X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FFinder.java;h=cad734b297d7ae1932e621f0f5251a09a9b21c31;hb=6a7ed84443875e35d61de7f57c4aa6898c68775a;hp=c5a2cf4e0c090630bf0e255f5ecd119432b4e065;hpb=3e313eab680734bb0bd49d3366c5ae6ad8330ef4;p=jalview.git

diff --git a/src/jalview/gui/Finder.java b/src/jalview/gui/Finder.java
index c5a2cf4..cad734b 100755
--- a/src/jalview/gui/Finder.java
+++ b/src/jalview/gui/Finder.java
@@ -1,129 +1,214 @@
-package jalview.gui;
-
-import jalview.jbgui.GFinder;
-import jalview.datamodel.*;
-import java.awt.event.*;
-import javax.swing.*;
-import javax.swing.event.*;
-import java.util.*;
-
-
-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()
-    {
-      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())
-    {
-      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;
-      }
-    }
-
-    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());
-
-
-      ap.highlightSearchResults( allResults );
-    }
-    else
-    {
-      JOptionPane.showInternalMessageDialog(this, "Finished searching", null,
-                                            JOptionPane.INFORMATION_MESSAGE);
-      resIndex=0;
-      seqIndex=0;
-    }
-
-
-  }
-
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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);
+    }
+
+  }
+}