X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fext%2Fedu%2Fucsf%2Frbvi%2Fstrucviz2%2FChimeraManager.java;h=2e5dbeb19d4fb9bfdce8d648918f5d20f78a9fa1;hb=42f7bb953f9562f9ff80f0d3c833a0b364f399a2;hp=7cc72cff5d198e41f5d7f3358a69a3e0fd36c042;hpb=fddf3084802b37e5cee17829e32692a4aac3e60d;p=jalview.git

diff --git a/src/ext/edu/ucsf/rbvi/strucviz2/ChimeraManager.java b/src/ext/edu/ucsf/rbvi/strucviz2/ChimeraManager.java
index 7cc72cf..2e5dbeb 100644
--- a/src/ext/edu/ucsf/rbvi/strucviz2/ChimeraManager.java
+++ b/src/ext/edu/ucsf/rbvi/strucviz2/ChimeraManager.java
@@ -197,76 +197,21 @@ public class ChimeraManager
       logger.warn("Could not open " + modelPath);
       return null;
     }
-    List<ChimeraModel> models = new ArrayList<ChimeraModel>();
-    int[] modelNumbers = null;
-    if (type == ModelType.PDB_MODEL)
-    {
-      for (String line : response)
-      {
-        if (line.startsWith("#"))
-        {
-          modelNumbers = ChimUtils.parseOpenedModelNumber(line);
-          if (modelNumbers != null)
-          {
-            int modelNumber = ChimUtils.makeModelKey(modelNumbers[0],
-                    modelNumbers[1]);
-            if (currentModelsMap.containsKey(modelNumber))
-            {
-              continue;
-            }
-            ChimeraModel newModel = new ChimeraModel(modelName, type,
-                    modelNumbers[0], modelNumbers[1]);
-            currentModelsMap.put(modelNumber, newModel);
-            models.add(newModel);
-
-            //
-            // patch for Jalview - set model name in Chimera
-            // TODO: find a variant that works for sub-models
-            sendChimeraCommand("setattr M name " + modelName + " #"
-                    + modelNumbers[0], false);
-            // end patch for Jalview
-
-            modelNumbers = null;
-          }
-        }
-      }
-    }
-    else
-    {
-      // TODO: [Optional] Open smiles from file would fail. Do we need it?
-      // If parsing fails, iterate over all open models to get the right one
-      List<ChimeraModel> openModels = getModelList();
-      for (ChimeraModel openModel : openModels)
-      {
-        String openModelName = openModel.getModelName();
-        if (openModelName.endsWith("..."))
-        {
-          openModelName = openModelName.substring(0,
-                  openModelName.length() - 3);
-        }
-        if (modelPath.startsWith(openModelName))
-        {
-          openModel.setModelName(modelPath);
-          int modelNumber = ChimUtils
-                  .makeModelKey(openModel.getModelNumber(),
-                          openModel.getSubModelNumber());
-          if (!currentModelsMap.containsKey(modelNumber))
-          {
-            currentModelsMap.put(modelNumber, openModel);
-            models.add(openModel);
-          }
-        }
-      }
-    }
-
+    List<ChimeraModel> chimeraModels = getModelList();
     // assign color and residues to open models
-    for (ChimeraModel newModel : models)
-    {
+    for (ChimeraModel chimeraModel : chimeraModels)
+    {
+      // // 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(newModel);
+      Color modelColor = getModelColor(chimeraModel);
       if (modelColor != null)
       {
-        newModel.setModelColor(modelColor);
+        chimeraModel.setModelColor(modelColor);
       }
 
       // Get our properties (default color scheme, etc.)
@@ -276,13 +221,13 @@ public class ChimeraManager
       // Create the information we need for the navigator
       if (type != ModelType.SMILES)
       {
-        addResidues(newModel);
+        addResidues(chimeraModel);
       }
     }
 
     sendChimeraCommand("focus", false);
     // startListening(); // see ChimeraListener
-    return models;
+    return chimeraModels;
   }
 
   /**
@@ -302,13 +247,12 @@ public class ChimeraManager
     // TODO: [Optional] Convert path to name in a better way
     if (modelPath.lastIndexOf(File.separator) > 0)
     {
-      modelName = modelPath.substring(modelPath
-              .lastIndexOf(File.separator) + 1);
+      modelName = modelPath
+              .substring(modelPath.lastIndexOf(File.separator) + 1);
     }
     else if (modelPath.lastIndexOf("/") > 0)
     {
-      modelName = modelPath
-              .substring(modelPath.lastIndexOf("/") + 1);
+      modelName = modelPath.substring(modelPath.lastIndexOf("/") + 1);
     }
     return modelName;
   }
@@ -355,7 +299,8 @@ public class ChimeraManager
   public void startListening(String uri)
   {
     sendChimeraCommand("listen start models url " + uri
-    + ";listen start select prefix SelectionChanged url " + uri, false);
+            + ";listen start select prefix SelectionChanged url " + uri,
+            false);
   }
 
   /**
@@ -379,7 +324,7 @@ public class ChimeraManager
   {
     chimera = null;
     currentModelsMap.clear();
-      this.chimeraRestPort = 0;
+    this.chimeraRestPort = 0;
     structureManager.clearOnChimeraExit();
   }
 
@@ -630,8 +575,7 @@ public class ChimeraManager
     } catch (Exception e)
     {
       logger.error("Failed to get REST port number from " + responses
-              + ": "
-              + e.getMessage());
+              + ": " + e.getMessage());
     } finally
     {
       try
@@ -776,7 +720,7 @@ public class ChimeraManager
    */
   public List<String> sendChimeraCommand(String command, boolean reply)
   {
-//    System.out.println("chimeradebug>> " + command);
+    // System.out.println("chimeradebug>> " + command);
     if (!isChimeraLaunched() || command == null
             || "".equals(command.trim()))
     {
@@ -827,16 +771,18 @@ public class ChimeraManager
 
     List<String> reply = new ArrayList<String>();
     BufferedReader response = null;
-    try {
+    try
+    {
       response = HttpClientUtils
               .doHttpUrlPost(restUrl, commands, 100, 5000);
       String line = "";
-      while ((line = response.readLine()) != null) {
+      while ((line = response.readLine()) != null)
+      {
         reply.add(line);
       }
     } catch (Exception e)
     {
-      logger.error("REST call " + command + " failed: " + e.getMessage());
+      logger.error("REST call '" + command + "' failed: " + e.getMessage());
     } finally
     {
       if (response != null)