From d629fa9b3d6abf5cd060136729921aebd1fb2a5d Mon Sep 17 00:00:00 2001
From: asadeg02 <arezu.sadeghi@gmail.com>
Date: Thu, 6 Dec 2018 01:59:29 -0500
Subject: [PATCH] resolve the bug regarding non-covelant-binding

---
 lib/interactions/non-covelant-binding.js | 11 ++++++++---
 lib/interactions/stimulation.js          |  3 +--
 lib/segment.js                           |  3 ++-
 3 files changed, 11 insertions(+), 6 deletions(-)

diff --git a/lib/interactions/non-covelant-binding.js b/lib/interactions/non-covelant-binding.js
index b251d29..3417c9f 100644
--- a/lib/interactions/non-covelant-binding.js
+++ b/lib/interactions/non-covelant-binding.js
@@ -21,9 +21,14 @@ function render(design, interaction, segments, interactions) {
       let productOffset = 0;
       let width = 0;
       for (let i in interaction.participants) {
-              
+           
+          if (!interaction.participants[i].segment) {
+              console.log(interaction.participants[i], "partcipant")
+              console.log(interaction, "interaction")
+          }   
           //clear all the previous rolles attached to participant segment
           interaction.participants[i].segment.role = null;
+          
 
           if (interaction.participants[i].role === "reactant") {
               reactantNumber++;
@@ -36,7 +41,7 @@ function render(design, interaction, segments, interactions) {
           var segment = Segment.render(design, interaction.participants[i].segment, interactions);
          
            if (i == 0) {
-            productOffset = interaction.participants.segmentWidth;
+            productOffset = interaction.segmentWidth;
             
            }
           
@@ -44,7 +49,7 @@ function render(design, interaction, segments, interactions) {
 
              //segment.dx(110);
              segment.dx(productOffset);
-             
+                          
          }
 
           else if (interaction.participants[i].segment.role === "reactant2") {
diff --git a/lib/interactions/stimulation.js b/lib/interactions/stimulation.js
index 7f2f731..1cae515 100644
--- a/lib/interactions/stimulation.js
+++ b/lib/interactions/stimulation.js
@@ -46,7 +46,6 @@ function render(design, interaction, segments, interactions) {
             //update participant offset       
             design.geom.participantOffset = Helper.find_participant_offset(interaction.participants[i], interaction.displayId, "simulation"); 
             var segment = Segment.render(design, interaction.participants[i].segment, interactions);
-            console.log(sgment.bbox().height)
             nonDNAVerticalOffset = segment.bbox().height + 30;
             nonDNAshorizontalOffset = (segment.bbox().width)/2;       
           }
@@ -62,7 +61,7 @@ function render(design, interaction, segments, interactions) {
             if (isCircuit ) {
               //segment.dx( (design.geom.participantOffset -1) * (design.geom.defaultGlyphSize.x + design.geom.glyphPadding) + design.geom.glyphPadding + design.geom.defaultGlyphSize.x/2)
               segment.dx(nonDNAshorizontalOffset - segment.bbox().width);
-              segment.dy(-nonDNAVerticalOffset - segment.bbox().height);
+              segment.dy(-nonDNAVerticalOffset);
             }
             else if (!isCircuit) {
               segment.dx(0)
diff --git a/lib/segment.js b/lib/segment.js
index 84263c7..9257a95 100755
--- a/lib/segment.js
+++ b/lib/segment.js
@@ -280,7 +280,8 @@ function renderSegment(design, segment, interactions,) {
            var arrowGlyph = arrowProps.glyph;
            arrowGlyph.transform({ matrix: Matrix.toSVGString(arrowTransform) });
            group.add(arrowGlyph);
-           interaction.participants.segmentWidth =  group.bbox().width
+           //interaction.participants.segmentWidth =  group.bbox().width
+           interaction.segmentWidth =  group.bbox().width
         }
 
         //if glyph is the first reactant in a non-covelant-binding-reaction modify direction of arrow