Merge branch 'develop' into features/JAL-4220_showSymbolsBelowConsensusThresholdAsGaps

[jalview.git] / src / jalview / bin / Commands.java

diff --git a/src/jalview/bin/Commands.java b/src/jalview/bin/Commands.java
index 7f493e0..84effe0 100644 (file)
--- a/src/jalview/bin/Commands.java
+++ b/src/jalview/bin/Commands.java
@@ -574,17 +574,22 @@ public class Commands
             Console.error("Failed to import and open structure view.");
             continue;
           }
-          while (sv.isBusy())
+          try
           {
-            try {
-              Thread.sleep(25);
-            }
-            catch (Exception x)
             {
-              
+              while (sv.isBusy())
+                Thread.sleep(25);
+              if (sv.isBusy())
+              {
+                Console.debug(
+                        "Waiting for viewer for " + structureFilepath);
+              }
             }
-          }
+          } catch (Exception x)
+          {
 
+          }
+          Console.debug("Successfully opened viewer for "+structureFilepath);
           String structureImageFilename = ArgParser.getValueFromSubValOrArg(
                   avm, av, Arg.STRUCTUREIMAGE, subVals);
           if (sv != null && structureImageFilename != null)
@@ -624,12 +629,13 @@ public class Commands
             }
             BitmapImageSizing userBis = ImageMaker
                     .parseScaleWidthHeightStrings(scale, width, height);
+            // TODO MAKE THIS VIEWER INDEPENDENT!!
             switch (StructureViewer.getViewerType())
             {
             case JMOL:
               try
               {
-                Thread.sleep(1000);
+                Thread.sleep(1000); // WHY ???
               } catch (InterruptedException e)
               {
                 // TODO Auto-generated catch block
@@ -641,8 +647,11 @@ public class Commands
               {
                 AppJmol jmol = (AppJmol) sview;
                 try { 
+                  Console.debug("Rendering image to "+structureImageFile);
                   jmol.makePDBImage(structureImageFile, imageType, renderer,
                         userBis);
+                  Console.debug("Finished Rendering image to "+structureImageFile);
+
                 }
                 catch (ImageOutputException ioexc)
                 {