X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fgui%2FFinder.java;h=869755280b39292b96b631e045839322191e7cd1;hb=5e0c372a53e267a798bdb3e96fe7789a54b89109;hp=d20cb6517093acf8117fb416e3b53289ae74816f;hpb=99c58ee0ae2a848f982552e53feaf6d5cb9925e5;p=jalview.git

diff --git a/src/jalview/gui/Finder.java b/src/jalview/gui/Finder.java
index d20cb65..8697552 100755
--- a/src/jalview/gui/Finder.java
+++ b/src/jalview/gui/Finder.java
@@ -1,288 +1,333 @@
 /*
-* 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
-*/
-
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * Copyright (C) 2006 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.*;
-import java.awt.*;
 
+
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
 public class Finder extends GFinder
 {
-  AlignViewport av;
-  AlignmentPanel ap;
-  JInternalFrame frame;
-  SuperGroup searchGroup;
-  Vector searchResults;
-
-  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;
+    int seqIndex = 0;
+    int resIndex = 0;
+
+    SearchResults searchResults;
+
+    /**
+     * 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 internalFrameClosing(InternalFrameEvent evt)
-     {
-       cancel_actionPerformed(null);
-     }
-});
-
-  }
-
-  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{
-      // if allResults is null, this effectively switches displaySearch flag in seqCanvas
-      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);
+        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();
+                            }
+                        });
+                }
+            });
+    }
 
 
-    for(int i=0; i<searchResults.size(); i+=3)
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void findNext_actionPerformed(ActionEvent e)
     {
-      // 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 );
-
+        doSearch(false);
     }
 
-    ap.av.alignment.addSuperGroup(searchGroup);
-    ap.highlightSearchResults( null );
-  }
-
-
-  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 ) );
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void findAll_actionPerformed(ActionEvent e)
+    {
+        resIndex = 0;
+        seqIndex = 0;
+        doSearch(true);
+    }
 
-    }catch(NumberFormatException ex){}
-    ///////////////////////////////////////////////
 
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void createNewGroup_actionPerformed(ActionEvent e)
+    {
+        JLabel label = new JLabel("Enter name of new sequence feature");
+        JTextField textinput = new JTextField(textfield.getText());
+        JPanel panel = new JPanel(new BorderLayout());
+        panel.add(label, BorderLayout.NORTH);
+        panel.add(textinput, BorderLayout.SOUTH);
 
 
-    Color [] newColors = new Color[24];
-    for(int i=0; i<24; i++)
-      newColors[i] = new Color(60,160,115);
+        SequenceI [] seqs = new SequenceI[searchResults.getSize()];
+        SequenceFeature [] features = new SequenceFeature[searchResults.getSize()];
 
-    jalview.schemes.UserColourScheme ucs = new jalview.schemes.UserColourScheme(newColors);
 
-    searchGroup = new SuperGroup(searchString, ucs , true, true, false);
+        for (int i = 0; i < searchResults.getSize(); i ++ )
+        {
+            seqs[i] = searchResults.getResultSequence(i).getDatasetSequence();
 
-    int end = av.alignment.getHeight();
+            features[i] = new SequenceFeature(textinput.getText(),
+                "Search Results", null,
+                searchResults.getResultStart(i),
+                searchResults.getResultEnd(i),
+               "Search Results");
+        }
 
-    SequenceGroup selection = av.getSelectionGroup();
-    if(selection!=null)
-     if(selection.getSize()<1 || (selection.getEndRes()-selection.getStartRes()<2))
-      selection = null;
+        if( ap.seqPanel.seqCanvas.getFeatureRenderer()
+            .createNewFeatures(seqs, features))
+        {
+          ap.alignFrame.showSeqFeatures.setSelected(true);
+          av.setShowSequenceFeatures(true);
+          ap.highlightSearchResults(null);
+        }
+    }
 
-    while( !found && seqIndex<end)
+    /**
+     * DOCUMENT ME!
+     *
+     * @param findAll DOCUMENT ME!
+     */
+    void doSearch(boolean findAll)
     {
-      seq = (Sequence)av.alignment.getSequenceAt(seqIndex);
+        createNewGroup.setEnabled(false);
 
+        String searchString = textfield.getText().trim();
+        if(!caseSensitive.isSelected())
+          searchString = searchString.toUpperCase();
 
-      if(selection!=null && !selection.sequences.contains(seq))
-      {
-        seqIndex++;
-        resIndex=0;
-        continue;
-      }
+        if(searchString.length()<1)
+          return;
 
-      item = seq.getSequence().toUpperCase();
+        com.stevesoft.pat.Regex regex = new com.stevesoft.pat.Regex(searchString);
 
-      if(selection!=null && selection.getEndRes()<av.alignment.getWidth())
-          item = item.substring(0, selection.getEndRes()+1);
+        searchResults = new SearchResults();
 
-      ///Shall we ignore gaps????
-      StringBuffer noGaps = new StringBuffer();
-      int insertCount=0;
-      Vector spaces = new Vector();
+        Sequence seq;
+        String item = null;
+        boolean found = false;
 
-      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) );
+        ////// is the searchString a residue number?
+        try
+        {
+            int res = Integer.parseInt(searchString);
+            found = true;
+            if (av.getSelectionGroup() == null || av.getSelectionGroup().getSize(false) < 1)
+            {
+              seq = (Sequence) av.getAlignment().getSequenceAt(0);
+            }
+            else
+            {
+              seq = (Sequence) (av.getSelectionGroup().getSequenceAt(0));
+            }
+
+            searchResults.addResult(seq, res, res);
+        }
+        catch (NumberFormatException ex)
+        {
+        }
 
-         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+"" );
+        int end = av.alignment.getHeight();
 
-         if(!findAll)
-         {
-           // thats enough, break and display the result
-           found = true;
-           resIndex++;
-           break;
-         }
+        SequenceGroup selection = av.getSelectionGroup();
 
-         r=resIndex;
-       }
-      }
-      if(!found)
-      {
-        seqIndex++;
-        resIndex = 0;
-      }
-    }
+        if (selection != null)
+        {
+            if ((selection.getSize(false) < 1) ||
+                    ((selection.getEndRes() - selection.getStartRes()) < 2))
+            {
+                selection = null;
+            }
+        }
+
+        while (!found && (seqIndex < end))
+        {
+            seq = (Sequence) av.alignment.getSequenceAt(seqIndex);
+
+            if ((selection != null) && !selection.getSequences(false).contains(seq))
+            {
+                seqIndex++;
+                resIndex = 0;
+
+                continue;
+            }
+
+            item = seq.getSequence();
+            if(!caseSensitive.isSelected())
+              item = item.toUpperCase();
+
+            if ((selection != null) &&
+                    (selection.getEndRes() < av.alignment.getWidth()-1))
+            {
+                item = item.substring(0, selection.getEndRes() + 1);
+            }
+
+            ///Shall we ignore gaps????
+            StringBuffer noGapsSB = 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)))
+                {
+                    noGapsSB.append(item.charAt(j));
+                    spaces.add(new Integer(insertCount));
+                }
+                else
+                {
+                    insertCount++;
+                }
+            }
+
+            String noGaps = noGapsSB.toString();
+
+            for (int r = resIndex; r < noGaps.length(); r++)
+            {
+
+                if (regex.searchFrom(noGaps, r))
+                {
+                    resIndex = regex.matchedFrom();
+
+                    if ((selection != null) &&
+                            ((resIndex +
+                            Integer.parseInt(spaces.get(resIndex).toString())) < selection.getStartRes()))
+                    {
+                        continue;
+                    }
+
+
+                    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.addResult(seq, sres, eres);
+
+                    if (!findAll)
+                    {
+                        // thats enough, break and display the result
+                        found = true;
+                        resIndex++;
+
+                        break;
+                    }
+
+                    r = resIndex;
+                }
+                else
+                {
+                  break;
+                }
+            }
+
+            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.getSize() == 0) && (idMatch.size() > 0))
+        {
+            ap.idPanel.highlightSearchResults(idMatch);
+        }
 
-    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 );
+        int resultSize = searchResults.getSize();
 
+        if (searchResults.getSize() > 0)
+          createNewGroup.setEnabled(true);
+        else
+          searchResults = null;
 
-    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 allResults is null, this effectively switches displaySearch flag in seqCanvas
+        ap.highlightSearchResults(searchResults);
 
-      createNewGroup.setEnabled(true);
-    }
-    else
-    {
-      JOptionPane.showInternalMessageDialog(this, "Finished searching", null, JOptionPane.INFORMATION_MESSAGE);
-      resIndex=0;
-      seqIndex=0;
-    }
+        if(!findAll && resultSize==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 );
+        if (findAll)
+        {
+          String message = resultSize + " matches found.";
+          JOptionPane.showInternalMessageDialog(this, message, null,
+                                                JOptionPane.INFORMATION_MESSAGE);
+        }
 
-    if (findAll)
-    {
-      String message =  (searchResults.size()/3) + " matches found.";
-      JOptionPane.showInternalMessageDialog(this, message, null,
-                                            JOptionPane.INFORMATION_MESSAGE);
     }
-
-  }
-
 }