X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fgui%2FFinder.java;h=5668b42312a9e64c0b75ec0ffbc0fe9afed0c93f;hb=7000ea3223f2f6a390f56341ba26850d2a137ae0;hp=d20cb6517093acf8117fb416e3b53289ae74816f;hpb=99c58ee0ae2a848f982552e53feaf6d5cb9925e5;p=jalview.git

diff --git a/src/jalview/gui/Finder.java b/src/jalview/gui/Finder.java
index d20cb65..5668b42 100755
--- a/src/jalview/gui/Finder.java
+++ b/src/jalview/gui/Finder.java
@@ -1,288 +1,201 @@
-/*
-* 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.awt.event.*;
-import javax.swing.*;
-import javax.swing.event.*;
-import java.util.*;
-import java.awt.*;
-
-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()
-    {
-      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);
-
-
-    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 );
-  }
-
-
-  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);
-    }
-
-  }
-
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * Copyright (C) 2007 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 java.util.*;
+
+import java.awt.*;
+import java.awt.event.*;
+import javax.swing.*;
+
+import jalview.datamodel.*;
+import jalview.jbgui.*;
+
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class Finder
+    extends GFinder
+{
+  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()
+  {
+    frame = new JInternalFrame();
+    frame.setContentPane(this);
+    frame.setLayer(JLayeredPane.PALETTE_LAYER);
+    Desktop.addInternalFrame(frame, "Find", 340, 110);
+
+    textfield.requestFocus();
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  public void findNext_actionPerformed(ActionEvent e)
+  {
+    if (getFocusedViewport())
+    {
+      doSearch(false);
+    }
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  public void findAll_actionPerformed(ActionEvent e)
+  {
+    if (getFocusedViewport())
+    {
+      resIndex = 0;
+      seqIndex = 0;
+      doSearch(true);
+    }
+  }
+
+  boolean getFocusedViewport()
+  {
+    JInternalFrame frame = Desktop.desktop.getAllFrames()[1];
+
+    if (frame != null && frame instanceof AlignFrame)
+    {
+      av = ( (AlignFrame) frame).viewport;
+      ap = ( (AlignFrame) frame).alignPanel;
+      return true;
+    }
+    return false;
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  public void createNewGroup_actionPerformed(ActionEvent e)
+  {
+    SequenceI[] seqs = new SequenceI[searchResults.getSize()];
+    SequenceFeature[] features = new SequenceFeature[searchResults.getSize()];
+
+    for (int i = 0; i < searchResults.getSize(); i++)
+    {
+      seqs[i] = searchResults.getResultSequence(i).getDatasetSequence();
+
+      features[i] = new SequenceFeature(textfield.getText().trim(),
+                                        "Search Results", null,
+                                        searchResults.getResultStart(i),
+                                        searchResults.getResultEnd(i),
+                                        "Search Results");
+    }
+
+    if (ap.seqPanel.seqCanvas.getFeatureRenderer()
+        .amendFeatures(seqs, features, true, ap))
+    {
+      ap.alignFrame.showSeqFeatures.setSelected(true);
+      av.setShowSequenceFeatures(true);
+      ap.highlightSearchResults(null);
+    }
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param findAll DOCUMENT ME!
+   */
+  void doSearch(boolean findAll)
+  {
+    createNewGroup.setEnabled(false);
+
+    String searchString = textfield.getText().trim();
+
+    if (searchString.length() < 1)
+    {
+      return;
+    }
+    // TODO: extend finder to match descriptions, features and annotation, and other stuff
+    // TODO: add switches to control what is searched - sequences, IDS, descriptions, features
+    jalview.analysis.Finder finder = new jalview.analysis.Finder(av.alignment,
+        av.getSelectionGroup(), seqIndex, resIndex);
+    finder.setCaseSensitive(caseSensitive.isSelected());
+    finder.setFindAll(findAll);
+
+    finder.find(searchString); // returns true if anything was actually found
+
+    seqIndex = finder.getSeqIndex();
+    resIndex = finder.getResIndex();
+
+    searchResults = finder.getSearchResults(); // find(regex, caseSensitive.isSelected(), )
+    Vector idMatch = finder.getIdMatch();
+    // set or reset the GUI
+    if ( (searchResults.getSize() == 0) && (idMatch.size() > 0))
+    {
+      ap.idPanel.highlightSearchResults(idMatch);
+    }
+
+    int resultSize = searchResults.getSize();
+
+    if (searchResults.getSize() > 0)
+    {
+      createNewGroup.setEnabled(true);
+    }
+    else
+    {
+      searchResults = null;
+    }
+
+    // if allResults is null, this effectively switches displaySearch flag in seqCanvas
+    ap.highlightSearchResults(searchResults);
+    // TODO: add enablers for 'SelectSequences' or 'SelectColumns' or 'SelectRegion' selection
+    if (!findAll && resultSize == 0)
+    {
+      JOptionPane.showInternalMessageDialog(this, "Finished searching",
+                                            null,
+                                            JOptionPane.INFORMATION_MESSAGE);
+      resIndex = 0;
+      seqIndex = 0;
+    }
+
+    if (findAll)
+    {
+      String message = resultSize + " matches found.";
+      JOptionPane.showInternalMessageDialog(this, message, null,
+                                            JOptionPane.INFORMATION_MESSAGE);
+    }
+
+  }
+}