } = data.error;
@@ -2421,6 +2455,23 @@ var PathsBetweenQueryView = Backbone.View.extend({
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currentGeneralProperties.inferNestingOnLoad =
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currentInferNestingOnLoad;
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chiseInstance.endSpinner("paths-between-spinner");
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// Highlighting feature
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eles = cy.collection();
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geneSymbolsArray.forEach(function (gene) {
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eles.merge(cy.nodes().filter(function (ele) {
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if(ele.data('label') && ele.data('label').toLowerCase().indexOf(gene.toLowerCase()) >= 0){
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return true;
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}
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return false;
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}))
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})
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var x = cy.elements().pathsBetween(eles, self.currentQueryParameters.lengthLimit, 'UNDIRECTED');
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cy.viewUtilities('get').highlight(x.resultEdges, 2);
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cy.viewUtilities('get').highlight(x.resultNodes, 2);
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cy.viewUtilities('get').highlight(eles, 0);
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// Highlighting feature end
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$(document).trigger("sbgnvizLoadFileEnd", [filename, cy]);
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} else {
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new PromptEmptyQueryResultView({
@@ -2486,6 +2537,23 @@ var PathsBetweenQueryView = Backbone.View.extend({
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currentGeneralProperties.inferNestingOnLoad =
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currentInferNestingOnLoad;
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chiseInstance.endSpinner("paths-between-spinner");
2540+
2541+
// Highlighting feature
2542+
eles = cy.collection();
2543+
geneSymbolsArray.forEach(function (gene) {
2544+
eles.merge(cy.nodes().filter(function (ele) {
2545+
if(ele.data('label') && ele.data('label').toLowerCase().indexOf(gene.toLowerCase()) >= 0){
2546+
return true;
2547+
}
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return false;
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}))
2550+
})
2551+
var x = cy.elements().pathsBetween(eles, self.currentQueryParameters.lengthLimit, 'UNDIRECTED');
2552+
cy.viewUtilities('get').highlight(x.resultEdges, 2);
2553+
cy.viewUtilities('get').highlight(x.resultNodes, 2);
2554+
cy.viewUtilities('get').highlight(eles, 0);
2555+
// Highlighting feature end
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$(document).trigger("sbgnvizLoadFileEnd", [filename, cy]);
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} else {
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new PromptEmptyQueryResultView({
@@ -2702,6 +2770,33 @@ var PathsFromToQueryView = Backbone.View.extend({
27022770
currentGeneralProperties.inferNestingOnLoad =
27032771
currentInferNestingOnLoad;
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chiseInstance.endSpinner("paths-fromto-spinner");
2773+
2774+
// Highlighting feature
2775+
source_eles = cy.collection();
2776+
sourceSymbolsArray.forEach(function (gene) {
2777+
source_eles.merge(cy.nodes().filter(function (ele) {
2778+
if(ele.data('label') && ele.data('label').toLowerCase().indexOf(gene.toLowerCase()) >= 0){
2779+
return true;
2780+
}
2781+
return false;
2782+
}))
2783+
})
2784+
target_eles = cy.collection();
2785+
targetSymbolsArray.forEach(function (gene) {
2786+
target_eles.merge(cy.nodes().filter(function (ele) {
2787+
if(ele.data('label') && ele.data('label').toLowerCase().indexOf(gene.toLowerCase()) >= 0){
2788+
return true;
2789+
}
2790+
return false;
2791+
}))
2792+
})
2793+
var x = cy.elements().pathsFromTo(source_eles, target_eles, self.currentQueryParameters.lengthLimit, self.currentQueryParameters.lengthLimit, 'UNDIRECTED');
2794+
cy.viewUtilities('get').highlight(x.edgesOnThePaths, 2);
2795+
// cy.viewUtilities('get').highlight(x.nodesOnThePaths, 2);
2796+
cy.viewUtilities('get').highlight(source_eles, 0);
2797+
cy.viewUtilities('get').highlight(target_eles, 1);
2798+
// Highlighting feature end
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$(document).trigger("sbgnvizLoadFileEnd", [filename, cy]);
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} else {
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new PromptEmptyQueryResultView({
@@ -2767,6 +2862,32 @@ var PathsFromToQueryView = Backbone.View.extend({
27672862
currentGeneralProperties.inferNestingOnLoad =
27682863
currentInferNestingOnLoad;
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chiseInstance.endSpinner("paths-fromto-spinner");
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2866+
// Highlighting feature
2867+
source_eles = cy.collection();
2868+
sourceSymbolsArray.forEach(function (gene) {
2869+
source_eles.merge(cy.nodes().filter(function (ele) {
2870+
if(ele.data('label') && ele.data('label').toLowerCase().indexOf(gene.toLowerCase()) >= 0){
2871+
return true;
2872+
}
2873+
return false;
2874+
}))
2875+
})
2876+
target_eles = cy.collection();
2877+
targetSymbolsArray.forEach(function (gene) {
2878+
target_eles.merge(cy.nodes().filter(function (ele) {
2879+
if(ele.data('label') && ele.data('label').toLowerCase().indexOf(gene.toLowerCase()) >= 0){
2880+
return true;
2881+
}
2882+
return false;
2883+
}))
2884+
})
2885+
cy.viewUtilities('get').highlight(source_eles, 0);
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cy.viewUtilities('get').highlight(target_eles, 1);
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var x = cy.elements().pathsFromTo(source_eles, target_eles, self.currentQueryParameters.lengthLimit, 1, 'UNDIRECTED');
2888+
cy.viewUtilities('get').highlight(x.edgesOnThePaths, 2);
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// Highlighting feature end
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$(document).trigger("sbgnvizLoadFileEnd", [filename, cy]);
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} else {
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new PromptEmptyQueryResultView({
@@ -2940,6 +3061,24 @@ var CommonStreamQueryView = Backbone.View.extend({
29403061
currentGeneralProperties.inferNestingOnLoad =
29413062
currentInferNestingOnLoad;
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chiseInstance.endSpinner("common-stream-spinner");
3064+
3065+
// Highlighting feature
3066+
eles = cy.collection();
3067+
geneSymbolsArray.forEach(function (gene) {
3068+
eles.merge(cy.nodes().filter(function (ele) {
3069+
if(ele.data('label') && ele.data('label').toLowerCase().indexOf(gene.toLowerCase()) >= 0){
3070+
return true;
3071+
}
3072+
return false;
3073+
}))
3074+
})
3075+
var x = cy.elements().commonStream(eles, self.currentQueryParameters.lengthLimit, 'BOTHSTREAM');
3076+
cy.viewUtilities('get').highlight(x.nodesOnPath, 2);
3077+
cy.viewUtilities('get').highlight(x.edgesOnPath, 2);
3078+
cy.viewUtilities('get').highlight(x.commonNodes, 1);
3079+
cy.viewUtilities('get').highlight(eles, 0);
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// Highlighting feature end
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$(document).trigger("sbgnvizLoadFileEnd", [filename, cy]);
29443083
} else {
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new PromptEmptyQueryResultView({
@@ -3005,6 +3144,24 @@ var CommonStreamQueryView = Backbone.View.extend({
30053144
currentGeneralProperties.inferNestingOnLoad =
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currentInferNestingOnLoad;
30073146
chiseInstance.endSpinner("common-stream-spinner");
3147+
3148+
// Highlighting feature
3149+
eles = cy.collection();
3150+
geneSymbolsArray.forEach(function (gene) {
3151+
eles.merge(cy.nodes().filter(function (ele) {
3152+
if(ele.data('label') && ele.data('label').toLowerCase().indexOf(gene.toLowerCase()) >= 0){
3153+
return true;
3154+
}
3155+
return false;
3156+
}))
3157+
})
3158+
var x = cy.elements().commonStream(eles, self.currentQueryParameters.lengthLimit, 'BOTHSTREAM');
3159+
cy.viewUtilities('get').highlight(x.nodesOnPath, 2);
3160+
cy.viewUtilities('get').highlight(x.edgesOnPath, 2);
3161+
cy.viewUtilities('get').highlight(x.commonNodes, 1);
3162+
cy.viewUtilities('get').highlight(eles, 0);
3163+
// Highlighting feature end
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$(document).trigger("sbgnvizLoadFileEnd", [filename, cy]);
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} else {
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new PromptEmptyQueryResultView({

‎app/main.js

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Original file line numberDiff line numberDiff line change
@@ -28,6 +28,7 @@ var cyAutopanOnDrag = require('cytoscape-autopan-on-drag');
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var cyNodeEditing = require('cytoscape-node-editing');
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var cyPopper = require('cytoscape-popper');
3030
var cyLayoutUtilities = require('cytoscape-layout-utilities');
31+
var cyGraphAlgos = require('cytoscape-graph-algos');
3132

3233
// Register cy extensions
3334
cyPanzoom( cytoscape, $ );
@@ -45,6 +46,7 @@ cyAutopanOnDrag( cytoscape );
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cyNodeEditing( cytoscape, $, konva );
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cyPopper( cytoscape );
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cyLayoutUtilities( cytoscape );
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cyGraphAlgos( cytoscape );
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// Libraries to pass sbgnviz
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var libs = {};

‎package.json

Lines changed: 1 addition & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -32,6 +32,7 @@
3232
"cytoscape-edgehandles": "~2.13.1",
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"cytoscape-expand-collapse": "github:iVis-at-Bilkent/cytoscape.js-expand-collapse#unstable",
3434
"cytoscape-fcose": "github:iVis-at-Bilkent/cytoscape.js-fcose#unstable",
35+
"cytoscape-graph-algos": "github:iVis-at-Bilkent/cytoscape.js-graph-algos#master",
3536
"cytoscape-grid-guide": "github:iVis-at-Bilkent/cytoscape.js-grid-guide#unstable",
3637
"cytoscape-layout-utilities": "github:iVis-at-Bilkent/cytoscape.js-layout-utilities#unstable",
3738
"cytoscape-node-editing": "github:iVis-at-Bilkent/cytoscape.js-node-editing#unstable",

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