X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FFinder.java;h=ef28ebe745e471a6a5f29b8af2895f91d5ae32f5;hb=fe5db5e87fc726b1560d21f97f19b0e04963b72c;hp=2311a9f532f1a4220fec634e46fe41ae97973979;hpb=183b98840a8ee8d03a2c7f7f42044190d52f2595;p=jalview.git

diff --git a/src/jalview/gui/Finder.java b/src/jalview/gui/Finder.java
index 2311a9f..ef28ebe 100755
--- a/src/jalview/gui/Finder.java
+++ b/src/jalview/gui/Finder.java
@@ -13,8 +13,8 @@ public class Finder extends GFinder
   AlignViewport av;
   AlignmentPanel ap;
   JInternalFrame frame;
-  String searchString;
   SuperGroup searchGroup;
+  Vector searchResults;
 
   int seqIndex = 0;
   int resIndex = 0;
@@ -67,6 +67,7 @@ public class Finder extends GFinder
     try{
       // if allResults is null, this effectively switches displaySearch flag in seqCanvas
       ap.highlightSearchResults( null );
+      ap.idPanel.highlightSearchResults( null );
      // frame.setClosed(true);
     }catch(Exception ex){ }
   }
@@ -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));
+
+   Color [] newColors = new Color[24];
+   for(int i=0; i<24; i++)
+     newColors[i] = new Color(60,160,115);
+
+   jalview.schemes.UserColourScheme ucs = new jalview.schemes.UserColourScheme(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 );
@@ -85,22 +110,25 @@ public class Finder extends GFinder
   void doSearch(boolean findAll)
   {
     createNewGroup.setEnabled(false);
-    searchString = textfield.getText().toUpperCase();
 
-    ArrayList searchResults = new ArrayList();
+    String searchString = textfield.getText().toUpperCase();
+
+    com.stevesoft.pat.Regex regex = new  com.stevesoft.pat.Regex(searchString);
+
+    searchResults = new Vector();
     int [] allResults = null;
 
     Sequence seq;
     String item=null;
     boolean found = false;
 
-    /// is the searchString a residue number?
+    ////// is the searchString a residue number?
     try{
       int res = Integer.parseInt(searchString);
       found = true;
 
-      if(av.getSelection().size()>0)
-        seq = (Sequence)(av.getSelection().sequenceAt(0));
+      if(av.getSelectionGroup().getSize()>0)
+        seq = (Sequence)(av.getSelectionGroup().getSequenceAt(0));
       else
         seq = (Sequence)av.getAlignment().getSequenceAt(0);
 
@@ -109,47 +137,46 @@ public class Finder extends GFinder
       searchResults.add( Integer.toString( seq.findIndex(res)-1 ) );
 
     }catch(NumberFormatException ex){}
+    ///////////////////////////////////////////////
+
+
 
-    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);
+    jalview.schemes.UserColourScheme ucs = new jalview.schemes.UserColourScheme(newColors);
 
     searchGroup = new SuperGroup(searchString, ucs , true, true, false);
 
     int end = av.alignment.getHeight();
 
-
-    SequenceGroup rubberband = av.getRubberbandGroup();
-    if(rubberband!=null)
-      end = rubberband.getEndRes();
-
-
+    SequenceGroup selection = av.getSelectionGroup();
+    if(selection!=null)
+     if(selection.getSize()<1 || (selection.getEndRes()-selection.getStartRes()<2))
+      selection = null;
 
     while( !found && seqIndex<end)
     {
-      seq = (Sequence)av.getAlignment().getSequenceAt(seqIndex);
+      seq = (Sequence)av.alignment.getSequenceAt(seqIndex);
+
 
-      if(   av.getSelection().size()>0 && !av.getSelection().contains(seq)
-            || (rubberband!=null && !rubberband.sequences.contains(seq))  )
+      if(selection!=null && !selection.sequences.contains(seq))
       {
-        // if a selection has been made, only search within that selection
         seqIndex++;
         resIndex=0;
         continue;
       }
 
-      item = seq.getSequence();
+      item = seq.getSequence().toUpperCase();
 
-      if(rubberband!=null)
-        item = item.substring(0, rubberband.getEndRes()+1);
+      if(selection!=null && selection.getEndRes()<av.alignment.getWidth())
+          item = item.substring(0, selection.getEndRes()+1);
 
       ///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++)
       {
@@ -164,7 +191,6 @@ public class Finder extends GFinder
       }
 
 
-      com.stevesoft.pat.Regex regex = new  com.stevesoft.pat.Regex(searchString);
 
       for(int r = resIndex; r<noGaps.length(); r++)
       {
@@ -172,21 +198,16 @@ public class Finder extends GFinder
        if( regex.searchFrom( noGaps.toString(), r ) )
        {
          resIndex = regex.matchedFrom();
-
-
-         if(rubberband!=null && ( resIndex+ Integer.parseInt(spaces.get(resIndex).toString()) )<rubberband.getStartRes())
+         if(selection!=null && ( resIndex+ Integer.parseInt(spaces.get(resIndex).toString()) )<selection.getStartRes())
            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)
          {
@@ -206,6 +227,18 @@ public class Finder extends GFinder
       }
     }
 
+
+    Vector idMatch = new Vector();
+    for(int id = 0; id<av.alignment.getHeight(); id++)
+    {
+      if(   regex.search( av.alignment.getSequenceAt(id).getName() ) )
+        idMatch.add( av.alignment.getSequenceAt(id) );
+    }
+
+    if(searchResults.size()==0 && idMatch.size()>0)
+      ap.idPanel.highlightSearchResults( idMatch );
+
+
     if(searchResults.size()>0)
     {
       allResults = new int[searchResults.size()];