X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FFinder.java;h=1aceb80e734677eb339ee9ef8aa175d27ab08fc8;hb=effd8d76f34bc7fd4e069603d80565b7ea9d3ff0;hp=c5a2cf4e0c090630bf0e255f5ecd119432b4e065;hpb=3e313eab680734bb0bd49d3366c5ae6ad8330ef4;p=jalview.git

diff --git a/src/jalview/gui/Finder.java b/src/jalview/gui/Finder.java
index c5a2cf4..1aceb80 100755
--- a/src/jalview/gui/Finder.java
+++ b/src/jalview/gui/Finder.java
@@ -1,129 +1,379 @@
+/*
+ * 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 jalview.jbgui.*;
+
+import java.awt.*;
 import java.awt.event.*;
+
+import java.util.*;
+
 import javax.swing.*;
 import javax.swing.event.*;
-import java.util.*;
 
 
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
 public class Finder extends GFinder
 {
-  AlignViewport av;
-  AlignmentPanel ap;
-  JInternalFrame frame;
-  String searchString;
-
-  int seqIndex = 0;
-  int resIndex = 0;
-  public Finder(AlignViewport av, AlignmentPanel ap, JInternalFrame f)
-  {
-    this.av = av;
-    this.ap = ap;
-    frame = f;
-
-    // all a big pain, but we need to wait until the frame is visible before the textfield can
-    // obtain the focus/////////////////////////
-    frame.addInternalFrameListener(new InternalFrameAdapter()
+    AlignViewport av;
+    AlignmentPanel ap;
+    JInternalFrame frame;
+    SuperGroup searchGroup;
+    Vector searchResults;
+    int seqIndex = 0;
+    int resIndex = 0;
+
+    /**
+     * Creates a new Finder object.
+     *
+     * @param av DOCUMENT ME!
+     * @param ap DOCUMENT ME!
+     * @param f DOCUMENT ME!
+     */
+    public Finder(AlignViewport av, AlignmentPanel ap, JInternalFrame f)
     {
-      public void internalFrameOpened(InternalFrameEvent evt)
-      {
-        SwingUtilities.invokeLater(new Runnable()
-        {
-          public void run()
-          {
-            textfield.requestFocus();
-          }
-       });
-   }
-});
-
-  }
-
-  public void textfield_actionPerformed(ActionEvent e)
-  {
-    doSearch(false);
-  }
-
-  public void findNext_actionPerformed(ActionEvent e)
-  {
-    doSearch(false);
-  }
-
-  public void findAll_actionPerformed(ActionEvent e)
-  {
-    resIndex=0;
-    seqIndex=0;
-    doSearch(true);
-  }
-
-  public void cancel_actionPerformed(ActionEvent e)
-  {
-    try{
-      frame.setClosed(true);
-    }catch(Exception ex){}
-
-  }
-
-  void doSearch(boolean findAll)
-  {
-    searchString = textfield.getText().toUpperCase();
-
-    ArrayList searchResults = new ArrayList();
-    int [] allResults = null;
-
-    Sequence seq;
-    String item;
-    boolean found = false;
-    while( !found && seqIndex<av.getAlignment().getHeight())
+        this.av = av;
+        this.ap = ap;
+        frame = f;
+
+        // all a big pain, but we need to wait until the frame is visible before the textfield can
+        // obtain the focus/////////////////////////
+        frame.addInternalFrameListener(new InternalFrameAdapter()
+            {
+                public void internalFrameOpened(InternalFrameEvent evt)
+                {
+                    SwingUtilities.invokeLater(new Runnable()
+                        {
+                            public void run()
+                            {
+                                textfield.requestFocus();
+                            }
+                        });
+                }
+
+                /**
+                 * DOCUMENT ME!
+                 *
+                 * @param evt DOCUMENT ME!
+                 */
+                public void internalFrameClosing(InternalFrameEvent evt)
+                {
+                    cancel_actionPerformed(null);
+                }
+            });
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void textfield_actionPerformed(ActionEvent e)
     {
-      seq = (Sequence)av.getAlignment().getSequenceAt(seqIndex);
-      item = seq.getSequence();
-
-      for(int r = resIndex; r<item.length(); r++)
-      {
-       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;
-         }
-       }
-      }
-      if(!found)
-      {
-        seqIndex++;
-        resIndex = 0;
-      }
+        doSearch(false);
     }
 
-    if(searchResults.size()>0)
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void findNext_actionPerformed(ActionEvent e)
     {
+        doSearch(false);
+    }
 
-      allResults = new int[searchResults.size()];
-      for(int i=0; i<searchResults.size(); i++)
-        allResults[i] = Integer.parseInt(searchResults.get(i).toString());
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void findAll_actionPerformed(ActionEvent e)
+    {
+        resIndex = 0;
+        seqIndex = 0;
+        doSearch(true);
+    }
 
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void cancel_actionPerformed(ActionEvent e)
+    {
+        try
+        {
+            // if allResults is null, this effectively switches displaySearch flag in seqCanvas
+            ap.highlightSearchResults(null);
+            ap.idPanel.highlightSearchResults(null);
 
-      ap.highlightSearchResults( allResults );
+            // frame.setClosed(true);
+        }
+        catch (Exception ex)
+        {
+        }
     }
-    else
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void createNewGroup_actionPerformed(ActionEvent e)
     {
-      JOptionPane.showInternalMessageDialog(this, "Finished searching", null,
-                                            JOptionPane.INFORMATION_MESSAGE);
-      resIndex=0;
-      seqIndex=0;
+        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);
     }
 
+    /**
+     * DOCUMENT ME!
+     *
+     * @param findAll DOCUMENT ME!
+     */
+    void doSearch(boolean findAll)
+    {
+        createNewGroup.setEnabled(false);
+
+        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?
+        try
+        {
+            int res = Integer.parseInt(searchString);
+            found = true;
+
+            if (av.getSelectionGroup().getSize() > 0)
+            {
+                seq = (Sequence) (av.getSelectionGroup().getSequenceAt(0));
+            }
+            else
+            {
+                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);
+
+        searchGroup = new SuperGroup(searchString, ucs, true, true, false);
+
+        int end = av.alignment.getHeight();
+
+        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.alignment.getSequenceAt(seqIndex);
+
+            if ((selection != null) && !selection.sequences.contains(seq))
+            {
+                seqIndex++;
+                resIndex = 0;
+
+                continue;
+            }
+
+            item = seq.getSequence().toUpperCase();
+
+            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;
+            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++;
+                }
+            }
+
+            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;
+            }
+        }
+
+        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());
+            }
+
+            createNewGroup.setEnabled(true);
+        }
+        else
+        {
+            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);
+
+        if (findAll)
+        {
+            String message = (searchResults.size() / 3) + " matches found.";
+            JOptionPane.showInternalMessageDialog(this, message, null,
+                JOptionPane.INFORMATION_MESSAGE);
+        }
+    }
 }