From 86ce701110991d006f506c585e13128996a01477 Mon Sep 17 00:00:00 2001
From: tcofoegbu <tcnofoegbu@dundee.ac.uk>
Date: Thu, 31 Mar 2016 12:36:25 +0100
Subject: [PATCH] JAL-2035 improvement to add binding to multiple model

---
 .../edu/ucsf/rbvi/strucviz2/ChimeraManager.java    |   25 ++++++++++----
 src/ext/edu/ucsf/rbvi/strucviz2/ChimeraModel.java  |   34 ++++++++++++++++++++
 2 files changed, 52 insertions(+), 7 deletions(-)

diff --git a/src/ext/edu/ucsf/rbvi/strucviz2/ChimeraManager.java b/src/ext/edu/ucsf/rbvi/strucviz2/ChimeraManager.java
index 2e5dbeb..4201f43 100644
--- a/src/ext/edu/ucsf/rbvi/strucviz2/ChimeraManager.java
+++ b/src/ext/edu/ucsf/rbvi/strucviz2/ChimeraManager.java
@@ -178,6 +178,7 @@ public class ChimeraManager
   {
     logger.info("chimera open " + modelPath);
     // stopListening();
+    List<ChimeraModel> modelList = getModelList();
     List<String> response = null;
     // TODO: [Optional] Handle modbase models
     if (type == ModelType.MODBASE_MODEL)
@@ -197,16 +198,26 @@ public class ChimeraManager
       logger.warn("Could not open " + modelPath);
       return null;
     }
-    List<ChimeraModel> chimeraModels = getModelList();
+
+    List<ChimeraModel> newModelList = getModelList();
+    for (ChimeraModel newModel : newModelList)
+    {
+      if (!modelList.contains(newModel))
+      {
+        newModel.setModelName(modelName);
+        sendChimeraCommand(
+                "setattr M name " + modelName + " #"
+                        + newModel.getModelNumber(), false);
+        modelList.add(newModel);
+
+      }
+    }
+
     // assign color and residues to open models
-    for (ChimeraModel chimeraModel : chimeraModels)
+    for (ChimeraModel chimeraModel : modelList)
     {
       // // patch for Jalview - set model name in Chimera
       // // TODO: find a variant that works for sub-models
-      chimeraModel.setModelName(modelName);
-      sendChimeraCommand(
-              "setattr M name " + modelName + " #"
-                      + chimeraModel.getModelNumber(), false);
       // get model color
       Color modelColor = getModelColor(chimeraModel);
       if (modelColor != null)
@@ -227,7 +238,7 @@ public class ChimeraManager
 
     sendChimeraCommand("focus", false);
     // startListening(); // see ChimeraListener
-    return chimeraModels;
+    return modelList;
   }
 
   /**
diff --git a/src/ext/edu/ucsf/rbvi/strucviz2/ChimeraModel.java b/src/ext/edu/ucsf/rbvi/strucviz2/ChimeraModel.java
index 0700565..7da7a48 100644
--- a/src/ext/edu/ucsf/rbvi/strucviz2/ChimeraModel.java
+++ b/src/ext/edu/ucsf/rbvi/strucviz2/ChimeraModel.java
@@ -145,6 +145,7 @@ public class ChimeraModel implements ChimeraStructuralObject
    * 
    * @return ChimeraModel
    */
+  @Override
   public ChimeraModel getChimeraModel()
   {
     return this;
@@ -272,6 +273,7 @@ public class ChimeraModel implements ChimeraStructuralObject
    * 
    * @return user data
    */
+  @Override
   public Object getUserData()
   {
     return userData;
@@ -283,6 +285,7 @@ public class ChimeraModel implements ChimeraStructuralObject
    * @param data
    *          user data to associate with this model
    */
+  @Override
   public void setUserData(Object data)
   {
     this.userData = data;
@@ -293,6 +296,7 @@ public class ChimeraModel implements ChimeraStructuralObject
    * 
    * @return the selected state
    */
+  @Override
   public boolean isSelected()
   {
     return selected;
@@ -304,6 +308,7 @@ public class ChimeraModel implements ChimeraStructuralObject
    * @param selected
    *          a boolean to set the selected state to
    */
+  @Override
   public void setSelected(boolean selected)
   {
     this.selected = selected;
@@ -314,6 +319,7 @@ public class ChimeraModel implements ChimeraStructuralObject
    * 
    * @return the chains in this model as a list
    */
+  @Override
   public List<ChimeraStructuralObject> getChildren()
   {
     return new ArrayList<ChimeraStructuralObject>(chainMap.values());
@@ -414,6 +420,7 @@ public class ChimeraModel implements ChimeraStructuralObject
   /**
    * Checks if this model has selected children.
    */
+  @Override
   public boolean hasSelectedChildren()
   {
     if (selected)
@@ -458,10 +465,13 @@ public class ChimeraModel implements ChimeraStructuralObject
   /**
    * Return the Chimera specification for this model.
    */
+  @Override
   public String toSpec()
   {
     if (subModelNumber == 0)
+    {
       return ("#" + modelNumber);
+    }
     return ("#" + modelNumber + "." + subModelNumber);
   }
 
@@ -469,6 +479,7 @@ public class ChimeraModel implements ChimeraStructuralObject
    * Return a string representation for the model. Shorten if longer than 100
    * characters.
    */
+  @Override
   public String toString()
   {
     String modelName = "";
@@ -554,4 +565,27 @@ public class ChimeraModel implements ChimeraStructuralObject
     }
     return nodeName;
   }
+
+  @Override
+  public boolean equals(Object otherChimeraModel)
+  {
+    if (!(otherChimeraModel instanceof ChimeraModel))
+    {
+      return false;
+    }
+    ChimeraModel otherCM = ((ChimeraModel) otherChimeraModel);
+    return this.name.equals(otherCM.name)
+            && this.modelNumber == otherCM.modelNumber
+            && this.type == otherCM.type;
+  }
+
+  @Override
+  public int hashCode()
+  {
+    int hashCode = 1;
+    hashCode = hashCode * 37 + this.name.hashCode();
+    hashCode = hashCode * 37 + this.type.hashCode();
+    hashCode = (hashCode * 37) + modelNumber;
+    return hashCode;
+  }
 }
-- 
1.7.10.2