From 5150ffd5baa1f58bb6b4059616bc6b9050326553 Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Thu, 12 May 2005 09:08:34 +0000
Subject: [PATCH] corrections for find when edit takes place

---
 src/jalview/appletgui/AlignmentPanel.java |   18 ++++++----
 src/jalview/appletgui/Finder.java         |   54 ++++++++++++++++++-----------
 src/jalview/appletgui/SeqCanvas.java      |   10 ++++--
 src/jalview/appletgui/SeqPanel.java       |    4 +--
 src/jalview/gui/AlignmentPanel.java       |   17 +++++----
 src/jalview/gui/Finder.java               |   48 ++++++++++++++++++-------
 src/jalview/gui/IdCanvas.java             |    4 +--
 src/jalview/gui/IdPanel.java              |    2 +-
 src/jalview/gui/SeqCanvas.java            |   10 ++++--
 src/jalview/gui/SeqPanel.java             |    3 +-
 10 files changed, 112 insertions(+), 58 deletions(-)

diff --git a/src/jalview/appletgui/AlignmentPanel.java b/src/jalview/appletgui/AlignmentPanel.java
index ddfc432..68746e3 100755
--- a/src/jalview/appletgui/AlignmentPanel.java
+++ b/src/jalview/appletgui/AlignmentPanel.java
@@ -76,6 +76,7 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
   {
      public void keyPressed(KeyEvent evt)
      {
+       System.out.println(evt.getKeyCode());
        switch(evt.getKeyCode())
        {
          case  27: // escape key
@@ -192,12 +193,17 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
    seqPanel.seqCanvas.highlightSearchResults( results );
 
    // do we need to scroll the panel?
-   if(results!=null && (av.getStartSeq()>results[0]
-                        || av.getEndSeq()<results[0]
-                        || av.getStartRes()>results[1]
-                        || av.getEndRes()<results[2]))
-       setScrollValues(results[1], results[0]);
-
+   if(results!=null)
+    {
+      SequenceI seq = av.alignment.getSequenceAt(results[0]);
+      int start = seq.findIndex( results[1] )-1;
+      int end = seq.findIndex( results[2] )-1;
+      if( av.getStartRes() > start
+          || av.getEndRes() < end
+          || (av.getStartSeq() > results[0]
+          || av.getEndSeq() < results[0]))
+        setScrollValues(start, results[0]);
+    }
 
  }
 
diff --git a/src/jalview/appletgui/Finder.java b/src/jalview/appletgui/Finder.java
index 0b1e319..ab4cd7b 100755
--- a/src/jalview/appletgui/Finder.java
+++ b/src/jalview/appletgui/Finder.java
@@ -12,6 +12,7 @@ public class Finder extends GFinder
   AlignmentPanel ap;
   Frame frame;
   SuperGroup searchGroup;
+  Vector searchResults;
 
   int seqIndex = 0;
   int resIndex = 0;
@@ -59,8 +60,32 @@ public class Finder extends GFinder
 
   public void createNewGroup_actionPerformed(ActionEvent e)
   {
-    for(int i=0; i<searchGroup.getSize(); i++)
-      av.alignment.addGroup( searchGroup.getGroupeAt(i));
+    jalview.schemes.UserColourScheme ucs = new jalview.schemes.UserColourScheme();
+   Color [] newColors = new Color[24];
+   for(int i=0; i<24; i++)
+     newColors[i] = new Color(60,160,115);
+
+   ucs.setColourScheme(newColors);
+   String searchString = textfield.getText();
+
+   searchGroup = new SuperGroup(searchString, ucs , true, true, false);
+
+
+    for(int i=0; i<searchResults.size(); i+=3)
+    {
+      // its possible edits may have occurred since search was performed
+      // account for this here
+
+      SequenceI seq = av.alignment.getSequenceAt( Integer.parseInt(searchResults.elementAt(i).toString()) );
+      int startRes = seq.findIndex( Integer.parseInt(searchResults.elementAt(i+1).toString()) )-1;
+      int endRes = seq.findIndex(   Integer.parseInt(searchResults.elementAt(i+2).toString()) )-1;
+
+      SequenceGroup sg = new SequenceGroup(searchString, ucs, true, true, false, startRes , endRes  );
+      sg.addSequence(seq);
+      av.alignment.addGroup(sg);
+      searchGroup.addGroup( sg );
+
+    }
 
     ap.av.alignment.addSuperGroup(searchGroup);
     ap.highlightSearchResults( null );
@@ -75,7 +100,7 @@ public class Finder extends GFinder
 
     com.stevesoft.pat.Regex regex = new  com.stevesoft.pat.Regex(searchString);
 
-    Vector searchResults = new Vector();
+    searchResults = new Vector();
     int [] allResults = null;
 
     Sequence seq;
@@ -100,15 +125,6 @@ public class Finder extends GFinder
     ///////////////////////////////////////////////
 
 
-    jalview.schemes.UserColourScheme ucs = new jalview.schemes.UserColourScheme();
-    Color [] newColors = new Color[24];
-    for(int i=0; i<24; i++)
-      newColors[i] = new Color(60,160,115);
-
-    ucs.setColourScheme(newColors);
-
-    searchGroup = new SuperGroup(searchString, ucs , true, true, false);
-
     int end = av.alignment.getHeight();
 
     SequenceGroup selection = av.getSelectionGroup();
@@ -162,15 +178,11 @@ public class Finder extends GFinder
            continue;
 
          searchResults.addElement( Integer.toString( seqIndex) );
-         searchResults.addElement( Integer.toString( resIndex+ Integer.parseInt(spaces.elementAt(resIndex).toString()) ) );
-         searchResults.addElement( Integer.toString( regex.matchedTo()-1 + Integer.parseInt(spaces.elementAt(regex.matchedTo()-1).toString()) ) );
-
-         SequenceGroup sg = new SequenceGroup(searchString, ucs, true, true, false,
-                                             resIndex+ Integer.parseInt(spaces.elementAt(resIndex).toString()) ,
-                                      regex.matchedTo()-1 + Integer.parseInt(spaces.elementAt(regex.matchedTo()-1).toString())
-            );
-         sg.addSequence((Sequence)av.getAlignment().getSequenceAt(seqIndex));
-         searchGroup.addGroup( sg );
+         int sres = seq.findPosition( resIndex+ Integer.parseInt(spaces.elementAt(resIndex).toString()) );
+         int eres = seq.findPosition( regex.matchedTo()-1 + Integer.parseInt(spaces.elementAt(regex.matchedTo()-1).toString()) );
+          searchResults.addElement( sres+"" );
+          searchResults.addElement( eres+"" );
+
 
          if(!findAll)
          {
diff --git a/src/jalview/appletgui/SeqCanvas.java b/src/jalview/appletgui/SeqCanvas.java
index 679d48b..db91d08 100755
--- a/src/jalview/appletgui/SeqCanvas.java
+++ b/src/jalview/appletgui/SeqCanvas.java
@@ -444,17 +444,21 @@ public void fastPaint(int horizontal, int vertical)
       for(int r=0; r<searchResults.length; r+=3)
       {
         int searchSeq = searchResults[r];
-        int searchStart = searchResults[r+1];
-        int searchEnd = searchResults[r+2];
 
         if (searchSeq >= y1 && searchSeq < y2)
         {
+          SequenceI seq = av.getAlignment().getSequenceAt(searchSeq);
+
+          int searchStart = seq.findIndex( searchResults[r+1] )-1;
+          int searchEnd =  seq.findIndex(  searchResults[r+2] )-1;
+
           SequenceRenderer ssr = (SequenceRenderer) sr;
           if(searchStart<x1)
             searchStart = x1;
           if(searchEnd > x2)
             searchEnd = x2;
-          ssr.drawHighlightedText(av.getAlignment().getSequenceAt(searchSeq),
+
+          ssr.drawHighlightedText(seq,
                                   searchStart,
                                   searchEnd,
                                   (searchStart - startx) * av.charWidth,
diff --git a/src/jalview/appletgui/SeqPanel.java b/src/jalview/appletgui/SeqPanel.java
index 6e4a34f..7df2254 100755
--- a/src/jalview/appletgui/SeqPanel.java
+++ b/src/jalview/appletgui/SeqPanel.java
@@ -344,10 +344,10 @@ public class SeqPanel extends Panel
   {
 
     if ( jalview.util.Comparison.isGap( av.alignment.getSequenceAt(seq).getSequence().charAt(j)))
-        av.alignment.getSequenceAt(seq).deleteCharAt(j);
+      av.alignment.getSequenceAt(seq).deleteCharAt(j);
 
     av.alignment.getWidth();
-    seqCanvas.repaint();
+    repaint();
     seqEditOccurred=seq;
   }
 
diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java
index 26b470a..b339e51 100755
--- a/src/jalview/gui/AlignmentPanel.java
+++ b/src/jalview/gui/AlignmentPanel.java
@@ -156,12 +156,17 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
    seqPanel.seqCanvas.highlightSearchResults( results );
 
    // do we need to scroll the panel?
-   if(results!=null && (av.getStartSeq()>results[0]
-                        || av.getEndSeq()<results[0]
-                        || av.getStartRes()>results[1]
-                        || av.getEndRes()<results[2]))
-       setScrollValues(results[1], results[0]);
-
+   if(results!=null)
+    {
+      SequenceI seq = av.alignment.getSequenceAt(results[0]);
+      int start = seq.findIndex( results[1] )-1;
+      int end = seq.findIndex( results[2] )-1;
+      if( av.getStartRes() > start
+          || av.getEndRes() < end
+          || (av.getStartSeq() > results[0]
+          || av.getEndSeq() < results[0]))
+        setScrollValues(start, results[0]);
+    }
 
  }
 
diff --git a/src/jalview/gui/Finder.java b/src/jalview/gui/Finder.java
index 5a2dfe9..594baf8 100755
--- a/src/jalview/gui/Finder.java
+++ b/src/jalview/gui/Finder.java
@@ -14,6 +14,7 @@ public class Finder extends GFinder
   AlignmentPanel ap;
   JInternalFrame frame;
   SuperGroup searchGroup;
+  Vector searchResults;
 
   int seqIndex = 0;
   int resIndex = 0;
@@ -74,8 +75,32 @@ public class Finder extends GFinder
 
   public void createNewGroup_actionPerformed(ActionEvent e)
   {
-    for(int i=0; i<searchGroup.getSize(); i++)
-      av.alignment.addGroup( searchGroup.getGroupeAt(i));
+    jalview.schemes.UserColourScheme ucs = new jalview.schemes.UserColourScheme();
+   Color [] newColors = new Color[24];
+   for(int i=0; i<24; i++)
+     newColors[i] = new Color(60,160,115);
+
+   ucs.setColourScheme(newColors);
+   String searchString = textfield.getText();
+
+   searchGroup = new SuperGroup(searchString, ucs , true, true, false);
+
+
+    for(int i=0; i<searchResults.size(); i+=3)
+    {
+      // its possible edits may have occurred since search was performed
+      // account for this here
+
+      SequenceI seq = av.alignment.getSequenceAt( Integer.parseInt(searchResults.elementAt(i).toString()) );
+      int startRes = seq.findIndex( Integer.parseInt(searchResults.elementAt(i+1).toString()) )-1;
+      int endRes = seq.findIndex(   Integer.parseInt(searchResults.elementAt(i+2).toString()) )-1;
+
+      SequenceGroup sg = new SequenceGroup(searchString, ucs, true, true, false, startRes , endRes  );
+      sg.addSequence(seq);
+      av.alignment.addGroup(sg);
+      searchGroup.addGroup( sg );
+
+    }
 
     ap.av.alignment.addSuperGroup(searchGroup);
     ap.highlightSearchResults( null );
@@ -90,7 +115,7 @@ public class Finder extends GFinder
 
     com.stevesoft.pat.Regex regex = new  com.stevesoft.pat.Regex(searchString);
 
-    ArrayList searchResults = new ArrayList();
+    searchResults = new Vector();
     int [] allResults = null;
 
     Sequence seq;
@@ -151,7 +176,7 @@ public class Finder extends GFinder
       ///Shall we ignore gaps????
       StringBuffer noGaps = new StringBuffer();
       int insertCount=0;
-      ArrayList spaces = new ArrayList();
+      Vector spaces = new Vector();
 
       for (int j=0; j < item.length(); j++)
       {
@@ -177,15 +202,12 @@ public class Finder extends GFinder
            continue;
 
          searchResults.add( Integer.toString( seqIndex) );
-         searchResults.add( Integer.toString( resIndex+ Integer.parseInt(spaces.get(resIndex).toString()) ) );
-         searchResults.add( Integer.toString( regex.matchedTo()-1 + Integer.parseInt(spaces.get(regex.matchedTo()-1).toString()) ) );
 
-         SequenceGroup sg = new SequenceGroup(searchString, ucs, true, true, false,
-                                             resIndex+ Integer.parseInt(spaces.get(resIndex).toString()) ,
-                                      regex.matchedTo()-1 + Integer.parseInt(spaces.get(regex.matchedTo()-1).toString())
-            );
-         sg.addSequence((Sequence)av.getAlignment().getSequenceAt(seqIndex));
-         searchGroup.addGroup( sg );
+         int sres = seq.findPosition( resIndex+ Integer.parseInt(spaces.elementAt(resIndex).toString()) );
+         int eres = seq.findPosition( regex.matchedTo()-1 + Integer.parseInt(spaces.elementAt(regex.matchedTo()-1).toString()) );
+
+          searchResults.addElement( sres+"" );
+          searchResults.addElement( eres+"" );
 
          if(!findAll)
          {
@@ -206,7 +228,7 @@ public class Finder extends GFinder
     }
 
 
-    ArrayList idMatch = new ArrayList();
+    Vector idMatch = new Vector();
     for(int id = 0; id<av.alignment.getHeight(); id++)
     {
       if(   regex.search( av.alignment.getSequenceAt(id).getName() ) )
diff --git a/src/jalview/gui/IdCanvas.java b/src/jalview/gui/IdCanvas.java
index 048fb37..882ed7a 100755
--- a/src/jalview/gui/IdCanvas.java
+++ b/src/jalview/gui/IdCanvas.java
@@ -19,7 +19,7 @@ public class IdCanvas extends JPanel
   int imgHeight=0;
   boolean fastPaint = false;
 
-  java.util.ArrayList searchResults;
+  java.util.Vector searchResults;
 
   public IdCanvas(AlignViewport av)
   {
@@ -193,7 +193,7 @@ public class IdCanvas extends JPanel
 
   }
 
-  public void setHighlighted(java.util.ArrayList found)
+  public void setHighlighted(java.util.Vector found)
   {
     searchResults = found;
     repaint();
diff --git a/src/jalview/gui/IdPanel.java b/src/jalview/gui/IdPanel.java
index fcf8e92..0b5d956 100755
--- a/src/jalview/gui/IdPanel.java
+++ b/src/jalview/gui/IdPanel.java
@@ -176,7 +176,7 @@ public class IdPanel extends JPanel implements MouseListener, MouseMotionListene
     PaintRefresher.Refresh(this);
   }
 
-  public void highlightSearchResults( java.util.ArrayList found )
+  public void highlightSearchResults( java.util.Vector found )
   {
     idCanvas.setHighlighted( found );
 
diff --git a/src/jalview/gui/SeqCanvas.java b/src/jalview/gui/SeqCanvas.java
index 74f6274..12659a8 100755
--- a/src/jalview/gui/SeqCanvas.java
+++ b/src/jalview/gui/SeqCanvas.java
@@ -450,17 +450,21 @@ public void fastPaint(int horizontal, int vertical)
       for(int r=0; r<searchResults.length; r+=3)
       {
         int searchSeq = searchResults[r];
-        int searchStart = searchResults[r+1];
-        int searchEnd = searchResults[r+2];
 
         if (searchSeq >= y1 && searchSeq < y2)
         {
+          SequenceI seq = av.getAlignment().getSequenceAt(searchSeq);
+
+          int searchStart = seq.findIndex( searchResults[r+1] )-1;
+          int searchEnd =  seq.findIndex(  searchResults[r+2] )-1;
+
           SequenceRenderer ssr = (SequenceRenderer) sr;
           if(searchStart<x1)
             searchStart = x1;
           if(searchEnd > x2)
             searchEnd = x2;
-          ssr.drawHighlightedText(av.getAlignment().getSequenceAt(searchSeq),
+
+          ssr.drawHighlightedText(seq,
                                   searchStart,
                                   searchEnd,
                                   (searchStart - startx) * av.charWidth,
diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java
index ddbd97c..162f978 100755
--- a/src/jalview/gui/SeqPanel.java
+++ b/src/jalview/gui/SeqPanel.java
@@ -347,11 +347,12 @@ public class SeqPanel extends JPanel
   {
 
     if ( jalview.util.Comparison.isGap( av.alignment.getSequenceAt(seq).getSequence().charAt(j)))
-        av.alignment.getSequenceAt(seq).deleteCharAt(j);
+      av.alignment.getSequenceAt(seq).deleteCharAt(j);
 
     av.alignment.getWidth();
     repaint();
     seqEditOccurred=seq;
+
   }
 
 
-- 
1.7.10.2