v2.2.2, suplicate complxes same colour, stoich expand complexes,toolt…

…ip bug fix
colin-combe · Jul 4, 2024 · 5e38e02 · 5e38e02
1 parent a4f5a59
commit 5e38e02
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Showing 10 changed files with 1,627 additions and 8,561 deletions.
diff --git a/data/CPX-7083.json b/data/CPX-7083.json
diff --git a/data/EBI-25570228.json b/data/EBI-25570228.json
diff --git a/data/index.js b/data/index.js
@@ -20,6 +20,11 @@ const exampleIndex = [
         "name": "CPX-5897",
         "url": "https://www.ebi.ac.uk/complexportal/complex/CPX-5897",
     },
+    {
+        "ac": "CPX-7083",
+        "name": "CPX-7083",
+        "url": "https://www.ebi.ac.uk/complexportal/complex/CPX-7083",
+    },
     {
         "ac": "EBI-25776165",
         "name": "EBI-25776165",

diff --git a/dist/complexviewer.js b/dist/complexviewer.js
diff --git a/package.json b/package.json
@@ -1,6 +1,6 @@
 {
   "name": "complexviewer",
-  "version": "2.2.2dev",
+  "version": "2.2.2",
   "description": "A network visualisation that displays molecular interaction data, including detailed residue-level information such as binding sites. Used in EBI's Complex Portal and elsewhere.",
   "author": {
     "name": "Colin Combe",

diff --git a/src/js/clone-complex-refs.js b/src/js/clone-complex-refs.js
@@ -11,38 +11,38 @@ export function cloneComplexRefs(json) {
     interactions.forEach(function (interaction) {
 
         // Get a collection of participants with 'complex' in interactorRef - not ideal way to get complexes
-        const complexesToCloneParticipantsOf = interaction.participants.filter(function (participant) {
+        const complexesToClone = interaction.participants.filter(function (participant) {
             if (participant.interactorRef.indexOf("complex") !== -1) {
                 return participant;
             }
         });
 
         // Loop through our participants that need expanding
-        complexesToCloneParticipantsOf.forEach(function (complexToCloneParticipantsOf) {
+        complexesToClone.forEach(function (complexToClone) {
 
             // Do we have an interaction
-            const foundInteraction = findFirstObjWithAttr(interactions, "id", complexToCloneParticipantsOf.interactorRef);
+            const foundInteraction = findFirstObjWithAttr(interactions, "id", complexToClone.interactorRef);
 
             // If we found an interaction then we need to clone it.
             if (foundInteraction) {
 
-                let count = instanceCount.get(complexToCloneParticipantsOf.interactorRef);
+                let count = instanceCount.get(complexToClone.interactorRef);
                 if (count) {
                     count = count + 1;
                 } else {
                     count = 1;
                 }
-                instanceCount.set(complexToCloneParticipantsOf.interactorRef, count);
+                instanceCount.set(complexToClone.interactorRef, count);
 
                 let i = count;
 
                 if (i > 1) {
                     // this looks weird, don't think it'll work if more than 2 refs to complex?
-                    complexToCloneParticipantsOf.interactorRef = `${complexToCloneParticipantsOf.interactorRef}_${i}`;
+                    complexToClone.interactorRef = `${complexToClone.interactorRef}_${i}`;
 
                     // update features of complex
-                    if (complexToCloneParticipantsOf.features) {
-                        complexToCloneParticipantsOf.features.forEach(function (feature) {
+                    if (complexToClone.features) {
+                        complexToClone.features.forEach(function (feature) {
                             feature.copiedfrom = feature.id;
                             // feature.id = `${feature.id}_${i}`;
                             // Also, adjust our sequence data
@@ -54,6 +54,7 @@ export function cloneComplexRefs(json) {
                     }
 
                     const clonedInteraction = JSON.parse(JSON.stringify(foundInteraction));
+                    clonedInteraction.sourceId = clonedInteraction.id;
                     clonedInteraction.id = `${clonedInteraction.id}_${i}`;
 
                     json.data.push(clonedInteraction);

diff --git a/src/js/clone-complex-stoich.js b/src/js/clone-complex-stoich.js
@@ -41,6 +41,7 @@ export function cloneComplexesStoich(json) {
                         }
 
                         const clonedInteraction = JSON.parse(JSON.stringify(foundInteraction));
+                        clonedInteraction.sourceId = clonedInteraction.id;
                         clonedInteraction.id = `${clonedInteraction.id}_${i}`;
                         clonedInteraction.interactorRef = `${complexToClone.interactorRef}_${i}`;
 

diff --git a/src/js/read-mijson.js b/src/js/read-mijson.js
@@ -186,7 +186,7 @@ export function readMijson(/*miJson*/miJson, /*App*/ app, expand = true) {
                 let nLink = app.allNaryLinks.get(nLinkId);
                 if (typeof nLink === "undefined") {
                     //doesn't already exist, make new nLink
-                    nLink = new NaryLink(nLinkId, app);
+                    nLink = new NaryLink(nLinkId, app, datum.sourceId);
                     app.allNaryLinks.set(nLinkId, nLink);
                     //alot of time is being spent on creating these IDs, stash them in the interaction object?
                     datum.naryId = nLinkId;

diff --git a/src/js/viz/link/nary-link.js b/src/js/viz/link/nary-link.js
@@ -4,8 +4,11 @@ import {Link} from "./link";
 import {rotatePointAboutPoint} from "../../geom";
 
 export class NaryLink extends Link {
-    constructor(id, app) {
+    constructor(id, app, sourceId) {
         super(id, app);
+        if (sourceId) {
+            this.sourceId = sourceId;
+        }
         this.binaryLinks = new Map();
         this.unaryLinks = new Map();
     }
@@ -31,7 +34,7 @@ export class NaryLink extends Link {
         if (!this._path) {
             this._path = this._createElement("path");
             if (this.app.stoichiometryExpanded) {
-                this.color = NaryLink.naryColors(this.id);
+                this.color = NaryLink.naryColors(this.sourceId?this.sourceId:this.id);
                 this._path.setAttribute("fill", this.color);
             } else {
                 this._path.setAttribute("fill", "none");

diff --git a/src/js/viz/sequence-datum.js b/src/js/viz/sequence-datum.js
@@ -34,50 +34,60 @@ export class SequenceDatum {
             const firstPart = sequenceDatumString.substring(0, dashPosition);
             const secondPart = sequenceDatumString.substring(dashPosition + 1);
 
-            let firstDotPosition;
-            if (firstPart.indexOf(".") === -1) {
-                this.begin = tidyPosition(firstPart);
-            } else {
-                firstDotPosition = firstPart.indexOf(".");
-                this.uncertainBegin = tidyPosition(firstPart.substring(0, firstDotPosition));
-                this.begin = tidyPosition(firstPart.substring(firstDotPosition + 2));
-            }
-
-            if (secondPart.indexOf(".") === -1) {
-                this.end = tidyPosition(secondPart);
-            } else {
-                firstDotPosition = secondPart.indexOf(".");
-                this.end = tidyPosition(secondPart.substring(0, firstDotPosition));
-                this.uncertainEnd = tidyPosition(secondPart.substring(firstDotPosition + 2));
-            }
-
-            if (this.begin === "n") {
+            if (firstPart == '?') {
                 this.uncertainBegin = 1;
-                this.begin = tidyPosition(this.end);
-                // this.uncertainEnd = this.end;
+                this.begin = tidyPosition(secondPart);
                 this.end = null;
-            }
-
-            if (this.end === "c") {
+            } else if (secondPart == '?') {
                 this.uncertainEnd = participant.size;
-                this.end = tidyPosition(this.begin);
-                // this.uncertainBegin = this.begin;
+                this.end = tidyPosition(firstPart);
                 this.begin = null;
-            }
-
-            if (firstPart.indexOf("<") > -1) {
-                this.uncertainBegin = 0;
-                this.begin = tidyPosition(firstPart.substring(1, firstPart.length));
-            }
-            if (secondPart.indexOf(">") > -1) {
-                this.end = tidyPosition(secondPart.substring(1, firstPart.length));
-                this.uncertainEnd = participant.size;
-            }
-
-            if (firstPart.indexOf(">") > -1 && secondPart.indexOf("<") > -1) {
-                this.uncertainBegin = tidyPosition(firstPart.substring(1, firstPart.length));
-                this.begin = tidyPosition(secondPart.substring(1, firstPart.length));
-                this.end = null;//this.begin;
+            } else {
+                let firstDotPosition;
+                if (firstPart.indexOf(".") === -1) {
+                    this.begin = tidyPosition(firstPart);
+                } else {
+                    firstDotPosition = firstPart.indexOf(".");
+                    this.uncertainBegin = tidyPosition(firstPart.substring(0, firstDotPosition));
+                    this.begin = tidyPosition(firstPart.substring(firstDotPosition + 2));
+                }
+
+                if (secondPart.indexOf(".") === -1) {
+                    this.end = tidyPosition(secondPart);
+                } else {
+                    firstDotPosition = secondPart.indexOf(".");
+                    this.end = tidyPosition(secondPart.substring(0, firstDotPosition));
+                    this.uncertainEnd = tidyPosition(secondPart.substring(firstDotPosition + 2));
+                }
+
+                if (this.begin === "n") {
+                    this.uncertainBegin = 1;
+                    this.begin = tidyPosition(this.end);
+                    // this.uncertainEnd = this.end;
+                    this.end = null;
+                }
+
+                if (this.end === "c") {
+                    this.uncertainEnd = participant.size;
+                    this.end = tidyPosition(this.begin);
+                    // this.uncertainBegin = this.begin;
+                    this.begin = null;
+                }
+
+                if (firstPart.indexOf("<") > -1) {
+                    this.uncertainBegin = 1;
+                    this.begin = tidyPosition(firstPart.substring(1, firstPart.length));
+                }
+                if (secondPart.indexOf(">") > -1) {
+                    this.end = tidyPosition(secondPart.substring(1, firstPart.length));
+                    this.uncertainEnd = participant.size;
+                }
+
+                if (firstPart.indexOf(">") > -1 && secondPart.indexOf("<") > -1) {
+                    this.uncertainBegin = tidyPosition(firstPart.substring(1, firstPart.length));
+                    this.begin = tidyPosition(secondPart.substring(1, firstPart.length));
+                    this.end = null;//this.begin;
+                }
             }
         }
     }