JAL-2325 tidy up release notes

[jalview.git] / src / ext / edu / ucsf / rbvi / strucviz2 / ChimeraManager.java

diff --git a/src/ext/edu/ucsf/rbvi/strucviz2/ChimeraManager.java b/src/ext/edu/ucsf/rbvi/strucviz2/ChimeraManager.java
index 4201f43..fdcf34f 100644 (file)
--- a/src/ext/edu/ucsf/rbvi/strucviz2/ChimeraManager.java
+++ b/src/ext/edu/ucsf/rbvi/strucviz2/ChimeraManager.java
@@ -27,6 +27,10 @@ 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;
@@ -199,8 +203,9 @@ public class ChimeraManager
       return null;
     }
 
-    List<ChimeraModel> newModelList = getModelList();
-    for (ChimeraModel newModel : newModelList)
+    // 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))
       {
@@ -209,15 +214,12 @@ public class ChimeraManager
                 "setattr M name " + modelName + " #"
                         + newModel.getModelNumber(), false);
         modelList.add(newModel);
-
       }
     }
 
     // assign color and residues to open models
     for (ChimeraModel chimeraModel : modelList)
     {
-      // // patch for Jalview - set model name in Chimera
-      // // TODO: find a variant that works for sub-models
       // get model color
       Color modelColor = getModelColor(chimeraModel);
       if (modelColor != null)
@@ -731,7 +733,7 @@ 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()))
     {
@@ -784,8 +786,8 @@ 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)
       {