X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FJalview.java;h=3d80589a2aac0323ee57911de9151a16b3c759de;hb=cb51e62fe2166b236ef488e0a8f35081fcd71388;hp=bb2038e889e71e34af4d4edb7275eaba5b1f17bf;hpb=26ee59562604fa9164e895e3ca07e11398a6c8a0;p=jalview.git

diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index bb2038e..3d80589 100755
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -20,6 +20,7 @@
  */
 package jalview.bin;
 
+import jalview.api.AlignCalcWorkerI;
 import jalview.api.AlignFrameI;
 import jalview.api.AlignViewportI;
 import jalview.api.JalviewApp;
@@ -83,9 +84,6 @@ import java.util.HashMap;
 import java.util.Hashtable;
 import java.util.Map;
 import java.util.Vector;
-import java.util.logging.ConsoleHandler;
-import java.util.logging.Level;
-import java.util.logging.Logger;
 
 import javax.swing.LookAndFeel;
 import javax.swing.UIManager;
@@ -146,6 +144,30 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi
 
   protected JSFunctionExec jsFunctionExec;
 
+  private boolean noCalculation, noMenuBar, noStatus;
+
+  private boolean noAnnotation;
+
+  public boolean getStartCalculations()
+  {
+    return !noCalculation;
+  }
+
+  public boolean getAllowMenuBar()
+  {
+    return !noMenuBar;
+  }
+
+  public boolean getShowStatus()
+  {
+    return !noStatus;
+  }
+
+  public boolean getShowAnnotation()
+  {
+    return !noAnnotation;
+  }
+
   public static AlignFrame getCurrentAlignFrame()
   {
     return getInstance().currentAlignFrame;
@@ -251,71 +273,12 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi
    */
   public static void main(String[] args)
   {
-    // setLogging(); // BH - for event debugging in JavaScript
+    // Platform.startJavaLogging();
     getInstance().doMain(args);
   }
 
-  /**
-   * Allow an outside entity to initiate the second half of argument parsing
-   * (only).
-   * 
-   * @param args
-   * @return null is good
-   */
-  @Override
-  public Object parseArguments(String[] args)
-  {
-
-    try
-    {
-      ArgsParser aparser = new ArgsParser(args);
-      return parseArguments(aparser, false);
-    } catch (Throwable t)
-    {
-      return t;
-    }
-  }
-
-  private static void logClass(String name)
-  {
-    // BH - for event debugging in JavaScript
-    ConsoleHandler consoleHandler = new ConsoleHandler();
-    consoleHandler.setLevel(Level.ALL);
-    Logger logger = Logger.getLogger(name);
-    logger.setLevel(Level.ALL);
-    logger.addHandler(consoleHandler);
-  }
 
   @SuppressWarnings("unused")
-  private static void setLogging()
-  {
-
-    /**
-     * @j2sIgnore
-     * 
-     */
-    {
-      System.out.println("not in js");
-    }
-
-    // BH - for event debugging in JavaScript (Java mode only)
-    if (!Platform.isJS())
-    /**
-     * Java only
-     * 
-     * @j2sIgnore
-     */
-    {
-      Logger.getLogger("").setLevel(Level.ALL);
-      logClass("java.awt.EventDispatchThread");
-      logClass("java.awt.EventQueue");
-      logClass("java.awt.Component");
-      logClass("java.awt.focus.Component");
-      logClass("java.awt.focus.DefaultKeyboardFocusManager");
-    }
-
-  }
-
   /**
    * @param args
    */
@@ -323,7 +286,11 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi
   {
 
     boolean isJS = Platform.isJS();
-    if (!isJS)
+    if (isJS)
+    {
+      Platform.setAppClass(this);
+    }
+    else
     {
       System.setSecurityManager(null);
     }
@@ -338,6 +305,15 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi
 
     String usrPropsFile = aparser.getValue(ArgsParser.PROPS);
     Cache.loadProperties(usrPropsFile);
+
+    if (aparser.contains(ArgsParser.NODISPLAY)
+            || aparser.contains(ArgsParser.NOGUI)
+            || aparser.contains(ArgsParser.HEADLESS)
+            || "true".equals(System.getProperty("java.awt.headless")))
+    {
+      headless = true;
+    }
+
     if (isJS)
     {
       isJavaAppletTag = aparser.isApplet();
@@ -369,13 +345,7 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi
         showUsage();
         System.exit(0);
       }
-      if (aparser.contains(ArgsParser.NODISPLAY)
-              || aparser.contains(ArgsParser.NOGUI)
-              || aparser.contains(ArgsParser.HEADLESS)
-              || "true".equals(System.getProperty("java.awt.headless")))
-      {
-        headless = true;
-      }
+
 
       // anything else!
 
@@ -431,7 +401,13 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi
 
     try
     {
-      UIManager.setLookAndFeel(UIManager.getSystemLookAndFeelClassName());
+      if (!isJS && Platform.isWin())
+       {
+        UIManager.setLookAndFeel(
+                headless ? "javax.swing.plaf.metal.MetalLookAndFeel"
+                        : UIManager.getSystemLookAndFeelClassName());
+//      UIManager.setLookAndFeel(UIManager.getSystemLookAndFeelClassName());
+      }
     } catch (Exception ex)
     {
       System.err.println("Unexpected Look and Feel Exception");
@@ -553,6 +529,33 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi
     parseArguments(aparser, true);
   }
 
+  /**
+   * Allow an outside entity to initiate the second half of argument parsing
+   * (only).
+   * 
+   * @param args
+   * @return null is good
+   */
+  @Override
+  public Object parseArguments(String[] args)
+  {
+
+    try
+    {
+      ArgsParser aparser = new ArgsParser(args);
+      return parseArguments(aparser, false);
+    } catch (Throwable t)
+    {
+      return t;
+    }
+  }
+
+  /**
+   * 
+   * @param aparser
+   * @param isStartup
+   * @return
+   */
   private Object parseArguments(ArgsParser aparser, boolean isStartup)
   {
     boolean isJS = Platform.isJS();
@@ -569,7 +572,6 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi
     String fileFormat = (isJavaAppletTag
             ? aparser.getAppletValue("format", null)
             : null);
-
     FileFormatI format = null;
     DataSourceType protocol = null;
 
@@ -597,8 +599,11 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi
       }
     }
 
+    String data;
+
     if (file != null)
     {
+
       if (!headless)
       {
         desktop.setProgressBar(
@@ -645,6 +650,30 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi
         // TODO ?
       }
 
+      if (aparser.contains(ArgsParser.NOMENUBAR))
+      {
+        noMenuBar = true;
+        System.out.println("CMD [nomenu] executed successfully!");
+      }
+
+      if (aparser.contains(ArgsParser.NOSTATUS))
+      {
+        noStatus = true;
+        System.out.println("CMD [nostatus] executed successfully!");
+      }
+
+      if (aparser.contains(ArgsParser.NOANNOTATION)
+              || aparser.contains(ArgsParser.NOANNOTATION2))
+      {
+        noAnnotation = true;
+        System.out.println("CMD no-annotation executed successfully!");
+      }
+      if (aparser.contains(ArgsParser.NOCALCULATION))
+      {
+        noCalculation = true;
+        System.out.println("CMD [nocalculation] executed successfully!");
+      }
+
       AlignFrame af = new FileLoader(!headless).loadFileWaitTillLoaded(file,
               protocol, format);
       if (af == null)
@@ -686,7 +715,7 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi
 
         // TODO: file2 How to implement file2 for the applet spit screen?
 
-        String data = aparser.getValue(ArgsParser.COLOUR, true);
+        data = aparser.getValue(ArgsParser.COLOUR, true);
         if (data != null)
         {
           data.replaceAll("%20", " ");
@@ -730,6 +759,13 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi
           System.out.println(
                   "CMD [-annotations " + data + "] executed successfully!");
         }
+
+        if (aparser.contains(ArgsParser.SHOWOVERVIEW))
+        {
+          af.overviewMenuItem_actionPerformed(null);
+          System.out.println("CMD [showoverview] executed successfully!");
+        }
+
         // set or clear the sortbytree flag.
         if (aparser.contains(ArgsParser.SORTBYTREE))
         {
@@ -739,18 +775,30 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi
             System.out.println("CMD [-sortbytree] executed successfully!");
           }
         }
-        
+
         boolean doUpdateAnnotation = false;
-        
 
-        if (aparser.contains(ArgsParser.NOANNOTATION)
-                || aparser.contains(ArgsParser.NOANNOTATION2))
+        /**
+         * we do this earlier in JalviewJS because of a complication with
+         * SHOWOVERVIEW
+         * 
+         * For now, just fixing this in JalviewJS.
+         *
+         * 
+         * @j2sIgnore
+         * 
+         */
         {
-          af.getViewport().setShowAnnotation(false);
-          if (!af.getViewport().isShowAnnotation())
+          if (aparser.contains(ArgsParser.NOANNOTATION)
+                  || aparser.contains(ArgsParser.NOANNOTATION2))
           {
-            doUpdateAnnotation = true;
-            System.out.println("CMD no-annotation executed successfully!");
+            af.getViewport().setShowAnnotation(false);
+            if (!af.getViewport().isShowAnnotation())
+            {
+              doUpdateAnnotation = true;
+              System.out
+                      .println("CMD no-annotation executed successfully!");
+            }
           }
         }
         if (aparser.contains(ArgsParser.NOSORTBYTREE))
@@ -810,11 +858,11 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi
                     + "] executed successfully!");
             groovyscript = null;
           }
-          checkOutputFile(aparser, af, format);
-          while (aparser.getSize() > 0)
-          {
-            System.out.println("Unknown arg: " + aparser.nextValue());
-          }
+        }
+        checkOutputFile(aparser, af, format);
+        while (aparser.getSize() > 0)
+        {
+          System.out.println("Unknown arg: " + aparser.nextValue());
         }
       }
     }
@@ -1004,6 +1052,8 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi
       // biojsmsa filename
       String outputFormat = aparser.nextValue();
       String file = aparser.nextValue();
+      System.out.println("format " + outputFormat);
+
       if (outputFormat.equalsIgnoreCase("png"))
       {
         af.createPNG(new File(file));
@@ -1593,6 +1643,10 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi
   @Override
   public String getSelectedSequencesFrom(AlignFrameI alf)
   {
+    if (alf == null)
+    {
+      alf = getCurrentAlignFrame();
+    }
     return getSelectedSequencesFrom(alf, null);
   }
 
@@ -1604,6 +1658,10 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi
   @Override
   public String getSelectedSequencesFrom(AlignFrameI alf, String sep)
   {
+    if (alf == null)
+    {
+      alf = getCurrentAlignFrame();
+    }
     return appLoader.getSelectedSequencesFrom(alf, sep);
   }
 
@@ -1616,7 +1674,7 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi
   public void highlight(String sequenceId, String position,
           String alignedPosition)
   {
-    highlightIn(getCurrentAlignFrame(), sequenceId, position,
+    highlightIn(null, sequenceId, position,
             alignedPosition);
   }
 
@@ -1624,6 +1682,10 @@ 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);
   }
 
@@ -1636,7 +1698,7 @@ 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
@@ -1649,6 +1711,10 @@ 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);
   }
 
@@ -1656,7 +1722,7 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi
   public String getSelectedSequencesAsAlignment(String format,
           String suffix)
   {
-    return getSelectedSequencesAsAlignmentFrom(getCurrentAlignFrame(),
+    return getSelectedSequencesAsAlignmentFrom(null,
             format, suffix);
   }
 
@@ -1664,6 +1730,10 @@ 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);
   }
 
@@ -1682,6 +1752,10 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi
   @Override
   public String getAlignmentOrderFrom(AlignFrameI alf, String sep)
   {
+    if (alf == null)
+    {
+      alf = getCurrentAlignFrame();
+    }
     return appLoader.getAlignmentOrderFrom(alf, sep);
   }
 
@@ -1701,6 +1775,10 @@ 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);
   }
 
@@ -1738,6 +1816,10 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi
   @Override
   public void loadAnnotationFrom(AlignFrameI alf, String annotation)
   {
+    if (alf == null)
+    {
+      alf = getCurrentAlignFrame();
+    }
     appLoader.loadAnnotationFrom(alf, annotation);
   }
 
@@ -1751,43 +1833,55 @@ 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)
   {
+    if (alf == null)
+    {
+      alf = getCurrentAlignFrame();
+    }
     return appLoader.getFeaturesFrom(alf, format);
   }
 
   @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
@@ -1799,6 +1893,10 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi
   @Override
   public AlignFrameI newViewFrom(AlignFrameI alf, String name)
   {
+    if (alf == null)
+    {
+      alf = getCurrentAlignFrame();
+    }
     return appLoader.newViewFrom(alf, name);
   }
 
@@ -1813,6 +1911,10 @@ 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);
   }
@@ -1821,56 +1923,80 @@ 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
@@ -1905,7 +2031,11 @@ 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);
   }
 
@@ -1921,6 +2051,10 @@ 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);
   }
 
@@ -1928,7 +2062,7 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi
   public String getSelectedSequencesAsAlignment(String format,
           boolean suffix)
   {
-    return getSelectedSequencesAsAlignmentFrom(getCurrentAlignFrame(),
+    return getSelectedSequencesAsAlignmentFrom(null,
             format, suffix);
   }
 
@@ -1936,6 +2070,10 @@ 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);
   }
@@ -2005,4 +2143,17 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi
 
   }
 
+  @Override
+  public void showOverview()
+  {
+    currentAlignFrame.overviewMenuItem_actionPerformed(null);
+  }
+
+  public void notifyWorker(AlignCalcWorkerI worker, String status)
+  {
+    // System.out.println("Jalview worker " + worker.getClass().getSimpleName()
+    // + " " + status);
+  }
+
 }
+