X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FCommands.java;h=d7d1ea34fa42e9ad2d238a32c5650ad9ac2c3d9f;hb=8f5766ed1f40e637824924ae810b5c033d185d60;hp=3d475051b7874b0611456869a9a547b84ee76958;hpb=9fd03d86789221ae4f6cf720cadf3d99cc68ac33;p=jalview.git

diff --git a/src/jalview/bin/Commands.java b/src/jalview/bin/Commands.java
index 3d47505..d7d1ea3 100644
--- a/src/jalview/bin/Commands.java
+++ b/src/jalview/bin/Commands.java
@@ -44,6 +44,9 @@ import jalview.io.FileLoader;
 import jalview.io.HtmlSvgOutput;
 import jalview.io.IdentifyFile;
 import jalview.io.NewickFile;
+import jalview.io.exceptions.ImageOutputException;
+import jalview.schemes.ColourSchemeI;
+import jalview.schemes.ColourSchemeProperty;
 import jalview.structure.StructureImportSettings.TFType;
 import jalview.structure.StructureSelectionManager;
 import jalview.util.FileUtils;
@@ -100,6 +103,16 @@ public class Commands
         theseArgsWereParsed &= processLinked(id);
         processGroovyScript(id);
         boolean processLinkedOkay = theseArgsWereParsed;
+        
+        // wait around until alignFrame isn't busy
+        AlignFrame af=afMap.get(id);
+        while (af!=null && af.getViewport().isCalcInProgress())
+        {
+          try {
+            Thread.sleep(25);
+          } catch (Exception q) {};
+        }
+        
         theseArgsWereParsed &= processImages(id);
         if (processLinkedOkay)
           theseArgsWereParsed &= processOutput(id);
@@ -107,7 +120,7 @@ public class Commands
         // close ap
         if (avm.getBoolean(Arg.CLOSE))
         {
-          AlignFrame af = afMap.get(id);
+          af = afMap.get(id);
           if (af != null)
           {
             af.closeMenuItem_actionPerformed(true);
@@ -249,7 +262,15 @@ public class Commands
                   Arg.COLOUR, sv, null, "DEFAULT_COLOUR_PROT", "");
           if ("" != colour)
           {
-            af.changeColour_actionPerformed(colour);
+            ColourSchemeI cs = ColourSchemeProperty.getColourScheme(
+                    af.getViewport(), af.getViewport().getAlignment(), colour);
+            
+            if (cs==null && !"None".equals(colour))
+            {
+              Console.warn("Couldn't parse '"+colour+"' as a colourscheme.");
+            } else {
+              af.changeColour(cs);
+            }
             Jalview.testoutput(argParser, Arg.COLOUR, "zappo", colour);
           }
 
@@ -548,11 +569,33 @@ public class Commands
                           structureFilepath, tft, paeFilepath, false,
                           ssFromStructure, false, viewerType);
 
-          if (headless)
+          if (sv==null)
           {
-            sv.setAsync(false);
+            Console.error("Failed to import and open structure view.");
+            continue;
           }
-
+          try
+          {
+            long tries=1000;
+            while (sv.isBusy() && tries>0)
+            {
+              Thread.sleep(25);
+              if (sv.isBusy())
+              {
+                tries--;
+                Console.debug(
+                        "Waiting for viewer for " + structureFilepath);
+              }
+            }
+            if (tries==0 && sv.isBusy())
+            {
+              Console.warn("Gave up waiting for structure viewer to load. Something may have gone wrong.");
+            }
+          } catch (Exception x)
+          {
+            Console.warn("Exception whilst waiting for structure viewer "+structureFilepath,x);
+          }
+          Console.debug("Successfully opened viewer for "+structureFilepath);
           String structureImageFilename = ArgParser.getValueFromSubValOrArg(
                   avm, av, Arg.STRUCTUREIMAGE, subVals);
           if (sv != null && structureImageFilename != null)
@@ -592,12 +635,13 @@ 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
@@ -608,8 +652,18 @@ public class Commands
               if (sview instanceof AppJmol)
               {
                 AppJmol jmol = (AppJmol) sview;
-                jmol.makePDBImage(structureImageFile, imageType, renderer,
+                try { 
+                  Console.debug("Rendering image to "+structureImageFile);
+                  jmol.makePDBImage(structureImageFile, imageType, renderer,
                         userBis);
+                  Console.debug("Finished Rendering image to "+structureImageFile);
+
+                }
+                catch (ImageOutputException ioexc)
+                {
+                  Console.warn("Unexpected error whilst exporting image to "+structureImageFile,ioexc);
+                }
+
               }
               break;
             default:
@@ -717,7 +771,7 @@ public class Commands
         Cache.setProperty("EXPORT_EMBBED_BIOJSON", "false");
 
         Console.info("Writing " + file);
-
+        try {
         switch (type)
         {
 
@@ -766,6 +820,9 @@ public class Commands
                   + "' not known. Ignoring");
           break;
         }
+        } catch (Exception ioex) {
+          Console.warn("Unexpected error during export",ioex);
+        }
       }
     }
     return true;