X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Frbvi%2Fchimera%2FJalviewChimeraBinding.java;h=399bad9d9c9d7cd0982644529885594e7bedea43;hb=db5d68a77f571ee8f419d2fa36ee1fe03d830123;hp=7169fa2974379fd8460efc25495235d1b295a523;hpb=05e40b4dd4e216024024fb921d797917d74daa76;p=jalview.git

diff --git a/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java b/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java
index 7169fa2..399bad9 100644
--- 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;
@@ -311,7 +311,7 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
   @Override
   public boolean isViewerRunning()
   {
-    return chimeraManager.isChimeraLaunched();
+    return chimeraManager!=null && chimeraManager.isChimeraLaunched();
   }
 
   /**
@@ -337,16 +337,16 @@ 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 (Cache.log.isDebugEnabled())
+      if (Console.isDebugEnabled())
       {
-        Cache.log.debug("Command executed: " + cmd);
+        Console.debug("Command executed: " + cmd);
       }
     }
 
@@ -527,7 +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;
@@ -679,7 +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;
       }