X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=46b2cc5acc64c83758cbdc75c04b6d9385141090;hb=7e129811d6ff01074428462284dffc2a6c2395a4;hp=3475e7a1b5c73aa6e31246c09fb8c498068f53ff;hpb=9b9afd73c1bad3a4a098f3bc3185cf9315a9b1a8;p=jalview.git

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 3475e7a..46b2cc5 100755
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -13,7 +13,7 @@
  * GNU General Public License for more details.
  *
  * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
+ * along with this program; if not, write to the Free Softwarechang
  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  */
 package jalview.gui;
@@ -68,6 +68,17 @@ public class AlignFrame
   {
     viewport = new AlignViewport(al);
 
+    if(viewport.vconsensus==null)
+    {
+      //Out of memory caluclating consensus.
+      BLOSUM62Colour.setEnabled(false);
+      PIDColour.setEnabled(false);
+      conservationMenuItem.setEnabled(false);
+      modifyConservation.setEnabled(false);
+      abovePIDThreshold.setEnabled(false);
+      modifyPID.setEnabled(false);
+    }
+
     alignPanel = new AlignmentPanel(this, viewport);
     alignPanel.annotationPanel.adjustPanelHeight();
     alignPanel.annotationSpaceFillerHolder.setPreferredSize(alignPanel.
@@ -76,32 +87,36 @@ public class AlignFrame
         getPreferredSize());
     alignPanel.setAnnotationVisible(viewport.getShowAnnotation());
 
+    String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT", "No sort");
+
+    if(sortby.equals("Id"))
+      sortIDMenuItem_actionPerformed(null);
+    else if(sortby.equals("Pairwise Identity"))
+      sortPairwiseMenuItem_actionPerformed(null);
+
     getContentPane().add(alignPanel, java.awt.BorderLayout.CENTER);
 
-    addInternalFrameListener(new InternalFrameAdapter()
+    viewport.addPropertyChangeListener(new PropertyChangeListener()
     {
-      public void internalFrameActivated(InternalFrameEvent evt)
-      {
-        javax.swing.SwingUtilities.invokeLater(new Runnable()
-        {
-          public void run()
-          {
-            alignPanel.requestFocus();
-          }
-        });
-      }
-    });
+     public void propertyChange(PropertyChangeEvent evt)
+     {
+       if (evt.getPropertyName().equals("alignment"))
+       {
+         alignmentChanged();
+       }
+     }
+   });
+
+
     addServiceListeners();
   }
 
   /* Set up intrinsic listeners for dynamically generated GUI bits. */
   private void addServiceListeners()
   {
-
-    final AlignFrame thisFrame = this;
     final java.beans.PropertyChangeListener thisListener;
     // Do this once to get current state
-    thisFrame.BuildWebServiceMenu();
+    BuildWebServiceMenu();
     Desktop.discoverer.addPropertyChangeListener(
         thisListener = new java.beans.PropertyChangeListener()
     {
@@ -111,7 +126,7 @@ public class AlignFrame
         if (evt.getPropertyName().equals("services"))
         {
           // System.out.println("Rebuilding web service menu");
-          thisFrame.BuildWebServiceMenu();
+          BuildWebServiceMenu();
         }
       }
     });
@@ -123,6 +138,7 @@ public class AlignFrame
       {
         // System.out.println("deregistering discoverer listener");
         Desktop.discoverer.removePropertyChangeListener(thisListener);
+        closeMenuItem_actionPerformed(null);
       }
       ;
     });
@@ -264,7 +280,8 @@ public class AlignFrame
       {
         java.io.PrintWriter out = new java.io.PrintWriter(
             new java.io.FileWriter(file));
-        out.println(output);
+
+        out.print(output);
         out.close();
         return true;
       }
@@ -348,6 +365,7 @@ public class AlignFrame
   {
     try
     {
+      PaintRefresher.components.remove(viewport.alignment);
       this.setClosed(true);
     }
     catch (Exception ex)
@@ -409,6 +427,7 @@ public class AlignFrame
     redoList.push(new HistoryItem(hi.getDescription(), viewport.alignment,
                                   HistoryItem.HIDE));
     restoreHistoryItem(hi);
+    viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
   }
 
   /**
@@ -421,9 +440,7 @@ public class AlignFrame
     HistoryItem hi = (HistoryItem) redoList.pop();
     restoreHistoryItem(hi);
     updateEditMenuBar();
-    viewport.updateConsensus();
-    alignPanel.repaint();
-    alignPanel.repaint();
+    viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
   }
 
   // used by undo and redo
@@ -468,9 +485,6 @@ public class AlignFrame
 
     updateEditMenuBar();
 
-    viewport.updateConsensus();
-    viewport.updateConservation();
-    alignPanel.repaint();
     viewport.firePropertyChange("alignment", null,
                                 viewport.getAlignment().getSequences());
   }
@@ -699,20 +713,17 @@ public class AlignFrame
       }
       else
       {
-        viewport.firePropertyChange("alignment", null,
-                                    viewport.getAlignment().getSequences());
         viewport.setEndSeq(viewport.alignment.getHeight());
         viewport.alignment.getWidth();
-        viewport.updateConservation();
-        viewport.updateConsensus();
-        alignPanel.repaint();
+        viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
       }
     }
     catch (Exception ex)
     {
+        // could be anything being pasted in here
     }
 
-    // could be anything being pasted in here
+
   }
 
   /**
@@ -777,13 +788,10 @@ public class AlignFrame
     viewport.setSelectionGroup(null);
     viewport.alignment.deleteGroup(sg);
 
-    if (seqsdeleted)
-    {
-      viewport.firePropertyChange("alignment", null,
+    viewport.firePropertyChange("alignment", null,
                                   viewport.getAlignment().getSequences());
-    }
 
-    viewport.resetSeqLimits(alignPanel.seqPanel.seqCanvas.getHeight());
+
 
     if (viewport.getAlignment().getHeight() < 1)
     {
@@ -795,10 +803,6 @@ public class AlignFrame
       {
       }
     }
-
-    viewport.updateConservation();
-    viewport.updateConsensus();
-    alignPanel.repaint();
   }
 
   /**
@@ -907,7 +911,7 @@ public class AlignFrame
         }
       }
 
-      alignPanel.repaint();
+      viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
     }
   }
 
@@ -945,7 +949,7 @@ public class AlignFrame
         }
       }
 
-      alignPanel.repaint();
+      viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
     }
   }
 
@@ -959,10 +963,16 @@ public class AlignFrame
     addHistoryItem(new HistoryItem("Remove Gapped Columns",
                                    viewport.alignment, HistoryItem.HIDE));
 
+    //This is to maintain viewport position on first residue
+    //of first sequence
+    SequenceI seq = viewport.alignment.getSequenceAt(0);
+    int startRes = seq.findPosition(viewport.startRes);
+
     viewport.getAlignment().removeGaps();
-    viewport.updateConservation();
-    viewport.updateConsensus();
-    alignPanel.repaint();
+
+    viewport.setStartRes(seq.findIndex(startRes)-1);
+
+   viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
   }
 
   /**
@@ -975,6 +985,12 @@ public class AlignFrame
     addHistoryItem(new HistoryItem("Remove Gaps", viewport.alignment,
                                    HistoryItem.HIDE));
 
+    //This is to maintain viewport position on first residue
+    //of first sequence
+    SequenceI seq = viewport.alignment.getSequenceAt(0);
+    int startRes = seq.findPosition(viewport.startRes);
+
+
     SequenceI current;
     int jSize;
 
@@ -1016,9 +1032,59 @@ public class AlignFrame
       while (j < end && j < jSize);
     }
 
-    viewport.updateConservation();
-    viewport.updateConsensus();
-    alignPanel.repaint();
+    viewport.setStartRes(seq.findIndex(startRes)-1);
+
+    viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
+  }
+
+ public void alignmentChanged()
+ {
+   if(viewport.vconsensus!=null)
+   {
+     viewport.updateConsensus();
+     viewport.updateConservation();
+   }
+   resetAllColourSchemes();
+   alignPanel.repaint();
+ }
+
+  void resetAllColourSchemes()
+  {
+    ColourSchemeI cs = viewport.globalColourScheme;
+    if(cs!=null)
+    {
+      if (cs instanceof ClustalxColourScheme)
+      {
+        ( (ClustalxColourScheme) viewport.getGlobalColourScheme()).
+            resetClustalX(viewport.alignment.getSequences(),
+                          viewport.alignment.getWidth());
+      }
+
+      cs.setConsensus(viewport.vconsensus);
+      if (cs.conservationApplied())
+      {
+        Alignment al = (Alignment) viewport.alignment;
+        Conservation c = new Conservation("All",
+                                          ResidueProperties.propHash, 3,
+                                          al.getSequences(), 0,
+                                          al.getWidth() - 1);
+        c.calculate();
+        c.verdict(false, viewport.ConsPercGaps);
+
+        cs.setConservation(c);
+      }
+    }
+
+    int s, sSize = viewport.alignment.getGroups().size();
+    for(s=0; s<sSize; s++)
+    {
+      SequenceGroup sg = (SequenceGroup)viewport.alignment.getGroups().elementAt(s);
+      if(sg.cs!=null && sg.cs instanceof ClustalxColourScheme)
+      {
+        ((ClustalxColourScheme)sg.cs).resetClustalX(sg.sequences, sg.getWidth());
+      }
+      sg.recalcConservation();
+    }
   }
 
   /**
@@ -1045,9 +1111,7 @@ public class AlignFrame
       }
     }
 
-    viewport.updateConservation();
-    viewport.updateConsensus();
-    alignPanel.repaint();
+    alignmentChanged();
   }
 
   /**
@@ -1371,66 +1435,50 @@ public class AlignFrame
   {
     int threshold = 0;
 
-    if (viewport.getAbovePIDThreshold())
+    if(cs!=null)
     {
-      threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
-                                                 "Background");
-
-      if (cs instanceof ResidueColourScheme)
+      if (viewport.getAbovePIDThreshold())
       {
-        ( (ResidueColourScheme) cs).setThreshold(threshold,
-                                                 viewport.
-                                                 getIgnoreGapsConsensus());
+        threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
+                                                   "Background");
+
+        cs.setThreshold(threshold,
+                        viewport.getIgnoreGapsConsensus());
+
+        viewport.setGlobalColourScheme(cs);
       }
-      else if (cs instanceof ScoreColourScheme)
+      else
       {
-        ( (ScoreColourScheme) cs).setThreshold(threshold,
-                                               viewport.getIgnoreGapsConsensus());
+        cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
       }
 
-      viewport.setGlobalColourScheme(cs);
-    }
-    else if (cs instanceof ResidueColourScheme)
-    {
-      ( (ResidueColourScheme) cs).setThreshold(0,
-                                               viewport.getIgnoreGapsConsensus());
-    }
-    else if (cs instanceof ScoreColourScheme)
-    {
-      ( (ScoreColourScheme) cs).setThreshold(0, viewport.getIgnoreGapsConsensus());
-    }
-
-    if (viewport.getConservationSelected())
-    {
-      ConservationColourScheme ccs = null;
-
-      Alignment al = (Alignment) viewport.alignment;
-      Conservation c = new Conservation("All",
-                                        ResidueProperties.propHash, 3,
-                                        al.getSequences(), 0,
-                                        al.getWidth() - 1);
+      if (viewport.getConservationSelected())
+      {
 
-      c.calculate();
-      c.verdict(false, viewport.ConsPercGaps);
+        Alignment al = (Alignment) viewport.alignment;
+        Conservation c = new Conservation("All",
+                                          ResidueProperties.propHash, 3,
+                                          al.getSequences(), 0,
+                                          al.getWidth() - 1);
 
-      ccs = new ConservationColourScheme(c, cs);
+        c.calculate();
+        c.verdict(false, viewport.ConsPercGaps);
 
-      viewport.setGlobalColourScheme(ccs);
+        cs.setConservation(c);
 
-      ccs.inc = SliderPanel.setConservationSlider(alignPanel, ccs,
-                                                  "Background");
-    }
-    else
-    {
-      // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!
-      if (cs != null)
+        cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel, cs,
+            "Background"));
+      }
+      else
       {
-        cs.setConsensus(viewport.vconsensus);
+        cs.setConservation(null);
       }
 
-      viewport.setGlobalColourScheme(cs);
+      cs.setConsensus(viewport.vconsensus);
     }
 
+    viewport.setGlobalColourScheme(cs);
+
     if (viewport.getColourAppliesToAllGroups())
     {
       Vector groups = viewport.alignment.getGroups();
@@ -1442,8 +1490,10 @@ public class AlignFrame
         if (cs == null)
         {
           sg.cs = null;
+          continue;
         }
-        else if (cs instanceof ClustalxColourScheme)
+
+        if (cs instanceof ClustalxColourScheme)
         {
           sg.cs = new ClustalxColourScheme(sg.sequences, sg.getWidth());
         }
@@ -1462,22 +1512,19 @@ public class AlignFrame
           }
         }
 
-        if (viewport.getAbovePIDThreshold())
+        if (viewport.getAbovePIDThreshold()
+            || cs instanceof PIDColourScheme
+            || cs instanceof Blosum62ColourScheme)
         {
-          if (sg.cs instanceof ResidueColourScheme)
-          {
-            ( (ResidueColourScheme) sg.cs).setThreshold(threshold,
-                viewport.getIgnoreGapsConsensus());
-          }
-          else if (sg.cs instanceof ScoreColourScheme)
-          {
-            ( (ScoreColourScheme) sg.cs).setThreshold(threshold,
+         sg.cs.setThreshold(threshold,
                 viewport.getIgnoreGapsConsensus());
-          }
 
           sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,
               sg.getWidth()));
         }
+        else
+          sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
+
 
         if (viewport.getConservationSelected())
         {
@@ -1487,21 +1534,10 @@ public class AlignFrame
                                             viewport.alignment.getWidth() - 1);
           c.calculate();
           c.verdict(false, viewport.ConsPercGaps);
-
-          ConservationColourScheme ccs = new ConservationColourScheme(c,
-              sg.cs);
-
-          // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!
-          ccs.setConsensus(AAFrequency.calculate(sg.sequences, 0,
-                                                 sg.getWidth()));
-          sg.cs = ccs;
-        }
-        else if (cs != null)
-        {
-          // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!
-          sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,
-              sg.getWidth()));
+          sg.cs.setConservation(c);
         }
+        else
+          sg.cs.setConservation(null);
       }
     }
 
@@ -1520,7 +1556,7 @@ public class AlignFrame
    */
   protected void modifyPID_actionPerformed(ActionEvent e)
   {
-    if (viewport.getAbovePIDThreshold())
+    if (viewport.getAbovePIDThreshold() && viewport.globalColourScheme!=null)
     {
       SliderPanel.setPIDSliderSource(alignPanel,
                                      viewport.getGlobalColourScheme(),
@@ -1536,7 +1572,7 @@ public class AlignFrame
    */
   protected void modifyConservation_actionPerformed(ActionEvent e)
   {
-    if (viewport.getConservationSelected())
+    if (viewport.getConservationSelected() && viewport.globalColourScheme!=null)
     {
       SliderPanel.setConservationSlider(alignPanel,
                                         viewport.globalColourScheme,
@@ -1557,16 +1593,7 @@ public class AlignFrame
     viewport.setAbovePIDThreshold(false);
     abovePIDThreshold.setSelected(false);
 
-    ColourSchemeI cs = viewport.getGlobalColourScheme();
-
-    if (cs instanceof ConservationColourScheme)
-    {
-      changeColour( ( (ConservationColourScheme) cs).cs);
-    }
-    else
-    {
-      changeColour(cs);
-    }
+    changeColour(viewport.getGlobalColourScheme());
 
     modifyConservation_actionPerformed(null);
   }
@@ -1585,14 +1612,7 @@ public class AlignFrame
 
     ColourSchemeI cs = viewport.getGlobalColourScheme();
 
-    if (cs instanceof ConservationColourScheme)
-    {
-      changeColour( ( (ConservationColourScheme) cs).cs);
-    }
-    else
-    {
-      changeColour(cs);
-    }
+    changeColour(viewport.getGlobalColourScheme());
 
     modifyPID_actionPerformed(null);
   }
@@ -1638,8 +1658,37 @@ public class AlignFrame
 
       while (userColours.hasMoreElements())
       {
-        JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(userColours.
+        final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(userColours.
             nextElement().toString());
+        radioItem.setName("USER_DEFINED");
+        radioItem.addMouseListener(new MouseAdapter()
+            {
+              public void mousePressed(MouseEvent evt)
+              {
+                if(evt.isControlDown() || SwingUtilities.isRightMouseButton(evt))
+                {
+                  radioItem.removeActionListener(radioItem.getActionListeners()[0]);
+
+                  int option = JOptionPane.showInternalConfirmDialog(jalview.gui.Desktop.desktop,
+                      "Remove from default list?",
+                      "Remove user defined colour",
+                      JOptionPane.YES_NO_OPTION);
+                  if(option == JOptionPane.YES_OPTION)
+                  {
+                    jalview.gui.UserDefinedColours.removeColourFromDefaults(radioItem.getText());
+                    colourMenu.remove(radioItem);
+                  }
+                  else
+                    radioItem.addActionListener(new ActionListener()
+                    {
+                      public void actionPerformed(ActionEvent evt)
+                      {
+                        userDefinedColour_actionPerformed(evt);
+                      }
+                    });
+                }
+              }
+            });
         radioItem.addActionListener(new ActionListener()
         {
           public void actionPerformed(ActionEvent evt)
@@ -1647,6 +1696,7 @@ public class AlignFrame
             userDefinedColour_actionPerformed(evt);
           }
         });
+
         colourMenu.insert(radioItem, 15);
         colours.add(radioItem);
       }
@@ -2125,6 +2175,11 @@ public class AlignFrame
     }
   }
 
+
+  public TreePanel ShowNewickTree(NewickFile nf, String title)
+  {
+    return ShowNewickTree(nf,title,600,500,4,5);
+  }
   /**
    * DOCUMENT ME!
    *
@@ -2133,7 +2188,7 @@ public class AlignFrame
    *
    * @return DOCUMENT ME!
    */
-  public TreePanel ShowNewickTree(NewickFile nf, String title)
+  public TreePanel ShowNewickTree(NewickFile nf, String title, int w,int h,int x, int y)
   {
     TreePanel tp = null;
 
@@ -2147,7 +2202,14 @@ public class AlignFrame
                            viewport.getAlignment().getSequences(), nf,
                            "FromFile",
                            title);
-        Desktop.addInternalFrame(tp, title, 600, 500);
+
+        tp.setSize(w,h);
+
+        if(x>0 && y>0)
+          tp.setLocation(x,y);
+
+
+        Desktop.addInternalFrame(tp, title, w, h);
         addTreeMenuItem(tp, title);
       }
     }
@@ -2219,7 +2281,7 @@ public class AlignFrame
           if (sh.getName().indexOf("lustal") > -1)
           {
             // We know that ClustalWS can accept partial alignments for refinement.
-            final JMenuItem methodR = new JMenuItem(sh.getName() + " realign");
+            final JMenuItem methodR = new JMenuItem(sh.getName()+" Realign");
             methodR.addActionListener(new ActionListener()
             {
               public void actionPerformed(ActionEvent e)