X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fext%2Fedu%2Fucsf%2Frbvi%2Fstrucviz2%2FChimeraManager.java;h=736e45965d3d56cfe4d9a0d6e3f39e549655f182;hb=36c3f2b9e9081149762bac7b69b5890f34eb53a9;hp=2e5dbeb19d4fb9bfdce8d648918f5d20f78a9fa1;hpb=42f7bb953f9562f9ff80f0d3c833a0b364f399a2;p=jalview.git

diff --git a/src/ext/edu/ucsf/rbvi/strucviz2/ChimeraManager.java b/src/ext/edu/ucsf/rbvi/strucviz2/ChimeraManager.java
index 2e5dbeb..736e459 100644
--- a/src/ext/edu/ucsf/rbvi/strucviz2/ChimeraManager.java
+++ b/src/ext/edu/ucsf/rbvi/strucviz2/ChimeraManager.java
@@ -1,3 +1,35 @@
+/* vim: set ts=2: */
+/**
+ * Copyright (c) 2006 The Regents of the University of California.
+ * All rights reserved.
+ *
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions
+ * are met:
+ *   1. Redistributions of source code must retain the above copyright
+ *      notice, this list of conditions, and the following disclaimer.
+ *   2. Redistributions in binary form must reproduce the above
+ *      copyright notice, this list of conditions, and the following
+ *      disclaimer in the documentation and/or other materials provided
+ *      with the distribution.
+ *   3. Redistributions must acknowledge that this software was
+ *      originally developed by the UCSF Computer Graphics Laboratory
+ *      under support by the NIH National Center for Research Resources,
+ *      grant P41-RR01081.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDER "AS IS" AND ANY
+ * EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+ * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+ * PURPOSE ARE DISCLAIMED.  IN NO EVENT SHALL THE REGENTS BE LIABLE
+ * FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+ * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT
+ * OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR
+ * BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+ * WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE
+ * OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE,
+ * EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+ *
+ */
 package ext.edu.ucsf.rbvi.strucviz2;
 
 import jalview.ws.HttpClientUtils;
@@ -27,6 +59,10 @@ import ext.edu.ucsf.rbvi.strucviz2.port.ListenerThreads;
  */
 public class ChimeraManager
 {
+  private static final int REST_REPLY_TIMEOUT_MS = 15000;
+
+  private static final int CONNECTION_TIMEOUT_MS = 100;
+
   private static final boolean debug = false;
 
   private int chimeraRestPort;
@@ -178,6 +214,7 @@ 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 +234,24 @@ public class ChimeraManager
       logger.warn("Could not open " + modelPath);
       return null;
     }
-    List<ChimeraModel> chimeraModels = getModelList();
+
+    // patch for Jalview - set model name in Chimera
+    // TODO: find a variant that works for sub-models
+    for (ChimeraModel newModel : getModelList())
+    {
+      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)
-    {
-      // // 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);
+    for (ChimeraModel chimeraModel : modelList)
+    {
       // get model color
       Color modelColor = getModelColor(chimeraModel);
       if (modelColor != null)
@@ -227,7 +272,7 @@ public class ChimeraManager
 
     sendChimeraCommand("focus", false);
     // startListening(); // see ChimeraListener
-    return chimeraModels;
+    return modelList;
   }
 
   /**
@@ -720,7 +765,7 @@ 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()))
     {
@@ -773,8 +818,8 @@ public class ChimeraManager
     BufferedReader response = null;
     try
     {
-      response = HttpClientUtils
-              .doHttpUrlPost(restUrl, commands, 100, 5000);
+      response = HttpClientUtils.doHttpUrlPost(restUrl, commands, CONNECTION_TIMEOUT_MS,
+              REST_REPLY_TIMEOUT_MS);
       String line = "";
       while ((line = response.readLine()) != null)
       {