X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FFinder.java;h=3161271ac7593ba3f7bea5ddcb8d2a0c3504d27a;hb=b2f9a8d7bce642ff4011bc6d49e02bb0569fbb11;hp=d20cb6517093acf8117fb416e3b53289ae74816f;hpb=99c58ee0ae2a848f982552e53feaf6d5cb9925e5;p=jalview.git

diff --git a/src/jalview/gui/Finder.java b/src/jalview/gui/Finder.java
index d20cb65..3161271 100755
--- a/src/jalview/gui/Finder.java
+++ b/src/jalview/gui/Finder.java
@@ -1,288 +1,267 @@
-/*
-* 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 (Version 2.8.1)
+ * Copyright (C) 2014 The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview 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 3 of the License, or (at your option) any later version.
+ *  
+ * Jalview 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 Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.gui;
+
+import java.util.*;
+import java.awt.event.*;
+
+import javax.swing.*;
+
+import jalview.datamodel.*;
+import jalview.jbgui.*;
+import jalview.util.MessageManager;
+
+/**
+ * DOCUMENT ME!
+ * 
+ * @author $author$
+ * @version $Revision$
+ */
+public class Finder extends GFinder
+{
+  AlignViewport av;
+
+  AlignmentPanel ap;
+
+  JInternalFrame frame;
+
+  int seqIndex = 0;
+
+  int resIndex = -1;
+
+  SearchResults searchResults;
+
+  /**
+   * Creates a new Finder object.
+   * 
+   * @param av
+   *          DOCUMENT ME!
+   * @param ap
+   *          DOCUMENT ME!
+   * @param f
+   *          DOCUMENT ME!
+   */
+  public Finder()
+  {
+    this(null, null);
+    focusfixed = false;
+  }
+
+  public Finder(AlignViewport viewport, AlignmentPanel alignPanel)
+  {
+    av = viewport;
+    ap = alignPanel;
+    focusfixed = true;
+    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 = -1;
+      seqIndex = 0;
+      doSearch(true);
+    }
+  }
+
+  /**
+   * do we only search a given alignment view ?
+   */
+  private boolean focusfixed;
+
+  /**
+   * if !focusfixed and not in a desktop environment, checks that av and ap are
+   * valid. Otherwise, gets the topmost alignment window and sets av and ap
+   * accordingly
+   * 
+   * @return false if no alignment window was found
+   */
+  boolean getFocusedViewport()
+  {
+    if (focusfixed || Desktop.desktop == null)
+    {
+      if (ap != null && av != null)
+      {
+        return true;
+      }
+      // we aren't in a desktop environment, so give up now.
+      return false;
+    }
+    // now checks further down the window stack to fix bug
+    // https://mantis.lifesci.dundee.ac.uk/view.php?id=36008
+    JInternalFrame[] frames = Desktop.desktop.getAllFrames();
+    for (int f = 0; f < frames.length; f++)
+    {
+      JInternalFrame frame = frames[f];
+      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);
+    }
+  }
+
+  /**
+   * incrementally search the alignment
+   * 
+   * @param findAll
+   *          true means find all results and raise a dialog box
+   */
+  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.getAlignment(), 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();
+    boolean haveResults = false;
+    // set or reset the GUI
+    if ((idMatch.size() > 0))
+    {
+      haveResults = true;
+      ap.idPanel.highlightSearchResults(idMatch);
+    }
+    else
+    {
+      ap.idPanel.highlightSearchResults(null);
+    }
+
+    if (searchResults.getSize() > 0)
+    {
+      haveResults = true;
+      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 (!haveResults)
+    {
+      JOptionPane.showInternalMessageDialog(this, MessageManager.getString("label.finished_searching"),
+              null, JOptionPane.INFORMATION_MESSAGE);
+      resIndex = -1;
+      seqIndex = 0;
+    } else {
+      if (findAll)
+      {
+        // then we report the matches that were found
+        String message = (idMatch.size() > 0) ? "" + idMatch.size()
+                + " IDs" : "";
+        if (searchResults != null)
+        {
+          if (idMatch.size() > 0 && searchResults.getSize() > 0)
+          {
+            message += " and ";
+          }
+          message += searchResults.getSize()
+                  + " subsequence matches found.";
+        }
+        JOptionPane.showInternalMessageDialog(this, message, null,
+                JOptionPane.INFORMATION_MESSAGE);
+        resIndex = -1;
+        seqIndex = 0;
+      }
+    }
+
+  }
+}