X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAlignFrame.java;h=bda314d9c4b34785b7b11b52c0510e0b4ea98966;hb=ee53965807b83bf93a21cbc341cee9a9e005b2cb;hp=1b5629f4a418b4944f5cef7a66237537b88e7662;hpb=4f0f6c493f753878483fb75d943e5e5f9fd73cca;p=jalview.git

diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index 1b5629f..bda314d 100755
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -35,28 +35,10 @@ public class AlignFrame
 {
   final AlignmentPanel alignPanel;
   final AlignViewport viewport;
-  public static final int NEW_WINDOW_WIDTH = 700;
-  public static final int NEW_WINDOW_HEIGHT = 500;
+  public static int NEW_WINDOW_WIDTH = 700;
+  public static int NEW_WINDOW_HEIGHT = 500;
   jalview.bin.JalviewLite applet;
 
-  public AlignFrame(AlignmentI al)
-  {
-    this.applet = null;
-    viewport = new AlignViewport(al, null);
-    alignPanel = new AlignmentPanel(this, viewport);
-    add(alignPanel);
-    alignPanel.validate();
-
-    this.addWindowListener(new WindowAdapter()
-    {
-      public void windowClosing(WindowEvent e)
-      {
-        closeMenuItem_actionPerformed(null);
-      }
-    });
-
-  }
-
 
   public AlignFrame(AlignmentI al, jalview.bin.JalviewLite applet)
   {
@@ -66,28 +48,50 @@ public class AlignFrame
     add(alignPanel);
     alignPanel.validate();
 
-    String treeFile = applet.getParameter("treeFile");
-    if (treeFile != null)
+    if(applet!=null)
     {
-      try
+      String treeFile = applet.getParameter("treeFile");
+      if (treeFile != null)
       {
-        treeFile = treeFile;
-        jalview.io.NewickFile fin = new jalview.io.NewickFile(applet.
-            getCodeBase() + treeFile, "URL");
-        fin.parse();
+        try
+        {
+          treeFile = treeFile;
+          jalview.io.NewickFile fin = new jalview.io.NewickFile(applet.
+              getCodeBase() + treeFile, "URL");
+          fin.parse();
 
-        if (fin.getTree() != null)
+          if (fin.getTree() != null)
+          {
+            TreePanel tp = null;
+            tp = new TreePanel(viewport, viewport.getAlignment().getSequences(),
+                               fin, "FromFile", applet.getCodeBase() + treeFile);
+            jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);
+            addTreeMenuItem(tp, treeFile);
+          }
+        }
+        catch (Exception ex)
         {
-          TreePanel tp = null;
-          tp = new TreePanel(viewport, viewport.getAlignment().getSequences(),
-                             fin, "FromFile", applet.getCodeBase() + treeFile);
-          jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);
-          addTreeMenuItem(tp, treeFile);
+          ex.printStackTrace();
         }
       }
-      catch (Exception ex)
+
+      String param = applet.getParameter("sortBy");
+      if (param != null)
       {
-        ex.printStackTrace();
+        if (param.equalsIgnoreCase("Id"))
+          sortIDMenuItem_actionPerformed(null);
+        else if (param.equalsIgnoreCase("Pairwise Identity"))
+          sortPairwiseMenuItem_actionPerformed(null);
+      }
+
+      param = applet.getParameter("wrap");
+      if (param != null)
+      {
+        if (param.equalsIgnoreCase("true"))
+        {
+          wrapMenuItem.setState(true);
+          wrapMenuItem_actionPerformed(null);
+        }
       }
     }
 
@@ -99,13 +103,21 @@ public class AlignFrame
           }
     });
 
-
-
+    viewport.addPropertyChangeListener(new java.beans.PropertyChangeListener()
+    {
+     public void propertyChange(java.beans.PropertyChangeEvent evt)
+     {
+       if (evt.getPropertyName().equals("alignment"))
+       {
+         alignmentChanged();
+       }
+     }
+   });
   }
 
   public void inputText_actionPerformed(ActionEvent e)
   {
-    CutAndPasteTransfer cap = new CutAndPasteTransfer(true);
+    CutAndPasteTransfer cap = new CutAndPasteTransfer(true, applet);
     Frame frame = new Frame();
     frame.add(cap);
     jalview.bin.JalviewLite.addFrame(frame, "Cut & Paste Input", 500, 500);
@@ -113,13 +125,13 @@ public class AlignFrame
 
   protected void outputText_actionPerformed(ActionEvent e)
   {
-    CutAndPasteTransfer cap = new CutAndPasteTransfer(false);
+    CutAndPasteTransfer cap = new CutAndPasteTransfer(false, applet);
     Frame frame = new Frame();
     frame.add(cap);
     jalview.bin.JalviewLite.addFrame(frame,
                                      "Alignment output - " + e.getActionCommand(),
                                      600, 500);
-    cap.setText(FormatAdapter.formatSequences(e.getActionCommand(),
+    cap.setText(new FormatAdapter().formatSequences(e.getActionCommand(),
                                               viewport.getAlignment().
                                               getSequences()));
   }
@@ -128,6 +140,8 @@ public class AlignFrame
   {
     PaintRefresher.components.remove(viewport.alignment);
     dispose();
+    if(PaintRefresher.components.size()==0 && applet==null)
+      System.exit(0);
   }
 
   Stack historyList = new Stack();
@@ -172,6 +186,7 @@ public class AlignFrame
     redoList.push(new HistoryItem(hi.getDescription(), viewport.alignment,
                                   HistoryItem.HIDE));
     restoreHistoryItem(hi);
+    viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
   }
 
   protected void redoMenuItem_actionPerformed(ActionEvent e)
@@ -179,9 +194,7 @@ 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
@@ -225,9 +238,7 @@ public class AlignFrame
 
     updateEditMenuBar();
 
-    viewport.updateConsensus();
-    viewport.updateConservation();
-    alignPanel.repaint();
+    viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
   }
 
   public void moveSelectedSequences(boolean up)
@@ -418,9 +429,7 @@ public class AlignFrame
       {
         viewport.setEndSeq(viewport.alignment.getHeight());
         viewport.alignment.getWidth();
-        viewport.updateConservation();
-        viewport.updateConsensus();
-        alignPanel.repaint();
+        viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
       }
 
     }
@@ -486,9 +495,7 @@ public class AlignFrame
       catch (Exception ex)
       {}
     }
-    viewport.updateConservation();
-    viewport.updateConsensus();
-    alignPanel.repaint();
+    viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
 
   }
 
@@ -507,7 +514,7 @@ public class AlignFrame
     {
       sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
     }
-    sg.setEndRes(viewport.alignment.getWidth());
+    sg.setEndRes(viewport.alignment.getWidth()-1);
     viewport.setSelectionGroup(sg);
     alignPanel.repaint();
     PaintRefresher.Refresh(null, viewport.alignment);
@@ -518,6 +525,7 @@ public class AlignFrame
     viewport.setSelectionGroup(null);
     viewport.getColumnSelection().clear();
     viewport.setSelectionGroup(null);
+    alignPanel.repaint();
     PaintRefresher.Refresh(null, viewport.alignment);
   }
 
@@ -557,8 +565,7 @@ public class AlignFrame
           viewport.alignment.deleteGroup(sg);
         }
       }
-
-      alignPanel.repaint();
+      viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
     }
   }
 
@@ -585,8 +592,7 @@ public class AlignFrame
           viewport.alignment.deleteGroup(sg);
         }
       }
-
-      alignPanel.repaint();
+      viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
     }
 
   }
@@ -596,10 +602,17 @@ 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());
   }
 
   public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
@@ -607,6 +620,11 @@ 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;
 
@@ -620,35 +638,110 @@ public class AlignFrame
     {
       seqs = viewport.getSelectionGroup().sequences;
       start = viewport.getSelectionGroup().getStartRes();
-      end = viewport.getSelectionGroup().getEndRes();
+      end = viewport.getSelectionGroup().getEndRes()+1;
     }
     else
       seqs = viewport.alignment.getSequences();
 
-    for (int i = 0; i <seqs.size(); i++)
+    for (int i = 0; i < seqs.size(); i++)
     {
-      current = (SequenceI)seqs.elementAt(i);
+      current = (SequenceI) seqs.elementAt(i);
       jSize = current.getLength();
 
+      // Removing a range is much quicker than removing gaps
+      // one by one for long sequences
       int j = start;
+      int rangeStart=-1, rangeEnd=-1;
+
       do
       {
         if (jalview.util.Comparison.isGap(current.getCharAt(j)))
         {
-          current.deleteCharAt(j);
-          j--;
-          jSize--;
+          if(rangeStart==-1)
+           {
+             rangeStart = j;
+             rangeEnd = j+1;
+           }
+           else
+           {
+             rangeEnd++;
+           }
+           j++;
+        }
+        else
+        {
+          if(rangeStart>-1)
+          {
+            current.deleteChars(rangeStart, rangeEnd);
+            j-=rangeEnd-rangeStart;
+            jSize-=rangeEnd-rangeStart;
+            rangeStart = -1;
+            rangeEnd = -1;
+          }
+          else
+            j++;
         }
-        j++;
       }
-      while(j < end && j < jSize) ;
+      while (j < end && j < jSize);
+      if(rangeStart>-1)
+      {
+       current.deleteChars(rangeStart, rangeEnd);
+      }
     }
+    viewport.setStartRes(seq.findIndex(startRes)-1);
+    viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
+  }
 
-    viewport.updateConservation();
+  public void alignmentChanged()
+  {
     viewport.updateConsensus();
+    viewport.updateConservation ();
+    resetAllColourSchemes();
+    if(alignPanel.overviewPanel!=null)
+      alignPanel.overviewPanel.updateOverviewImage();
     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();
+    }
+  }
+
+
 
   public void findMenuItem_actionPerformed(ActionEvent e)
   {
@@ -657,11 +750,7 @@ public class AlignFrame
 
   public void font_actionPerformed(ActionEvent e)
   {
-    Frame frame = new Frame();
-    FontChooser fc = new FontChooser(alignPanel, frame);
-    frame.add(fc);
-    jalview.bin.JalviewLite.addFrame(frame, "Change Font", 440, 100);
-
+    new FontChooser(alignPanel);
   }
 
   protected void fullSeqId_actionPerformed(ActionEvent e)
@@ -725,11 +814,6 @@ public class AlignFrame
 
   public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
   {
-    if (annotationPanelMenuItem.getState() && viewport.getWrapAlignment())
-    {
-      annotationPanelMenuItem.setState(false);
-      return;
-    }
     viewport.setShowAnnotation(annotationPanelMenuItem.getState());
     alignPanel.setAnnotationVisible(annotationPanelMenuItem.getState());
   }
@@ -918,6 +1002,7 @@ public class AlignFrame
         else
         {
           sg.cs.setConservation(null);
+          sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
         }
 
       }
@@ -1034,13 +1119,31 @@ public class AlignFrame
     if (viewport.getSelectionGroup().getSize() > 1)
     {
       Frame frame = new Frame();
-      frame.add(new PairwiseAlignPanel(viewport));
+      frame.add(new PairwiseAlignPanel(alignPanel));
       jalview.bin.JalviewLite.addFrame(frame, "Pairwise Alignment", 600, 500);
     }
   }
 
   public void PCAMenuItem_actionPerformed(ActionEvent e)
   {
+    //are the sequences aligned?
+    if (!viewport.alignment.isAligned())
+    {
+      SequenceI current;
+      int Width = viewport.getAlignment().getWidth();
+
+      for (int i = 0; i < viewport.getAlignment().getSequences().size();
+           i++)
+      {
+        current = viewport.getAlignment().getSequenceAt(i);
+
+        if (current.getLength() < Width)
+        {
+          current.insertCharAt(Width - 1, viewport.getGapCharacter());
+        }
+      }
+      alignPanel.repaint();
+    }
 
     if ( (viewport.getSelectionGroup() != null &&
           viewport.getSelectionGroup().getSize() < 4 &&
@@ -1052,11 +1155,7 @@ public class AlignFrame
 
     try
     {
-      PCAPanel pcaPanel = new PCAPanel(viewport, null);
-      Frame frame = new Frame();
-      frame.add(pcaPanel);
-      jalview.bin.JalviewLite.addFrame(frame, "Principal component analysis",
-                                       400, 400);
+      new PCAPanel(viewport);
     }
     catch (java.lang.OutOfMemoryError ex)
     {