Merge pull request #103 from VisBOL/merged-interaction

Merged interaction
VisBOL · Dec 20, 2018 · a736aaa · a736aaa
2 parents b016f78 + 6e9258e
commit a736aaa
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Showing 16 changed files with 276 additions and 179 deletions.
diff --git a/font/sbolv/interaction-arrows/inhibitorArrow.js b/font/sbolv/interaction-arrows/inhibitorArrow.js
@@ -7,9 +7,9 @@ function createGeometry(boxSize) {
     return {
 
         top: Vec2(boxSize.x/2,0),
-        bottomLeft: Vec2(boxSize.x/4,(2*boxSize.y)/4),
-        bottomRight: Vec2((boxSize.x * 3 )/4, (2*boxSize.y)/4),
-        middleBottom: Vec2(boxSize.x/2, (2*boxSize.y)/4)
+        bottomLeft: Vec2(boxSize.x/4,boxSize.y * 0.6),
+        bottomRight: Vec2((boxSize.x * 3 )/4, boxSize.y * 0.6),
+        middleBottom: Vec2(boxSize.x/2, boxSize.y * 0.6)
 
     };
 }

diff --git a/font/sbolv/interaction-arrows/main.js b/font/sbolv/interaction-arrows/main.js
@@ -2,7 +2,7 @@
 module.exports = {
 'InhibitorArrow': require('./inhibitorArrow'),
 'ProductArrow': require('./productArrow'),
-'SimulatorArrow': require('./simulatorArrow'),
+'StimulatorArrow': require('./stimulatorArrow'),
 'ReactantArrow': require('./reactantArrow'),
 'DegradationArrow': require('./degradationArrow')
 }
diff --git a/font/sbolv/interaction-arrows/productArrow.js b/font/sbolv/interaction-arrows/productArrow.js
@@ -7,7 +7,7 @@ function createGeometry(boxSize) {
     return {
 
         top: Vec2(boxSize.x/2, boxSize.y/4),
-        bottom: Vec2(boxSize.x/2, boxSize.y),
+        bottom: Vec2(boxSize.x/2, boxSize.y * 0.8),
 
         left: Vec2(boxSize.x/3,boxSize.y/4),
         right: Vec2((boxSize.x * 2 )/3, boxSize.y/4),

diff --git a/...bolv/interaction-arrows/simulatorArrow.js → ...olv/interaction-arrows/stimulatorArrow.js b/...bolv/interaction-arrows/simulatorArrow.js → ...olv/interaction-arrows/stimulatorArrow.js
@@ -6,7 +6,7 @@ function createGeometry(boxSize) {
 
     return {
 
-        top: Vec2(boxSize.x/2, boxSize.y * 0.1),
+        top: Vec2(boxSize.x/2, boxSize.y * 0.2),
         bottom: Vec2(boxSize.x/2, boxSize.y * 0.8),
 
         left: Vec2(boxSize.x/3,boxSize.y * 0.8),

diff --git a/lib/component.js b/lib/component.js
@@ -55,7 +55,7 @@ helper.circuit_is_participant = function(segment, interactions) {
    else {
      for (interaction of interactions) {
        for (participant of interaction.participants) {
-         if (participant.SO && segment.name === participant.name) {
+         if (participant.SO && segment.name === participant.segment.name) {
            return true; 
          }
        }

diff --git a/lib/design.js b/lib/design.js
@@ -141,7 +141,8 @@ Design.prototype = {
         * otherwise it doesn't know where to render them
         */
         let componentBoxHeight = this.geom.componentBoxHeight;
-        this.interactions = this.displayList.interactions.map(function(interactionObject) {
+        console.log(this.displayList.combinedInteractions, 'interactions')
+        this.interactions = this.displayList.combinedInteractions.map(function(interactionObject) {
 
            var interaction = Interaction.render(design, interactionObject, design.displayList.interactions);
            let interactionPosition = design.geom.interactionPosition;

diff --git a/lib/displayList.js b/lib/displayList.js
@@ -6,6 +6,7 @@ function DisplayList(displayListObject) {
     this.components = [];
     this.processes = [];
     this.interactions = [];
+    this.combinedInteractions = [];
 
     this.refs = Object.create(null);
 
@@ -36,27 +37,10 @@ function DisplayList(displayListObject) {
    * Add rendering Info to participants of the interaction, right now it's just for inhibition
    */
    if(displayListObject.interactions !== undefined) {
-
-
-        this.interactions = displayListObject.interactions.map(function(interaction) {
-
-            //this is the set of interaction types that currently our code is able to rende
-            /*let AvailableInteractions = ["SBO:0000169", "SBO:0000170", "SBO:0000177", "SBO:0000179", "SBO:0000589"];
-
-            if (AvailableInteractions.indexOf(interaction.SBO) !== -1) {
-              for (let i in interaction.participants) {
-                 
-                //find the segment for the circuit participating in the interaction, this way we can simply render the segment using renderSegment
-                for ( let j in displayList.components[0].segments ) {
-                   
-                   if (displayList.components[0].segments[j].name === interaction.participants[i].name ) {
-                      interaction.participants[i].segment = displayList.components[0].segments[j];
-                   }
-                } 
-              }
-            }*/
-        return interaction;    
-      });
+
+        this.interactions = displayListObject.interactions;
+        this.combinedInteractions = DisplayList.combinedInteractions(displayList, displayListObject.interactions)
+
    }
 
 
@@ -194,6 +178,81 @@ DisplayList.Entity = function Entity(displayList, entity) {
     this.name = entity.name;
 }
 
+/*
+*******************************************************************************************
+*/
+DisplayList.combinedInteractions = function combinedInteractions(displayList, interactions) {
+
+        let combinedInteractionsDict = {}
+        let combinedInteractionsList = []
+        let degradationsDict = {}
+        let degraded_NonDNAs = []
+        for(interaction of interactions) {
+
+            //this is the set of interaction types that currently our code is able to rende
+            let AvailableInteractions = ["SBO:0000169", "SBO:0000170", "SBO:0000589"];
+            //let AvailableInteractions = ["SBO:0000169", "SBO:0000170", "SBO:0000177", "SBO:0000179", "SBO:0000589"];
+
+            if (AvailableInteractions.indexOf(interaction.SBO) !== -1) {
+
+              for (participant of interaction.participants) {
+
+                   if (participant.SO) {
+
+                      if (participant.segment.segmentId in combinedInteractionsDict) {
+
+                         combinedInteractionsDict[participant.segment.segmentId]['interactions'].push(interaction)
+
+                      }
+                      else {
+                         segmentInfoDict = {}
+                         segmentInfoDict['segment'] = participant.segment
+                         segmentInfoDict['interactions'] = []
+                         segmentInfoDict['interactions'].push(interaction)
+                         combinedInteractionsDict[participant.segment.segmentId] = segmentInfoDict
+
+                     }
+                  }
+               }
+            }
+
+            if (interaction.SBO === "SBO:0000179") {
+                degraded_NonDNAs.push(interaction.participants[0].segment.segmentId)
+                degradationsDict[interaction.participants[0].segment.segmentId] = interaction
+            }
+
+            if (interaction.SBO === "SBO:0000177") {
+                combinedInteractionsList.push(interaction)
+            }
+        }
+
+        for (key in combinedInteractionsDict) {            
+            for (interaction of combinedInteractionsDict[key]['interactions']) {
+                for (participant of interaction.participants) {
+                    if (!participant.SO && degraded_NonDNAs.indexOf(participant.segment.segmentId) != -1) {
+                        participant.isDegraded = true
+                        degradationsDict[participant.segment.segmentId] = null
+                    }
+                }
+            }
+        }
+
+        //add interactions of type degradation which are not participating in circiut interactions
+        for (key in degradationsDict) {
+            if (degradationsDict[key] !== null) {
+                combinedInteractionsList.push(degradationsDict[key])
+            }
+        }
+
+        //get the values aa a list
+        for (key in combinedInteractionsDict) {
+            combinedInteractionsList.push(combinedInteractionsDict[key])
+        }
+
+        return combinedInteractionsList   
+}
+
+///////////////////////////////////////////////////////////////////////////////////////
 DisplayList.prototype = {
 
     getObjectByID: function getObjectByID(id) {

diff --git a/lib/getDisplayList.js b/lib/getDisplayList.js
@@ -54,7 +54,7 @@ function recurseGetDisplayList(componentDefinition, segments, config, share, max
 
                 }
             }
-
+            
             segments = recurseGetDisplayList(component.definition, segments, config, share)
         }
 
@@ -63,7 +63,7 @@ function recurseGetDisplayList(componentDefinition, segments, config, share, max
     return segments.map(segment => trimSequence(segment, max))
 }
 
-function getDisplayListSegment(componentDefinition, config, share) {
+function getDisplayListSegment(componentDefinition, config, share,i) {
     var displayName = componentDefinition.displayId
 
     if (componentDefinition.name != '' && componentDefinition.name != componentDefinition.displayId) {
@@ -105,7 +105,6 @@ function getDisplayListSegment(componentDefinition, config, share) {
 
     if (componentDefinition.sequenceAnnotations.length === 0 && componentDefinition.components.length === 0) {
 
-        //console.log(componentDefinition);
         var glyph = 'unspecified'
         var name = componentDefinition.name != '' ? componentDefinition.name : componentDefinition.displayId
         var roles = componentDefinition.roles
@@ -173,6 +172,8 @@ function getDisplayListSegment(componentDefinition, config, share) {
 
         return {
             name: displayName,
+            //extra field for identity of a segment
+            segmentId: componentDefinition.uri.toString(),
             sequence: [{
                 strand: "positive",
                 type: glyph,
@@ -189,6 +190,8 @@ function getDisplayListSegment(componentDefinition, config, share) {
 
     return {
         name: displayName,
+        //extra field for identity of a segment
+        segmentId: componentDefinition.uri.toString(),
         sequence: sortedSequenceAnnotations(componentDefinition).map((sequenceAnnotation) => {
 
             var glyph = 'unspecified'

diff --git a/lib/getInteractionList.js b/lib/getInteractionList.js
@@ -3,7 +3,7 @@ var sboToInteractionType = require('./sboToInteractionType')
 var sboToRole = require('./sboToRole')
 var getDisplayListSegment = require('./getDisplayList').getDisplayListSegment
 
-function getInteractionList(moduleDefinition) {
+function getInteractionList(moduleDefinition, config, share) {
 
   let interactions = [];
 
@@ -30,30 +30,34 @@ function getInteractionList(moduleDefinition) {
 
 
               let participantObj = {};
-              participantObj.displayId = participation.displayId;
-              participantObj.segment = getDisplayListSegment(participation.participant.definition)     
-              participantObj.name = participation.participant.definition.displayId;
+              if (participation.displayId !== undefined) {
+                  participantObj.displayId = participation.displayId;
+              }
+
+              if (participation.participant.definition) {
+                  participantObj.segment = getDisplayListSegment(participation.participant.definition,config,share)     
+                  participantObj.name = participation.participant.definition.displayId;
 
-              //Attaching type when participant is Non-DNA
-              if( /*participation.participant.definition.roles.length === 0 */participation.participant.definition.types[0]._parts.fragment != "DnaRegion") {
+                  //Attaching type when participant is Non-DNA
+                  if(participation.participant.definition.types[0]._parts.fragment != "DnaRegion") {
 
-                if (participation.participant.definition.types.length === 1) {
-                  //Attaching type
-                  participantObj.type = participation.participant.definition.types[0]._parts.fragment;
-                 }
-              }
+                    if (participation.participant.definition.types.length === 1) {
+                      //Attaching type
+                      participantObj.type = participation.participant.definition.types[0]._parts.fragment;
+                    }
+                  }
 
-             //Attaching type when participant is DNA 
-              else if( participation.participant.definition.roles.length === 1 ) {
+                 //Attaching type when participant is DNA 
+                 else if( participation.participant.definition.roles.length === 1 ) {
 
 
-                var SOCode = participation.participant.definition.roles[0]._parts.path.split('/').pop();
-                 //var SOCode = participation._roles[0]._parts.path.split('/').pop();
-                // This property only exists for DNA parts 
-                 participantObj.SO = SOCode ;
-                 participantObj.type = soToGlyphType(SOCode); 
-                 
-              }
+                    var SOCode = participation.participant.definition.roles[0]._parts.path.split('/').pop();
+                    //var SOCode = participation._roles[0]._parts.path.split('/').pop();
+                    // This property only exists for DNA parts 
+                    participantObj.SO = SOCode ;
+                    participantObj.type = soToGlyphType(SOCode);                  
+                }
+            }
 
               if (participation.roles.length === 1) {