X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FCommands.java;fp=src%2Fjalview%2Fbin%2FCommands.java;h=dbc4953ee489616d2b4eb02333b910f223af868c;hb=a65cf4f5da37aba7b52abf2cc3c8a06a469f64ed;hp=d7d1ea34fa42e9ad2d238a32c5650ad9ac2c3d9f;hpb=ac2ebf05c1262b96c1a1b3e3d20b87d84f286a85;p=jalview.git

diff --git a/src/jalview/bin/Commands.java b/src/jalview/bin/Commands.java
index d7d1ea3..dbc4953 100644
--- a/src/jalview/bin/Commands.java
+++ b/src/jalview/bin/Commands.java
@@ -103,16 +103,20 @@ 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())
+        AlignFrame af = afMap.get(id);
+        while (af != null && af.getViewport().isCalcInProgress())
         {
-          try {
+          try
+          {
             Thread.sleep(25);
-          } catch (Exception q) {};
+          } catch (Exception q)
+          {
+          }
+          ;
         }
-        
+
         theseArgsWereParsed &= processImages(id);
         if (processLinkedOkay)
           theseArgsWereParsed &= processOutput(id);
@@ -263,12 +267,16 @@ public class Commands
           if ("" != colour)
           {
             ColourSchemeI cs = ColourSchemeProperty.getColourScheme(
-                    af.getViewport(), af.getViewport().getAlignment(), colour);
-            
-            if (cs==null && !"None".equals(colour))
+                    af.getViewport(), af.getViewport().getAlignment(),
+                    colour);
+
+            if (cs == null && !"None".equals(colour))
+            {
+              Console.warn(
+                      "Couldn't parse '" + colour + "' as a colourscheme.");
+            }
+            else
             {
-              Console.warn("Couldn't parse '"+colour+"' as a colourscheme.");
-            } else {
               af.changeColour(cs);
             }
             Jalview.testoutput(argParser, Arg.COLOUR, "zappo", colour);
@@ -569,15 +577,15 @@ public class Commands
                           structureFilepath, tft, paeFilepath, false,
                           ssFromStructure, false, viewerType);
 
-          if (sv==null)
+          if (sv == null)
           {
             Console.error("Failed to import and open structure view.");
             continue;
           }
           try
           {
-            long tries=1000;
-            while (sv.isBusy() && tries>0)
+            long tries = 1000;
+            while (sv.isBusy() && tries > 0)
             {
               Thread.sleep(25);
               if (sv.isBusy())
@@ -587,15 +595,18 @@ public class Commands
                         "Waiting for viewer for " + structureFilepath);
               }
             }
-            if (tries==0 && sv.isBusy())
+            if (tries == 0 && sv.isBusy())
             {
-              Console.warn("Gave up waiting for structure viewer to load. Something may have gone wrong.");
+              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.warn("Exception whilst waiting for structure viewer "
+                    + structureFilepath, x);
           }
-          Console.debug("Successfully opened viewer for "+structureFilepath);
+          Console.debug(
+                  "Successfully opened viewer for " + structureFilepath);
           String structureImageFilename = ArgParser.getValueFromSubValOrArg(
                   avm, av, Arg.STRUCTUREIMAGE, subVals);
           if (sv != null && structureImageFilename != null)
@@ -652,16 +663,18 @@ public class Commands
               if (sview instanceof AppJmol)
               {
                 AppJmol jmol = (AppJmol) sview;
-                try { 
-                  Console.debug("Rendering image to "+structureImageFile);
+                try
+                {
+                  Console.debug("Rendering image to " + structureImageFile);
                   jmol.makePDBImage(structureImageFile, imageType, renderer,
-                        userBis);
-                  Console.debug("Finished Rendering image to "+structureImageFile);
+                          userBis);
+                  Console.debug("Finished Rendering image to "
+                          + structureImageFile);
 
-                }
-                catch (ImageOutputException ioexc)
+                } catch (ImageOutputException ioexc)
                 {
-                  Console.warn("Unexpected error whilst exporting image to "+structureImageFile,ioexc);
+                  Console.warn("Unexpected error whilst exporting image to "
+                          + structureImageFile, ioexc);
                 }
 
               }
@@ -771,57 +784,60 @@ public class Commands
         Cache.setProperty("EXPORT_EMBBED_BIOJSON", "false");
 
         Console.info("Writing " + file);
-        try {
-        switch (type)
+        try
         {
-
-        case "svg":
-          Console.debug("Outputting type '" + type + "' to " + fileName);
-          af.createSVG(file, renderer);
-          break;
-
-        case "png":
-          Console.debug("Outputting type '" + type + "' to " + fileName);
-          af.createPNG(file, null, userBis);
-          break;
-
-        case "html":
-          Console.debug("Outputting type '" + type + "' to " + fileName);
-          HtmlSvgOutput htmlSVG = new HtmlSvgOutput(af.alignPanel);
-          htmlSVG.exportHTML(fileName, renderer);
-          break;
-
-        case "biojs":
-          Console.debug("Creating BioJS MSA Viwer HTML file: " + fileName);
-          try
-          {
-            BioJsHTMLOutput.refreshVersionInfo(
-                    BioJsHTMLOutput.BJS_TEMPLATES_LOCAL_DIRECTORY);
-          } catch (URISyntaxException e)
+          switch (type)
           {
-            e.printStackTrace();
+
+          case "svg":
+            Console.debug("Outputting type '" + type + "' to " + fileName);
+            af.createSVG(file, renderer);
+            break;
+
+          case "png":
+            Console.debug("Outputting type '" + type + "' to " + fileName);
+            af.createPNG(file, null, userBis);
+            break;
+
+          case "html":
+            Console.debug("Outputting type '" + type + "' to " + fileName);
+            HtmlSvgOutput htmlSVG = new HtmlSvgOutput(af.alignPanel);
+            htmlSVG.exportHTML(fileName, renderer);
+            break;
+
+          case "biojs":
+            Console.debug(
+                    "Outputting BioJS MSA Viwer HTML file: " + fileName);
+            try
+            {
+              BioJsHTMLOutput.refreshVersionInfo(
+                      BioJsHTMLOutput.BJS_TEMPLATES_LOCAL_DIRECTORY);
+            } catch (URISyntaxException e)
+            {
+              e.printStackTrace();
+            }
+            BioJsHTMLOutput bjs = new BioJsHTMLOutput(af.alignPanel);
+            bjs.exportHTML(fileName);
+            break;
+
+          case "eps":
+            Console.debug("Outputting EPS file: " + fileName);
+            af.createEPS(file, renderer);
+            break;
+
+          case "imagemap":
+            Console.debug("Outputting ImageMap file: " + fileName);
+            af.createImageMap(file, name);
+            break;
+
+          default:
+            Console.warn(Arg.IMAGE.argString() + " type '" + type
+                    + "' not known. Ignoring");
+            break;
           }
-          BioJsHTMLOutput bjs = new BioJsHTMLOutput(af.alignPanel);
-          bjs.exportHTML(fileName);
-          break;
-
-        case "eps":
-          Console.debug("Creating EPS file: " + fileName);
-          af.createEPS(file, name);
-          break;
-
-        case "imagemap":
-          Console.debug("Creating ImageMap file: " + fileName);
-          af.createImageMap(file, name);
-          break;
-
-        default:
-          Console.warn(Arg.IMAGE.argString() + " type '" + type
-                  + "' not known. Ignoring");
-          break;
-        }
-        } catch (Exception ioex) {
-          Console.warn("Unexpected error during export",ioex);
+        } catch (Exception ioex)
+        {
+          Console.warn("Unexpected error during export", ioex);
         }
       }
     }