Merge branch 'develop' into feature/r2_11_2/JAL-3808_gff2_exonerate

[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 66420b0..c78a82b 100644 (file)
--- a/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java
+++ b/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java
@@ -36,7 +36,7 @@ import ext.edu.ucsf.rbvi.strucviz2.ChimeraModel;
 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.bin.Console;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.SearchResultMatchI;
 import jalview.datamodel.SearchResultsI;
@@ -337,11 +337,18 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
     if (getResponse)
     {
       reply = lastReply;
-      if (Cache.log.isDebugEnabled()) {
-        Cache.log.debug(
+      if (Console.isDebugEnabled()) {
+        Console.debug(
               "Response from command ('" + cmd + "') was:\n" + lastReply); 
       }
     }
+    else
+    {
+      if (Console.isDebugEnabled())
+      {
+        Console.debug("Command executed: " + cmd);
+      }
+    }
 
     return reply;
   }
@@ -418,19 +425,29 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
     {
       return;
     }
-
+    if (!found)
+    {
+      // not a valid residue label command, so clear
+      cmd.setLength(0);
+    }
     /*
-     * unshow the label for the previous residue
+     * prepend with command
+     * to unshow the label for the previous residue
      */
     if (lastHighlightCommand != null)
     {
-      executeCommand(false,  null,  new StructureCommand("~" + lastHighlightCommand));
+      cmd.insert(0, ";");
+      cmd.insert(0,lastHighlightCommand);
+      cmd.insert(0,"~");
+      
     }
-    if (found)
-    {
-      executeCommand(false,  null,  new StructureCommand(command));
+    if (cmd.length()>0) {
+      executeCommand(true,  null,  new StructureCommand(cmd.toString()));
+    }
+    
+    if (found) {
+      this.lastHighlightCommand = command;
     }
-    this.lastHighlightCommand = command;
   }
 
   /**
@@ -510,7 +527,7 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
         atomSpecs.add(spec);
       } catch (IllegalArgumentException e)
       {
-        Cache.log.error("Failed to parse atomspec: " + atomSpec);
+        Console.error("Failed to parse atomspec: " + atomSpec);
       }
     }
     return atomSpecs;
@@ -662,7 +679,7 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
         spec = parseAtomSpec(atomSpec);
       } catch (IllegalArgumentException e)
       {
-        Cache.log.error("Problem parsing atomspec " + atomSpec);
+        Console.error("Problem parsing atomspec " + atomSpec);
         continue;
       }