X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=src%2Fjalview%2Fgui%2FFinder.java;h=71a52e9209abf3db764f85cf790b290def4e7fa0;hb=b14411143cbfb4d311f68b3d3b73a645bf8200e8;hp=909ba1f39957075ebbecdf01ca16db114944ffde;hpb=587fef46179c0daf041e240c10b03ac5910718a8;p=jalview.git

diff --git a/src/jalview/gui/Finder.java b/src/jalview/gui/Finder.java
index 909ba1f..71a52e9 100755
--- a/src/jalview/gui/Finder.java
+++ b/src/jalview/gui/Finder.java
@@ -1,22 +1,44 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
 package jalview.gui;
 
-import jalview.jbgui.GFinder;
-import jalview.datamodel.*;
+import java.util.*;
+
+import java.awt.*;
 import java.awt.event.*;
 import javax.swing.*;
 import javax.swing.event.*;
-import java.util.*;
 
+import jalview.datamodel.*;
+import jalview.jbgui.*;
 
-public class Finder extends GFinder
+public class Finder
+    extends GFinder
 {
   AlignViewport av;
   AlignmentPanel ap;
   JInternalFrame frame;
-  String searchString;
-
+  SuperGroup searchGroup;
+  Vector searchResults;
   int seqIndex = 0;
   int resIndex = 0;
+
   public Finder(AlignViewport av, AlignmentPanel ap, JInternalFrame f)
   {
     this.av = av;
@@ -35,10 +57,14 @@ public class Finder extends GFinder
           {
             textfield.requestFocus();
           }
-       });
-   }
-});
+        });
+      }
 
+      public void internalFrameClosing(InternalFrameEvent evt)
+      {
+        cancel_actionPerformed(null);
+      }
+    });
   }
 
   public void textfield_actionPerformed(ActionEvent e)
@@ -53,119 +79,257 @@ public class Finder extends GFinder
 
   public void findAll_actionPerformed(ActionEvent e)
   {
-    resIndex=0;
-    seqIndex=0;
+    resIndex = 0;
+    seqIndex = 0;
     doSearch(true);
   }
 
   public void cancel_actionPerformed(ActionEvent e)
   {
-    try{
+    try
+    {
       // if allResults is null, this effectively switches displaySearch flag in seqCanvas
-      ap.highlightSearchResults( null );
-      frame.setClosed(true);
-    }catch(Exception ex){ }
+      ap.highlightSearchResults(null);
+      ap.idPanel.highlightSearchResults(null);
 
+      // frame.setClosed(true);
+    }
+    catch (Exception ex)
+    {
+    }
+  }
+
+  public void createNewGroup_actionPerformed(ActionEvent e)
+  {
+    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, false);
+      av.alignment.addGroup(sg);
+      searchGroup.addGroup(sg);
+    }
+
+    ap.av.alignment.addSuperGroup(searchGroup);
+    ap.highlightSearchResults(null);
   }
 
   void doSearch(boolean findAll)
   {
-    searchString = textfield.getText().toUpperCase();
+    createNewGroup.setEnabled(false);
+
+    String searchString = textfield.getText().toUpperCase();
+
+    com.stevesoft.pat.Regex regex = new com.stevesoft.pat.Regex(searchString);
 
-    ArrayList searchResults = new ArrayList();
-    int [] allResults = null;
+    searchResults = new Vector();
+
+    int[] allResults = null;
 
     Sequence seq;
-    String item;
+    String item = null;
     boolean found = false;
 
-    /// is the searchString a residue number?
-    try{
+    ////// 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);
+      {
+        seq = (Sequence) av.getAlignment().getSequenceAt(0);
+      }
+
+      searchResults.add(Integer.toString(av.getAlignment().findIndex(seq)));
+      searchResults.add(Integer.toString(seq.findIndex(res) - 1));
+      searchResults.add(Integer.toString(seq.findIndex(res) - 1));
+    }
+    catch (NumberFormatException ex)
+    {
+    }
+
+    ///////////////////////////////////////////////
+    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);
 
-      searchResults.add( Integer.toString( av.getAlignment().findIndex(seq) ) );
-      searchResults.add( Integer.toString( seq.findIndex(res)-1 ) );
-      searchResults.add( Integer.toString( seq.findIndex(res)-1 ) );
+    searchGroup = new SuperGroup(searchString, ucs, true, true, false);
 
+    int end = av.alignment.getHeight();
 
-      //av.getAlignment().getSequenceAt(seq).findPosition(res)
-    }catch(NumberFormatException ex){}
+    SequenceGroup selection = av.getSelectionGroup();
 
+    if (selection != null)
+    {
+      if ( (selection.getSize() < 1) ||
+          ( (selection.getEndRes() - selection.getStartRes()) < 2))
+      {
+        selection = null;
+      }
+    }
 
-    while( !found && seqIndex<av.getAlignment().getHeight())
+    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))
+      if ( (selection != null) && !selection.sequences.contains(seq))
       {
-        // if a selection has been made, only search within that selection
         seqIndex++;
-        resIndex=0;
+        resIndex = 0;
+
         continue;
       }
 
-      item = seq.getSequence();
+      item = seq.getSequence().toUpperCase();
 
-      for(int r = resIndex; r<item.length(); r++)
+      if ( (selection != null) &&
+          (selection.getEndRes() < av.alignment.getWidth()))
       {
-       if(item.indexOf(searchString,r)>-1)
-       {
-         resIndex = item.indexOf(searchString,r);
-
-         searchResults.add( Integer.toString(seqIndex) );
-         searchResults.add( Integer.toString( resIndex) );
-         searchResults.add( Integer.toString( (resIndex+searchString.length()-1) ) );
-         if(!findAll)
-         {
-           // thats enough, break and display the result
-           found = true;
-           resIndex++;
-           break;
-         }
-
-         r=resIndex+1;
-       }
+        item = item.substring(0, selection.getEndRes() + 1);
+      }
+
+      ///Shall we ignore gaps????
+      StringBuffer noGaps = new StringBuffer();
+      int insertCount = 0;
+      Vector spaces = new Vector();
+
+      for (int j = 0; j < item.length(); j++)
+      {
+        if (!jalview.util.Comparison.isGap(item.charAt(j)))
+        {
+          noGaps.append(item.charAt(j));
+          spaces.add(new Integer(insertCount));
+        }
+        else
+        {
+          insertCount++;
+        }
       }
-      if(!found)
+
+      for (int r = resIndex; r < noGaps.length(); r++)
+      {
+        if (regex.searchFrom(noGaps.toString(), r))
+        {
+          resIndex = regex.matchedFrom();
+
+          if ( (selection != null) &&
+              ( (resIndex +
+                 Integer.parseInt(spaces.get(resIndex).toString())) <
+               selection.getStartRes()))
+          {
+            continue;
+          }
+
+          searchResults.add(Integer.toString(seqIndex));
+
+          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)
+          {
+            // thats enough, break and display the result
+            found = true;
+            resIndex++;
+
+            break;
+          }
+
+          r = resIndex;
+        }
+      }
+
+      if (!found)
       {
         seqIndex++;
         resIndex = 0;
       }
     }
 
-    if(searchResults.size()>0)
+    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()];
-      for(int i=0; i<searchResults.size(); i++)
-        allResults[i] = Integer.parseInt(searchResults.get(i).toString());
 
-      if (findAll)
+      for (int i = 0; i < searchResults.size(); i++)
       {
-        String message =  (searchResults.size()/3) + " matches found.";
-        JOptionPane.showInternalMessageDialog(this, message, null,
-                                              JOptionPane.INFORMATION_MESSAGE);
+        allResults[i] = Integer.parseInt(searchResults.get(i).toString());
       }
 
-
+      createNewGroup.setEnabled(true);
     }
     else
     {
-      JOptionPane.showInternalMessageDialog(this, "Finished searching", null, JOptionPane.INFORMATION_MESSAGE);
-      resIndex=0;
-      seqIndex=0;
+      JOptionPane.showInternalMessageDialog(this, "Finished searching",
+                                            null,
+                                            JOptionPane.INFORMATION_MESSAGE);
+      resIndex = 0;
+      seqIndex = 0;
     }
 
     // if allResults is null, this effectively switches displaySearch flag in seqCanvas
-    ap.highlightSearchResults( allResults );
-
+    ap.highlightSearchResults(allResults);
 
+    if (findAll)
+    {
+      String message = (searchResults.size() / 3) + " matches found.";
+      JOptionPane.showInternalMessageDialog(this, message, null,
+                                            JOptionPane.INFORMATION_MESSAGE);
+    }
   }
-
 }