X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FJalview.java;h=07fd4d68310a87eb29647b4807c87271b33c7216;hb=2b08c849bd54a0799ddf251f602a421d4696005e;hp=402f9bfcdba5ccc23927f06504d9cc9283c402d8;hpb=f6a84063f10ea1ae9898310c541961cd1d53dd8a;p=jalview.git

diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index 402f9bf..07fd4d6 100755
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -27,15 +27,18 @@ import jalview.datamodel.PDBEntry;
 import jalview.datamodel.SequenceI;
 import jalview.ext.so.SequenceOntology;
 import jalview.gui.AlignFrame;
+import jalview.gui.AlignViewport;
 import jalview.gui.Desktop;
 import jalview.gui.Preferences;
 import jalview.gui.PromptUserConfig;
+import jalview.gui.StructureViewer;
 import jalview.io.AppletFormatAdapter;
 import jalview.io.BioJsHTMLOutput;
 import jalview.io.DataSourceType;
 import jalview.io.FileFormat;
 import jalview.io.FileFormatException;
 import jalview.io.FileFormatI;
+import jalview.io.FileFormats;
 import jalview.io.FileLoader;
 import jalview.io.HtmlSvgOutput;
 import jalview.io.IdentifyFile;
@@ -279,7 +282,8 @@ public class Jalview implements ApplicationSingletonI
   void doMain(String[] args)
   {
 
-    if (!Platform.isJS())
+    boolean isJS = Platform.isJS();
+    if (!isJS)
     {
       System.setSecurityManager(null);
     }
@@ -294,7 +298,7 @@ public class Jalview implements ApplicationSingletonI
 
     String usrPropsFile = aparser.getValue(ArgsParser.PROPS);
     Cache.loadProperties(usrPropsFile);
-    if (Platform.isJS())
+    if (isJS)
     {
       isJavaAppletTag = aparser.isApplet();
       if (isJavaAppletTag)
@@ -363,7 +367,7 @@ public class Jalview implements ApplicationSingletonI
       else
       {
         System.out.println("Executing setprop argument: " + defs);
-        if (Platform.isJS())
+        if (isJS)
         {
           Cache.setProperty(defs.substring(0, p), defs.substring(p + 1));
         }
@@ -446,7 +450,7 @@ public class Jalview implements ApplicationSingletonI
       desktop.setInBatchMode(true); // indicate we are starting up
       desktop.setVisible(true);
 
-      if (!Platform.isJS())
+      if (!isJS)
       /**
        * Java only
        * 
@@ -477,7 +481,7 @@ public class Jalview implements ApplicationSingletonI
           }
           else
           {
-            if (Cache.getProperty("NOQUESTIONNAIRES") == null)
+            if (Cache.getProperty(Preferences.NOQUESTIONNAIRES) == null)
             {
               // Start the desktop questionnaire prompter with the specified
               // questionnaire
@@ -506,109 +510,29 @@ public class Jalview implements ApplicationSingletonI
       }
     }
 
-    String data = null;
-    FileFormatI format = null;
-    DataSourceType protocol = null;
-    FileLoader fileLoader = new FileLoader(!headless);
 
     // script to execute after all loading is
     // completed one way or another
     // extract groovy argument and execute if necessary
-    String groovyscript = aparser.getValue(ArgsParser.GROOVY, true);
+    String groovyscript = (isJS ? null
+            : aparser.getValue(ArgsParser.GROOVY, true));
     String file = aparser.getValue(ArgsParser.OPEN, true);
+    String file2 = (isJavaAppletTag ? aparser.getAppletValue("file2", null)
+            : null);
+    String fileFormat = (isJavaAppletTag
+            ? aparser.getAppletValue("format", null)
+            : null);
+    FileFormatI format = null;
+    DataSourceType protocol = null;
 
     if (file == null && desktop == null)
     {
       System.out.println("No files to open!");
       System.exit(1);
     }
-    String vamsasImport = aparser.getValue(ArgsParser.VDOC);
-    String vamsasSession = aparser.getValue(ArgsParser.VSESS);
-    if (vamsasImport != null || vamsasSession != null)
-    {
-      if (desktop == null || headless)
-      {
-        System.out.println(
-                "Headless vamsas sessions not yet supported. Sorry.");
-        System.exit(1);
-      }
-      // if we have a file, start a new session and import it.
-      boolean inSession = false;
-      if (vamsasImport != null)
-      {
-        try
-        {
-          DataSourceType viprotocol = AppletFormatAdapter
-                  .checkProtocol(vamsasImport);
-          if (viprotocol == DataSourceType.FILE)
-          {
-            inSession = desktop.vamsasImport(new File(vamsasImport));
-          }
-          else if (viprotocol == DataSourceType.URL)
-          {
-            inSession = desktop.vamsasImport(new URL(vamsasImport));
-          }
-
-        } catch (Exception e)
-        {
-          System.err.println("Exeption when importing " + vamsasImport
-                  + " as a vamsas document.");
-          e.printStackTrace();
-        }
-        if (!inSession)
-        {
-          System.err.println("Failed to import " + vamsasImport
-                  + " as a vamsas document.");
-        }
-        else
-        {
-          System.out.println("Imported Successfully into new session "
-                  + desktop.getVamsasApplication().getCurrentSession());
-        }
-      }
-      if (vamsasSession != null)
-      {
-        if (vamsasImport != null)
-        {
-          // close the newly imported session and import the Jalview specific
-          // remnants into the new session later on.
-          desktop.vamsasStop_actionPerformed(null);
-        }
-        // now join the new session
-        try
-        {
-          if (desktop.joinVamsasSession(vamsasSession))
-          {
-            System.out.println(
-                    "Successfully joined vamsas session " + vamsasSession);
-          }
-          else
-          {
-            System.err.println("WARNING: Failed to join vamsas session "
-                    + vamsasSession);
-          }
-        } catch (Exception e)
-        {
-          System.err.println(
-                  "ERROR: Failed to join vamsas session " + vamsasSession);
-          e.printStackTrace();
-        }
-        if (vamsasImport != null)
-        {
-          // the Jalview specific remnants can now be imported into the new
-          // session at the user's leisure.
-          Cache.log.info(
-                  "Skipping Push for import of data into existing vamsas session."); // TODO:
-          // enable
-          // this
-          // when
-          // debugged
-          // desktop.getVamsasApplication().push_update();
-        }
-      }
-    }
-    long progress = -1;
+    boolean haveImport = checkStartVamas(aparser);
     // Finally, deal with the remaining input data.
+    long progress = -1;
     if (file != null)
     {
       if (!headless)
@@ -618,9 +542,8 @@ public class Jalview implements ApplicationSingletonI
                         .getString("status.processing_commandline_args"),
                 progress = System.currentTimeMillis());
       }
-      System.out.println("CMD [-open " + file + "] executed successfully!");
 
-      if (!Platform.isJS())
+      if (!isJS)
       /**
        * ignore in JavaScript -- can't just check file existence - could load
        * it?
@@ -646,13 +569,20 @@ public class Jalview implements ApplicationSingletonI
 
       try
       {
-        format = new IdentifyFile().identify(file, protocol);
+        format = (isJavaAppletTag && fileFormat != null
+                ? FileFormats.getInstance().forName(fileFormat)
+                : null);
+        if (format == null)
+        {
+          format = new IdentifyFile().identify(file, protocol);
+        }
       } catch (FileFormatException e1)
       {
         // TODO ?
       }
 
-      AlignFrame af = fileLoader.LoadFileWaitTillLoaded(file, protocol,
+      AlignFrame af = new FileLoader(!headless).loadFileWaitTillLoaded(file,
+              protocol,
               format);
       if (af == null)
       {
@@ -660,8 +590,39 @@ public class Jalview implements ApplicationSingletonI
       }
       else
       {
+        System.out
+                .println("CMD [-open " + file + "] executed successfully!");
+        if (file2 != null)
+        {
+          protocol = AppletFormatAdapter.checkProtocol(file2);
+          try
+          {
+            format = new IdentifyFile().identify(file2, protocol);
+          } catch (FileFormatException e1)
+          {
+            // TODO ?
+          }
+          AlignFrame af2 = new FileLoader(!headless).loadFileWaitTillLoaded(
+                  file2,
+                  protocol, format);
+          if (af2 == null)
+          {
+            System.out.println("error");
+          }
+          else
+          {
+            AlignViewport.openLinkedAlignmentAs(af,
+                    af.getViewport().getAlignment(),
+                    af2.getViewport().getAlignment(), "",
+                    AlignViewport.SPLIT_FRAME);
+          }
+        }
+
         setCurrentAlignFrame(af);
-        data = aparser.getValue(ArgsParser.COLOUR, true);
+
+        // TODO: file2 How to implement file2 for the applet spit screen?
+
+        String data = aparser.getValue(ArgsParser.COLOUR, true);
         if (data != null)
         {
           data.replaceAll("%20", " ");
@@ -752,109 +713,29 @@ public class Jalview implements ApplicationSingletonI
         // 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
-          // and before any images or figures are generated.
-          System.out.println("Executing script " + groovyscript);
-          executeGroovyScript(groovyscript, af);
-          System.out.println("CMD groovy[" + groovyscript
-                  + "] executed successfully!");
-          groovyscript = null;
-        }
-
         if (isJavaAppletTag)
         {
           loadAppletParams(aparser, af);
         }
-        else
+        else if (!isJS)
+        /**
+         * Java only
+         * 
+         * @j2sIgnore
+         */
         {
-
-          String imageName = "unnamed.png";
-          while (aparser.getSize() > 1)
+          if (groovyscript != null)
           {
-            // PNG filename
-            // SVG filename
-            // HTML filename
-            // biojsmsa filename
-            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"))
-            {
-              File imageFile = new File(file);
-              imageName = imageFile.getName();
-              HtmlSvgOutput htmlSVG = new HtmlSvgOutput(af.alignPanel);
-              htmlSVG.exportHTML(file);
-
-              System.out.println("Creating HTML image: " + file);
-              continue;
-            }
-            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);
-              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;
-            }
-
-            af.saveAlignment(file, format);
-            if (af.isSaveAlignmentSuccessful())
-            {
-              System.out.println("Written alignment in " + format
-                      + " format to " + file);
-            }
-            else
-            {
-              System.out.println("Error writing file " + file + " in "
-                      + format + " format!!");
-            }
-
+            // Execute the groovy script after we've done all the rendering
+            // stuff
+            // and before any images or figures are generated.
+            System.out.println("Executing script " + groovyscript);
+            executeGroovyScript(groovyscript, af);
+            System.out.println("CMD groovy[" + groovyscript
+                    + "] executed successfully!");
+            groovyscript = null;
           }
-
+          checkOutputFile(aparser, af, format);
           while (aparser.getSize() > 0)
           {
             System.out.println("Unknown arg: " + aparser.nextValue());
@@ -867,8 +748,7 @@ public class Jalview implements ApplicationSingletonI
     // And the user
     // ////////////////////
 
-    if (!Platform.isJS() && !headless && file == null
-            && vamsasImport == null
+    if (!isJS && !headless && file == null && !haveImport
             && jalview.bin.Cache.getDefault("SHOW_STARTUP_FILE", true))
     /**
      * Java only
@@ -911,7 +791,8 @@ public class Jalview implements ApplicationSingletonI
         }
       }
 
-      startUpAlframe = fileLoader.LoadFileWaitTillLoaded(file, protocol,
+      startUpAlframe = new FileLoader(!headless)
+              .loadFileWaitTillLoaded(file, protocol,
               format);
       // extract groovy arguments before anything else.
     }
@@ -942,6 +823,185 @@ public class Jalview implements ApplicationSingletonI
     }
   }
 
+  private boolean checkStartVamas(ArgsParser aparser)
+  {
+    String vamsasImport = aparser.getValue(ArgsParser.VDOC);
+    String vamsasSession = aparser.getValue(ArgsParser.VSESS);
+    if (vamsasImport == null && vamsasSession == null)
+    {
+      return false;
+    }
+    if (desktop == null || headless)
+    {
+      System.out.println(
+              "Headless vamsas sessions not yet supported. Sorry.");
+      System.exit(1);
+    }
+    boolean haveImport = (vamsasImport != null);
+    if (haveImport)
+    {
+      // if we have a file, start a new session and import it.
+      boolean inSession = false;
+      try
+      {
+        DataSourceType viprotocol = AppletFormatAdapter
+                .checkProtocol(vamsasImport);
+        if (viprotocol == DataSourceType.FILE)
+        {
+          inSession = desktop.vamsasImport(new File(vamsasImport));
+        }
+        else if (viprotocol == DataSourceType.URL)
+        {
+          inSession = desktop.vamsasImport(new URL(vamsasImport));
+        }
+
+      } catch (Exception e)
+      {
+        System.err.println("Exeption when importing " + vamsasImport
+                + " as a vamsas document.");
+        e.printStackTrace();
+      }
+      if (!inSession)
+      {
+        System.err.println("Failed to import " + vamsasImport
+                + " as a vamsas document.");
+      }
+      else
+      {
+        System.out.println("Imported Successfully into new session "
+                + desktop.getVamsasApplication().getCurrentSession());
+      }
+    }
+    if (vamsasSession != null)
+    {
+      if (vamsasImport != null)
+      {
+        // close the newly imported session and import the Jalview specific
+        // remnants into the new session later on.
+        desktop.vamsasStop_actionPerformed(null);
+      }
+      // now join the new session
+      try
+      {
+        if (desktop.joinVamsasSession(vamsasSession))
+        {
+          System.out.println(
+                  "Successfully joined vamsas session " + vamsasSession);
+        }
+        else
+        {
+          System.err.println("WARNING: Failed to join vamsas session "
+                  + vamsasSession);
+        }
+      } catch (Exception e)
+      {
+        System.err.println(
+                "ERROR: Failed to join vamsas session " + vamsasSession);
+        e.printStackTrace();
+      }
+      if (vamsasImport != null)
+      {
+        // the Jalview specific remnants can now be imported into the new
+        // session at the user's leisure.
+        Cache.log.info(
+                "Skipping Push for import of data into existing vamsas session."); // TODO:
+        // enable
+        // this
+        // when
+        // debugged
+        // desktop.getVamsasApplication().push_update();
+      }
+    }
+    return haveImport;
+  }
+
+  private void checkOutputFile(ArgsParser aparser, AlignFrame af,
+          FileFormatI format)
+  {
+    String imageName = "unnamed.png";
+    while (aparser.getSize() > 1)
+    {
+      // PNG filename
+      // SVG filename
+      // HTML filename
+      // biojsmsa filename
+      String outputFormat = aparser.nextValue();
+      String 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"))
+      {
+        File imageFile = new File(file);
+        imageName = imageFile.getName();
+        HtmlSvgOutput htmlSVG = new HtmlSvgOutput(af.alignPanel);
+        htmlSVG.exportHTML(file);
+
+        System.out.println("Creating HTML image: " + file);
+        continue;
+      }
+      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);
+        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;
+      }
+
+      af.saveAlignment(file, format);
+      if (af.isSaveAlignmentSuccessful())
+      {
+        System.out.println(
+                "Written alignment in " + format + " format to " + file);
+      }
+      else
+      {
+        System.out.println("Error writing file " + file + " in " + format
+                + " format!!");
+      }
+
+    }
+  }
+
   private static void showUsage()
   {
     System.out.println(
@@ -1177,12 +1237,18 @@ public class Jalview implements ApplicationSingletonI
     return id + (frameType == null ? "" : "-" + frameType);
   }
 
+  /**
+   * Handle all JalviewLite applet parameters
+   * 
+   * @param aparser
+   * @param af
+   */
   private void loadAppletParams(ArgsParser aparser, AlignFrame af)
   {
-    Jalview me = this;
     JalviewApp app = new JalviewApp()
     {
 
+      private boolean alignPDBStructures; // From JalviewLite; not implemented
 
       @Override
       public String getParameter(String name)
@@ -1198,12 +1264,18 @@ public class Jalview implements ApplicationSingletonI
                 : "true".equalsIgnoreCase(stn));
       }
 
+      /**
+       * Get the applet-like document base even though this is an application.
+       */
       @Override
       public URL getDocumentBase()
       {
         return Platform.getDocumentBase();
       }
 
+      /**
+       * Get the applet-like code base even though this is an application.
+       */
       @Override
       public URL getCodeBase()
       {
@@ -1213,79 +1285,85 @@ public class Jalview implements ApplicationSingletonI
       @Override
       public AlignViewportI getViewport()
       {
-        return Jalview.getCurrentAlignFrame().getViewport();
+        return af.getViewport();
       }
 
+      /**
+       * features
+       * 
+       */
+      @Override
+      public boolean parseFeaturesFile(String filename,
+              DataSourceType protocol)
+      {
+        return af.parseFeaturesFile(filename, protocol);
+      }
+
+      /**
+       * scorefile
+       * 
+       */
       @Override
       public boolean loadScoreFile(String sScoreFile) throws IOException
       {
-        Jalview.getCurrentAlignFrame().loadJalviewDataFile(sScoreFile, null,
-                null, null);
+        af.loadJalviewDataFile(sScoreFile, null, null, null);
         return true;
       }
 
+      /**
+       * annotations, jpredfile, jnetfile
+       * 
+       */
       @Override
-      public boolean parseFeaturesFile(String filename,
-              DataSourceType protocol)
+      public void updateForAnnotations()
       {
-        return af.parseFeaturesFile(filename, protocol);
+        af.updateForAnnotations();
       }
 
       @Override
       public void loadTree(NewickFile fin, String treeFile)
               throws IOException
       {
-        // n/a -- already done
+        // n/a -- already done by standard Jalview command line processing
       }
 
       @Override
       public void setAlignPdbStructures(boolean defaultParameter)
       {
-        // TODO Auto-generated method stub
-
+        alignPDBStructures = true;
       }
 
       @Override
       public void newStructureView(PDBEntry pdb, SequenceI[] seqs,
               String[] chains, DataSourceType protocol)
       {
-        // TODO Auto-generated method stub
-
-      }
-
-      @Override
-      public void alignedStructureView(PDBEntry[] pdb, SequenceI[][] seqs,
-              String[][] chains, String[] protocols)
-      {
-        // TODO Auto-generated method stub
-
+        StructureViewer.launchStructureViewer(af.alignPanel, pdb, seqs);
       }
 
       @Override
-      public void updateForLoader()
+      public void setFeatureGroupState(String[] groups, boolean state)
       {
-        // TODO Auto-generated method stub
-
+        af.setFeatureGroupState(groups, state);
       }
 
       @Override
-      public void setFeatureGroupState(String[] groups, boolean state)
+      public void alignedStructureView(PDBEntry[] pdb, SequenceI[][] seqs,
+              String[][] chains, String[] protocols)
       {
-        // TODO Auto-generated method stub
-
+        System.err.println(
+                "Jalview applet interface alignedStructureView not implemented");
       }
 
       @Override
       public void newFeatureSettings()
       {
-        // TODO Auto-generated method stub
-
+        System.err.println(
+                "Jalview applet interface newFeatureSettings not implemented");
       }
 
     };
 
     new JalviewAppLoader(true).load(app);
-
   }
 
 }