X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FJalview.java;h=74babbbdc8d9ffe8a82f2ad44d852d2e9782641c;hb=8e98fa5a09e06ac59c965d030ed71b0158178a24;hp=3d80589a2aac0323ee57911de9151a16b3c759de;hpb=cb51e62fe2166b236ef488e0a8f35081fcd71388;p=jalview.git

diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index 3d80589..74babbb 100755
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -21,7 +21,6 @@
 package jalview.bin;
 
 import jalview.api.AlignCalcWorkerI;
-import jalview.api.AlignFrameI;
 import jalview.api.AlignViewportI;
 import jalview.api.JalviewApp;
 import jalview.api.StructureSelectionManagerProvider;
@@ -110,6 +109,22 @@ import netscape.javascript.JSObject;
 public class Jalview implements ApplicationSingletonI, JalviewJSApi
 {
 
+  // for testing those nasty messages you cannot ever find.
+  // static
+  // {
+  // System.setOut(new PrintStream(new ByteArrayOutputStream())
+  // {
+  // @Override
+  // public void println(Object o)
+  // {
+  // if (o != null)
+  // {
+  // System.err.println(o);
+  // }
+  // }
+  //
+  // });
+  // }
   public static Jalview getInstance()
   {
     return (Jalview) ApplicationSingletonProvider
@@ -271,9 +286,13 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi
    * @param args
    *          open <em>filename</em>
    */
+  @SuppressWarnings("unused")
   public static void main(String[] args)
   {
-    // Platform.startJavaLogging();
+    if (false)
+    {
+      Platform.startJavaLogging();
+    }
     getInstance().doMain(args);
   }
 
@@ -455,7 +474,9 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi
      * configure 'full' SO model if preferences say to, 
      * else use the default (SO Lite)
      */
-    if (Cache.getDefault(Preferences.USE_FULL_SO, false))
+    // BH NOTE 2020.06.01 Jalview-JS/develop has this true for Java, false for
+    // JavaScript
+    if (Cache.getDefault(Preferences.USE_FULL_SO, !isJS))
     {
       SequenceOntologyFactory.setSequenceOntology(new SequenceOntology());
     }
@@ -543,7 +564,8 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi
     try
     {
       ArgsParser aparser = new ArgsParser(args);
-      return parseArguments(aparser, false);
+      parseArguments(aparser, false);
+      return null;
     } catch (Throwable t)
     {
       return t;
@@ -554,9 +576,9 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi
    * 
    * @param aparser
    * @param isStartup
-   * @return
+   * @return null, indicating no error
    */
-  private Object parseArguments(ArgsParser aparser, boolean isStartup)
+  private void parseArguments(ArgsParser aparser, boolean isStartup)
   {
     boolean isJS = Platform.isJS();
 
@@ -580,7 +602,6 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi
       System.out.println("No files to open!");
       System.exit(1);
     }
-    boolean haveImport = checkStartVamas(aparser);
     // Finally, deal with the remaining input data.
     long progress = -1;
     if (file == null && isJavaAppletTag)
@@ -710,11 +731,8 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi
                     "CMD [-open2 " + file2 + "] executed successfully!");
           }
         }
-
         setCurrentAlignFrame(af);
 
-        // TODO: file2 How to implement file2 for the applet spit screen?
-
         data = aparser.getValue(ArgsParser.COLOUR, true);
         if (data != null)
         {
@@ -859,19 +877,20 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi
             groovyscript = null;
           }
         }
-        checkOutputFile(aparser, af, format);
+        createOutputFiles(aparser, af, format);
         while (aparser.getSize() > 0)
         {
           System.out.println("Unknown arg: " + aparser.nextValue());
         }
       }
     }
+
     AlignFrame startUpAlframe = null;
     // We'll only open the default file if the desktop is visible.
     // And the user
     // ////////////////////
 
-    if (!isJS && !headless && file == null && !haveImport
+    if (!isJS && !headless && file == null
             && jalview.bin.Cache.getDefault("SHOW_STARTUP_FILE", true))
     /**
      * Java only
@@ -944,115 +963,36 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi
       desktop.setInBatchMode(false);
     }
 
-    return null;
   }
 
-  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,
+  /**
+   * Writes an output file for each format (if any) specified in the
+   * command-line arguments. Supported formats are currently
+   * <ul>
+   * <li>png</li>
+   * <li>svg</li>
+   * <li>html</li>
+   * <li>biojsmsa</li>
+   * <li>imgMap</li>
+   * <li>eps</li>
+   * </ul>
+   * A format parameter should be followed by a parameter specifying the output
+   * file name. {@code imgMap} parameters should follow those for the
+   * corresponding alignment image output.
+   * 
+   * @param aparser
+   * @param af
+   * @param format
+   */
+  private void createOutputFiles(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();
-      System.out.println("format " + outputFormat);
+      // System.out.println("format " + outputFormat);
 
       if (outputFormat.equalsIgnoreCase("png"))
       {
@@ -1075,7 +1015,6 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi
         imageName = imageFile.getName();
         HtmlSvgOutput htmlSVG = new HtmlSvgOutput(af.alignPanel);
         htmlSVG.exportHTML(file);
-
         System.out.println("Creating HTML image: " + file);
         continue;
       }
@@ -1641,7 +1580,7 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi
    *      .AlignFrame)
    */
   @Override
-  public String getSelectedSequencesFrom(AlignFrameI alf)
+  public String getSelectedSequencesFrom(AlignFrame alf)
   {
     if (alf == null)
     {
@@ -1656,7 +1595,7 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi
    *      .AlignFrame, java.lang.String)
    */
   @Override
-  public String getSelectedSequencesFrom(AlignFrameI alf, String sep)
+  public String getSelectedSequencesFrom(AlignFrame alf, String sep)
   {
     if (alf == null)
     {
@@ -1679,7 +1618,7 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi
   }
 
   @Override
-  public void highlightIn(AlignFrameI alf, String sequenceId,
+  public void highlightIn(AlignFrame alf, String sequenceId,
           String position, String alignedPosition)
   {
     if (alf == null)
@@ -1702,13 +1641,13 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi
   }
 
   @Override
-  public void selectIn(AlignFrameI alf, String sequenceIds, String columns)
+  public void selectIn(AlignFrame alf, String sequenceIds, String columns)
   {
     selectIn(alf, sequenceIds, columns, null);
   }
 
   @Override
-  public void selectIn(AlignFrameI alf, String sequenceIds, String columns,
+  public void selectIn(AlignFrame alf, String sequenceIds, String columns,
           String sep)
   {
     if (alf == null)
@@ -1727,7 +1666,7 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi
   }
 
   @Override
-  public String getSelectedSequencesAsAlignmentFrom(AlignFrameI alf,
+  public String getSelectedSequencesAsAlignmentFrom(AlignFrame alf,
           String format, String sep)
   {
     if (alf == null)
@@ -1744,13 +1683,13 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi
   }
 
   @Override
-  public String getAlignmentOrderFrom(AlignFrameI alf)
+  public String getAlignmentOrderFrom(AlignFrame alf)
   {
     return getAlignmentFrom(alf, null);
   }
 
   @Override
-  public String getAlignmentOrderFrom(AlignFrameI alf, String sep)
+  public String getAlignmentOrderFrom(AlignFrame alf, String sep)
   {
     if (alf == null)
     {
@@ -1772,7 +1711,7 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi
   }
 
   @Override
-  public String orderAlignmentBy(AlignFrameI alf, String order,
+  public String orderAlignmentBy(AlignFrame alf, String order,
           String undoName, String sep)
   {
     if (alf == null)
@@ -1789,7 +1728,7 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi
   }
 
   @Override
-  public String getAlignmentFrom(AlignFrameI alf, String format)
+  public String getAlignmentFrom(AlignFrame alf, String format)
   {
     return getAlignmentFrom(alf, format, null);
   }
@@ -1801,7 +1740,7 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi
   }
 
   @Override
-  public String getAlignmentFrom(AlignFrameI alf, String format,
+  public String getAlignmentFrom(AlignFrame alf, String format,
           String suffix)
   {
     return appLoader.getAlignmentFrom(alf, format, suffix);
@@ -1814,7 +1753,7 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi
   }
 
   @Override
-  public void loadAnnotationFrom(AlignFrameI alf, String annotation)
+  public void loadAnnotationFrom(AlignFrame alf, String annotation)
   {
     if (alf == null)
     {
@@ -1830,7 +1769,7 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi
   }
 
   @Override
-  public boolean loadFeaturesFrom(AlignFrameI alf, String features,
+  public boolean loadFeaturesFrom(AlignFrame alf, String features,
           boolean autoenabledisplay)
   {
     if (alf == null)
@@ -1847,7 +1786,7 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi
   }
 
   @Override
-  public String getFeaturesFrom(AlignFrameI alf, String format)
+  public String getFeaturesFrom(AlignFrame alf, String format)
   {
     if (alf == null)
     {
@@ -1863,7 +1802,7 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi
   }
 
   @Override
-  public String getAnnotationFrom(AlignFrameI alf)
+  public String getAnnotationFrom(AlignFrame alf)
   {
     if (alf == null)
     {
@@ -1872,43 +1811,43 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi
     return appLoader.getAnnotationFrom(alf);
   }
 
-  @Override
-  public AlignFrameI newView()
-  {
-    return newViewFrom(null, null);
-  }
-
-  @Override
-  public AlignFrameI newView(String name)
-  {
-    return newViewFrom(null, name);
-  }
-
-  @Override
-  public AlignFrameI newViewFrom(AlignFrameI alf)
-  {
-    return newViewFrom(alf, null);
-  }
-
-  @Override
-  public AlignFrameI newViewFrom(AlignFrameI alf, String name)
-  {
-    if (alf == null)
-    {
-      alf = getCurrentAlignFrame();
-    }
-    return appLoader.newViewFrom(alf, name);
-  }
+  // @Override
+  // public AlignFrame newView()
+  // {
+  // return newViewFrom(null, null);
+  // }
+  //
+  // @Override
+  // public AlignFrame newView(String name)
+  // {
+  // return newViewFrom(null, name);
+  // }
+  //
+  // @Override
+  // public AlignFrame newViewFrom(AlignFrame alf)
+  // {
+  // return newViewFrom(alf, null);
+  // }
+
+  // @Override
+  // public AlignFrame newViewFrom(AlignFrame alf, String name)
+  // {
+  // if (alf == null)
+  // {
+  // alf = getCurrentAlignFrame();
+  // }
+  // return appLoader.newViewFrom(alf, name);
+  // }
 
   @Override
-  public AlignFrameI loadAlignment(String text, String title)
+  public AlignFrame loadAlignment(String text, String title)
   {
     return appLoader.loadAlignment(text, AlignFrame.DEFAULT_WIDTH,
             AlignFrame.DEFAULT_HEIGHT, title);
   }
 
   @Override
-  public boolean addPdbFile(AlignFrameI alFrame, String sequenceId,
+  public boolean addPdbFile(AlignFrame alFrame, String sequenceId,
           String pdbEntryString, String pdbFile)
   {
     if (alFrame == null)
@@ -1920,7 +1859,7 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi
   }
 
   @Override
-  public void scrollViewToIn(AlignFrameI alf, String topRow,
+  public void scrollViewToIn(AlignFrame alf, String topRow,
           String leftHandColumn)
   {
     if (alf == null)
@@ -1931,7 +1870,7 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi
   }
 
   @Override
-  public void scrollViewToRowIn(AlignFrameI alf, String topRow)
+  public void scrollViewToRowIn(AlignFrame alf, String topRow)
   {
     if (alf == null)
     {
@@ -1941,7 +1880,7 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi
   }
 
   @Override
-  public void scrollViewToColumnIn(AlignFrameI alf, String leftHandColumn)
+  public void scrollViewToColumnIn(AlignFrame alf, String leftHandColumn)
   {
     if (alf == null)
     {
@@ -1957,7 +1896,7 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi
   }
 
   @Override
-  public String getFeatureGroupsOn(AlignFrameI alf)
+  public String getFeatureGroupsOn(AlignFrame alf)
   {
     if (alf == null)
     {
@@ -1973,7 +1912,7 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi
   }
 
   @Override
-  public String getFeatureGroupsOfStateOn(AlignFrameI alf, boolean visible)
+  public String getFeatureGroupsOfStateOn(AlignFrame alf, boolean visible)
   {
     if (alf == null)
     {
@@ -1989,7 +1928,7 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi
   }
 
   @Override
-  public void setFeatureGroupStateOn(AlignFrameI alf, String groups,
+  public void setFeatureGroupStateOn(AlignFrame alf, String groups,
           boolean state)
   {
     if (alf == null)
@@ -2067,7 +2006,7 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi
   }
 
   @Override
-  public String getSelectedSequencesAsAlignmentFrom(AlignFrameI alf,
+  public String getSelectedSequencesAsAlignmentFrom(AlignFrame alf,
           String format, boolean suffix)
   {
     if (alf == null)
@@ -2101,7 +2040,7 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi
   }
 
   @Override
-  public void setMouseoverListener(AlignFrameI af, String listener)
+  public void setMouseoverListener(AlignFrame af, String listener)
   {
     // TODO Auto-generated method stub
 
@@ -2115,7 +2054,7 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi
   }
 
   @Override
-  public void setSelectionListener(AlignFrameI af, String listener)
+  public void setSelectionListener(AlignFrame af, String listener)
   {
     // TODO Auto-generated method stub
 
@@ -2129,7 +2068,7 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi
   }
 
   @Override
-  public void removeJavascriptListener(AlignFrameI af, String listener)
+  public void removeJavascriptListener(AlignFrame af, String listener)
   {
     // TODO Auto-generated method stub