X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=7b1dfeb10c4a81e1b87b0a7390eeb5a3ac5f81b4;hb=c858b2b71816055429bd496a7158973ad8acec57;hp=6b8eb09a357c744213c62d7a32bed349a2c75d0a;hpb=24caafeb32f8531894aeead29c1932a57348c1d9;p=jalview.git

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 6b8eb09..7b1dfeb 100755
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -64,7 +64,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
 
   String fileName = null;
 
-  private int treeCount = 0;
 
   /**
    * Creates a new AlignFrame object.
@@ -311,7 +310,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
               SequenceGroup sg = viewport.getSelectionGroup();
               if (toggleSeqs)
               {
-                if (sg != null && sg.getSize(false) != viewport.alignment.getHeight())
+                if (sg != null && sg.getSize() != viewport.alignment.getHeight())
                 {
                   hideSelSequences_actionPerformed(null);
                   hide = true;
@@ -381,7 +380,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
 
       expandViews.setEnabled(true);
       gatherViews.setEnabled(true);
-      tabbedPane.addTab(ap.av.viewName==null?"Original":ap.av.viewName, ap);
+      tabbedPane.addTab(ap.av.viewName, ap);
 
       ap.setVisible(false);
     }
@@ -401,7 +400,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
     gatherViews.setEnabled(true);
     tabbedPane.setVisible(true);
     AlignmentPanel first = (AlignmentPanel) alignPanels.firstElement();
-    tabbedPane.addTab(first.av.viewName==null?"Original":first.av.viewName,first);
+    tabbedPane.addTab(first.av.viewName,first);
     this.getContentPane().add(tabbedPane, BorderLayout.CENTER);
   }
 
@@ -593,7 +592,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
           dset.deleteSequence(0);
         }
 
-        firePropertyChange("Alignment", null, null);
+        firePropertyChange("Alignment", null, viewport.alignment.getSequences());
 
         updateEditMenuBar();
       }
@@ -619,7 +618,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
 
   public void save_actionPerformed(ActionEvent e)
   {
-    if(fileName==null || currentFileFormat==null)
+    if(fileName==null
+       || currentFileFormat==null
+       || fileName.startsWith("http")
+        )
       saveAs_actionPerformed(null);
     else
       saveAlignment(fileName, currentFileFormat);
@@ -674,6 +676,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
 
   public boolean saveAlignment(String file, String format)
   {
+    boolean success = true;
+
     if (format.equalsIgnoreCase("Jalview"))
     {
       String shortName = title;
@@ -684,15 +688,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
             java.io.File.separatorChar) + 1);
       }
 
-      new Jalview2XML().SaveAlignment(this, file, shortName);
+      success = new Jalview2XML().SaveAlignment(this, file, shortName);
 
       statusBar.setText("Successfully saved to file: "
                           +fileName+" in "
                           +format +" format.");
 
-
-      // USE Jalview2XML to save this file
-      return true;
     }
     else
     {
@@ -718,28 +719,37 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
 
       if (output == null)
       {
-        return false;
-      }
-
-      try
-      {
-        java.io.PrintWriter out = new java.io.PrintWriter(
-            new java.io.FileWriter(file));
-
-        out.print(output);
-        out.close();
-        this.setTitle(file);
-        statusBar.setText("Successfully saved to file: "
-                          +fileName+" in "
-                          +format +" format.");
-        return true;
+        success = false;
       }
-      catch (Exception ex)
+      else
       {
-        ex.printStackTrace();
+        try
+        {
+          java.io.PrintWriter out = new java.io.PrintWriter(
+              new java.io.FileWriter(file));
+
+          out.print(output);
+          out.close();
+          this.setTitle(file);
+          statusBar.setText("Successfully saved to file: "
+                            + fileName + " in "
+                            + format + " format.");
+        }
+        catch (Exception ex)
+        {
+          success = false;
+          ex.printStackTrace();
+        }
       }
     }
-    return false;
+
+    if (!success)
+      JOptionPane.showInternalMessageDialog(
+          this, "Couldn't save file: " + fileName,
+          "Error Saving File",
+          JOptionPane.WARNING_MESSAGE);
+
+    return success;
   }
 
   /**
@@ -815,6 +825,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
     alignPanel.makeEPS(f);
   }
 
+
+  public void pageSetup_actionPerformed(ActionEvent e)
+  {
+    PrinterJob printJob = PrinterJob.getPrinterJob();
+    PrintThread.pf = printJob.pageDialog(printJob.defaultPage());
+  }
+
   /**
    * DOCUMENT ME!
    *
@@ -823,7 +840,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
   public void printMenuItem_actionPerformed(ActionEvent e)
   {
     //Putting in a thread avoids Swing painting problems
-    PrintThread thread = new PrintThread();
+    PrintThread thread = new PrintThread(alignPanel);
     thread.start();
   }
 
@@ -890,13 +907,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
         {
           int index = tabbedPane.getSelectedIndex();
 
-          tabbedPane.removeTabAt(index);
           alignPanels.removeElement(alignPanel);
           PaintRefresher.RemoveComponent(alignPanel.seqPanel.seqCanvas);
           PaintRefresher.RemoveComponent(alignPanel.idPanel.idCanvas);
           PaintRefresher.RemoveComponent(alignPanel);
           alignPanel = null;
           viewport = null;
+
+          tabbedPane.removeTabAt(index);
           tabbedPane.validate();
 
           if(index==tabbedPane.getTabCount())
@@ -974,10 +992,15 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
     command.undoCommand();
 
     AlignViewport originalSource = getOriginatingSource(command);
-
-    originalSource.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null;
     updateEditMenuBar();
-    originalSource.firePropertyChange("alignment", null,null);
+
+    if(originalSource!=null)
+    {
+      originalSource.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null;
+      originalSource.firePropertyChange("alignment",
+                                        null,
+                                        originalSource.alignment.getSequences());
+    }
   }
 
   /**
@@ -987,29 +1010,39 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
    */
   protected void redoMenuItem_actionPerformed(ActionEvent e)
   {
+    if(viewport.redoList.size()<1)
+      return;
+
     CommandI command = (CommandI) viewport.redoList.pop();
     viewport.historyList.push(command);
     command.doCommand();
 
     AlignViewport originalSource = getOriginatingSource(command);
-    originalSource.hasHiddenColumns = viewport.colSel.getHiddenColumns()!=null;
-
     updateEditMenuBar();
-    originalSource.firePropertyChange("alignment", null, null);
+
+    if(originalSource!=null)
+    {
+      originalSource.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null;
+      originalSource.firePropertyChange("alignment",
+                                        null,
+                                        originalSource.alignment.getSequences());
+    }
   }
 
   AlignViewport getOriginatingSource(CommandI command)
   {
-    AlignViewport originalSource = viewport;
+    AlignViewport originalSource = null;
     //For sequence removal and addition, we need to fire
    //the property change event FROM the viewport where the
    //original alignment was altered
+    AlignmentI al=null;
     if (command instanceof EditCommand)
     {
       EditCommand editCommand = (EditCommand) command;
-      AlignmentI al = editCommand.getAlignment();
+      al = editCommand.getAlignment();
       Vector comps = (Vector) PaintRefresher.components
           .get(viewport.getSequenceSetId());
+
       for (int i = 0; i < comps.size(); i++)
       {
         if (comps.elementAt(i) instanceof AlignmentPanel)
@@ -1022,6 +1055,17 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
         }
       }
     }
+
+    if (originalSource == null)
+    {
+      //The original view is closed, we must validate
+      //the current view against the closed view first
+      if (al != null)
+        PaintRefresher.validateSequences(al, viewport.alignment);
+
+      originalSource = viewport;
+    }
+
     return originalSource;
   }
 
@@ -1045,14 +1089,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
       {
         SequenceI seq = viewport.alignment.getSequenceAt(i);
 
-        if (!sg.getSequences(false).contains(seq))
+        if (!sg.getSequences(null).contains(seq))
         {
           continue;
         }
 
         SequenceI temp = viewport.alignment.getSequenceAt(i - 1);
 
-        if (sg.getSequences(false).contains(temp))
+        if (sg.getSequences(null).contains(temp))
         {
           continue;
         }
@@ -1067,14 +1111,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
       {
         SequenceI seq = viewport.alignment.getSequenceAt(i);
 
-        if (!sg.getSequences(false).contains(seq))
+        if (!sg.getSequences(null).contains(seq))
         {
           continue;
         }
 
         SequenceI temp = viewport.alignment.getSequenceAt(i + 1);
 
-        if (sg.getSequences(false).contains(temp))
+        if (sg.getSequences(null).contains(temp))
         {
           continue;
         }
@@ -1119,6 +1163,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
 
     try
     {
+      jalview.gui.Desktop.internalCopy = true;
       //Its really worth setting the clipboard contents
       //to empty before setting the large StringSelection!!
       Toolkit.getDefaultToolkit().getSystemClipboard()
@@ -1246,7 +1291,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
      }
      else
      {
-       sequences = new FormatAdapter().readFile(str, "Paste", format);
+       sequences = new FormatAdapter().readFile(str, "Paste", format).getSequencesArray();
      }
 
      AlignmentI alignment = null;
@@ -1398,7 +1443,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
 
     Vector seqs = new Vector();
     SequenceI seq;
-    for (int i = 0; i < sg.getSize(false); i++)
+    for (int i = 0; i < sg.getSize(); i++)
     {
       seq = sg.getSequenceAt(i);
       seqs.addElement(seq);
@@ -1406,7 +1451,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
 
 
    // If the cut affects all sequences, remove highlighted columns
-   if (sg.getSize(false) == viewport.alignment.getHeight())
+   if (sg.getSize() == viewport.alignment.getHeight())
    {
      viewport.getColumnSelection().removeElements(sg.getStartRes(),
          sg.getEndRes() + 1);
@@ -1455,7 +1500,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
   protected void deleteGroups_actionPerformed(ActionEvent e)
   {
     viewport.alignment.deleteAllGroups();
-    viewport.sequenceColours.clear();
+    viewport.sequenceColours = null;
     viewport.setSelectionGroup(null);
     PaintRefresher.Refresh(this, viewport.getSequenceSetId());
     alignPanel.repaint();
@@ -1525,6 +1570,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
       sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
     }
 
+    alignPanel.repaint();
+
     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
   }
 
@@ -1569,7 +1616,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
 
       SequenceI [] seqs;
       if(viewport.getSelectionGroup()!=null)
-        seqs = viewport.getSelectionGroup().getSequencesAsArray(true);
+        seqs = viewport.getSelectionGroup().getSequencesAsArray(viewport.hiddenRepSequences);
       else
         seqs = viewport.alignment.getSequencesArray();
 
@@ -1632,7 +1679,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
     SequenceI[] seqs;
     if (viewport.getSelectionGroup() != null)
     {
-      seqs = viewport.getSelectionGroup().getSequencesAsArray(true);
+      seqs = viewport.getSelectionGroup().getSequencesAsArray(viewport.hiddenRepSequences);
       start = viewport.getSelectionGroup().getStartRes();
       end = viewport.getSelectionGroup().getEndRes();
     }
@@ -1644,7 +1691,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
         new RemoveGapColCommand("Remove Gapped Columns",
                                 seqs,
                                 start, end,
-                                viewport.getGapCharacter());
+                                viewport.alignment);
 
     addHistoryItem(removeGapCols);
 
@@ -1676,7 +1723,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
     SequenceI[] seqs;
     if (viewport.getSelectionGroup() != null)
     {
-      seqs = viewport.getSelectionGroup().getSequencesAsArray(true);
+      seqs = viewport.getSelectionGroup().getSequencesAsArray(viewport.hiddenRepSequences);
       start = viewport.getSelectionGroup().getStartRes();
       end = viewport.getSelectionGroup().getEndRes();
     }
@@ -1689,9 +1736,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
     int startRes = seq.findPosition(viewport.startRes);
 
     addHistoryItem(new RemoveGapsCommand("Remove Gaps",
-                                           seqs,
-                                           start, end,
-                     viewport.getGapCharacter()));
+                                         seqs,
+                                         start, end,
+                                         viewport.alignment));
 
     viewport.setStartRes(seq.findIndex(startRes)-1);
 
@@ -1729,12 +1776,32 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
         new Jalview2XML().copyAlignPanel(alignPanel, true);
 
     if (viewport.viewName == null)
-      viewport.viewName = "View 1";
+      viewport.viewName = "Original";
 
     newap.av.historyList = viewport.historyList;
     newap.av.redoList = viewport.redoList;
-    newap.av.viewName = "View " +
-        (Desktop.getViewCount(viewport.getSequenceSetId()) + 1);
+
+    int index = Desktop.getViewCount(viewport.getSequenceSetId());
+    String newViewName = "View " +index;
+
+    Vector comps = (Vector)PaintRefresher.components.get(viewport.getSequenceSetId());
+    Vector existingNames = new Vector();
+    for(int i=0; i<comps.size(); i++)
+    {
+      if(comps.elementAt(i) instanceof AlignmentPanel)
+      {
+        AlignmentPanel ap = (AlignmentPanel)comps.elementAt(i);
+        if(!existingNames.contains(ap.av.viewName))
+          existingNames.addElement(ap.av.viewName);
+      }
+    }
+
+    while(existingNames.contains(newViewName))
+    {
+      newViewName = "View "+ (++index);
+    }
+
+    newap.av.viewName = newViewName;
 
     addAlignmentPanel(newap, false);
 
@@ -2171,7 +2238,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
         if (cs instanceof ClustalxColourScheme)
         {
           sg.cs = new ClustalxColourScheme(
-              sg.getSequences(true), sg.getWidth());
+              sg.getSequences(viewport.hiddenRepSequences), sg.getWidth());
         }
         else if (cs instanceof UserColourScheme)
         {
@@ -2196,7 +2263,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
                 viewport.getIgnoreGapsConsensus());
 
          sg.cs.setConsensus(AAFrequency.calculate(
-             sg.getSequences(true), sg.getStartRes(),
+             sg.getSequences(viewport.hiddenRepSequences), sg.getStartRes(),
              sg.getEndRes()+1));
        }
         else
@@ -2207,7 +2274,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
         {
           Conservation c = new Conservation("Group",
                                             ResidueProperties.propHash, 3,
-                                            sg.getSequences(true),
+                                            sg.getSequences(viewport.hiddenRepSequences),
                                             sg.getStartRes(),
                                             sg.getEndRes()+1);
           c.calculate();
@@ -2459,7 +2526,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
   public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
   {
     if ( (viewport.getSelectionGroup() == null) ||
-        (viewport.getSelectionGroup().getSize(false) < 2))
+        (viewport.getSelectionGroup().getSize() < 2))
     {
       JOptionPane.showInternalMessageDialog(this,
                                             "You must select at least 2 sequences.",
@@ -2482,8 +2549,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
   public void PCAMenuItem_actionPerformed(ActionEvent e)
   {
     if ( ( (viewport.getSelectionGroup() != null) &&
-          (viewport.getSelectionGroup().getSize(false) < 4) &&
-          (viewport.getSelectionGroup().getSize(false) > 0)) ||
+          (viewport.getSelectionGroup().getSize() < 4) &&
+          (viewport.getSelectionGroup().getSize() > 0)) ||
         (viewport.getAlignment().getHeight() < 4))
     {
       JOptionPane.showInternalMessageDialog(this,
@@ -2495,7 +2562,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
       return;
     }
 
-     new PCAPanel(viewport);
+     new PCAPanel(alignPanel);
   }
 
 
@@ -2563,7 +2630,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
     TreePanel tp;
 
     if (viewport.getSelectionGroup() != null) {
-      if (viewport.getSelectionGroup().getSize(false) < 3) {
+      if (viewport.getSelectionGroup().getSize() < 3) {
         JOptionPane.showMessageDialog(Desktop.desktop,
                                       "You need to have more than two sequences selected to build a tree!",
                                       "Not enough sequences",
@@ -2575,9 +2642,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
       SequenceGroup sg = viewport.getSelectionGroup();
 
       /* Decide if the selection is a column region */
-      while (s < sg.getSize(false))
+      while (s < sg.getSize())
       {
-        if ( ( (SequenceI) sg.getSequences(false).elementAt(s++)).getLength() <
+        if ( ( (SequenceI) sg.getSequences(null).elementAt(s++)).getLength() <
             sg.getEndRes())
         {
           JOptionPane.showMessageDialog(Desktop.desktop,
@@ -2615,9 +2682,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
       tp = new TreePanel(alignPanel, type, pwType);
     }
 
-    addTreeMenuItem(tp, title);
+    title += " from ";
+
+    if(viewport.viewName!=null)
+      title+= viewport.viewName+" of ";
 
-    Desktop.addInternalFrame(tp, title + " from " + this.title, 600, 500);
+    title += this.title;
+
+    Desktop.addInternalFrame(tp, title, 600, 500);
   }
 
   /**
@@ -2655,51 +2727,53 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
    * @param treePanel Displayed tree window.
    * @param title SortBy menu item title.
    */
-  void addTreeMenuItem(final TreePanel treePanel, String title)
+  public void buildTreeMenu()
   {
-    final JMenuItem item = new JMenuItem(title);
-
-    treeCount++;
+    sortByTreeMenu.removeAll();
 
-    if (treeCount == 1)
+    Vector comps = (Vector)PaintRefresher.components.get(viewport.getSequenceSetId());
+    Vector treePanels = new Vector();
+    int i, iSize = comps.size();
+    for(i=0; i<iSize; i++)
     {
-      sort.add(sortByTreeMenu);
-    }
-
-    sortByTreeMenu.add(item);
-    item.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
+      if(comps.elementAt(i) instanceof TreePanel)
       {
-        SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
-        AlignmentSorter.sortByTree(viewport.getAlignment(),
-                                   treePanel.getTree());
+        treePanels.add(comps.elementAt(i));
+      }
+    }
 
-        addHistoryItem(new OrderCommand("Tree Sort",
-                                        oldOrder,
-                                        viewport.alignment));
+    iSize = treePanels.size();
 
+    if(iSize<1)
+    {
+      sortByTreeMenu.setVisible(false);
+      return;
+    }
 
-        alignPanel.repaint();
-      }
-    });
+    sortByTreeMenu.setVisible(true);
 
-    treePanel.addInternalFrameListener(new javax.swing.event.
-                                       InternalFrameAdapter()
+    for(i=0; i<treePanels.size(); i++)
     {
-      public void internalFrameClosed(
-          javax.swing.event.InternalFrameEvent evt)
+      TreePanel tp = (TreePanel)treePanels.elementAt(i);
+      final JMenuItem item = new JMenuItem(tp.getTitle());
+      final NJTree tree = ((TreePanel)treePanels.elementAt(i)).getTree();
+      item.addActionListener(new java.awt.event.ActionListener()
       {
-        treeCount--;
-        sortByTreeMenu.remove(item);
-
-        if (treeCount == 0)
+        public void actionPerformed(ActionEvent e)
         {
-          sort.remove(sortByTreeMenu);
+          SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
+          AlignmentSorter.sortByTree(viewport.getAlignment(), tree);
+
+          addHistoryItem(new OrderCommand("Tree Sort",
+                                          oldOrder,
+                                          viewport.alignment));
+
+          alignPanel.repaint();
         }
-      }
-      ;
-    });
+      });
+
+      sortByTreeMenu.add(item);
+    }
   }
 
   /**
@@ -2713,7 +2787,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
     AlignmentView msa = null;
 
     if ( (viewport.getSelectionGroup() != null) &&
-        (viewport.getSelectionGroup().getSize(false) > 1))
+        (viewport.getSelectionGroup().getSize() > 1))
     {
       // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to some common interface!
       /*SequenceGroup seqs = viewport.getSelectionGroup();
@@ -2755,7 +2829,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
    AlignmentView seqs = null;
 
     if ( (viewport.getSelectionGroup() != null) &&
-        (viewport.getSelectionGroup().getSize(false) > 0))
+        (viewport.getSelectionGroup().getSize() > 0))
     {
       seqs = viewport.getAlignmentView(true);
     }
@@ -2855,7 +2929,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
 
 
         Desktop.addInternalFrame(tp, title, w, h);
-        addTreeMenuItem(tp, title);
       }
     }
     catch (Exception ex)
@@ -2866,28 +2939,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
     return tp;
   }
 
-  class PrintThread
-      extends Thread
-  {
-    public void run()
-    {
-      PrinterJob printJob = PrinterJob.getPrinterJob();
-      PageFormat pf = printJob.pageDialog(printJob.defaultPage());
-      printJob.setPrintable(alignPanel, pf);
-
-      if (printJob.printDialog())
-      {
-        try
-        {
-          printJob.print();
-        }
-        catch (Exception PrintException)
-        {
-          PrintException.printStackTrace();
-        }
-      }
-    }
-  }
 
   /**
    * Generates menu items and listener event actions for web service clients
@@ -3222,7 +3273,7 @@ public void drop(DropTargetDropEvent evt)
       }
 
       boolean isAnnotation = new AnnotationFile().readAnnotationFile(viewport.
-          alignment, file);
+          alignment, file, protocol);
 
       if (!isAnnotation)
       {
@@ -3290,3 +3341,34 @@ public void drop(DropTargetDropEvent evt)
     return viewport;
   }
 }
+
+class PrintThread extends Thread
+{
+  AlignmentPanel ap;
+  public PrintThread(AlignmentPanel ap)
+  {
+   this.ap = ap;
+  }
+  static PageFormat pf;
+  public void run()
+  {
+    PrinterJob printJob = PrinterJob.getPrinterJob();
+
+    if (pf != null)
+      printJob.setPrintable(ap, pf);
+    else
+      printJob.setPrintable(ap);
+
+    if (printJob.printDialog())
+    {
+      try
+      {
+        printJob.print();
+      }
+      catch (Exception PrintException)
+      {
+        PrintException.printStackTrace();
+      }
+    }
+  }
+}