X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FJalview.java;h=0ec9ee0e685c5e38f347014808b105283af6f945;hb=refs%2Fheads%2FJAL-3253-applet-SwingJS-omnibus;hp=f59c37f16cae5d38c3848d231c4e168a08e9f57c;hpb=a3d82d30b2bc55f250bbf1c94975308407e8aae7;p=jalview.git

diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index f59c37f..0ec9ee0 100755
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -86,6 +86,7 @@ import java.util.Map;
 import java.util.Vector;
 
 import javax.swing.LookAndFeel;
+import javax.swing.SwingUtilities;
 import javax.swing.UIManager;
 
 import groovy.lang.Binding;
@@ -148,6 +149,8 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi
 
   private boolean noAnnotation;
 
+  public static final String TERMINATOR_LINE = "Jalview argument parsing complete.";
+
   public boolean getStartCalculations()
   {
     return !noCalculation;
@@ -312,6 +315,7 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi
             || "true".equals(System.getProperty("java.awt.headless")))
     {
       headless = true;
+      setSynchronous(true);
     }
 
     if (isJS)
@@ -346,7 +350,6 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi
         System.exit(0);
       }
 
-
       // anything else!
 
       final String jabawsUrl = aparser.getValue(ArgsParser.JABAWS);
@@ -402,11 +405,11 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi
     try
     {
       if (!isJS && Platform.isWin())
-       {
+      {
         UIManager.setLookAndFeel(
                 headless ? "javax.swing.plaf.metal.MetalLookAndFeel"
                         : UIManager.getSystemLookAndFeelClassName());
-//      UIManager.setLookAndFeel(UIManager.getSystemLookAndFeelClassName());
+        // UIManager.setLookAndFeel(UIManager.getSystemLookAndFeelClassName());
       }
     } catch (Exception ex)
     {
@@ -460,7 +463,21 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi
       SequenceOntologyFactory.setSequenceOntology(new SequenceOntology());
     }
 
-    if (!headless)
+    if (headless)
+    {
+      // If this is not tested, then
+
+      if (aparser.contains(ArgsParser.NOUSAGESTATS))
+      {
+        System.err.println("CMD [-nousagestats] executed successfully!");
+      }
+      if (aparser.contains(ArgsParser.NOQUESTIONNAIRE))
+      {
+        System.err.println("CMD [-noquestionnaire] executed successfully!");
+      }
+
+    }
+    else
     {
       desktop = Desktop.getInstance();
       desktop.setInBatchMode(true); // indicate we are starting up
@@ -527,6 +544,7 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi
     }
 
     parseArguments(aparser, true);
+    System.err.println(TERMINATOR_LINE);
   }
 
   /**
@@ -580,7 +598,7 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi
       System.out.println("No files to open!");
       System.exit(1);
     }
-    boolean haveImport = checkStartVamas(aparser);
+    boolean haveImport = false;// checkStartVamas(aparser);
     // Finally, deal with the remaining input data.
     long progress = -1;
     if (file == null && isJavaAppletTag)
@@ -674,7 +692,7 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi
         System.out.println("CMD [nocalculation] executed successfully!");
       }
 
-      AlignFrame af = new FileLoader(!headless).loadFileWaitTillLoaded(file,
+      AlignFrame af = new FileLoader(!headless).LoadFileWaitTillLoaded(file,
               protocol, format);
       if (af == null)
       {
@@ -695,7 +713,7 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi
             // TODO ?
           }
           AlignFrame af2 = new FileLoader(!headless)
-                  .loadFileWaitTillLoaded(file2, protocol, format);
+                  .LoadFileWaitTillLoaded(file2, protocol, format);
           if (af2 == null)
           {
             System.out.println("error");
@@ -859,7 +877,7 @@ 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());
@@ -915,7 +933,7 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi
       }
 
       startUpAlframe = new FileLoader(!headless)
-              .loadFileWaitTillLoaded(file, protocol, format);
+              .LoadFileWaitTillLoaded(file, protocol, format);
       // extract groovy arguments before anything else.
     }
 
@@ -947,112 +965,34 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi
     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"))
       {
@@ -1354,23 +1294,6 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi
   }
 
   /**
-   * Get the SwingJS applet ID and combine that with the frameType
-   * 
-   * @param frameType
-   *          "alignment", "desktop", etc., or null
-   * @return
-   */
-  public static String getAppID(String frameType)
-  {
-    String id = Cache.getProperty("Info.j2sAppletID");
-    if (id == null)
-    {
-      id = "jalview";
-    }
-    return id + (frameType == null ? "" : "-" + frameType);
-  }
-
-  /**
    * Handle all JalviewLite applet parameters
    * 
    * @param aparser
@@ -1643,6 +1566,10 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi
   @Override
   public String getSelectedSequencesFrom(AlignFrameI alf)
   {
+    if (alf == null)
+    {
+      alf = getCurrentAlignFrame();
+    }
     return getSelectedSequencesFrom(alf, null);
   }
 
@@ -1654,6 +1581,10 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi
   @Override
   public String getSelectedSequencesFrom(AlignFrameI alf, String sep)
   {
+    if (alf == null)
+    {
+      alf = getCurrentAlignFrame();
+    }
     return appLoader.getSelectedSequencesFrom(alf, sep);
   }
 
@@ -1666,7 +1597,7 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi
   public void highlight(String sequenceId, String position,
           String alignedPosition)
   {
-    highlightIn(getCurrentAlignFrame(), sequenceId, position,
+    highlightIn(null, sequenceId, position,
             alignedPosition);
   }
 
@@ -1674,6 +1605,10 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi
   public void highlightIn(AlignFrameI alf, String sequenceId,
           String position, String alignedPosition)
   {
+    if (alf == null)
+    {
+      alf = getCurrentAlignFrame();
+    }
     appLoader.highlightIn(alf, sequenceId, position, alignedPosition);
   }
 
@@ -1686,7 +1621,7 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi
   @Override
   public void select(String sequenceIds, String columns, String sep)
   {
-    selectIn(getCurrentAlignFrame(), sequenceIds, columns, sep);
+    selectIn(null, sequenceIds, columns, sep);
   }
 
   @Override
@@ -1699,6 +1634,10 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi
   public void selectIn(AlignFrameI alf, String sequenceIds, String columns,
           String sep)
   {
+    if (alf == null)
+    {
+      alf = getCurrentAlignFrame();
+    }
     appLoader.selectIn(alf, sequenceIds, columns, sep);
   }
 
@@ -1706,7 +1645,7 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi
   public String getSelectedSequencesAsAlignment(String format,
           String suffix)
   {
-    return getSelectedSequencesAsAlignmentFrom(getCurrentAlignFrame(),
+    return getSelectedSequencesAsAlignmentFrom(null,
             format, suffix);
   }
 
@@ -1714,6 +1653,10 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi
   public String getSelectedSequencesAsAlignmentFrom(AlignFrameI alf,
           String format, String sep)
   {
+    if (alf == null)
+    {
+      alf = getCurrentAlignFrame();
+    }
     return appLoader.getSelectedSequencesAsAlignmentFrom(alf, format, sep);
   }
 
@@ -1732,6 +1675,10 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi
   @Override
   public String getAlignmentOrderFrom(AlignFrameI alf, String sep)
   {
+    if (alf == null)
+    {
+      alf = getCurrentAlignFrame();
+    }
     return appLoader.getAlignmentOrderFrom(alf, sep);
   }
 
@@ -1751,6 +1698,10 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi
   public String orderAlignmentBy(AlignFrameI alf, String order,
           String undoName, String sep)
   {
+    if (alf == null)
+    {
+      alf = getCurrentAlignFrame();
+    }
     return appLoader.orderAlignmentBy(alf, order, undoName, sep);
   }
 
@@ -1788,6 +1739,10 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi
   @Override
   public void loadAnnotationFrom(AlignFrameI alf, String annotation)
   {
+    if (alf == null)
+    {
+      alf = getCurrentAlignFrame();
+    }
     appLoader.loadAnnotationFrom(alf, annotation);
   }
 
@@ -1801,43 +1756,55 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi
   public boolean loadFeaturesFrom(AlignFrameI alf, String features,
           boolean autoenabledisplay)
   {
+    if (alf == null)
+    {
+      alf = getCurrentAlignFrame();
+    }
     return appLoader.loadFeaturesFrom(alf, features, autoenabledisplay);
   }
 
   @Override
   public String getFeatures(String format)
   {
-    return getFeaturesFrom(getCurrentAlignFrame(), format);
+    return getFeaturesFrom(null, format);
   }
 
   @Override
   public String getFeaturesFrom(AlignFrameI alf, String format)
   {
-    return appLoader.getFeaturesFrom(alf, format);
+    if (alf == null)
+    {
+      alf = getCurrentAlignFrame();
+    }
+    return appLoader.getFeaturesFrom(alf, format, true, false);
   }
 
   @Override
   public String getAnnotation()
   {
-    return getAnnotationFrom(getCurrentAlignFrame());
+    return getAnnotationFrom(null);
   }
 
   @Override
   public String getAnnotationFrom(AlignFrameI alf)
   {
+    if (alf == null)
+    {
+      alf = getCurrentAlignFrame();
+    }
     return appLoader.getAnnotationFrom(alf);
   }
 
   @Override
   public AlignFrameI newView()
   {
-    return newViewFrom(getCurrentAlignFrame(), null);
+    return newViewFrom(null, null);
   }
 
   @Override
   public AlignFrameI newView(String name)
   {
-    return newViewFrom(getCurrentAlignFrame(), name);
+    return newViewFrom(null, name);
   }
 
   @Override
@@ -1849,6 +1816,10 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi
   @Override
   public AlignFrameI newViewFrom(AlignFrameI alf, String name)
   {
+    if (alf == null)
+    {
+      alf = getCurrentAlignFrame();
+    }
     return appLoader.newViewFrom(alf, name);
   }
 
@@ -1863,6 +1834,10 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi
   public boolean addPdbFile(AlignFrameI alFrame, String sequenceId,
           String pdbEntryString, String pdbFile)
   {
+    if (alFrame == null)
+    {
+      alFrame = getCurrentAlignFrame();
+    }
     return appLoader.addPdbFile(alFrame, sequenceId, pdbEntryString,
             pdbFile);
   }
@@ -1871,56 +1846,80 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi
   public void scrollViewToIn(AlignFrameI alf, String topRow,
           String leftHandColumn)
   {
+    if (alf == null)
+    {
+      alf = getCurrentAlignFrame();
+    }
     appLoader.scrollViewToIn(alf, topRow, leftHandColumn);
   }
 
   @Override
   public void scrollViewToRowIn(AlignFrameI alf, String topRow)
   {
+    if (alf == null)
+    {
+      alf = getCurrentAlignFrame();
+    }
     appLoader.scrollViewToRowIn(alf, topRow);
   }
 
   @Override
   public void scrollViewToColumnIn(AlignFrameI alf, String leftHandColumn)
   {
+    if (alf == null)
+    {
+      alf = getCurrentAlignFrame();
+    }
     appLoader.scrollViewToColumnIn(alf, leftHandColumn);
   }
 
   @Override
   public String getFeatureGroups()
   {
-    return getFeatureGroupsOn(getCurrentAlignFrame());
+    return getFeatureGroupsOn(null);
   }
 
   @Override
   public String getFeatureGroupsOn(AlignFrameI alf)
   {
+    if (alf == null)
+    {
+      alf = getCurrentAlignFrame();
+    }
     return appLoader.getFeatureGroupsOn(alf);
   }
 
   @Override
   public String getFeatureGroupsOfState(boolean visible)
   {
-    return getFeatureGroupsOfStateOn(getCurrentAlignFrame(), visible);
+    return getFeatureGroupsOfStateOn(null, visible);
   }
 
   @Override
   public String getFeatureGroupsOfStateOn(AlignFrameI alf, boolean visible)
   {
+    if (alf == null)
+    {
+      alf = getCurrentAlignFrame();
+    }
     return appLoader.getFeatureGroupsOfStateOn(alf, visible);
   }
 
   @Override
-  public void setFeatureGroupStateOn(AlignFrameI alf, String groups,
-          boolean state)
-  {
-    setFeatureGroupStateOn(alf, groups, state);
+  public void setFeatureGroupState(String groups, boolean state)
+  { // JalviewLite API
+    setFeatureGroupStateOn(null, groups, state);
   }
 
   @Override
-  public void setFeatureGroupState(String groups, boolean state)
+  public void setFeatureGroupStateOn(AlignFrameI alf, String groups,
+          boolean state)
   {
-    appLoader.setFeatureGroupStateOn(getCurrentAlignFrame(), groups, state);
+    if (alf == null)
+    {
+      alf = getCurrentAlignFrame();
+    }
+    appLoader.setFeatureGroupStateOn(alf, groups, state);
   }
 
   @Override
@@ -1955,7 +1954,11 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi
   @Override
   public Object openTreePanel(AlignFrame af, String treeType,
           String modelName)
-  {
+  { // JalviewJS api
+    if (af == null)
+    {
+      af = getCurrentAlignFrame();
+    }
     return CalculationChooser.openTreePanel(af, treeType, modelName, null);
   }
 
@@ -1971,6 +1974,10 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi
   @Override
   public Object openPcaPanel(AlignFrame af, String modelName)
   {
+    if (af == null)
+    {
+      af = getCurrentAlignFrame();
+    }
     return CalculationChooser.openPcaPanel(af, modelName, null);
   }
 
@@ -1978,7 +1985,7 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi
   public String getSelectedSequencesAsAlignment(String format,
           boolean suffix)
   {
-    return getSelectedSequencesAsAlignmentFrom(getCurrentAlignFrame(),
+    return getSelectedSequencesAsAlignmentFrom(null,
             format, suffix);
   }
 
@@ -1986,6 +1993,10 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi
   public String getSelectedSequencesAsAlignmentFrom(AlignFrameI alf,
           String format, boolean suffix)
   {
+    if (alf == null)
+    {
+      alf = getCurrentAlignFrame();
+    }
     return appLoader.getSelectedSequencesAsAlignmentFrom(alf, format,
             "" + suffix);
   }
@@ -2067,5 +2078,99 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi
     // + " " + status);
   }
 
-}
+  /**
+   * flag to allow selected Runnable and Thread processes to run synchronously
+   * 
+   * JAL-3563
+   * 
+   */
+  private static boolean isSynchronous = false;
+
+  /**
+   * Set Jalview to run selected processes synchronously in test and headless
+   * environments.
+   * 
+   * JAL-3563
+   * 
+   * @param b
+   * @author Bob Hanson
+   */
+  public static void setSynchronous(boolean b)
+  {
+    isSynchronous = b;
+  }
+
+  /**
+   * Allows optional synchronous running of a Runnable that would otherwise use
+   * SwingUtilities.invokeLater.
+   * 
+   * JAL-3563
+   * 
+   * @param t
+   * @author Bob Hanson
+   */
+  public static boolean isSynchronous()
+  {
+    return isSynchronous;
+  }
+
+  /**
+   * Allows optional synchronous running of a Runnable that would otherwise use
+   * SwingUtilities.invokeLater.
+   * 
+   * JAL-3563
+   * 
+   * @param t
+   * @author Bob Hanson
+   */
+  public static void execRunnable(Runnable r)
+  {
+    if (isSynchronous())
+    {
+      r.run();
+    }
+    else
+    {
+      SwingUtilities.invokeLater(r);
+    }
+  }
+
+  /**
+   * Allows optional synchronous running of a thread that would otherwise be run
+   * using start().
+   * 
+   * JAL-3563
+   * 
+   * @param t
+   * @author Bob Hanson
+   */
+  public static void execThread(Thread t)
+  {
+    if (isSynchronous())
+    {
+      t.run();
+    }
+    else
+    {
+      t.start();
+    }
+  }
+
+  /**
+   * Get the SwingJS applet ID and combine that with the frameType
+   * 
+   * @param frameType
+   *          "alignment", "desktop", etc., or null
+   * @return
+   */
+  public static String getAppID(String frameType)
+  {
+    String id = Cache.getProperty("Info.j2sAppletID");
+    if (id == null)
+    {
+      id = "jalview";
+    }
+    return id + (frameType == null ? "" : "-" + frameType);
+  }
 
+}
\ No newline at end of file