From 6e0940dc80f8a43208cdc07ebf8722fa8542904e Mon Sep 17 00:00:00 2001
From: kinimesi <kinimesi@users.noreply.github.com>
Date: Tue, 7 Nov 2017 16:27:48 +0300
Subject: [PATCH 1/4] Updated version to 1.0.4

---
 index.html | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/index.html b/index.html
index a499112b3..8c6126bfa 100644
--- a/index.html
+++ b/index.html
@@ -623,7 +623,7 @@ <h2 class="sbgn-text">About</h2>
                             <table width="100%" height="100%" align="center" valign="center">
                             <tbody>
                                 <tr><td>
-                                        <p id="about-newt-version" class="sbgn-text">Newt Editor version 1.0.3</p>
+                                        <p id="about-newt-version" class="sbgn-text">Newt Editor version 1.0.4</p>
                                     </td></tr>
 
                                 <tr><td>

From a8db82e5f1234304035df8b73a3e8e0529151f28 Mon Sep 17 00:00:00 2001
From: hasanbalci <balcihasan99@gmail.com>
Date: Fri, 10 Nov 2017 13:27:22 +0200
Subject: [PATCH 2/4] Fixes #195

---
 app/js/app-cy.js | 8 +++++---
 1 file changed, 5 insertions(+), 3 deletions(-)

diff --git a/app/js/app-cy.js b/app/js/app-cy.js
index 8638ee5dd..1983b8f78 100644
--- a/app/js/app-cy.js
+++ b/app/js/app-cy.js
@@ -704,9 +704,11 @@ module.exports = function () {
                 && cyTarget.id() !== convenientProcessSource.id()
                 && chise.elementUtilities.isPNClass(nodeType)
                 && chise.elementUtilities.isEPNClass(cyTarget) 
-                && chise.elementUtilities.isEPNClass(convenientProcessSource) ) {
-
-          chise.addProcessWithConvenientEdges(convenientProcessSource, cyTarget, nodeType);
+                && chise.elementUtilities.isEPNClass(convenientProcessSource)
+                && !(cyTarget.parent()[0] != undefined && chise.elementUtilities.isEPNClass(cyTarget.parent()[0]) || 
+                  convenientProcessSource.parent()[0] != undefined && chise.elementUtilities.isEPNClass(convenientProcessSource.parent()[0]))
+          ){
+            chise.addProcessWithConvenientEdges(convenientProcessSource, cyTarget, nodeType);
         }
         else {
           var cyPosX;

From 7a73b00fb53703fa0935043c1a78ca4e1933388f Mon Sep 17 00:00:00 2001
From: hasanbalci <balcihasan99@gmail.com>
Date: Tue, 14 Nov 2017 14:39:43 +0200
Subject: [PATCH 3/4] Increase size threshold for disabling auto arrange #192

---
 app/js/app-menu.js | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/app/js/app-menu.js b/app/js/app-menu.js
index f18facaf9..e021b4cee 100644
--- a/app/js/app-menu.js
+++ b/app/js/app-menu.js
@@ -237,7 +237,7 @@ module.exports = function () {
       mapTabGeneralPanel.render();
 
       // set reaggange on complexity managment based on map size
-      if (cy.nodes().length > 100){
+      if (cy.nodes().length > 1250){
         appUtilities.currentGeneralProperties.rearrangeAfterExpandCollapse = false;
         mapTabRearrangementPanel.render();
       }

From 0c86f6c5ae6e969729941402c4c16db1be93b37d Mon Sep 17 00:00:00 2001
From: kinimesi <kinimesi@users.noreply.github.com>
Date: Sun, 19 Nov 2017 18:08:15 +0300
Subject: [PATCH 4/4] Fixes iVis-at-Bilkent/newt/issues/193

---
 app/js/app-cy.js           | 4 ++--
 app/js/app-mode-handler.js | 7 ++++---
 2 files changed, 6 insertions(+), 5 deletions(-)

diff --git a/app/js/app-cy.js b/app/js/app-cy.js
index 1983b8f78..1ac8580b7 100644
--- a/app/js/app-cy.js
+++ b/app/js/app-cy.js
@@ -435,7 +435,7 @@ module.exports = function () {
           // fired when edgehandles is done and entities are added
           var source = sourceNode.id();
           var target = targetNodes[0].id();
-          var edgeParams = {class : modeHandler.selectedEdgeType, language : modeHandler.selectedLanguage};
+          var edgeParams = {class : modeHandler.selectedEdgeType, language : modeHandler.selectedEdgeLanguage};
 
           // if added edge changes map type, warn user
           if (chise.getMapType() && chise.getMapType() != "Unknown" && edgeParams.language != chise.getMapType()){
@@ -749,7 +749,7 @@ module.exports = function () {
           
           // If the parent class is valid for the node type then add the node
           if (chise.elementUtilities.isValidParent(nodeType, parentClass)) {
-            var nodeParams = {class : nodeType, language : modeHandler.selectedLanguage};
+            var nodeParams = {class : nodeType, language : modeHandler.selectedNodeLanguage};
 
             // if added node changes map type, warn user
             if (chise.getMapType() && chise.getMapType() != "Unknown" && nodeParams.language != chise.getMapType()){
diff --git a/app/js/app-mode-handler.js b/app/js/app-mode-handler.js
index a043fcb93..ca2ec4790 100644
--- a/app/js/app-mode-handler.js
+++ b/app/js/app-mode-handler.js
@@ -3,7 +3,8 @@ var modeHandler = {
   sustainMode: false,
   selectedNodeType: "macromolecule",
   selectedEdgeType: "consumption",
-  selectedLanguage: "PD",
+  selectedNodeLanguage: "PD",
+  selectedEdgeLanguage: "PD",
   // Initilize mode handler
   initilize: function () {
     $('#select-mode-icon').parent().addClass('selected-mode'); // Initial mode is selection mode.
@@ -62,7 +63,7 @@ var modeHandler = {
       modeHandler.selectedNodeType = nodeType;
     }
     if (language)
-      modeHandler.selectedLanguage = language;
+      modeHandler.selectedNodeLanguage = language;
   },
   // Set the current mode to add edge mode, if edgeType is specified than switch the current edge type to the given value,
   // if the edgeType will remain same, add edge mode is already enabled and sustain mode is not set before, then set the sustain mode
@@ -106,7 +107,7 @@ var modeHandler = {
       modeHandler.selectedEdgeType = edgeType;
     }
     if (language)
-      modeHandler.selectedLanguage = language;
+      modeHandler.selectedEdgeLanguage = language;
   },
   // Set selection mode, disables sustainable mode.
   setSelectionMode: function () {