X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAlignFrame.java;h=fae50d9e45073d08a22f98813773b311637f8fdb;hb=4f8907121d304b0f9b499578578c3381b815db9d;hp=491d2beedd6f687b62d990c2b8b1acca4841c2be;hpb=187b75ac779575fa0399f7c3991dcd7bade8ca90;p=jalview.git

diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index 491d2be..fae50d9 100755
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -27,6 +27,8 @@ import jalview.io.*;
 import java.awt.*;
 import java.awt.event.*;
 import java.util.*;
+import java.io.InputStreamReader;
+import java.io.BufferedReader;
 
 public class AlignFrame
     extends GAlignFrame
@@ -44,8 +46,18 @@ public class AlignFrame
     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)
   {
     this.applet = applet;
@@ -55,7 +67,6 @@ public class AlignFrame
     alignPanel.validate();
 
     String treeFile = applet.getParameter("treeFile");
-    TreePanel treepanel = null;
     if (treeFile != null)
     {
       try
@@ -80,6 +91,16 @@ public class AlignFrame
       }
     }
 
+    this.addWindowListener(new WindowAdapter()
+    {
+      public void windowClosing(WindowEvent e)
+          {
+            closeMenuItem_actionPerformed(null);
+          }
+    });
+
+
+
   }
 
   public void inputText_actionPerformed(ActionEvent e)
@@ -105,6 +126,7 @@ public class AlignFrame
 
   public void closeMenuItem_actionPerformed(ActionEvent e)
   {
+    PaintRefresher.components.remove(viewport.alignment);
     dispose();
   }
 
@@ -278,30 +300,55 @@ public class AlignFrame
       orderedSeqs.put(index + "", seq);
     }
 
-    int index = 0;
+    int index = 0, startRes, endRes;
+    char ch;
+
     for (int i = 0; i < sg.getSize(); i++)
     {
-      SequenceI seq = null;
-      while (seq == null)
-      {
-        if (orderedSeqs.containsKey(index + ""))
+        SequenceI seq = null;
+
+        while (seq == null)
         {
-          seq = (SequenceI) orderedSeqs.get(index + "");
-          index++;
-          break;
+            if (orderedSeqs.containsKey(index + ""))
+            {
+                seq = (SequenceI) orderedSeqs.get(index + "");
+                index++;
+
+                break;
+            }
+            else
+            {
+                index++;
+            }
         }
-        else
+
+        //FIND START RES
+        //Returns residue following index if gap
+        startRes = seq.findPosition(sg.getStartRes());
+
+        //FIND END RES
+        //Need to find the residue preceeding index if gap
+        endRes = 0;
+
+        for (int j = 0; j < sg.getEndRes()+1 && j < seq.getLength(); j++)
         {
-          index++;
+          ch = seq.getCharAt(j);
+          if (!jalview.util.Comparison.isGap( (ch)))
+          {
+            endRes++;
+          }
+        }
+
+        if(endRes>0)
+        {
+          endRes += seq.getStart() -1;
         }
-      }
 
-      copiedSequences.append(seq.getName() + "\t" +
-                             seq.findPosition(sg.getStartRes()) + "\t"
-                             + seq.findPosition(sg.getEndRes()) + "\t"
-                             +
-                             sg.getSequenceAt(i).getSequence(sg.getStartRes(),
-          sg.getEndRes() + 1) + "\n");
+        copiedSequences.append(seq.getName() + "\t" +
+            startRes + "\t" +
+            endRes + "\t" +
+            seq.getSequence(sg.getStartRes(),
+                sg.getEndRes() + 1) + "\n");
     }
 
   }
@@ -460,10 +507,10 @@ 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);
+    PaintRefresher.Refresh(null, viewport.alignment);
   }
 
   public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
@@ -471,7 +518,7 @@ public class AlignFrame
     viewport.setSelectionGroup(null);
     viewport.getColumnSelection().clear();
     viewport.setSelectionGroup(null);
-    PaintRefresher.Refresh(null);
+    PaintRefresher.Refresh(null, viewport.alignment);
   }
 
   public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
@@ -482,7 +529,7 @@ public class AlignFrame
       sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
     }
 
-    PaintRefresher.Refresh(null);
+    PaintRefresher.Refresh(null, viewport.alignment);
   }
 
   public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
@@ -567,8 +614,9 @@ public class AlignFrame
 
     int start=0, end = viewport.alignment.getWidth();
 
-    if(viewport.getSelectionGroup()!=null
-     || viewport.getSelectionGroup().sequences.size()<1)
+    if (viewport.getSelectionGroup() != null
+        && viewport.getSelectionGroup().sequences != null
+        && viewport.getSelectionGroup().sequences.size()>0)
     {
       seqs = viewport.getSelectionGroup().sequences;
       start = viewport.getSelectionGroup().getStartRes();
@@ -775,53 +823,48 @@ 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);
-      }
+        threshold = SliderPanel.setPIDSliderSource(alignPanel, cs, "Background");
 
-      viewport.setGlobalColourScheme(cs);
-    }
-    else if (cs instanceof ResidueColourScheme)
-    {
-      ( (ResidueColourScheme) cs).setThreshold(0);
-    }
+        cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
 
-    if (viewport.getConservationSelected())
-    {
-      ConservationColourScheme ccs = null;
+        viewport.setGlobalColourScheme(cs);
+      }
+      else
+      {
+        cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
+      }
 
-      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);
 
-      // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!
-      ccs.setConsensus(viewport.vconsensus);
-      viewport.setGlobalColourScheme(ccs);
+        cs.setConservation(c);
 
-      SliderPanel.setConservationSlider(alignPanel, ccs, "Background");
+        cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel, cs,
+            "Background"));
 
-    }
-    else
-    {
-      // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!
-      if (cs != null)
+      }
+      else
       {
-        cs.setConsensus(viewport.vconsensus);
+        cs.setConservation(null);
       }
-      viewport.setGlobalColourScheme(cs);
+
+      cs.setConsensus(viewport.vconsensus);
+
     }
+    viewport.setGlobalColourScheme(cs);
 
     if (viewport.getColourAppliesToAllGroups())
     {
@@ -837,9 +880,7 @@ public class AlignFrame
         }
         if (cs instanceof ClustalxColourScheme)
         {
-          ClustalxColourScheme cxs = (ClustalxColourScheme) cs;
-          cxs.resetClustalX(viewport.alignment.getSequences(), viewport.alignment.getWidth());
-          sg.cs = cxs;
+          sg.cs = new ClustalxColourScheme(sg.sequences, sg.getWidth());
         }
         else
         {
@@ -854,15 +895,15 @@ 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);
-          }
-
+          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())
         {
@@ -872,21 +913,18 @@ 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;
+          sg.cs.setConservation(c);
         }
         else
         {
-          // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!
-          sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0, sg.getWidth()));
+          sg.cs.setConservation(null);
+          sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
         }
 
       }
     }
 
+
     if (alignPanel.getOverviewPanel() != null)
     {
       alignPanel.getOverviewPanel().updateOverviewImage();
@@ -895,9 +933,11 @@ public class AlignFrame
     alignPanel.repaint();
   }
 
+
+
   protected void modifyPID_actionPerformed(ActionEvent e)
   {
-    if (viewport.getAbovePIDThreshold())
+    if (viewport.getAbovePIDThreshold() && viewport.globalColourScheme!=null)
     {
       SliderPanel.setPIDSliderSource(alignPanel, viewport.getGlobalColourScheme(),
                                      "Background");
@@ -907,7 +947,7 @@ public class AlignFrame
 
   protected void modifyConservation_actionPerformed(ActionEvent e)
   {
-    if (viewport.getConservationSelected())
+    if (viewport.getConservationSelected() && viewport.globalColourScheme!=null)
     {
       SliderPanel.setConservationSlider(alignPanel, viewport.globalColourScheme,
                                         "Background");
@@ -922,15 +962,7 @@ public class AlignFrame
     viewport.setAbovePIDThreshold(false);
     abovePIDThreshold.setState(false);
 
-    ColourSchemeI cs = viewport.getGlobalColourScheme();
-    if (cs instanceof ConservationColourScheme)
-    {
-      changeColour( ( (ConservationColourScheme) cs).cs);
-    }
-    else
-    {
-      changeColour(cs);
-    }
+    changeColour(viewport.getGlobalColourScheme());
 
     modifyConservation_actionPerformed(null);
   }
@@ -942,16 +974,7 @@ public class AlignFrame
     conservationMenuItem.setState(false);
     viewport.setConservationSelected(false);
 
-    ColourSchemeI cs = viewport.getGlobalColourScheme();
-
-    if (cs instanceof ConservationColourScheme)
-    {
-      changeColour( ( (ConservationColourScheme) cs).cs);
-    }
-    else
-    {
-      changeColour(cs);
-    }
+    changeColour(viewport.getGlobalColourScheme());
 
     modifyPID_actionPerformed(null);
   }
@@ -1067,7 +1090,21 @@ public class AlignFrame
     //are the sequences aligned?
     if (!viewport.alignment.isAligned())
     {
-      return;
+      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();
+
     }
 
     final TreePanel tp;
@@ -1120,9 +1157,13 @@ public class AlignFrame
 
   protected void about_actionPerformed(ActionEvent e)
   {
-    class AboutPanel
-        extends Canvas
+
+    class AboutPanel extends Canvas
     {
+      String version;
+      public AboutPanel(String version)
+      { this.version = version; }
+
       public void paint(Graphics g)
       {
         g.setColor(Color.white);
@@ -1133,7 +1174,7 @@ public class AlignFrame
         int y = 5, x = 7;
         g.setColor(Color.black);
         g.setFont(new Font("Helvetica", Font.BOLD, 14));
-        g.drawString("JalView - Release 2.01", 200, y += fh);
+        g.drawString("Jalview - Release "+version, 200, y += fh);
         g.setFont(new Font("Helvetica", Font.PLAIN, 12));
         g.drawString("Authors:  Michele Clamp, James Cuff, Steve Searle, Andrew Waterhouse, Jim Procter & Geoff Barton.",
                      x, y += fh * 2);
@@ -1149,8 +1190,32 @@ public class AlignFrame
       }
     }
 
+    String version = "test";
+    java.net.URL url = getClass().getResource("/.build_properties");
+    if (url != null)
+    {
+      try
+      {
+        BufferedReader reader = new BufferedReader(new InputStreamReader(
+            url.openStream()));
+        String line;
+        while ( (line = reader.readLine()) != null)
+        {
+          if (line.indexOf("VERSION") > -1)
+          {
+            version = line.substring(line.indexOf("=") + 1);
+          }
+        }
+      }
+      catch (Exception ex)
+      {
+        ex.printStackTrace();
+      }
+    }
+
+
     Frame frame = new Frame();
-    frame.add(new AboutPanel());
+    frame.add(new AboutPanel(version));
     jalview.bin.JalviewLite.addFrame(frame, "Jalview", 580, 200);
 
   }