Merge branch 'develop' of http://source.jalview.org/git/jalview into develop

[jalview.git] / src / jalview / ext / rbvi / chimera / JalviewChimeraBinding.java

diff --git a/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java b/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java
index 549636b..66420b0 100644 (file)
--- a/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java
+++ b/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java
@@ -27,7 +27,6 @@ import java.io.PrintWriter;
 import java.net.BindException;
 import java.util.ArrayList;
 import java.util.Collections;
-import java.util.Iterator;
 import java.util.LinkedHashMap;
 import java.util.List;
 import java.util.Map;
@@ -38,7 +37,6 @@ import ext.edu.ucsf.rbvi.strucviz2.StructureManager;
 import ext.edu.ucsf.rbvi.strucviz2.StructureManager.ModelType;
 import jalview.api.AlignmentViewPanel;
 import jalview.bin.Cache;
-import jalview.datamodel.AlignmentI;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.SearchResultMatchI;
 import jalview.datamodel.SearchResultsI;
@@ -426,11 +424,11 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
      */
     if (lastHighlightCommand != null)
     {
-      chimeraManager.sendChimeraCommand("~" + lastHighlightCommand, false);
+      executeCommand(false,  null,  new StructureCommand("~" + lastHighlightCommand));
     }
     if (found)
     {
-      chimeraManager.sendChimeraCommand(command, false);
+      executeCommand(false,  null,  new StructureCommand(command));
     }
     this.lastHighlightCommand = command;
   }
@@ -572,10 +570,7 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
     }
     else
     {
-      for (StructureCommandI command : commands)
-      {
-        sendAsynchronousCommand(command, null);
-      }
+      executeCommands(commands, false, null);
     }
     return commands.size();
   }
@@ -603,7 +598,7 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
       String path = tmp.getAbsolutePath();
       StructureCommandI command = getCommandGenerator()
               .openCommandFile(path);
-      sendAsynchronousCommand(command, null);
+      executeCommand(false, null, command);
     } catch (IOException e)
     {
       System.err.println("Sending commands to Chimera via file failed with "