corrections for find when edit takes place

diff --git a/src/jalview/appletgui/AlignmentPanel.java b/src/jalview/appletgui/AlignmentPanel.java
index ddfc432..68746e3 100755 (executable)
--- a/src/jalview/appletgui/AlignmentPanel.java
+++ b/src/jalview/appletgui/AlignmentPanel.java
@@ -76,6 +76,7 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
   {\r
      public void keyPressed(KeyEvent evt)\r
      {\r
+       System.out.println(evt.getKeyCode());\r
        switch(evt.getKeyCode())\r
        {\r
          case  27: // escape key\r
@@ -192,12 +193,17 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
    seqPanel.seqCanvas.highlightSearchResults( results );\r
 \r
    // do we need to scroll the panel?\r
-   if(results!=null && (av.getStartSeq()>results[0]\r
-                        || av.getEndSeq()<results[0]\r
-                        || av.getStartRes()>results[1]\r
-                        || av.getEndRes()<results[2]))\r
-       setScrollValues(results[1], results[0]);\r
-\r
+   if(results!=null)\r
+    {\r
+      SequenceI seq = av.alignment.getSequenceAt(results[0]);\r
+      int start = seq.findIndex( results[1] )-1;\r
+      int end = seq.findIndex( results[2] )-1;\r
+      if( av.getStartRes() > start\r
+          || av.getEndRes() < end\r
+          || (av.getStartSeq() > results[0]\r
+          || av.getEndSeq() < results[0]))\r
+        setScrollValues(start, results[0]);\r
+    }\r
 \r
  }\r
 \r

diff --git a/src/jalview/appletgui/Finder.java b/src/jalview/appletgui/Finder.java
index 0b1e319..ab4cd7b 100755 (executable)
--- a/src/jalview/appletgui/Finder.java
+++ b/src/jalview/appletgui/Finder.java
@@ -12,6 +12,7 @@ public class Finder extends GFinder
   AlignmentPanel ap;\r
   Frame frame;\r
   SuperGroup searchGroup;\r
+  Vector searchResults;\r
 \r
   int seqIndex = 0;\r
   int resIndex = 0;\r
@@ -59,8 +60,32 @@ public class Finder extends GFinder
 \r
   public void createNewGroup_actionPerformed(ActionEvent e)\r
   {\r
-    for(int i=0; i<searchGroup.getSize(); i++)\r
-      av.alignment.addGroup( searchGroup.getGroupeAt(i));\r
+    jalview.schemes.UserColourScheme ucs = new jalview.schemes.UserColourScheme();\r
+   Color [] newColors = new Color[24];\r
+   for(int i=0; i<24; i++)\r
+     newColors[i] = new Color(60,160,115);\r
+\r
+   ucs.setColourScheme(newColors);\r
+   String searchString = textfield.getText();\r
+\r
+   searchGroup = new SuperGroup(searchString, ucs , true, true, false);\r
+\r
+\r
+    for(int i=0; i<searchResults.size(); i+=3)\r
+    {\r
+      // its possible edits may have occurred since search was performed\r
+      // account for this here\r
+\r
+      SequenceI seq = av.alignment.getSequenceAt( Integer.parseInt(searchResults.elementAt(i).toString()) );\r
+      int startRes = seq.findIndex( Integer.parseInt(searchResults.elementAt(i+1).toString()) )-1;\r
+      int endRes = seq.findIndex(   Integer.parseInt(searchResults.elementAt(i+2).toString()) )-1;\r
+\r
+      SequenceGroup sg = new SequenceGroup(searchString, ucs, true, true, false, startRes , endRes  );\r
+      sg.addSequence(seq);\r
+      av.alignment.addGroup(sg);\r
+      searchGroup.addGroup( sg );\r
+\r
+    }\r
 \r
     ap.av.alignment.addSuperGroup(searchGroup);\r
     ap.highlightSearchResults( null );\r
@@ -75,7 +100,7 @@ public class Finder extends GFinder
 \r
     com.stevesoft.pat.Regex regex = new  com.stevesoft.pat.Regex(searchString);\r
 \r
-    Vector searchResults = new Vector();\r
+    searchResults = new Vector();\r
     int [] allResults = null;\r
 \r
     Sequence seq;\r
@@ -100,15 +125,6 @@ public class Finder extends GFinder
     ///////////////////////////////////////////////\r
 \r
 \r
-    jalview.schemes.UserColourScheme ucs = new jalview.schemes.UserColourScheme();\r
-    Color [] newColors = new Color[24];\r
-    for(int i=0; i<24; i++)\r
-      newColors[i] = new Color(60,160,115);\r
-\r
-    ucs.setColourScheme(newColors);\r
-\r
-    searchGroup = new SuperGroup(searchString, ucs , true, true, false);\r
-\r
     int end = av.alignment.getHeight();\r
 \r
     SequenceGroup selection = av.getSelectionGroup();\r
@@ -162,15 +178,11 @@ public class Finder extends GFinder
            continue;\r
 \r
          searchResults.addElement( Integer.toString( seqIndex) );\r
-         searchResults.addElement( Integer.toString( resIndex+ Integer.parseInt(spaces.elementAt(resIndex).toString()) ) );\r
-         searchResults.addElement( Integer.toString( regex.matchedTo()-1 + Integer.parseInt(spaces.elementAt(regex.matchedTo()-1).toString()) ) );\r
-\r
-         SequenceGroup sg = new SequenceGroup(searchString, ucs, true, true, false,\r
-                                             resIndex+ Integer.parseInt(spaces.elementAt(resIndex).toString()) ,\r
-                                      regex.matchedTo()-1 + Integer.parseInt(spaces.elementAt(regex.matchedTo()-1).toString())\r
-            );\r
-         sg.addSequence((Sequence)av.getAlignment().getSequenceAt(seqIndex));\r
-         searchGroup.addGroup( sg );\r
+         int sres = seq.findPosition( resIndex+ Integer.parseInt(spaces.elementAt(resIndex).toString()) );\r
+         int eres = seq.findPosition( regex.matchedTo()-1 + Integer.parseInt(spaces.elementAt(regex.matchedTo()-1).toString()) );\r
+          searchResults.addElement( sres+"" );\r
+          searchResults.addElement( eres+"" );\r
+\r
 \r
          if(!findAll)\r
          {\r

diff --git a/src/jalview/appletgui/SeqCanvas.java b/src/jalview/appletgui/SeqCanvas.java
index 679d48b..db91d08 100755 (executable)
--- 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)\r
       {\r
         int searchSeq = searchResults[r];\r
-        int searchStart = searchResults[r+1];\r
-        int searchEnd = searchResults[r+2];\r
 \r
         if (searchSeq >= y1 && searchSeq < y2)\r
         {\r
+          SequenceI seq = av.getAlignment().getSequenceAt(searchSeq);\r
+\r
+          int searchStart = seq.findIndex( searchResults[r+1] )-1;\r
+          int searchEnd =  seq.findIndex(  searchResults[r+2] )-1;\r
+\r
           SequenceRenderer ssr = (SequenceRenderer) sr;\r
           if(searchStart<x1)\r
             searchStart = x1;\r
           if(searchEnd > x2)\r
             searchEnd = x2;\r
-          ssr.drawHighlightedText(av.getAlignment().getSequenceAt(searchSeq),\r
+\r
+          ssr.drawHighlightedText(seq,\r
                                   searchStart,\r
                                   searchEnd,\r
                                   (searchStart - startx) * av.charWidth,\r

diff --git a/src/jalview/appletgui/SeqPanel.java b/src/jalview/appletgui/SeqPanel.java
index 6e4a34f..7df2254 100755 (executable)
--- a/src/jalview/appletgui/SeqPanel.java
+++ b/src/jalview/appletgui/SeqPanel.java
@@ -344,10 +344,10 @@ public class SeqPanel extends Panel
   {\r
 \r
     if ( jalview.util.Comparison.isGap( av.alignment.getSequenceAt(seq).getSequence().charAt(j)))\r
-        av.alignment.getSequenceAt(seq).deleteCharAt(j);\r
+      av.alignment.getSequenceAt(seq).deleteCharAt(j);\r
 \r
     av.alignment.getWidth();\r
-    seqCanvas.repaint();\r
+    repaint();\r
     seqEditOccurred=seq;\r
   }\r
 \r

diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java
index 26b470a..b339e51 100755 (executable)
--- 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 );\r
 \r
    // do we need to scroll the panel?\r
-   if(results!=null && (av.getStartSeq()>results[0]\r
-                        || av.getEndSeq()<results[0]\r
-                        || av.getStartRes()>results[1]\r
-                        || av.getEndRes()<results[2]))\r
-       setScrollValues(results[1], results[0]);\r
-\r
+   if(results!=null)\r
+    {\r
+      SequenceI seq = av.alignment.getSequenceAt(results[0]);\r
+      int start = seq.findIndex( results[1] )-1;\r
+      int end = seq.findIndex( results[2] )-1;\r
+      if( av.getStartRes() > start\r
+          || av.getEndRes() < end\r
+          || (av.getStartSeq() > results[0]\r
+          || av.getEndSeq() < results[0]))\r
+        setScrollValues(start, results[0]);\r
+    }\r
 \r
  }\r
 \r

diff --git a/src/jalview/gui/Finder.java b/src/jalview/gui/Finder.java
index 5a2dfe9..594baf8 100755 (executable)
--- a/src/jalview/gui/Finder.java
+++ b/src/jalview/gui/Finder.java
@@ -14,6 +14,7 @@ public class Finder extends GFinder
   AlignmentPanel ap;\r
   JInternalFrame frame;\r
   SuperGroup searchGroup;\r
+  Vector searchResults;\r
 \r
   int seqIndex = 0;\r
   int resIndex = 0;\r
@@ -74,8 +75,32 @@ public class Finder extends GFinder
 \r
   public void createNewGroup_actionPerformed(ActionEvent e)\r
   {\r
-    for(int i=0; i<searchGroup.getSize(); i++)\r
-      av.alignment.addGroup( searchGroup.getGroupeAt(i));\r
+    jalview.schemes.UserColourScheme ucs = new jalview.schemes.UserColourScheme();\r
+   Color [] newColors = new Color[24];\r
+   for(int i=0; i<24; i++)\r
+     newColors[i] = new Color(60,160,115);\r
+\r
+   ucs.setColourScheme(newColors);\r
+   String searchString = textfield.getText();\r
+\r
+   searchGroup = new SuperGroup(searchString, ucs , true, true, false);\r
+\r
+\r
+    for(int i=0; i<searchResults.size(); i+=3)\r
+    {\r
+      // its possible edits may have occurred since search was performed\r
+      // account for this here\r
+\r
+      SequenceI seq = av.alignment.getSequenceAt( Integer.parseInt(searchResults.elementAt(i).toString()) );\r
+      int startRes = seq.findIndex( Integer.parseInt(searchResults.elementAt(i+1).toString()) )-1;\r
+      int endRes = seq.findIndex(   Integer.parseInt(searchResults.elementAt(i+2).toString()) )-1;\r
+\r
+      SequenceGroup sg = new SequenceGroup(searchString, ucs, true, true, false, startRes , endRes  );\r
+      sg.addSequence(seq);\r
+      av.alignment.addGroup(sg);\r
+      searchGroup.addGroup( sg );\r
+\r
+    }\r
 \r
     ap.av.alignment.addSuperGroup(searchGroup);\r
     ap.highlightSearchResults( null );\r
@@ -90,7 +115,7 @@ public class Finder extends GFinder
 \r
     com.stevesoft.pat.Regex regex = new  com.stevesoft.pat.Regex(searchString);\r
 \r
-    ArrayList searchResults = new ArrayList();\r
+    searchResults = new Vector();\r
     int [] allResults = null;\r
 \r
     Sequence seq;\r
@@ -151,7 +176,7 @@ public class Finder extends GFinder
       ///Shall we ignore gaps????\r
       StringBuffer noGaps = new StringBuffer();\r
       int insertCount=0;\r
-      ArrayList spaces = new ArrayList();\r
+      Vector spaces = new Vector();\r
 \r
       for (int j=0; j < item.length(); j++)\r
       {\r
@@ -177,15 +202,12 @@ public class Finder extends GFinder
            continue;\r
 \r
          searchResults.add( Integer.toString( seqIndex) );\r
-         searchResults.add( Integer.toString( resIndex+ Integer.parseInt(spaces.get(resIndex).toString()) ) );\r
-         searchResults.add( Integer.toString( regex.matchedTo()-1 + Integer.parseInt(spaces.get(regex.matchedTo()-1).toString()) ) );\r
 \r
-         SequenceGroup sg = new SequenceGroup(searchString, ucs, true, true, false,\r
-                                             resIndex+ Integer.parseInt(spaces.get(resIndex).toString()) ,\r
-                                      regex.matchedTo()-1 + Integer.parseInt(spaces.get(regex.matchedTo()-1).toString())\r
-            );\r
-         sg.addSequence((Sequence)av.getAlignment().getSequenceAt(seqIndex));\r
-         searchGroup.addGroup( sg );\r
+         int sres = seq.findPosition( resIndex+ Integer.parseInt(spaces.elementAt(resIndex).toString()) );\r
+         int eres = seq.findPosition( regex.matchedTo()-1 + Integer.parseInt(spaces.elementAt(regex.matchedTo()-1).toString()) );\r
+\r
+          searchResults.addElement( sres+"" );\r
+          searchResults.addElement( eres+"" );\r
 \r
          if(!findAll)\r
          {\r
@@ -206,7 +228,7 @@ public class Finder extends GFinder
     }\r
 \r
 \r
-    ArrayList idMatch = new ArrayList();\r
+    Vector idMatch = new Vector();\r
     for(int id = 0; id<av.alignment.getHeight(); id++)\r
     {\r
       if(   regex.search( av.alignment.getSequenceAt(id).getName() ) )\r

diff --git a/src/jalview/gui/IdCanvas.java b/src/jalview/gui/IdCanvas.java
index 048fb37..882ed7a 100755 (executable)
--- a/src/jalview/gui/IdCanvas.java
+++ b/src/jalview/gui/IdCanvas.java
@@ -19,7 +19,7 @@ public class IdCanvas extends JPanel
   int imgHeight=0;\r
   boolean fastPaint = false;\r
 \r
-  java.util.ArrayList searchResults;\r
+  java.util.Vector searchResults;\r
 \r
   public IdCanvas(AlignViewport av)\r
   {\r
@@ -193,7 +193,7 @@ public class IdCanvas extends JPanel
 \r
   }\r
 \r
-  public void setHighlighted(java.util.ArrayList found)\r
+  public void setHighlighted(java.util.Vector found)\r
   {\r
     searchResults = found;\r
     repaint();\r

diff --git a/src/jalview/gui/IdPanel.java b/src/jalview/gui/IdPanel.java
index fcf8e92..0b5d956 100755 (executable)
--- 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);\r
   }\r
 \r
-  public void highlightSearchResults( java.util.ArrayList found )\r
+  public void highlightSearchResults( java.util.Vector found )\r
   {\r
     idCanvas.setHighlighted( found );\r
 \r

diff --git a/src/jalview/gui/SeqCanvas.java b/src/jalview/gui/SeqCanvas.java
index 74f6274..12659a8 100755 (executable)
--- 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)\r
       {\r
         int searchSeq = searchResults[r];\r
-        int searchStart = searchResults[r+1];\r
-        int searchEnd = searchResults[r+2];\r
 \r
         if (searchSeq >= y1 && searchSeq < y2)\r
         {\r
+          SequenceI seq = av.getAlignment().getSequenceAt(searchSeq);\r
+\r
+          int searchStart = seq.findIndex( searchResults[r+1] )-1;\r
+          int searchEnd =  seq.findIndex(  searchResults[r+2] )-1;\r
+\r
           SequenceRenderer ssr = (SequenceRenderer) sr;\r
           if(searchStart<x1)\r
             searchStart = x1;\r
           if(searchEnd > x2)\r
             searchEnd = x2;\r
-          ssr.drawHighlightedText(av.getAlignment().getSequenceAt(searchSeq),\r
+\r
+          ssr.drawHighlightedText(seq,\r
                                   searchStart,\r
                                   searchEnd,\r
                                   (searchStart - startx) * av.charWidth,\r

diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java
index ddbd97c..162f978 100755 (executable)
--- a/src/jalview/gui/SeqPanel.java
+++ b/src/jalview/gui/SeqPanel.java
@@ -347,11 +347,12 @@ public class SeqPanel extends JPanel
   {\r
 \r
     if ( jalview.util.Comparison.isGap( av.alignment.getSequenceAt(seq).getSequence().charAt(j)))\r
-        av.alignment.getSequenceAt(seq).deleteCharAt(j);\r
+      av.alignment.getSequenceAt(seq).deleteCharAt(j);\r
 \r
     av.alignment.getWidth();\r
     repaint();\r
     seqEditOccurred=seq;\r
+\r
   }\r
 \r
 \r