X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAlignFrame.java;h=4fc6208a753a374ae5d785396aefc6bd8fc843dd;hb=6e21be7d86ab4ac3936e1e7691b31ebcf9080cdf;hp=dc8f72b78c35cd63fee4a65aa7e678c02202b9aa;hpb=81d90a3969ade80091512d829a4fd2850d85b7bc;p=jalview.git

diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index dc8f72b..4fc6208 100755
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -29,66 +29,89 @@ import java.awt.event.*;
 import java.util.*;
 import java.io.InputStreamReader;
 import java.io.BufferedReader;
+import java.net.URL;
 
 public class AlignFrame
     extends GAlignFrame
 {
   final AlignmentPanel alignPanel;
   final AlignViewport viewport;
-  public static final int NEW_WINDOW_WIDTH = 700;
-  public static final int NEW_WINDOW_HEIGHT = 500;
+  int NEW_WINDOW_WIDTH = 700;
+  int NEW_WINDOW_HEIGHT = 500;
   jalview.bin.JalviewLite applet;
 
-  public AlignFrame(AlignmentI al)
+
+  public AlignFrame(AlignmentI al, jalview.bin.JalviewLite applet, String title)
   {
-    this.applet = null;
-    viewport = new AlignViewport(al, null);
+    this.applet = applet;
+    viewport = new AlignViewport(al, applet);
     alignPanel = new AlignmentPanel(this, viewport);
     add(alignPanel);
     alignPanel.validate();
 
-    this.addWindowListener(new WindowAdapter()
+    if(applet!=null)
     {
-      public void windowClosing(WindowEvent e)
+      String treeFile = applet.getParameter("treeFile");
+      if (treeFile != null)
       {
-        closeMenuItem_actionPerformed(null);
-      }
-    });
+        try
+        {
+          jalview.io.NewickFile fin = new jalview.io.NewickFile(applet.
+              getCodeBase() + treeFile, "URL");
+          fin.parse();
 
-  }
+          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)
+        {
+          ex.printStackTrace();
+        }
+      }
 
+      String param = applet.getParameter("sortBy");
+      if (param != null)
+      {
+        if (param.equalsIgnoreCase("Id"))
+          sortIDMenuItem_actionPerformed(null);
+        else if (param.equalsIgnoreCase("Pairwise Identity"))
+          sortPairwiseMenuItem_actionPerformed(null);
+      }
 
-  public AlignFrame(AlignmentI al, jalview.bin.JalviewLite applet)
-  {
-    this.applet = applet;
-    viewport = new AlignViewport(al, applet);
-    alignPanel = new AlignmentPanel(this, viewport);
-    add(alignPanel);
-    alignPanel.validate();
+      param = applet.getParameter("wrap");
+      if (param != null)
+      {
+        if (param.equalsIgnoreCase("true"))
+        {
+          wrapMenuItem.setState(true);
+          wrapMenuItem_actionPerformed(null);
+        }
+      }
 
-    String treeFile = applet.getParameter("treeFile");
-    if (treeFile != null)
-    {
       try
       {
-        treeFile = treeFile;
-        jalview.io.NewickFile fin = new jalview.io.NewickFile(applet.
-            getCodeBase() + treeFile, "URL");
-        fin.parse();
-
-        if (fin.getTree() != null)
+        param = applet.getParameter("windowWidth");
+        if (param != null)
+        {
+          int width = Integer.parseInt(param);
+          NEW_WINDOW_WIDTH = width;
+        }
+        param = applet.getParameter("windowHeight");
+        if (param != 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);
+          int height = Integer.parseInt(param);
+          NEW_WINDOW_HEIGHT = height;
         }
       }
       catch (Exception ex)
-      {
-        ex.printStackTrace();
-      }
+      {}
+
     }
 
     this.addWindowListener(new WindowAdapter()
@@ -99,13 +122,111 @@ public class AlignFrame
           }
     });
 
+    viewport.addPropertyChangeListener(new java.beans.PropertyChangeListener()
+    {
+     public void propertyChange(java.beans.PropertyChangeEvent evt)
+     {
+       if (evt.getPropertyName().equals("alignment"))
+       {
+         alignmentChanged();
+       }
+     }
+   });
+
+   jalview.bin.JalviewLite.addFrame(this, title,
+                                    NEW_WINDOW_WIDTH,
+                                    NEW_WINDOW_HEIGHT);
 
 
   }
 
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param String DOCUMENT ME!
+   */
+
+  public void parseFeaturesFile(String file)
+  {
+    try
+    {
+      URL url = new URL(file);
+
+      BufferedReader in =  new BufferedReader(new InputStreamReader(url.openStream()));
+      SequenceI seq = null;
+      String line, type, desc, token;
+
+      int index, start, end;
+      StringTokenizer st;
+      SequenceFeature sf;
+      FeatureRenderer fr = alignPanel.seqPanel.seqCanvas.getFeatureRenderer();
+      int lineNo = 0;
+      while ( (line = in.readLine()) != null)
+      {
+        lineNo++;
+        st = new StringTokenizer(line, "\t");
+        if (st.countTokens() == 2)
+        {
+          type = st.nextToken();
+          UserColourScheme ucs = new UserColourScheme(st.nextToken());
+          fr.setColour(type, ucs.findColour("A"));
+          continue;
+        }
+
+        while (st.hasMoreElements())
+        {
+          desc = st.nextToken();
+          token = st.nextToken();
+          if (!token.equals("ID_NOT_SPECIFIED"))
+          {
+            index = viewport.alignment.findIndex(viewport.alignment.findName(
+                token));
+            st.nextToken();
+          }
+          else
+          {
+            index = Integer.parseInt(st.nextToken());
+          }
+
+          start = Integer.parseInt(st.nextToken());
+          end = Integer.parseInt(st.nextToken());
+
+          seq = viewport.alignment.getSequenceAt(index);
+          start = seq.findIndex(start) - 1;
+          end = seq.findIndex(end) - 1;
+
+          type = st.nextToken();
+
+          if(fr.getColour(type)==null)
+          {
+            // Probably the old style groups file
+            UserColourScheme ucs = new UserColourScheme(type);
+            fr.setColour(type, ucs.findColour("A"));
+          }
+
+          sf = new SequenceFeature(type, desc, "", start, end);
+
+          seq.addSequenceFeature(sf);
+        }
+      }
+
+      viewport.showSequenceFeatures = true;
+      ((Alignment)viewport.alignment).featuresAdded = true;
+
+      alignPanel.repaint();
+
+    }
+    catch (Exception ex)
+    {
+      System.out.println("Error parsing groups file: " + ex);
+    }
+  }
+
+
   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 +234,13 @@ 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 AppletFormatAdapter().formatSequences(e.getActionCommand(),
                                               viewport.getAlignment().
                                               getSequences()));
   }
@@ -128,6 +249,8 @@ 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 +295,7 @@ 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 +303,7 @@ 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 +347,7 @@ public class AlignFrame
 
     updateEditMenuBar();
 
-    viewport.updateConsensus();
-    viewport.updateConservation();
-    alignPanel.repaint();
+    viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
   }
 
   public void moveSelectedSequences(boolean up)
@@ -401,7 +521,6 @@ public class AlignFrame
           newSeqs[i] = (SequenceI) seqs.elementAt(i);
         }
 
-        AlignFrame af = new AlignFrame(new Alignment(newSeqs), applet);
         String newtitle = new String("Copied sequences");
         if (getTitle().startsWith("Copied sequences"))
         {
@@ -411,6 +530,8 @@ public class AlignFrame
         {
           newtitle = newtitle.concat("- from " + getTitle());
         }
+        AlignFrame af = new AlignFrame(new Alignment(newSeqs), applet, newtitle);
+
         jalview.bin.JalviewLite.addFrame(af, newtitle, NEW_WINDOW_WIDTH,
                                          NEW_WINDOW_HEIGHT);
       }
@@ -418,9 +539,7 @@ 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 +605,7 @@ public class AlignFrame
       catch (Exception ex)
       {}
     }
-    viewport.updateConservation();
-    viewport.updateConsensus();
-    alignPanel.repaint();
+    viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
 
   }
 
@@ -518,6 +635,7 @@ public class AlignFrame
     viewport.setSelectionGroup(null);
     viewport.getColumnSelection().clear();
     viewport.setSelectionGroup(null);
+    alignPanel.repaint();
     PaintRefresher.Refresh(null, viewport.alignment);
   }
 
@@ -557,8 +675,7 @@ public class AlignFrame
           viewport.alignment.deleteGroup(sg);
         }
       }
-
-      alignPanel.repaint();
+      viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
     }
   }
 
@@ -585,8 +702,7 @@ public class AlignFrame
           viewport.alignment.deleteGroup(sg);
         }
       }
-
-      alignPanel.repaint();
+      viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
     }
 
   }
@@ -606,10 +722,7 @@ public class AlignFrame
 
     viewport.setStartRes(seq.findIndex(startRes)-1);
 
-    viewport.updateConservation();
-    viewport.updateConsensus();
-    resetAllClustalSchemes();
-    alignPanel.repaint();
+    viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
   }
 
   public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
@@ -635,55 +748,106 @@ 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);
-    resetAllClustalSchemes();
-    viewport.updateConservation();
+    viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
+  }
+
+  public void alignmentChanged()
+  {
     viewport.updateConsensus();
+    viewport.updateConservation ();
+    resetAllColourSchemes();
+    if(alignPanel.overviewPanel!=null)
+      alignPanel.overviewPanel.updateOverviewImage();
     alignPanel.repaint();
   }
 
-  void resetAllClustalSchemes()
+  void resetAllColourSchemes()
   {
-    if(viewport.getGlobalColourScheme()!=null
-       && viewport.getGlobalColourScheme() instanceof ClustalxColourScheme)
+    ColourSchemeI cs = viewport.globalColourScheme;
+    if(cs!=null)
     {
-      ((ClustalxColourScheme)viewport.getGlobalColourScheme()).
-          resetClustalX(viewport.alignment.getSequences(),
-                        viewport.alignment.getWidth());
+      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 instanceof ClustalxColourScheme)
+      if(sg.cs!=null && sg.cs instanceof ClustalxColourScheme)
       {
         ((ClustalxColourScheme)sg.cs).resetClustalX(sg.sequences, sg.getWidth());
       }
+      sg.recalcConservation();
     }
   }
 
@@ -691,21 +855,17 @@ public class AlignFrame
 
   public void findMenuItem_actionPerformed(ActionEvent e)
   {
-    Finder finder = new Finder(alignPanel);
+    new Finder(alignPanel);
   }
 
   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)
   {
-    viewport.setShowFullId(fullSeqId.getState());
+    viewport.setShowJVSuffix(fullSeqId.getState());
     alignPanel.fontChanged();
     alignPanel.repaint();
   }
@@ -764,11 +924,6 @@ 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());
   }
@@ -1020,7 +1175,7 @@ public class AlignFrame
 
   public void userDefinedColour_actionPerformed(ActionEvent e)
   {
-    UserDefinedColours chooser = new UserDefinedColours(alignPanel, null);
+    new UserDefinedColours(alignPanel, null);
   }
 
   public void PIDColour_actionPerformed(ActionEvent e)
@@ -1074,13 +1229,31 @@ 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 &&
@@ -1092,11 +1265,7 @@ 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)
     {
@@ -1191,7 +1360,7 @@ public class AlignFrame
 
   protected void documentation_actionPerformed(ActionEvent e)
   {
-    jalview.bin.JalviewLite.showURL("http://www.jalview.org/help.html");
+    showURL("http://www.jalview.org/help.html");
   }
 
   protected void about_actionPerformed(ActionEvent e)
@@ -1258,4 +1427,36 @@ public class AlignFrame
     jalview.bin.JalviewLite.addFrame(frame, "Jalview", 580, 200);
 
   }
+
+  /**
+   * Displays the given URL in a new browser window
+   *
+   * @param url URL to display in browser window.
+   * <br>New window will be named "HELP_WINDOW"
+   */
+  public void showURL(String url)
+  {
+    showURL(url, "HELP");
+  }
+
+  public void showURL(String url, String target)
+  {
+    if (applet == null)
+    {
+      System.out.println("Not running as applet - no browser available.");
+    }
+    else
+    {
+      try
+      {
+        applet.getAppletContext().showDocument(new java.net.URL(url),
+                                               target);
+      }
+      catch (Exception ex)
+      {
+        ex.printStackTrace();
+      }
+    }
+  }
+
 }