X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FJalview.java;fp=src%2Fjalview%2Fbin%2FJalview.java;h=675a758033c13f100172c2e5085a54edfdfaca01;hb=bf478b2e1087fb03bf6b9fb07f14a9e4f096892c;hp=6952cfb5482e2be7d3fe1c63c6b614db50f0ed19;hpb=0f80d9d589f1e38f4977457f91ee20159ba9907a;p=jalview.git

diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index 6952cfb..675a758 100755
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -91,6 +91,7 @@ import jalview.io.FileLoader;
 import jalview.io.HtmlSvgOutput;
 import jalview.io.IdentifyFile;
 import jalview.io.NewickFile;
+import jalview.io.exceptions.ImageOutputException;
 import jalview.io.gff.SequenceOntologyFactory;
 import jalview.schemes.ColourSchemeI;
 import jalview.schemes.ColourSchemeProperty;
@@ -1005,9 +1006,7 @@ public class Jalview
             ex.printStackTrace(System.err);
           }
         }
-        // TODO - load PDB structure(s) to alignment JAL-629
-        // (associate with identical sequence in alignment, or a specified
-        // sequence)
+        
         if (groovyscript != null)
         {
           // Execute the groovy script after we've done all the rendering stuff
@@ -1021,100 +1020,109 @@ public class Jalview
         String imageName = "unnamed.png";
         while (aparser.getSize() > 1)
         {
-          String outputFormat = aparser.nextValue();
-          file = aparser.nextValue();
-
-          if (outputFormat.equalsIgnoreCase("png"))
-          {
-            af.createPNG(new File(file));
-            imageName = (new File(file)).getName();
-            System.out.println("Creating PNG image: " + file);
-            continue;
-          }
-          else if (outputFormat.equalsIgnoreCase("svg"))
-          {
-            File imageFile = new File(file);
-            imageName = imageFile.getName();
-            af.createSVG(imageFile);
-            System.out.println("Creating SVG image: " + file);
-            continue;
-          }
-          else if (outputFormat.equalsIgnoreCase("html"))
+          try
           {
-            File imageFile = new File(file);
-            imageName = imageFile.getName();
-            HtmlSvgOutput htmlSVG = new HtmlSvgOutput(af.alignPanel);
-            htmlSVG.exportHTML(file);
+            String outputFormat = aparser.nextValue();
+            file = aparser.nextValue();
 
-            System.out.println("Creating HTML image: " + file);
-            continue;
-          }
-          else if (outputFormat.equalsIgnoreCase("biojsmsa"))
-          {
-            if (file == null)
+            if (outputFormat.equalsIgnoreCase("png"))
             {
-              System.err.println("The output html file must not be null");
-              return;
+              System.out.println("Creating PNG image: " + file);
+              af.createPNG(new File(file));
+              imageName = (new File(file)).getName();
+              continue;
             }
-            try
+            else if (outputFormat.equalsIgnoreCase("svg"))
             {
-              BioJsHTMLOutput.refreshVersionInfo(
-                      BioJsHTMLOutput.BJS_TEMPLATES_LOCAL_DIRECTORY);
-            } catch (URISyntaxException e)
+              System.out.println("Creating SVG image: " + file);
+              File imageFile = new File(file);
+              imageName = imageFile.getName();
+              af.createSVG(imageFile);
+              continue;
+            }
+            else if (outputFormat.equalsIgnoreCase("html"))
             {
-              e.printStackTrace();
+              File imageFile = new File(file);
+              imageName = imageFile.getName();
+              HtmlSvgOutput htmlSVG = new HtmlSvgOutput(af.alignPanel);
+
+              System.out.println("Creating HTML image: " + file);
+              htmlSVG.exportHTML(file);
+              continue;
             }
-            BioJsHTMLOutput bjs = new BioJsHTMLOutput(af.alignPanel);
-            bjs.exportHTML(file);
-            System.out
-                    .println("Creating BioJS MSA Viwer HTML file: " + file);
-            continue;
-          }
-          else if (outputFormat.equalsIgnoreCase("imgMap"))
-          {
-            af.createImageMap(new File(file), imageName);
-            System.out.println("Creating image map: " + file);
-            continue;
-          }
-          else if (outputFormat.equalsIgnoreCase("eps"))
-          {
-            File outputFile = new File(file);
-            System.out.println(
-                    "Creating EPS file: " + outputFile.getAbsolutePath());
-            af.createEPS(outputFile);
-            continue;
-          }
-          FileFormatI outFormat = null;
-          try
-          {
-            outFormat = FileFormats.getInstance().forName(outputFormat);
-          } catch (Exception formatP)
-          {
-            System.out.println("Couldn't parse " + outFormat
-                    + " as a valid Jalview format string.");
-          }
-          if (outFormat != null)
-          {
-            if (!outFormat.isWritable())
+            else if (outputFormat.equalsIgnoreCase("biojsmsa"))
+            {
+              if (file == null)
+              {
+                System.err.println("The output html file must not be null");
+                return;
+              }
+              try
+              {
+                BioJsHTMLOutput.refreshVersionInfo(
+                        BioJsHTMLOutput.BJS_TEMPLATES_LOCAL_DIRECTORY);
+              } catch (URISyntaxException e)
+              {
+                e.printStackTrace();
+              }
+              BioJsHTMLOutput bjs = new BioJsHTMLOutput(af.alignPanel);
+              System.out.println(
+                      "Creating BioJS MSA Viwer HTML file: " + file);
+              bjs.exportHTML(file);
+              continue;
+            }
+            else if (outputFormat.equalsIgnoreCase("imgMap"))
             {
+              System.out.println("Creating image map: " + file);
+              af.createImageMap(new File(file), imageName);
+              continue;
+            }
+            else if (outputFormat.equalsIgnoreCase("eps"))
+            {
+              File outputFile = new File(file);
               System.out.println(
-                      "This version of Jalview does not support alignment export as "
-                              + outputFormat);
+                      "Creating EPS file: " + outputFile.getAbsolutePath());
+              af.createEPS(outputFile);
+              continue;
+            }
+
+            FileFormatI outFormat = null;
+            try
+            {
+              outFormat = FileFormats.getInstance().forName(outputFormat);
+            } catch (Exception formatP)
+            {
+              System.out.println("Couldn't parse " + outFormat
+                      + " as a valid Jalview format string.");
             }
-            else
+            if (outFormat != null)
             {
-              af.saveAlignment(file, outFormat);
-              if (af.isSaveAlignmentSuccessful())
+              if (!outFormat.isWritable())
               {
-                System.out.println("Written alignment in "
-                        + outFormat.getName() + " format to " + file);
+                System.out.println(
+                        "This version of Jalview does not support alignment export as "
+                                + outputFormat);
               }
               else
               {
-                System.out.println("Error writing file " + file + " in "
-                        + outFormat.getName() + " format!!");
+                af.saveAlignment(file, outFormat);
+                if (af.isSaveAlignmentSuccessful())
+                {
+                  System.out.println("Written alignment in "
+                          + outFormat.getName() + " format to " + file);
+                }
+                else
+                {
+                  System.out.println("Error writing file " + file + " in "
+                          + outFormat.getName() + " format!!");
+                }
               }
             }
+          } catch (ImageOutputException ioexc)
+          {
+            System.out.println(
+                    "Unexpected error whilst exporting image to " + file);
+            ioexc.printStackTrace();
           }
 
         }
@@ -1799,8 +1807,14 @@ public class Jalview
     }
   }
 
-  /*
-   * testoutput for string values
+  /******************************
+   * 
+   * TEST OUTPUT METHODS
+   * 
+   ******************************/
+  /**
+   * method for reporting string values parsed/processed during tests
+   * 
    */
   protected static void testoutput(ArgParser ap, Arg a, String s1,
           String s2)
@@ -1824,6 +1838,10 @@ public class Jalview
     testoutput(true, a, s1, s2);
   }
 
+  /**
+   * method for reporting string values parsed/processed during tests
+   */
+
   protected static void testoutput(BootstrapArgs bsa, Arg a, String s1,
           String s2)
   {
@@ -1848,6 +1866,9 @@ public class Jalview
     testoutput(true, a, s1, s2);
   }
 
+  /**
+   * report value set for string values parsed/processed during tests
+   */
   private static void testoutput(boolean yes, Arg a, String s1, String s2)
   {
     if (yes && ((s1 == null && s2 == null)