JAL-3446 from JAL-3253 Discoverers

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 93713d2..815b5ef 100644 (file)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -346,8 +346,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    */
   void init()
   {
    */
   void init()
   {

-//       setBackground(Color.white); // BH 2019
-                 
+    // setBackground(Color.white); // BH 2019
+

     if (!Jalview.isHeadlessMode())
     {
       progressBar = new ProgressBar(this.statusPanel, this.statusBar);
     if (!Jalview.isHeadlessMode())
     {
       progressBar = new ProgressBar(this.statusPanel, this.statusBar);

@@ -847,8 +847,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
               javax.swing.event.InternalFrameEvent evt)
       {
         // System.out.println("deregistering discoverer listener");
               javax.swing.event.InternalFrameEvent evt)
       {
         // System.out.println("deregistering discoverer listener");

-        Desktop.getInstance().removeJalviewPropertyChangeListener("services",
-                thisListener);
+        Desktop.getInstance().removeJalviewPropertyChangeListener(
+                "services", thisListener);

         closeMenuItem_actionPerformed(true);
       }
     });
         closeMenuItem_actionPerformed(true);
       }
     });

@@ -1242,15 +1242,16 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       String shortName = title;
       if (shortName.indexOf(File.separatorChar) > -1)
       {
       String shortName = title;
       if (shortName.indexOf(File.separatorChar) > -1)
       {

-        shortName = shortName.substring(
-                shortName.lastIndexOf(File.separatorChar) + 1);
+        shortName = shortName
+                .substring(shortName.lastIndexOf(File.separatorChar) + 1);

       }
       }

-      lastSaveSuccessful = new Jalview2XML().saveAlignment(this, file, shortName);
-      
+      lastSaveSuccessful = new Jalview2XML().saveAlignment(this, file,
+              shortName);
+

       statusBar.setText(MessageManager.formatMessage(
               "label.successfully_saved_to_file_in_format", new Object[]
               { fileName, format }));
       statusBar.setText(MessageManager.formatMessage(
               "label.successfully_saved_to_file_in_format", new Object[]
               { fileName, format }));

-      
+

       return;
     }
 
       return;
     }
 

@@ -1287,16 +1288,17 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
           BackupFiles backupfiles = doBackup ? new BackupFiles(file) : null;
           try
           {
           BackupFiles backupfiles = doBackup ? new BackupFiles(file) : null;
           try
           {

-            String tempFilePath = doBackup ? backupfiles.getTempFilePath() : file;
-                       PrintWriter out = new PrintWriter(
-                    new FileWriter(tempFilePath));
+            String tempFilePath = doBackup ? backupfiles.getTempFilePath()
+                    : file;
+            PrintWriter out = new PrintWriter(new FileWriter(tempFilePath));

 
             out.print(output);
             out.close();
             AlignFrame.this.setTitle(file);
             statusBar.setText(MessageManager.formatMessage(
 
             out.print(output);
             out.close();
             AlignFrame.this.setTitle(file);
             statusBar.setText(MessageManager.formatMessage(

-                  "label.successfully_saved_to_file_in_format", new Object[]
-                  { fileName, format.getName() }));
+                    "label.successfully_saved_to_file_in_format",
+                    new Object[]
+                    { fileName, format.getName() }));

             lastSaveSuccessful = true;
           } catch (Exception ex)
           {
             lastSaveSuccessful = true;
           } catch (Exception ex)
           {

@@ -1490,7 +1492,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     final JalviewFileChooser chooser = new JalviewFileChooser(
             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
     chooser.setFileView(new JalviewFileView());
     final JalviewFileChooser chooser = new JalviewFileChooser(
             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
     chooser.setFileView(new JalviewFileView());

-    String tooltip = MessageManager.getString("label.load_jalview_annotations");
+    String tooltip = MessageManager
+            .getString("label.load_jalview_annotations");

     chooser.setDialogTitle(tooltip);
     chooser.setToolTipText(tooltip);
     chooser.setResponseHandler(0, new Runnable()
     chooser.setDialogTitle(tooltip);
     chooser.setToolTipText(tooltip);
     chooser.setResponseHandler(0, new Runnable()

@@ -1936,7 +1939,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
     try
     {
 
     try
     {

-      jalview.gui.Desktop.internalCopy = true;
+      Desktop.getInstance().internalCopy = true;

       // Its really worth setting the clipboard contents
       // to empty before setting the large StringSelection!!
       Toolkit.getDefaultToolkit().getSystemClipboard()
       // Its really worth setting the clipboard contents
       // to empty before setting the large StringSelection!!
       Toolkit.getDefaultToolkit().getSystemClipboard()

@@ -1963,7 +1966,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
               hiddenCutoff, hiddenOffset);
     }
 
               hiddenCutoff, hiddenOffset);
     }
 

-    Desktop.jalviewClipboard = new Object[] { seqs,
+    Desktop.getInstance().jalviewClipboard = new Object[] { seqs,

         viewport.getAlignment().getDataset(), hiddenColumns };
     setStatus(MessageManager.formatMessage(
             "label.copied_sequences_to_clipboard", new Object[]
         viewport.getAlignment().getDataset(), hiddenColumns };
     setStatus(MessageManager.formatMessage(
             "label.copied_sequences_to_clipboard", new Object[]

@@ -2003,6 +2006,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   void paste(boolean newAlignment)
   {
     boolean externalPaste = true;
   void paste(boolean newAlignment)
   {
     boolean externalPaste = true;

+    Desktop d = Desktop.getInstance();

     try
     {
       Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
     try
     {
       Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();

@@ -2035,12 +2039,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       boolean annotationAdded = false;
       AlignmentI alignment = null;
 
       boolean annotationAdded = false;
       AlignmentI alignment = null;
 

-      if (Desktop.jalviewClipboard != null)
+      if (d.jalviewClipboard != null)

       {
         // The clipboard was filled from within Jalview, we must use the
         // sequences
         // And dataset from the copied alignment
       {
         // The clipboard was filled from within Jalview, we must use the
         // sequences
         // And dataset from the copied alignment

-        SequenceI[] newseq = (SequenceI[]) Desktop.jalviewClipboard[0];
+        SequenceI[] newseq = (SequenceI[]) d.jalviewClipboard[0];

         // be doubly sure that we create *new* sequence objects.
         sequences = new SequenceI[newseq.length];
         for (int i = 0; i < newseq.length; i++)
         // be doubly sure that we create *new* sequence objects.
         sequences = new SequenceI[newseq.length];
         for (int i = 0; i < newseq.length; i++)

@@ -2065,10 +2069,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       if (newAlignment)
       {
 
       if (newAlignment)
       {
 

-        if (Desktop.jalviewClipboard != null)
+        if (d.jalviewClipboard != null)

         {
           // dataset is inherited
         {
           // dataset is inherited

-          alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]);
+          alignment.setDataset((Alignment) d.jalviewClipboard[1]);

         }
         else
         {
         }
         else
         {

@@ -2084,8 +2088,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
         alignment = viewport.getAlignment();
         alwidth = alignment.getWidth() + 1;
         // decide if we need to import sequences from an existing dataset
         alignment = viewport.getAlignment();
         alwidth = alignment.getWidth() + 1;
         // decide if we need to import sequences from an existing dataset

-        boolean importDs = Desktop.jalviewClipboard != null
-                && Desktop.jalviewClipboard[1] != alignment.getDataset();
+        boolean importDs = d.jalviewClipboard != null
+                && d.jalviewClipboard[1] != alignment.getDataset();

         // importDs==true instructs us to copy over new dataset sequences from
         // an existing alignment
         Vector<SequenceI> newDs = (importDs) ? new Vector<>() : null; // used to
         // importDs==true instructs us to copy over new dataset sequences from
         // an existing alignment
         Vector<SequenceI> newDs = (importDs) ? new Vector<>() : null; // used to

@@ -2287,10 +2291,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                 DEFAULT_HEIGHT);
         String newtitle = new String("Copied sequences");
 
                 DEFAULT_HEIGHT);
         String newtitle = new String("Copied sequences");
 

-        if (Desktop.jalviewClipboard != null
-                && Desktop.jalviewClipboard[2] != null)
+        if (d.jalviewClipboard != null && d.jalviewClipboard[2] != null)

         {
         {

-          HiddenColumns hc = (HiddenColumns) Desktop.jalviewClipboard[2];
+          HiddenColumns hc = (HiddenColumns) d.jalviewClipboard[2];

           af.viewport.setHiddenColumns(hc);
         }
 
           af.viewport.setHiddenColumns(hc);
         }
 

@@ -2342,11 +2345,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
               DEFAULT_HEIGHT);
       String newtitle = new String("Flanking alignment");
       AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
               DEFAULT_HEIGHT);
       String newtitle = new String("Flanking alignment");

-
-      if (Desktop.jalviewClipboard != null
-              && Desktop.jalviewClipboard[2] != null)
+      Desktop d = Desktop.getInstance();
+      if (d.jalviewClipboard != null && d.jalviewClipboard[2] != null)

       {
       {

-        HiddenColumns hc = (HiddenColumns) Desktop.jalviewClipboard[2];
+        HiddenColumns hc = (HiddenColumns) d.jalviewClipboard[2];

         af.viewport.setHiddenColumns(hc);
       }
 
         af.viewport.setHiddenColumns(hc);
       }
 

@@ -2405,56 +2407,62 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       return;
     }
 
       return;
     }
 

-    Runnable okAction = new Runnable() 
-    {
-               @Override
-               public void run() 
-               {
-                   SequenceI[] cut = sg.getSequences()
-                           .toArray(new SequenceI[sg.getSize()]);
-
-                   addHistoryItem(new EditCommand(
-                           MessageManager.getString("label.cut_sequences"), Action.CUT,
-                           cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
-                           viewport.getAlignment()));
-
-                   viewport.setSelectionGroup(null);
-                   viewport.sendSelection();
-                   viewport.getAlignment().deleteGroup(sg);
-
-                   viewport.firePropertyChange("alignment", null,
-                           viewport.getAlignment().getSequences());
-                   if (viewport.getAlignment().getHeight() < 1)
-                   {
-                     try
-                     {
-                       AlignFrame.this.setClosed(true);
-                     } catch (Exception ex)
-                     {
-                     }
-                   }
-               }};
+    Runnable okAction = new Runnable()
+    {
+      @Override
+      public void run()
+      {
+        SequenceI[] cut = sg.getSequences()
+                .toArray(new SequenceI[sg.getSize()]);
+
+        addHistoryItem(new EditCommand(
+                MessageManager.getString("label.cut_sequences"), Action.CUT,
+                cut, sg.getStartRes(),
+                sg.getEndRes() - sg.getStartRes() + 1,
+                viewport.getAlignment()));
+
+        viewport.setSelectionGroup(null);
+        viewport.sendSelection();
+        viewport.getAlignment().deleteGroup(sg);
+
+        viewport.firePropertyChange("alignment", null,
+                viewport.getAlignment().getSequences());
+        if (viewport.getAlignment().getHeight() < 1)
+        {
+          try
+          {
+            AlignFrame.this.setClosed(true);
+          } catch (Exception ex)
+          {
+          }
+        }
+      }
+    };

 
     /*
      * If the cut affects all sequences, prompt for confirmation
      */
 
     /*
      * If the cut affects all sequences, prompt for confirmation
      */

-    boolean wholeHeight = sg.getSize() == viewport.getAlignment().getHeight();
+    boolean wholeHeight = sg.getSize() == viewport.getAlignment()
+            .getHeight();

     boolean wholeWidth = (((sg.getEndRes() - sg.getStartRes())
             + 1) == viewport.getAlignment().getWidth()) ? true : false;
     boolean wholeWidth = (((sg.getEndRes() - sg.getStartRes())
             + 1) == viewport.getAlignment().getWidth()) ? true : false;

-       if (wholeHeight && wholeWidth)
-       {
-           JvOptionPane dialog = JvOptionPane.newOptionDialog(Desktop.getDesktopPane());
-               dialog.setResponseHandler(0, okAction); // 0 = OK_OPTION
-           Object[] options = new Object[] { MessageManager.getString("action.ok"),
-                   MessageManager.getString("action.cancel") };
-               dialog.showDialog(MessageManager.getString("warn.delete_all"),
-                   MessageManager.getString("label.delete_all"),
-                   JvOptionPane.DEFAULT_OPTION, JvOptionPane.PLAIN_MESSAGE, null,
-                   options, options[0]);
-       } else 
-       {
-               okAction.run();
-       }
+    if (wholeHeight && wholeWidth)
+    {
+      JvOptionPane dialog = JvOptionPane
+              .newOptionDialog(Desktop.getDesktopPane());
+      dialog.setResponseHandler(0, okAction); // 0 = OK_OPTION
+      Object[] options = new Object[] {
+          MessageManager.getString("action.ok"),
+          MessageManager.getString("action.cancel") };
+      dialog.showDialog(MessageManager.getString("warn.delete_all"),
+              MessageManager.getString("label.delete_all"),
+              JvOptionPane.DEFAULT_OPTION, JvOptionPane.PLAIN_MESSAGE, null,
+              options, options[0]);
+    }
+    else
+    {
+      okAction.run();
+    }

   }
 
   /**
   }
 
   /**

@@ -2626,8 +2634,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                 column, viewport.getAlignment());
       }
 
                 column, viewport.getAlignment());
       }
 

-      setStatus(MessageManager
-              .formatMessage("label.removed_columns", new String[]
+      setStatus(MessageManager.formatMessage("label.removed_columns",
+              new String[]

               { Integer.valueOf(trimRegion.getSize()).toString() }));
 
       addHistoryItem(trimRegion);
               { Integer.valueOf(trimRegion.getSize()).toString() }));
 
       addHistoryItem(trimRegion);

@@ -2676,8 +2684,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
     addHistoryItem(removeGapCols);
 
 
     addHistoryItem(removeGapCols);
 

-    setStatus(MessageManager
-            .formatMessage("label.removed_empty_columns", new Object[]
+    setStatus(MessageManager.formatMessage("label.removed_empty_columns",
+            new Object[]

             { Integer.valueOf(removeGapCols.getSize()).toString() }));
 
     // This is to maintain viewport position on first residue
             { Integer.valueOf(removeGapCols.getSize()).toString() }));
 
     // This is to maintain viewport position on first residue

@@ -2799,8 +2807,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
     if (viewport.getViewName() == null)
     {
 
     if (viewport.getViewName() == null)
     {

-      viewport.setViewName(MessageManager
-              .getString("label.view_name_original"));
+      viewport.setViewName(
+              MessageManager.getString("label.view_name_original"));

     }
 
     /*
     }
 
     /*

@@ -3326,7 +3334,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       JLabel textLabel = new JLabel();
       textLabel.setText(content);
       textLabel.setBackground(Color.WHITE);
       JLabel textLabel = new JLabel();
       textLabel.setText(content);
       textLabel.setBackground(Color.WHITE);

-      
+

       pane = new JPanel(new BorderLayout());
       ((JPanel) pane).setOpaque(true);
       pane.setBackground(Color.WHITE);
       pane = new JPanel(new BorderLayout());
       ((JPanel) pane).setOpaque(true);
       pane.setBackground(Color.WHITE);

@@ -3369,8 +3377,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     }
 
     JInternalFrame frame = new JInternalFrame();
     }
 
     JInternalFrame frame = new JInternalFrame();

-    
-    

 
     // BH 2019.07.26 we allow for an embedded
     // undecorated overview with defined size
 
     // BH 2019.07.26 we allow for an embedded
     // undecorated overview with defined size

@@ -3482,8 +3488,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
      * otherwise set the chosen colour scheme (or null for 'None')
      */
     ColourSchemeI cs = ColourSchemes.getInstance().getColourScheme(name,
      * otherwise set the chosen colour scheme (or null for 'None')
      */
     ColourSchemeI cs = ColourSchemes.getInstance().getColourScheme(name,

-            viewport,
-            viewport.getAlignment(), viewport.getHiddenRepSequences());
+            viewport, viewport.getAlignment(),
+            viewport.getHiddenRepSequences());

     changeColour(cs);
   }
 
     changeColour(cs);
   }
 

@@ -3867,8 +3873,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       Enumeration<String> labels = scoreSorts.keys();
       while (labels.hasMoreElements())
       {
       Enumeration<String> labels = scoreSorts.keys();
       while (labels.hasMoreElements())
       {

-        addSortByAnnotScoreMenuItem(sortByAnnotScore,
-                labels.nextElement());
+        addSortByAnnotScoreMenuItem(sortByAnnotScore, labels.nextElement());

       }
       sortByAnnotScore.setVisible(scoreSorts.size() > 0);
       scoreSorts.clear();
       }
       sortByAnnotScore.setVisible(scoreSorts.size() > 0);
       scoreSorts.clear();

@@ -4035,7 +4040,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     chooser.setToolTipText(
             MessageManager.getString("label.load_tree_file"));
 
     chooser.setToolTipText(
             MessageManager.getString("label.load_tree_file"));
 

-    chooser.setResponseHandler(0,new Runnable()
+    chooser.setResponseHandler(0, new Runnable()

     {
       @Override
       public void run()
     {
       @Override
       public void run()

@@ -4050,7 +4055,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
           viewport.setCurrentTree(showNewickTree(fin, filePath).getTree());
         } catch (Exception ex)
         {
           viewport.setCurrentTree(showNewickTree(fin, filePath).getTree());
         } catch (Exception ex)
         {

-          JvOptionPane.showMessageDialog(Desktop.getDesktopPane(), ex.getMessage(),
+          JvOptionPane.showMessageDialog(Desktop.getDesktopPane(),
+                  ex.getMessage(),

                   MessageManager
                           .getString("label.problem_reading_tree_file"),
                   JvOptionPane.WARNING_MESSAGE);
                   MessageManager
                           .getString("label.problem_reading_tree_file"),
                   JvOptionPane.WARNING_MESSAGE);

@@ -4195,9 +4201,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
           final JMenu dismenu = new JMenu("Protein Disorder");
           // JAL-940 - only show secondary structure prediction services from
           // the legacy server
           final JMenu dismenu = new JMenu("Protein Disorder");
           // JAL-940 - only show secondary structure prediction services from
           // the legacy server

+          Hashtable<String, Vector<ServiceHandle>> ds = Discoverer
+                  .getServices();
+

           if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
               // &&
           if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
               // &&

-          Discoverer.services != null && (Discoverer.services.size() > 0))
+          ds != null && (ds.size() > 0))

           {
             // TODO: refactor to allow list of AbstractName/Handler bindings to
             // be
           {
             // TODO: refactor to allow list of AbstractName/Handler bindings to
             // be

@@ -4205,15 +4214,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
             // No MSAWS used any more:
             // Vector msaws = null; // (Vector)
             // Discoverer.services.get("MsaWS");
             // No MSAWS used any more:
             // Vector msaws = null; // (Vector)
             // Discoverer.services.get("MsaWS");

-            Vector<ServiceHandle> secstrpr = Discoverer.services
-                    .get("SecStrPred");
+            Vector<ServiceHandle> secstrpr = ds.get("SecStrPred");

             if (secstrpr != null)
             {
               // Add any secondary structure prediction services
               for (int i = 0, j = secstrpr.size(); i < j; i++)
               {
             if (secstrpr != null)
             {
               // Add any secondary structure prediction services
               for (int i = 0, j = secstrpr.size(); i < j; i++)
               {

-                final ext.vamsas.ServiceHandle sh = secstrpr
-                        .get(i);
+                final ext.vamsas.ServiceHandle sh = secstrpr.get(i);

                 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
                         .getServiceClient(sh);
                 int p = secstrmenu.getItemCount();
                 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
                         .getServiceClient(sh);
                 int p = secstrmenu.getItemCount();

@@ -4447,8 +4454,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       final String errorTitle = MessageManager
               .getString("label.implementation_error")
               + MessageManager.getString("label.translation_failed");
       final String errorTitle = MessageManager
               .getString("label.implementation_error")
               + MessageManager.getString("label.translation_failed");

-      JvOptionPane.showMessageDialog(Desktop.getDesktopPane(), msg, errorTitle,
-              JvOptionPane.ERROR_MESSAGE);
+      JvOptionPane.showMessageDialog(Desktop.getDesktopPane(), msg,
+              errorTitle, JvOptionPane.ERROR_MESSAGE);

       return;
     }
     if (al == null || al.getHeight() == 0)
       return;
     }
     if (al == null || al.getHeight() == 0)

@@ -4457,8 +4464,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
               "label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation");
       final String errorTitle = MessageManager
               .getString("label.translation_failed");
               "label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation");
       final String errorTitle = MessageManager
               .getString("label.translation_failed");

-      JvOptionPane.showMessageDialog(Desktop.getDesktopPane(), msg, errorTitle,
-              JvOptionPane.WARNING_MESSAGE);
+      JvOptionPane.showMessageDialog(Desktop.getDesktopPane(), msg,
+              errorTitle, JvOptionPane.WARNING_MESSAGE);

     }
     else
     {
     }
     else
     {

@@ -4550,184 +4557,190 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
     Transferable t = evt.getTransferable();
 
     evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
     Transferable t = evt.getTransferable();
 

-    final AlignFrame thisaf = this;

     final List<Object> files = new ArrayList<>();
     List<DataSourceType> protocols = new ArrayList<>();
 
     try
     {
       Desktop.transferFromDropTarget(files, protocols, evt, t);
     final List<Object> files = new ArrayList<>();
     List<DataSourceType> protocols = new ArrayList<>();
 
     try
     {
       Desktop.transferFromDropTarget(files, protocols, evt, t);

+      if (files.size() > 0)
+      {
+        new Thread(new Runnable()
+        {
+          @Override
+          public void run()
+          {
+            loadDroppedFiles(files, protocols, evt, t);
+          }
+        }).start();
+      }

     } catch (Exception e)
     {
       e.printStackTrace();
     }
     } catch (Exception e)
     {
       e.printStackTrace();
     }

-    if (files != null)
+  }
+
+  protected void loadDroppedFiles(List<Object> files,
+          List<DataSourceType> protocols, DropTargetDropEvent evt,
+          Transferable t)
+  {
+    try

     {
     {

-      new Thread(new Runnable()
+      // check to see if any of these files have names matching sequences
+      // in
+      // the alignment
+      SequenceIdMatcher idm = new SequenceIdMatcher(
+              viewport.getAlignment().getSequencesArray());
+      /**
+       * Object[] { String,SequenceI}
+       */
+      ArrayList<Object[]> filesmatched = new ArrayList<>();
+      ArrayList<Object> filesnotmatched = new ArrayList<>();
+      for (int i = 0; i < files.size(); i++)

       {
       {

-        @Override
-        public void run()
+        // BH 2018
+        Object file = files.get(i);
+        String fileName = file.toString();
+        String pdbfn = "";
+        DataSourceType protocol = (file instanceof File
+                ? DataSourceType.FILE
+                : FormatAdapter.checkProtocol(fileName));
+        if (protocol == DataSourceType.FILE)

         {
         {

-          try
+          File fl;
+          if (file instanceof File)
+          {
+            fl = (File) file;
+            Platform.cacheFileData(fl);
+          }
+          else

           {
           {

-            // check to see if any of these files have names matching sequences
-            // in
-            // the alignment
-            SequenceIdMatcher idm = new SequenceIdMatcher(
-                    viewport.getAlignment().getSequencesArray());
-            /**
-             * Object[] { String,SequenceI}
-             */
-            ArrayList<Object[]> filesmatched = new ArrayList<>();
-            ArrayList<Object> filesnotmatched = new ArrayList<>();
-            for (int i = 0; i < files.size(); i++)
+            fl = new File(fileName);
+          }
+          pdbfn = fl.getName();
+        }
+        else if (protocol == DataSourceType.URL)
+        {
+          URL url = new URL(fileName);
+          pdbfn = url.getFile();
+        }
+        if (pdbfn.length() > 0)
+        {
+          // attempt to find a match in the alignment
+          SequenceI[] mtch = idm.findAllIdMatches(pdbfn);
+          int l = 0, c = pdbfn.indexOf(".");
+          while (mtch == null && c != -1)
+          {
+            do

             {
             {

-              // BH 2018
-              Object file = files.get(i);
-              String fileName = file.toString();
-              String pdbfn = "";
-              DataSourceType protocol = (file instanceof File
-                      ? DataSourceType.FILE
-                      : FormatAdapter.checkProtocol(fileName));
-              if (protocol == DataSourceType.FILE)
-              {
-                File fl;
-                if (file instanceof File) {
-                  fl = (File) file;
-                  Platform.cacheFileData(fl);
-                } else {
-                  fl = new File(fileName);
-                }
-                pdbfn = fl.getName();
-              }
-              else if (protocol == DataSourceType.URL)
-              {
-                URL url = new URL(fileName);
-                pdbfn = url.getFile();
-              }
-              if (pdbfn.length() > 0)
-              {
-                // attempt to find a match in the alignment
-                SequenceI[] mtch = idm.findAllIdMatches(pdbfn);
-                int l = 0, c = pdbfn.indexOf(".");
-                while (mtch == null && c != -1)
-                {
-                  do
-                  {
-                    l = c;
-                  } while ((c = pdbfn.indexOf(".", l)) > l);
-                  if (l > -1)
-                  {
-                    pdbfn = pdbfn.substring(0, l);
-                  }
-                  mtch = idm.findAllIdMatches(pdbfn);
-                }
-                if (mtch != null)
-                {
-                  FileFormatI type;
-                  try
-                  {
-                    type = new IdentifyFile().identify(file, protocol);
-                  } catch (Exception ex)
-                  {
-                    type = null;
-                  }
-                  if (type != null && type.isStructureFile())
-                  {
-                    filesmatched.add(new Object[] { file, protocol, mtch });
-                    continue;
-                  }
-                }
-                // File wasn't named like one of the sequences or wasn't a PDB
-                // file.
-                filesnotmatched.add(file);
-              }
+              l = c;
+            } while ((c = pdbfn.indexOf(".", l)) > l);
+            if (l > -1)
+            {
+              pdbfn = pdbfn.substring(0, l);

             }
             }

-            int assocfiles = 0;
-            if (filesmatched.size() > 0)
+            mtch = idm.findAllIdMatches(pdbfn);
+          }
+          if (mtch != null)
+          {
+            FileFormatI type;
+            try

             {
             {

-              boolean autoAssociate = Cache
-                      .getDefault("AUTOASSOCIATE_PDBANDSEQS", false);
-              if (!autoAssociate)
-              {
-                String msg = MessageManager.formatMessage(
-                        "label.automatically_associate_structure_files_with_sequences_same_name",
-                        new Object[]
-                        { Integer.valueOf(filesmatched.size())
-                                .toString() });
-                String ttl = MessageManager.getString(
-                        "label.automatically_associate_structure_files_by_name");
-                int choice = JvOptionPane.showConfirmDialog(thisaf, msg,
-                        ttl, JvOptionPane.YES_NO_OPTION);
-                autoAssociate = choice == JvOptionPane.YES_OPTION;
-              }
-              if (autoAssociate)
-              {
-                for (Object[] fm : filesmatched)
-                {
-                  // try and associate
-                  // TODO: may want to set a standard ID naming formalism for
-                  // associating PDB files which have no IDs.
-                  for (SequenceI toassoc : (SequenceI[]) fm[2])
-                  {
-                    PDBEntry pe = new AssociatePdbFileWithSeq()
-                            .associatePdbWithSeq(fm[0].toString(),
-                                    (DataSourceType) fm[1], toassoc, false,
-                                    Desktop.getInstance());
-                    if (pe != null)
-                    {
-                      System.err.println("Associated file : "
-                              + (fm[0].toString()) + " with "
-                              + toassoc.getDisplayId(true));
-                      assocfiles++;
-                    }
-                  }
-                  // TODO: do we need to update overview ? only if features are
-                  // shown I guess
-                  alignPanel.paintAlignment(true, false);
-                }
-              }
-              else
-              {
-                /*
-                 * add declined structures as sequences
-                 */
-                for (Object[] o : filesmatched)
-                {
-                  filesnotmatched.add(o[0]);
-                }
-              }
+              type = new IdentifyFile().identify(file, protocol);
+            } catch (Exception ex)
+            {
+              type = null;

             }
             }

-            if (filesnotmatched.size() > 0)
+            if (type != null && type.isStructureFile())

             {
             {

-              if (assocfiles > 0 && (Cache.getDefault(
-                      "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false)
-                      || JvOptionPane.showConfirmDialog(thisaf,
-                              "<html>" + MessageManager.formatMessage(
-                                      "label.ignore_unmatched_dropped_files_info",
-                                      new Object[]
-                                      { Integer.valueOf(
-                                              filesnotmatched.size())
-                                              .toString() })
-                                      + "</html>",
-                              MessageManager.getString(
-                                      "label.ignore_unmatched_dropped_files"),
-                              JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION))
-              {
-                return;
-              }
-              for (Object fn : filesnotmatched)
+              filesmatched.add(new Object[] { file, protocol, mtch });
+              continue;
+            }
+          }
+          // File wasn't named like one of the sequences or wasn't a PDB
+          // file.
+          filesnotmatched.add(file);
+        }
+      }
+      int assocfiles = 0;
+      if (filesmatched.size() > 0)
+      {
+        boolean autoAssociate = Cache.getDefault("AUTOASSOCIATE_PDBANDSEQS",
+                false);
+        if (!autoAssociate)
+        {
+          String msg = MessageManager.formatMessage(
+                  "label.automatically_associate_structure_files_with_sequences_same_name",
+                  new Object[]
+                  { Integer.valueOf(filesmatched.size()).toString() });
+          String ttl = MessageManager.getString(
+                  "label.automatically_associate_structure_files_by_name");
+          int choice = JvOptionPane.showConfirmDialog(this, msg, ttl,
+                  JvOptionPane.YES_NO_OPTION);
+          autoAssociate = choice == JvOptionPane.YES_OPTION;
+        }
+        if (autoAssociate)
+        {
+          for (Object[] fm : filesmatched)
+          {
+            // try and associate
+            // TODO: may want to set a standard ID naming formalism for
+            // associating PDB files which have no IDs.
+            for (SequenceI toassoc : (SequenceI[]) fm[2])
+            {
+              PDBEntry pe = new AssociatePdbFileWithSeq()
+                      .associatePdbWithSeq(fm[0].toString(),
+                              (DataSourceType) fm[1], toassoc, false,
+                              Desktop.getInstance());
+              if (pe != null)

               {
               {

-                loadJalviewDataFile(fn, null, null, null);
+                System.err.println("Associated file : " + (fm[0].toString())
+                        + " with " + toassoc.getDisplayId(true));
+                assocfiles++;

               }
               }

-

             }
             }

-          } catch (Exception ex)
+            // TODO: do we need to update overview ? only if features are
+            // shown I guess
+            alignPanel.paintAlignment(true, false);
+          }
+        }
+        else
+        {
+          /*
+           * add declined structures as sequences
+           */
+          for (Object[] o : filesmatched)

           {
           {

-            ex.printStackTrace();
+            filesnotmatched.add(o[0]);

           }
         }
           }
         }

-      }).start();
+      }
+      if (filesnotmatched.size() > 0)
+      {
+        if (assocfiles > 0 && (Cache
+                .getDefault("AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false)
+                || JvOptionPane.showConfirmDialog(this,
+                        "<html>" + MessageManager.formatMessage(
+                                "label.ignore_unmatched_dropped_files_info",
+                                new Object[]
+                                { Integer.valueOf(filesnotmatched.size())
+                                        .toString() })
+                                + "</html>",
+                        MessageManager.getString(
+                                "label.ignore_unmatched_dropped_files"),
+                        JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION))
+        {
+          return;
+        }
+        for (Object fn : filesnotmatched)
+        {
+          loadJalviewDataFile(fn, null, null, null);
+        }
+
+      }
+    } catch (Exception ex)
+    {
+      ex.printStackTrace();

     }
   }
 
     }
   }
 

@@ -4924,7 +4937,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     }
   }
 
     }
   }
 

-

   /**
    * Method invoked by the ChangeListener on the tabbed pane, in other words
    * when a different tabbed pane is selected by the user or programmatically.
   /**
    * Method invoked by the ChangeListener on the tabbed pane, in other words
    * when a different tabbed pane is selected by the user or programmatically.

@@ -5868,6 +5880,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   }
 
   private Rectangle lastFeatureSettingsBounds = null;
   }
 
   private Rectangle lastFeatureSettingsBounds = null;

+

   @Override
   public void setFeatureSettingsGeometry(Rectangle bounds)
   {
   @Override
   public void setFeatureSettingsGeometry(Rectangle bounds)
   {

@@ -5908,8 +5921,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   {
     jalview.api.FeatureRenderer fr = null;
     if (alignPanel != null
   {
     jalview.api.FeatureRenderer fr = null;
     if (alignPanel != null

-            && (fr = alignPanel
-                    .getFeatureRenderer()) != null)
+            && (fr = alignPanel.getFeatureRenderer()) != null)

     {
       List<String> gps = fr.getGroups(visible);
       String[] _gps = gps.toArray(new String[gps.size()]);
     {
       List<String> gps = fr.getGroups(visible);
       String[] _gps = gps.toArray(new String[gps.size()]);

@@ -5941,7 +5953,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     alignPanel.getSeqPanel().selection(sel, csel, hidden, null);
   }
 
     alignPanel.getSeqPanel().selection(sel, csel, hidden, null);
   }
 

-

 }
 
 class PrintThread extends Thread
 }
 
 class PrintThread extends Thread

diff --git a/src/jalview/gui/AnnotationLabels.java b/src/jalview/gui/AnnotationLabels.java
index 27dcebf..c843f37 100755 (executable)
--- a/src/jalview/gui/AnnotationLabels.java
+++ b/src/jalview/gui/AnnotationLabels.java
@@ -20,21 +20,6 @@
  */
 package jalview.gui;
 
  */
 package jalview.gui;
 

-import jalview.analysis.AlignSeq;
-import jalview.analysis.AlignmentUtils;
-import jalview.datamodel.Alignment;
-import jalview.datamodel.AlignmentAnnotation;
-import jalview.datamodel.Annotation;
-import jalview.datamodel.HiddenColumns;
-import jalview.datamodel.Sequence;
-import jalview.datamodel.SequenceGroup;
-import jalview.datamodel.SequenceI;
-import jalview.io.FileFormat;
-import jalview.io.FormatAdapter;
-import jalview.util.Comparison;
-import jalview.util.MessageManager;
-import jalview.util.Platform;
-

 import java.awt.Color;
 import java.awt.Cursor;
 import java.awt.Dimension;
 import java.awt.Color;
 import java.awt.Cursor;
 import java.awt.Dimension;

@@ -62,6 +47,21 @@ import javax.swing.JPopupMenu;
 import javax.swing.SwingUtilities;
 import javax.swing.ToolTipManager;
 
 import javax.swing.SwingUtilities;
 import javax.swing.ToolTipManager;
 

+import jalview.analysis.AlignSeq;
+import jalview.analysis.AlignmentUtils;
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.Annotation;
+import jalview.datamodel.HiddenColumns;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+import jalview.io.FileFormat;
+import jalview.io.FormatAdapter;
+import jalview.util.Comparison;
+import jalview.util.MessageManager;
+import jalview.util.Platform;
+

 /**
  * The panel that holds the labels for alignment annotations, providing
  * tooltips, context menus, drag to reorder rows, and drag to adjust panel
 /**
  * The panel that holds the labels for alignment annotations, providing
  * tooltips, context menus, drag to reorder rows, and drag to adjust panel

@@ -981,20 +981,12 @@ public class AnnotationLabels extends JPanel
               av.getAlignment().getHiddenColumns());
     }
 
               av.getAlignment().getHiddenColumns());
     }
 

-    Desktop.jalviewClipboard = new Object[] { seqs, ds, // what is the dataset
-                                                        // of a consensus
-                                                        // sequence ? need to
-                                                        // flag
-        // sequence as special.
+    // what is the dataset of a consensus sequence? 
+    // need to flag sequence as special.
+    Desktop.getInstance().jalviewClipboard = new Object[] { seqs, ds, 

         hiddenColumns };
   }
 
         hiddenColumns };
   }
 

-  /**
-   * DOCUMENT ME!
-   * 
-   * @param g1
-   *          DOCUMENT ME!
-   */

   @Override
   public void paintComponent(Graphics g)
   {
   @Override
   public void paintComponent(Graphics g)
   {

diff --git a/src/jalview/gui/Desktop.java b/src/jalview/gui/Desktop.java
index 5df48a2..68313e1 100644 (file)
--- a/src/jalview/gui/Desktop.java
+++ b/src/jalview/gui/Desktop.java
@@ -235,19 +235,19 @@ public class Desktop extends GDesktop
             .getStructureSelectionManager(getInstance());
   }
 
             .getStructureSelectionManager(getInstance());
   }
 

-  static int openFrameCount = 0;
+  int openFrameCount = 0;

 
 

-  static final int xOffset = 30;
+  final int xOffset = 30;

 
 

-  static final int yOffset = 30;
+  final int yOffset = 30;

 
 

-  public static jalview.ws.jws1.Discoverer discoverer;
+  public jalview.ws.jws1.Discoverer discoverer;

 
 

-  public static Object[] jalviewClipboard;
+  public Object[] jalviewClipboard;

 
 

-  public static boolean internalCopy = false;
+  public boolean internalCopy = false;

 
 

-  static int fileLoadingCount = 0;
+  int fileLoadingCount = 0;

 
   class MyDesktopManager implements DesktopManager
   {
 
   class MyDesktopManager implements DesktopManager
   {

@@ -851,16 +851,21 @@ public class Desktop extends GDesktop
           final JInternalFrame frame, String title, boolean makeVisible,
           int w, int h, boolean resizable, boolean ignoreMinSize)
   {
           final JInternalFrame frame, String title, boolean makeVisible,
           int w, int h, boolean resizable, boolean ignoreMinSize)
   {

+    
+    getInstance().addFrame(frame, title, makeVisible, w, h, resizable, ignoreMinSize);
+  }
+  
+    private void addFrame(JInternalFrame frame, String title,
+          boolean makeVisible, int w, int h, boolean resizable,
+          boolean ignoreMinSize)
+  {
+      // TODO: allow callers to determine X and Y position of frame (eg. via
+      // bounds object).
+      // TODO: consider fixing method to update entries in the window submenu with
+      // the current window title

 
 

-
-
-    // TODO: allow callers to determine X and Y position of frame (eg. via
-    // bounds object).
-    // TODO: consider fixing method to update entries in the window submenu with
-    // the current window title
-
-    frame.setTitle(title);
-    if (frame.getWidth() < 1 || frame.getHeight() < 1)
+      frame.setTitle(title);
+      if (frame.getWidth() < 1 || frame.getHeight() < 1)

     {
       frame.setSize(w, h);
     }
     {
       frame.setSize(w, h);
     }

@@ -995,7 +1000,6 @@ public class Desktop extends GDesktop
    */
   private static void setKeyBindings(JInternalFrame frame)
   {
    */
   private static void setKeyBindings(JInternalFrame frame)
   {

-    @SuppressWarnings("serial")

     final Action closeAction = new AbstractAction()
     {
       @Override
     final Action closeAction = new AbstractAction()
     {
       @Override

@@ -2667,7 +2671,7 @@ public class Desktop extends GDesktop
       // todo: changesupport handlers need to be transferred
       if (discoverer == null)
       {
       // todo: changesupport handlers need to be transferred
       if (discoverer == null)
       {

-        discoverer = new jalview.ws.jws1.Discoverer();
+        discoverer = jalview.ws.jws1.Discoverer.getInstance();

         // register PCS handler for desktop.
         discoverer.addPropertyChangeListener(changeSupport);
       }
         // register PCS handler for desktop.
         discoverer.addPropertyChangeListener(changeSupport);
       }

@@ -3142,6 +3146,7 @@ public class Desktop extends GDesktop
    *          - the payload from the drop event
    * @throws Exception
    */
    *          - the payload from the drop event
    * @throws Exception
    */

+  @SuppressWarnings("unchecked")

   public static void transferFromDropTarget(List<Object> files,
           List<DataSourceType> protocols, DropTargetDropEvent evt,
           Transferable t) throws Exception
   public static void transferFromDropTarget(List<Object> files,
           List<DataSourceType> protocols, DropTargetDropEvent evt,
           Transferable t) throws Exception

@@ -3213,7 +3218,7 @@ public class Desktop extends GDesktop
     {
       // Works on Windows and MacOSX
       Cache.log.debug("Drop handled as javaFileListFlavor");
     {
       // Works on Windows and MacOSX
       Cache.log.debug("Drop handled as javaFileListFlavor");

-      for (Object file : (List) t
+      for (File file : (List<File>) t

               .getTransferData(DataFlavor.javaFileListFlavor))
       {
         files.add(file);
               .getTransferData(DataFlavor.javaFileListFlavor))
       {
         files.add(file);

diff --git a/src/jalview/urls/IdOrgSettings.java b/src/jalview/urls/IdOrgSettings.java
index 7dd1a19..cd7e98e 100644 (file)
--- a/src/jalview/urls/IdOrgSettings.java
+++ b/src/jalview/urls/IdOrgSettings.java
@@ -21,35 +21,46 @@
 
 package jalview.urls;
 
 
 package jalview.urls;
 

+import jalview.bin.ApplicationSingletonProvider;
+import jalview.bin.ApplicationSingletonProvider.ApplicationSingletonI;
+

 /**
  * Holds settings for identifiers.org e.g. url, download location
 /**
  * Holds settings for identifiers.org e.g. url, download location

- * 
- * @author $author$
- * @version $Revision$

  */
  */

-public class IdOrgSettings
+public class IdOrgSettings implements ApplicationSingletonI

 {
 {

-  private static String url;
+  private String url;

 
 

-  private static String location;
+  private String location;
+
+  private static IdOrgSettings getInstance()
+  {
+    return (IdOrgSettings) ApplicationSingletonProvider
+            .getInstance(IdOrgSettings.class);
+  }

 
   public static void setUrl(String seturl)
   {
 
   public static void setUrl(String seturl)
   {

-    url = seturl;
+    getInstance().url = seturl;

   }
 
   public static void setDownloadLocation(String setloc)
   {
   }
 
   public static void setDownloadLocation(String setloc)
   {

-    location = setloc;
+    getInstance().location = setloc;

   }
 
   public static String getUrl()
   {
   }
 
   public static String getUrl()
   {

-    return url;
+    return getInstance().url;

   }
 
   public static String getDownloadLocation()
   {
   }
 
   public static String getDownloadLocation()
   {

-    return location;
+    return getInstance().location;
+  }
+
+  private IdOrgSettings()
+  {
+    // private singleton

   }
 }
   }
 }

diff --git a/src/jalview/ws/jws1/Discoverer.java b/src/jalview/ws/jws1/Discoverer.java
index ec8c89c..6aa3f48 100644 (file)
--- a/src/jalview/ws/jws1/Discoverer.java
+++ b/src/jalview/ws/jws1/Discoverer.java
@@ -20,11 +20,15 @@
  */
 package jalview.ws.jws1;
 
  */
 package jalview.ws.jws1;
 

+import jalview.bin.ApplicationSingletonProvider;
+import jalview.bin.ApplicationSingletonProvider.ApplicationSingletonI;
+import jalview.gui.AlignmentPanel;

 import jalview.gui.JvOptionPane;
 import jalview.util.MessageManager;
 
 import java.net.URL;
 import java.util.Hashtable;
 import jalview.gui.JvOptionPane;
 import jalview.util.MessageManager;
 
 import java.net.URL;
 import java.util.Hashtable;

+import java.util.List;

 import java.util.StringTokenizer;
 import java.util.Vector;
 
 import java.util.StringTokenizer;
 import java.util.Vector;
 

@@ -34,8 +38,19 @@ import ext.vamsas.RegistryServiceSoapBindingStub;
 import ext.vamsas.ServiceHandle;
 import ext.vamsas.ServiceHandles;
 
 import ext.vamsas.ServiceHandle;
 import ext.vamsas.ServiceHandles;
 

-public class Discoverer implements Runnable
+public class Discoverer implements Runnable, ApplicationSingletonI

 {
 {

+
+  public static Discoverer getInstance()
+  {
+    return (Discoverer) ApplicationSingletonProvider.getInstance(Discoverer.class);
+  }
+
+  private Discoverer()
+  {
+    // use getInstance()
+  }
+

   ext.vamsas.IRegistry registry; // the root registry service.
 
   private java.beans.PropertyChangeSupport changeSupport = new java.beans.PropertyChangeSupport(
   ext.vamsas.IRegistry registry; // the root registry service.
 
   private java.beans.PropertyChangeSupport changeSupport = new java.beans.PropertyChangeSupport(

@@ -110,20 +125,24 @@ public class Discoverer implements Runnable
     return server;
   }
 
     return server;
   }
 

-  static private java.net.URL RootServiceURL = null;
+  private java.net.URL RootServiceURL = null;

 
 

-  static public Vector<URL> ServiceURLList = null;
+  private Vector<URL> ServiceURLList = null;

 
 

-  static private boolean reallyDiscoverServices = true;
+  public Vector<URL> getServiceURLList() {
+    return ServiceURLList;
+  }
+  
+  private boolean reallyDiscoverServices = true;

 
 

-  public static java.util.Hashtable<String, Vector<ServiceHandle>> services = null;
+  private java.util.Hashtable<String, Vector<ServiceHandle>> services = null;

   // stored by
   // abstractServiceType
   // string
 
   // stored by
   // abstractServiceType
   // string
 

-  public static java.util.Vector<ServiceHandle> serviceList = null;
+  public java.util.Vector<ServiceHandle> serviceList = null;

 
 

-  static private Vector<URL> getDiscoveryURLS()
+  private Vector<URL> getDiscoveryURLS()

   {
     Vector<URL> urls = new Vector<>();
     String RootServiceURLs = jalview.bin.Cache.getDefault("DISCOVERY_URLS",
   {
     Vector<URL> urls = new Vector<>();
     String RootServiceURLs = jalview.bin.Cache.getDefault("DISCOVERY_URLS",

@@ -176,10 +195,16 @@ public class Discoverer implements Runnable
    */
   static public void doDiscovery()
   {
    */
   static public void doDiscovery()
   {

+    getInstance().discovery();
+  }
+
+  private void discovery()
+  {

     jalview.bin.Cache.log
             .debug("(Re)-Initialising the discovery URL list.");
     try
     {
     jalview.bin.Cache.log
             .debug("(Re)-Initialising the discovery URL list.");
     try
     {

+      Discoverer d = getInstance();

       reallyDiscoverServices = jalview.bin.Cache
               .getDefault("DISCOVERY_START", false);
       if (reallyDiscoverServices)
       reallyDiscoverServices = jalview.bin.Cache
               .getDefault("DISCOVERY_START", false);
       if (reallyDiscoverServices)

@@ -284,7 +309,7 @@ public class Discoverer implements Runnable
    *          Hashtable
    * @return boolean
    */
    *          Hashtable
    * @return boolean
    */

-  static private boolean buildServiceLists(ServiceHandle[] sh,
+  private boolean buildServiceLists(ServiceHandle[] sh,

           Vector<ServiceHandle> cat,
           Hashtable<String, Vector<ServiceHandle>> sscat)
   {
           Vector<ServiceHandle> cat,
           Hashtable<String, Vector<ServiceHandle>> sscat)
   {

@@ -395,10 +420,32 @@ public class Discoverer implements Runnable
   /**
    * binding service abstract name to handler class
    */
   /**
    * binding service abstract name to handler class
    */

-  private static Hashtable<String, WS1Client> serviceClientBindings;
+  private Hashtable<String, WS1Client> serviceClientBindings;

 
   public static WS1Client getServiceClient(ServiceHandle sh)
   {
 
   public static WS1Client getServiceClient(ServiceHandle sh)
   {

+    return getInstance().getClient(sh);
+  }
+  
+  /**
+   * notes on discovery service 1. need to allow multiple discovery source urls.
+   * 2. user interface to add/control list of urls in preferences notes on
+   * wsclient discovery 1. need a classpath property with list of additional
+   * plugin directories 2. optional config to cite specific bindings between
+   * class name and Abstract service name. 3. precedence for automatic discovery
+   * by using getAbstractName for WSClient - user added plugins override default
+   * plugins ? notes on wsclient gui code for gui attachment now moved to
+   * wsclient implementation. Needs more abstraction but approach seems to work.
+   * is it possible to 'generalise' the data retrieval calls further ? current
+   * methods are very specific (gatherForMSA or gatherForSeqOrMsaSecStrPred),
+   * new methods for conservation (group or alignment), treecalc (aligned
+   * profile), seqannot (sequences selected from dataset, annotation back to
+   * dataset).
+   * 
+   */
+
+  private WS1Client getClient(ServiceHandle sh)
+  {

     if (serviceClientBindings == null)
     {
       // get a list from Config or create below
     if (serviceClientBindings == null)
     {
       // get a list from Config or create below

@@ -421,20 +468,9 @@ public class Discoverer implements Runnable
     }
     return instance;
   }
     }
     return instance;
   }

-  /**
-   * notes on discovery service 1. need to allow multiple discovery source urls.
-   * 2. user interface to add/control list of urls in preferences notes on
-   * wsclient discovery 1. need a classpath property with list of additional
-   * plugin directories 2. optional config to cite specific bindings between
-   * class name and Abstract service name. 3. precedence for automatic discovery
-   * by using getAbstractName for WSClient - user added plugins override default
-   * plugins ? notes on wsclient gui code for gui attachment now moved to
-   * wsclient implementation. Needs more abstraction but approach seems to work.
-   * is it possible to 'generalise' the data retrieval calls further ? current
-   * methods are very specific (gatherForMSA or gatherForSeqOrMsaSecStrPred),
-   * new methods for conservation (group or alignment), treecalc (aligned
-   * profile), seqannot (sequences selected from dataset, annotation back to
-   * dataset).
-   * 
-   */
+
+  public static Hashtable<String, Vector<ServiceHandle>> getServices()
+  {
+    return getInstance().services;
+  }

 }
 }

diff --git a/src/jalview/ws/jws2/Jws2Discoverer.java b/src/jalview/ws/jws2/Jws2Discoverer.java
index c3b0b30..255ef8f 100644 (file)
--- a/src/jalview/ws/jws2/Jws2Discoverer.java
+++ b/src/jalview/ws/jws2/Jws2Discoverer.java
@@ -21,6 +21,8 @@
 package jalview.ws.jws2;
 
 import jalview.bin.Cache;
 package jalview.ws.jws2;
 
 import jalview.bin.Cache;

+import jalview.bin.ApplicationSingletonProvider;
+import jalview.bin.ApplicationSingletonProvider.ApplicationSingletonI;

 import jalview.gui.AlignFrame;
 import jalview.gui.Desktop;
 import jalview.gui.JvSwingUtils;
 import jalview.gui.AlignFrame;
 import jalview.gui.Desktop;
 import jalview.gui.JvSwingUtils;

@@ -60,19 +62,9 @@ import compbio.ws.client.Services;
  * @author JimP
  * 
  */
  * @author JimP
  * 
  */

-public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
+public class Jws2Discoverer
+        implements Runnable, WSMenuEntryProviderI, ApplicationSingletonI

 {
 {

-  public static final String COMPBIO_JABAWS = "http://www.compbio.dundee.ac.uk/jabaws";
-
-  /*
-   * the .jalview_properties entry for JWS2 URLS
-   */
-  private final static String JWS2HOSTURLS = "JWS2HOSTURLS";
-
-  /*
-   * Singleton instance
-   */
-  private static Jws2Discoverer discoverer;

 
   /**
    * Returns the singleton instance of this class.
 
   /**
    * Returns the singleton instance of this class.

@@ -81,22 +73,34 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
    */
   public static Jws2Discoverer getInstance()
   {
    */
   public static Jws2Discoverer getInstance()
   {

-    if (discoverer == null)
-    {
-      discoverer = new Jws2Discoverer();
-    }
-    return discoverer;
+    return (Jws2Discoverer) ApplicationSingletonProvider
+            .getInstance(Jws2Discoverer.class);
+  }
+
+  /**
+   * Private constructor enforces use of singleton via getDiscoverer()
+   */
+  private Jws2Discoverer()
+  {
+    // use getInstance();

   }
 
   }
 

+  public static final String COMPBIO_JABAWS = "http://www.compbio.dundee.ac.uk/jabaws";
+
+  /*
+   * the .jalview_properties entry for JWS2 URLS
+   */
+  private final static String JWS2HOSTURLS = "JWS2HOSTURLS";
+

   /*
    * Override for testing only
    */
   /*
    * Override for testing only
    */

-  private static List<String> testUrls = null;
+  private List<String> testUrls = null;

 
   // preferred url has precedence over others
   private String preferredUrl;
 
 
   // preferred url has precedence over others
   private String preferredUrl;
 

-  private PropertyChangeSupport changeSupport = new PropertyChangeSupport(
+  protected PropertyChangeSupport changeSupport = new PropertyChangeSupport(

           this);
 
   private Vector<String> invalidServiceUrls = null;
           this);
 
   private Vector<String> invalidServiceUrls = null;

@@ -117,13 +121,6 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
   protected Vector<Jws2Instance> services;
 
   /**
   protected Vector<Jws2Instance> services;
 
   /**

-   * Private constructor enforces use of singleton via getDiscoverer()
-   */
-  private Jws2Discoverer()
-  {
-  }
-
-  /**

    * change listeners are notified of "services" property changes
    * 
    * @param listener
    * change listeners are notified of "services" property changes
    * 
    * @param listener

@@ -204,7 +201,7 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
     oldthread = Thread.currentThread();
     try
     {
     oldthread = Thread.currentThread();
     try
     {

-      Class foo = getClass().getClassLoader()
+      getClass().getClassLoader()

               .loadClass("compbio.ws.client.Jws2Client");
     } catch (ClassNotFoundException e)
     {
               .loadClass("compbio.ws.client.Jws2Client");
     } catch (ClassNotFoundException e)
     {

@@ -597,36 +594,36 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
    */
   public static void main(String[] args)
   {
    */
   public static void main(String[] args)
   {

+    Jws2Discoverer instance = getInstance();

     if (args.length > 0)
     {
     if (args.length > 0)
     {

-      testUrls = new ArrayList<>();
+      instance.testUrls = new ArrayList<>();

       for (String url : args)
       {
       for (String url : args)
       {

-        testUrls.add(url);
+        instance.testUrls.add(url);

       }
     }
       }
     }

-    Thread runner = getInstance()
-            .startDiscoverer(new PropertyChangeListener()
-            {
+    Thread runner = instance.startDiscoverer(new PropertyChangeListener()
+    {

 
 

-              @Override
-              public void propertyChange(PropertyChangeEvent evt)
-              {
-                if (getInstance().services != null)
-                {
-                  System.out.println("Changesupport: There are now "
-                          + getInstance().services.size() + " services");
-                  int i = 1;
-                  for (Jws2Instance instance : getInstance().services)
-                  {
-                    System.out.println("Service " + i++ + " "
-                            + instance.getClass() + "@" + instance.getHost()
-                            + ": " + instance.getActionText());
-                  }
+      @Override
+      public void propertyChange(PropertyChangeEvent evt)
+      {
+        if (getInstance().services != null)
+        {
+          System.out.println("Changesupport: There are now "
+                  + getInstance().services.size() + " services");
+          int i = 1;
+          for (Jws2Instance instance : getInstance().services)
+          {
+            System.out.println("Service " + i++ + " " + instance.getClass()
+                    + "@" + instance.getHost() + ": "
+                    + instance.getActionText());
+          }

 
 

-                }
-              }
-            });
+        }
+      }
+    });

     while (runner.isAlive())
     {
       try
     while (runner.isAlive())
     {
       try

@@ -644,7 +641,6 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
     }
   }
 
     }
   }
 

-

   public boolean hasServices()
   {
     return !running && services != null && services.size() > 0;
   public boolean hasServices()
   {
     return !running && services != null && services.size() > 0;

diff --git a/src/jalview/ws/jws2/jabaws2/Jws2InstanceFactory.java b/src/jalview/ws/jws2/jabaws2/Jws2InstanceFactory.java
index 623b8de..1983ff5 100644 (file)
--- a/src/jalview/ws/jws2/jabaws2/Jws2InstanceFactory.java
+++ b/src/jalview/ws/jws2/jabaws2/Jws2InstanceFactory.java
@@ -20,6 +20,8 @@
  */
 package jalview.ws.jws2.jabaws2;
 
  */
 package jalview.ws.jws2.jabaws2;
 

+import jalview.bin.ApplicationSingletonProvider;
+import jalview.bin.ApplicationSingletonProvider.ApplicationSingletonI;

 import jalview.ws.jws2.AAConClient;
 import jalview.ws.jws2.RNAalifoldClient;
 import jalview.ws.uimodel.AlignAnalysisUIText;
 import jalview.ws.jws2.AAConClient;
 import jalview.ws.jws2.RNAalifoldClient;
 import jalview.ws.uimodel.AlignAnalysisUIText;

@@ -29,11 +31,23 @@ import java.util.HashSet;
 
 import compbio.data.msa.JABAService;
 
 
 import compbio.data.msa.JABAService;
 

-public class Jws2InstanceFactory
+public class Jws2InstanceFactory implements ApplicationSingletonI

 {
 {

-  private static HashMap<String, AlignAnalysisUIText> aaConGUI;

 
 

-  private static HashSet<String> ignoreGUI;
+  private Jws2InstanceFactory()
+  {
+    // private singleton
+  }
+
+  private static Jws2InstanceFactory getInstance()
+  {
+    return (Jws2InstanceFactory) ApplicationSingletonProvider
+            .getInstance(Jws2InstanceFactory.class);
+  }
+
+  private HashMap<String, AlignAnalysisUIText> aaConGUI;
+
+  private HashSet<String> ignoreGUI;

 
   private static String category_rewrite(String cat_name)
   {
 
   private static String category_rewrite(String cat_name)
   {

@@ -42,17 +56,17 @@ public class Jws2InstanceFactory
             : cat_name;
   }
 
             : cat_name;
   }
 

-  private static void init()
+  private void init()

   {
     if (aaConGUI == null)
     {
   {
     if (aaConGUI == null)
     {

-      aaConGUI = new HashMap<String, AlignAnalysisUIText>();
+      aaConGUI = new HashMap<>();

       aaConGUI.put(compbio.ws.client.Services.AAConWS.toString(),
               AAConClient.getAlignAnalysisUITest());
       aaConGUI.put(compbio.ws.client.Services.RNAalifoldWS.toString(),
               RNAalifoldClient.getAlignAnalysisUITest());
       // ignore list for JABAWS services not supported in jalview ...
       aaConGUI.put(compbio.ws.client.Services.AAConWS.toString(),
               AAConClient.getAlignAnalysisUITest());
       aaConGUI.put(compbio.ws.client.Services.RNAalifoldWS.toString(),
               RNAalifoldClient.getAlignAnalysisUITest());
       // ignore list for JABAWS services not supported in jalview ...

-      ignoreGUI = new HashSet<String>();
+      ignoreGUI = new HashSet<>();

     }
   }
 
     }
   }
 

@@ -65,8 +79,8 @@ public class Jws2InstanceFactory
    */
   public static boolean ignoreService(String serviceType)
   {
    */
   public static boolean ignoreService(String serviceType)
   {

-    init();
-    return (ignoreGUI.contains(serviceType.toString()));
+    getInstance().init();
+    return (getInstance().ignoreGUI.contains(serviceType.toString()));

   }
 
   /**
   }
 
   /**

@@ -84,10 +98,10 @@ public class Jws2InstanceFactory
           String serviceType, String name, String description,
           JABAService service)
   {
           String serviceType, String name, String description,
           JABAService service)
   {

-    init();
+    getInstance().init();

     Jws2Instance svc = new Jws2Instance(jwsservers, serviceType,
             category_rewrite(name), description, service);
     Jws2Instance svc = new Jws2Instance(jwsservers, serviceType,
             category_rewrite(name), description, service);

-    svc.aaui = aaConGUI.get(serviceType.toString());
+    svc.aaui = getInstance().aaConGUI.get(serviceType.toString());

     return svc;
   }
 
     return svc;
   }
 

diff --git a/src/jalview/ws/rest/RestClient.java b/src/jalview/ws/rest/RestClient.java
index 08f137d..eea6474 100644 (file)
--- a/src/jalview/ws/rest/RestClient.java
+++ b/src/jalview/ws/rest/RestClient.java
@@ -20,6 +20,8 @@
  */
 package jalview.ws.rest;
 
  */
 package jalview.ws.rest;
 

+import jalview.bin.ApplicationSingletonProvider;
+import jalview.bin.ApplicationSingletonProvider.ApplicationSingletonI;

 import jalview.bin.Cache;
 import jalview.datamodel.AlignmentView;
 import jalview.gui.AlignFrame;
 import jalview.bin.Cache;
 import jalview.datamodel.AlignmentView;
 import jalview.gui.AlignFrame;

@@ -49,8 +51,20 @@ import javax.swing.event.MenuListener;
  * 
  */
 public class RestClient extends WSClient
  * 
  */
 public class RestClient extends WSClient

-        implements WSClientI, WSMenuEntryProviderI
+implements WSClientI, WSMenuEntryProviderI, ApplicationSingletonI

 {
 {

+
+private static RestClient getInstance()
+{
+return (RestClient) ApplicationSingletonProvider.getInstance(RestClient.class);
+}
+
+public static final String RSBS_SERVICES = "RSBS_SERVICES";
+
+
+  protected Vector<String> services = null;
+
+

   RestServiceDescription service;
 
   public RestClient(RestServiceDescription rsd)
   RestServiceDescription service;
 
   public RestClient(RestServiceDescription rsd)

@@ -399,12 +413,13 @@ public class RestClient extends WSClient
     return true;
   }
 
     return true;
   }
 

-  protected static Vector<String> services = null;
-
-  public static final String RSBS_SERVICES = "RSBS_SERVICES";
-

   public static RestClient[] getRestClients()
   {
   public static RestClient[] getRestClients()
   {

+    return getInstance().getClients();
+  }
+    
+  private RestClient[] getClients()
+  {

     if (services == null)
     {
       services = new Vector<String>();
     if (services == null)
     {
       services = new Vector<String>();

@@ -458,10 +473,11 @@ public class RestClient extends WSClient
   {
     if (rsbsUrls != null)
     {
   {
     if (rsbsUrls != null)
     {

+      

       // TODO: consider validating services ?
       // TODO: consider validating services ?

-      services = new Vector<String>(rsbsUrls);
+      getInstance().services = new Vector<String>(rsbsUrls);

       StringBuffer sprop = new StringBuffer();
       StringBuffer sprop = new StringBuffer();

-      for (String s : services)
+      for (String s : getInstance().services)

       {
         sprop.append(s);
       }
       {
         sprop.append(s);
       }

diff --git a/src/jalview/ws/sifts/SiftsSettings.java b/src/jalview/ws/sifts/SiftsSettings.java
index 5e2c526..a042bb9 100644 (file)
--- a/src/jalview/ws/sifts/SiftsSettings.java
+++ b/src/jalview/ws/sifts/SiftsSettings.java
@@ -20,59 +20,78 @@
  */
 package jalview.ws.sifts;
 
  */
 package jalview.ws.sifts;
 

+import jalview.bin.ApplicationSingletonProvider;
+import jalview.bin.ApplicationSingletonProvider.ApplicationSingletonI;
+

 import java.util.Objects;
 
 import java.util.Objects;
 

-public class SiftsSettings
+public class SiftsSettings implements ApplicationSingletonI

 {
 {

-  private static boolean mapWithSifts = false;
+  /**
+   * Constructor
+   * 
+   * @return
+   */
+  private static SiftsSettings getInstance()
+  {
+    return (SiftsSettings) ApplicationSingletonProvider
+            .getInstance(SiftsSettings.class);
+  }
+
+  private SiftsSettings()
+  {
+    // singleton; use getInstance()
+  }
+
+  private boolean mapWithSifts = false;

 
 

-  private static String siftDownloadDirectory;
+  private String siftDownloadDirectory;

 
 

-  private static int cacheThresholdInDays;
+  private int cacheThresholdInDays;

 
 

-  private static int failSafePIDThreshold;
+  private int failSafePIDThreshold;

 
   public static boolean isMapWithSifts()
   {
 
   public static boolean isMapWithSifts()
   {

-    return mapWithSifts;
+    return getInstance().mapWithSifts;

   }
 
   public static void setMapWithSifts(boolean mapWithSifts)
   {
   }
 
   public static void setMapWithSifts(boolean mapWithSifts)
   {

-    SiftsSettings.mapWithSifts = mapWithSifts;
+    getInstance().mapWithSifts = mapWithSifts;

   }
 
   public static String getSiftDownloadDirectory()
   {
   }
 
   public static String getSiftDownloadDirectory()
   {

-    return siftDownloadDirectory;
+    return getInstance().siftDownloadDirectory;

   }
 
   public static void setSiftDownloadDirectory(String siftDownloadDirectory)
   {
   }
 
   public static void setSiftDownloadDirectory(String siftDownloadDirectory)
   {

-    SiftsSettings.siftDownloadDirectory = siftDownloadDirectory;
+    getInstance().siftDownloadDirectory = siftDownloadDirectory;

   }
 
   public static int getCacheThresholdInDays()
   {
   }
 
   public static int getCacheThresholdInDays()
   {

-    return cacheThresholdInDays;
+    return getInstance().cacheThresholdInDays;

   }
 
   public static void setCacheThresholdInDays(String cacheThresholdInDays)
   {
     Objects.requireNonNull(cacheThresholdInDays);
   }
 
   public static void setCacheThresholdInDays(String cacheThresholdInDays)
   {
     Objects.requireNonNull(cacheThresholdInDays);

-    SiftsSettings.cacheThresholdInDays = Integer
+    getInstance().cacheThresholdInDays = Integer

             .valueOf(cacheThresholdInDays);
   }
 
   public static int getFailSafePIDThreshold()
   {
             .valueOf(cacheThresholdInDays);
   }
 
   public static int getFailSafePIDThreshold()
   {

-    return failSafePIDThreshold;
+    return getInstance().failSafePIDThreshold;

   }
 
   public static void setFailSafePIDThreshold(String failSafePIDThreshold)
   {
     Objects.requireNonNull(failSafePIDThreshold);
   }
 
   public static void setFailSafePIDThreshold(String failSafePIDThreshold)
   {
     Objects.requireNonNull(failSafePIDThreshold);

-    SiftsSettings.failSafePIDThreshold = Integer
+    getInstance().failSafePIDThreshold = Integer

             .valueOf(failSafePIDThreshold);
   }
 }
             .valueOf(failSafePIDThreshold);
   }
 }

diff --git a/test/jalview/ws/sifts/SiftsClientTest.java b/test/jalview/ws/sifts/SiftsClientTest.java
index 6122d6d..f661bde 100644 (file)
--- a/test/jalview/ws/sifts/SiftsClientTest.java
+++ b/test/jalview/ws/sifts/SiftsClientTest.java
@@ -189,7 +189,6 @@ public class SiftsClientTest
     Cache.loadProperties("test/jalview/io/testProps.jvprops");
     // SIFTs entries are updated weekly - so use saved SIFTs file to enforce
     // test reproducibility
     Cache.loadProperties("test/jalview/io/testProps.jvprops");
     // SIFTs entries are updated weekly - so use saved SIFTs file to enforce
     // test reproducibility

-    new SiftsSettings();

     SiftsSettings.setSiftDownloadDirectory(jalview.bin.Cache.getDefault(
             "sifts_download_dir", DEFAULT_SIFTS_DOWNLOAD_DIR));
     SiftsSettings.setMapWithSifts(true);
     SiftsSettings.setSiftDownloadDirectory(jalview.bin.Cache.getDefault(
             "sifts_download_dir", DEFAULT_SIFTS_DOWNLOAD_DIR));
     SiftsSettings.setMapWithSifts(true);