X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=bb722a50c87356fff370a471cd05f9b59bfabec7;hb=0a1d49ccc421184b23bcb45cee901f5313913aa1;hp=9e0bae63f95e8d4ed07c042303b78ee351589598;hpb=8ac358f8762f9a632d5dc70aa32df57ca0755244;p=jalview.git

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 9e0bae6..bb722a5 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.
@@ -159,7 +158,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
 
   void addKeyListener()
   {
-      final AlignFrame af = this;
       addKeyListener(new KeyAdapter()
       {
         public void keyPressed(KeyEvent evt)
@@ -173,17 +171,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
 
           switch (evt.getKeyCode())
           {
-            case KeyEvent.VK_G:
-              Desktop.instance.gatherViews(af);
-              break;
-
-            case KeyEvent.VK_X:
-              if (!evt.isControlDown())
-              {
-                Desktop.instance.explodeViews(af);
-              }
-              break;
-
 
             case 27: // escape key
               deselectAllSequenceMenuItem_actionPerformed(null);
@@ -374,6 +361,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
 
     alignPanels.addElement(ap);
 
+    PaintRefresher.Register(ap, ap.av.getSequenceSetId());
+
     int aSize = alignPanels.size();
 
     tabbedPane.setVisible(aSize>1 || ap.av.viewName!=null);
@@ -386,13 +375,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
     {
       if (aSize == 2)
       {
-        AlignmentPanel first = (AlignmentPanel) alignPanels.firstElement();
-        tabbedPane.addTab(first.av.viewName==null?"Original":first.av.viewName,first);
-
-        this.getContentPane().add(tabbedPane, BorderLayout.CENTER);
+        setInitialTabVisible();
       }
 
-      tabbedPane.addTab(ap.av.viewName==null?"Original":ap.av.viewName, ap);
+      expandViews.setEnabled(true);
+      gatherViews.setEnabled(true);
+      tabbedPane.addTab(ap.av.viewName, ap);
 
       ap.setVisible(false);
     }
@@ -406,6 +394,16 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
     }
   }
 
+  public void setInitialTabVisible()
+  {
+    expandViews.setEnabled(true);
+    gatherViews.setEnabled(true);
+    tabbedPane.setVisible(true);
+    AlignmentPanel first = (AlignmentPanel) alignPanels.firstElement();
+    tabbedPane.addTab(first.av.viewName,first);
+    this.getContentPane().add(tabbedPane, BorderLayout.CENTER);
+  }
+
 
   public AlignViewport getViewport()
   {
@@ -466,10 +464,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
    */
   void setMenusFromViewport(AlignViewport av)
   {
+    padGapsMenuitem.setSelected(av.padGaps);
     colourTextMenuItem.setSelected(av.showColourText);
     abovePIDThreshold.setSelected(av.getAbovePIDThreshold());
     conservationMenuItem.setSelected(av.getConservationSelected());
     seqLimits.setSelected(av.getShowJVSuffix());
+    idRightAlign.setSelected(av.rightAlignIds);
     renderGapsMenuItem.setSelected(av.renderGaps);
     wrapMenuItem.setSelected(av.wrapAlignment);
     annotationPanelMenuItem.setState(av.showAnnotation);
@@ -558,12 +558,27 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
     {
       if(currentFileFormat.equals("Jalview"))
       {
-        this.closeMenuItem_actionPerformed(true);
+        JInternalFrame [] frames = Desktop.desktop.getAllFrames();
+        for(int i=0; i<frames.length; i++)
+        {
+          if (frames[i] instanceof AlignFrame
+              && frames[i] != this
+              && ( (AlignFrame) frames[i]).fileName.equals(fileName))
+          {
+            try{
+              frames[i].setSelected(true);
+              Desktop.instance.closeAssociatedWindows();
+            }catch(java.beans.PropertyVetoException ex){}
+          }
+
+        }
+        Desktop.instance.closeAssociatedWindows();
+
       }
       else
       {
         viewport.alignment.deleteAllGroups();
-        viewport.sequenceColours.clear();
+        viewport.sequenceColours=null;
         while (viewport.alignment.getHeight() > 0)
         {
           viewport.alignment.deleteSequence(0);
@@ -577,13 +592,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
           dset.deleteSequence(0);
         }
 
-        firePropertyChange("Alignment", null, null);
+        firePropertyChange("Alignment", null, viewport.alignment.getSequences());
 
         updateEditMenuBar();
       }
 
       FileLoader loader = new FileLoader();
-      loader.LoadFile(viewport, fileName, "File", currentFileFormat);
+      String protocol = fileName.startsWith("http:")? "URL":"File";
+      loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
 
     }
   }
@@ -602,7 +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);
@@ -657,6 +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;
@@ -667,15 +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
     {
@@ -701,28 +719,37 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
 
       if (output == null)
       {
-        return false;
+        success = 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;
-      }
-      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;
   }
 
   /**
@@ -873,13 +900,14 @@ 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())
@@ -956,10 +984,16 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
     viewport.redoList.push(command);
     command.undoCommand();
 
-    viewport.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null;
+    AlignViewport originalSource = getOriginatingSource(command);
     updateEditMenuBar();
-    viewport.firePropertyChange("alignment", null,
-                                viewport.getAlignment().getSequences());
+
+    if(originalSource!=null)
+    {
+      originalSource.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null;
+      originalSource.firePropertyChange("alignment",
+                                        null,
+                                        originalSource.alignment.getSequences());
+    }
   }
 
   /**
@@ -969,15 +1003,64 @@ 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();
-    viewport.hasHiddenColumns = viewport.colSel.getHiddenColumns()!=null;
 
+    AlignViewport originalSource = getOriginatingSource(command);
     updateEditMenuBar();
-    viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
+
+    if(originalSource!=null)
+    {
+      originalSource.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null;
+      originalSource.firePropertyChange("alignment",
+                                        null,
+                                        originalSource.alignment.getSequences());
+    }
   }
 
+  AlignViewport getOriginatingSource(CommandI command)
+  {
+    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;
+      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)
+        {
+          if (al == ( (AlignmentPanel) comps.elementAt(i)).av.alignment)
+          {
+            originalSource = ( (AlignmentPanel) comps.elementAt(i)).av;
+            break;
+          }
+        }
+      }
+    }
+
+    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;
+  }
 
   /**
    * DOCUMENT ME!
@@ -1200,7 +1283,7 @@ 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;
@@ -1351,15 +1434,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
     }
 
     Vector seqs = new Vector();
-    int cutLength = sg.getEndRes()-sg.getStartRes()+1;
-    boolean seqsCut = false;
     SequenceI seq;
     for (int i = 0; i < sg.getSize(false); i++)
     {
       seq = sg.getSequenceAt(i);
       seqs.addElement(seq);
-      if(seq.getLength()<=cutLength)
-        seqsCut = true;
     }
 
 
@@ -1413,7 +1492,7 @@ 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();
@@ -1458,7 +1537,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
     alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
     alignPanel.idPanel.idCanvas.searchResults = null;
     alignPanel.repaint();
-    PaintRefresher.Refresh(this, viewport.getSequenceSetId());
+    PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
   }
 
   /**
@@ -1483,7 +1562,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
       sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
     }
 
-    PaintRefresher.Refresh(this, viewport.getSequenceSetId());
+    alignPanel.repaint();
+
+    PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
   }
 
   public void invertColSel_actionPerformed(ActionEvent e)
@@ -1678,11 +1759,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
    */
   public void findMenuItem_actionPerformed(ActionEvent e)
   {
-    JInternalFrame frame = new JInternalFrame();
-    Finder finder = new Finder(viewport, alignPanel, frame);
-    frame.setContentPane(finder);
-    frame.setLayer(JLayeredPane.PALETTE_LAYER);
-    Desktop.addInternalFrame(frame, "Find", 340, 110);
+    new Finder();
   }
 
   public void newView_actionPerformed(ActionEvent e)
@@ -1691,12 +1768,32 @@ 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);
 
@@ -1707,6 +1804,17 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
     tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
   }
 
+  public void expandViews_actionPerformed(ActionEvent e)
+  {
+        Desktop.instance.explodeViews(this);
+  }
+
+  public void gatherViews_actionPerformed(ActionEvent e)
+  {
+    Desktop.instance.gatherViews(this);
+  }
+
+
 
   /**
    * DOCUMENT ME!
@@ -1732,6 +1840,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
     alignPanel.repaint();
   }
 
+  public void idRightAlign_actionPerformed(ActionEvent e)
+  {
+    viewport.rightAlignIds = idRightAlign.isSelected();
+    alignPanel.repaint();
+  }
+
+
 
   /**
    * DOCUMENT ME!
@@ -1925,112 +2040,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
 
   public void textColour_actionPerformed(ActionEvent e)
   {
-    int original1 = viewport.textColour.getRGB();
-    int original2 = viewport.textColour2.getRGB();
-    int thresh = viewport.thresholdTextColour;
-    final JSlider slider = new JSlider(0, 750, viewport.thresholdTextColour);
-    final JButton col1 = new JButton("DARK");
-    col1.setBackground(viewport.textColour);
-    col1.setForeground(viewport.textColour);
-    final JButton col2 = new JButton("LIGHT");
-    col2.setBackground(viewport.textColour2);
-    col2.setForeground(viewport.textColour2);
-    final JPanel bigpanel = new JPanel(new BorderLayout());
-    JPanel panel = new JPanel();
-    bigpanel.add(panel, BorderLayout.CENTER);
-    bigpanel.add(new JLabel(
-      "<html><i>Select a dark and light text colour, then set the threshold to"
-     +"<br>switch between colours, based on background colour</i></html>"),
-                 BorderLayout.NORTH);
-    panel.add(col1);
-    panel.add(slider);
-    panel.add(col2);
-
-    col1.addActionListener(new ActionListener()
-        {
-          public void actionPerformed(ActionEvent e)
-          {
-            Color col = JColorChooser.showDialog(bigpanel,
-                                                 "Select Colour for Text",
-                                                 viewport.textColour);
-            if (col != null)
-            {
-              viewport.textColour = col;
-              col1.setBackground(col);
-              col1.setForeground(col);
-              if(viewport.colourAppliesToAllGroups)
-                setGroupTextColour();
-            }
-            alignPanel.repaint();
-          }
-        });
-
-    col2.addActionListener(new ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        Color col = JColorChooser.showDialog(bigpanel,
-                                             "Select Colour for Text",
-                                             viewport.textColour);
-        if (col != null)
-        {
-          viewport.textColour2 = col;
-          col2.setBackground(col);
-          col2.setForeground(col);
-          if(viewport.colourAppliesToAllGroups)
-                setGroupTextColour();
-        }
-        alignPanel.repaint();
-      }
-    });
-
-
-    slider.addChangeListener(new ChangeListener()
-    {
-      public void stateChanged(ChangeEvent evt)
-      {
-        viewport.thresholdTextColour = slider.getValue();
-        if(viewport.colourAppliesToAllGroups)
-                setGroupTextColour();
-        alignPanel.repaint();
-      }
-    });
-
-    int reply = JOptionPane.showInternalOptionDialog(this,
-                                                 bigpanel,
-                                                 "Adjust Foreground Text Colour Threshold",
-                                                 JOptionPane.OK_CANCEL_OPTION,
-                                                 JOptionPane.QUESTION_MESSAGE,
-                                                 null,
-                                                 null, null);
-
-    if(reply==JOptionPane.CANCEL_OPTION)
-    {
-      viewport.textColour = new Color(original1);
-      viewport.textColour2 = new Color(original2);
-      viewport.thresholdTextColour = thresh;
-    }
-  }
-
-  void setGroupTextColour()
-  {
-    if(viewport.alignment.getGroups()==null)
-      return;
-
-    Vector groups = viewport.alignment.getGroups();
-
-    for(int i=0; i<groups.size(); i++)
-    {
-      SequenceGroup sg = (SequenceGroup)groups.elementAt(i);
-      sg.textColour = viewport.textColour;
-      sg.textColour2 = viewport.textColour2;
-      sg.thresholdTextColour = viewport.thresholdTextColour;
-    }
-
-
+    new TextColourChooser().chooseColour(alignPanel, null);
   }
 
-
   /**
    * DOCUMENT ME!
    *
@@ -2542,7 +2554,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
       return;
     }
 
-     new PCAPanel(viewport);
+     new PCAPanel(alignPanel);
   }
 
 
@@ -2662,9 +2674,14 @@ 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 ";
+
+    title += this.title;
 
-    Desktop.addInternalFrame(tp, title + " from " + this.title, 600, 500);
+    Desktop.addInternalFrame(tp, title, 600, 500);
   }
 
   /**
@@ -2702,51 +2719,53 @@ 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);
+    sortByTreeMenu.removeAll();
 
-    treeCount++;
-
-    if (treeCount == 1)
-    {
-      sort.add(sortByTreeMenu);
-    }
-
-    sortByTreeMenu.add(item);
-    item.addActionListener(new java.awt.event.ActionListener()
+    Vector comps = (Vector)PaintRefresher.components.get(viewport.getSequenceSetId());
+    Vector treePanels = new Vector();
+    int i, iSize = comps.size();
+    for(i=0; i<iSize; i++)
     {
-      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);
+    }
   }
 
   /**
@@ -2902,7 +2921,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
 
 
         Desktop.addInternalFrame(tp, title, w, h);
-        addTreeMenuItem(tp, title);
       }
     }
     catch (Exception ex)
@@ -3269,7 +3287,7 @@ public void drop(DropTargetDropEvent evt)
       }
 
       boolean isAnnotation = new AnnotationFile().readAnnotationFile(viewport.
-          alignment, file);
+          alignment, file, protocol);
 
       if (!isAnnotation)
       {