X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fappletgui%2FFinder.java;h=e1236c9c65918f914c3e364e611da8f9d292668c;hb=7bc226b58110fa26d9dbd3f0c78095d06909ffc3;hp=58670d8803d735ffefdbe9534772adc4d77cb081;hpb=c7040936ee47d9d468638c39067b9f887be760a3;p=jalview.git

diff --git a/src/jalview/appletgui/Finder.java b/src/jalview/appletgui/Finder.java
index 58670d8..e1236c9 100755
--- a/src/jalview/appletgui/Finder.java
+++ b/src/jalview/appletgui/Finder.java
@@ -1,241 +1,241 @@
-package jalview.appletgui;
-
-import jalview.jbappletgui.GFinder;
-import jalview.datamodel.*;
-import java.awt.event.*;
-import java.util.*;
-import java.awt.*;
-
-public class Finder extends GFinder
-{
-  AlignViewport av;
-  AlignmentPanel ap;
-  Frame frame;
-  SuperGroup searchGroup;
-  Vector searchResults;
-
-  int seqIndex = 0;
-  int resIndex = 0;
-  public Finder(final AlignmentPanel ap)
-  {
-    this.av = ap.av;
-    this.ap = ap;
-    frame = new Frame();
-    frame.add(this);
-    jalview.bin.JalviewLite.addFrame(frame, "Find", 340,120);
-    frame.repaint();
-    frame.addWindowListener(new WindowAdapter()
-        {public void windowClosing(WindowEvent evt)
-              { ap.highlightSearchResults( 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.addElement( Integer.toString( av.getAlignment().findIndex(seq) ) );
-      searchResults.addElement( Integer.toString( seq.findIndex(res)-1 ) );
-      searchResults.addElement( Integer.toString( seq.findIndex(res)-1 ) );
-
-    }catch(NumberFormatException ex){}
-    ///////////////////////////////////////////////
-
-
-    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.addElement(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.elementAt(resIndex).toString()) )<selection.getStartRes())
-           continue;
-
-         searchResults.addElement( 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.addElement( 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.elementAt(i).toString());
-
-      createNewGroup.setEnabled(true);
-    }
-    else
-    {
-      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.";
-      System.out.println(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.appletgui;
+
+import java.util.*;
+
+import java.awt.*;
+import java.awt.event.*;
+
+import jalview.datamodel.*;
+
+public class Finder
+    extends Panel implements ActionListener
+{
+  AlignViewport av;
+  AlignmentPanel ap;
+  Frame frame;
+
+  SearchResults searchResults;
+
+  int seqIndex = 0;
+  int resIndex = 0;
+  public Finder(final AlignmentPanel ap)
+  {
+    try
+    {
+      jbInit();
+    }
+    catch (Exception e)
+    {
+      e.printStackTrace();
+    }
+
+    this.av = ap.av;
+    this.ap = ap;
+    frame = new Frame();
+    frame.add(this);
+    jalview.bin.JalviewLite.addFrame(frame, "Find", 340, 120);
+    frame.repaint();
+    frame.addWindowListener(new WindowAdapter()
+    {
+      public void windowClosing(WindowEvent evt)
+      {
+        ap.highlightSearchResults(null);
+      }
+    });
+  }
+
+  public void actionPerformed(ActionEvent evt)
+  {
+    if (evt.getSource() == textfield)
+    {
+      doSearch(false);
+    }
+
+    else if (evt.getSource() == findNext)
+    {
+      doSearch(false);
+    }
+
+    else if (evt.getSource() == findAll)
+    {
+      resIndex = 0;
+      seqIndex = 0;
+      doSearch(true);
+    }
+    else if (evt.getSource() == createNewGroup)
+    {
+      createNewGroup_actionPerformed();
+    }
+  }
+
+  public void createNewGroup_actionPerformed()
+  {
+
+    CutAndPasteTransfer cap = new CutAndPasteTransfer(true, null);
+    cap.accept.setLabel("Accept");
+    Dialog dialog = new Dialog(ap.alignFrame, "Enter New Feature Name", true);
+    dialog.add(cap);
+
+    cap.setText(textfield.getText());
+
+    dialog.setBounds(frame.getLocation().x + frame.getSize().width + 5,
+                     frame.getLocation().y + 20, 300, 100);
+    dialog.show();
+
+    String featureName = cap.getText().trim();
+    if (featureName.length() < 1)
+    {
+      return;
+    }
+
+    for (int i = 0; i < searchResults.getSize(); i++)
+    {
+      SequenceI seq = searchResults.getResultSequence(i);
+
+      SequenceFeature sf = new SequenceFeature(featureName,
+                                               null, null,
+                                               searchResults.getResultStart(i),
+                                               searchResults.getResultEnd(i),
+                                               "Search Results");
+
+      ap.seqPanel.seqCanvas.getFeatureRenderer().addNewFeature(
+          featureName, new Color(60, 160, 115));
+      seq.addSequenceFeature(sf);
+    }
+
+    ap.seqPanel.seqCanvas.getFeatureRenderer().findAllFeatures();
+    ap.alignFrame.sequenceFeatures.setState(true);
+    av.showSequenceFeatures(true);
+    ap.highlightSearchResults(null);
+  }
+
+  void doSearch(boolean findAll)
+  {
+    if (jalview.bin.JalviewLite.currentAlignFrame != null)
+    {
+      ap = jalview.bin.JalviewLite.currentAlignFrame.alignPanel;
+      av = ap.av;
+    }
+    createNewGroup.setEnabled(false);
+    jalview.analysis.Finder finder = new jalview.analysis.Finder(av.
+        getAlignment(), av.getSelectionGroup(), seqIndex, resIndex);
+    finder.setCaseSensitive(caseSensitive.getState());
+    finder.setFindAll(findAll);
+
+    String searchString = textfield.getText();
+
+    finder.find(searchString);
+    seqIndex = finder.getSeqIndex();
+    resIndex = finder.getResIndex();
+    searchResults = finder.getSearchResults();
+    Vector idMatch = finder.getIdMatch();
+
+    if (searchResults.getSize() == 0 && idMatch.size() > 0)
+    {
+      ap.idPanel.highlightSearchResults(idMatch);
+    }
+
+    if (searchResults.getSize() > 0)
+    {
+      createNewGroup.setEnabled(true);
+
+    }
+    else
+    {
+      searchResults = null;
+      resIndex = 0;
+      seqIndex = 0;
+    }
+
+    // if allResults is null, this effectively switches displaySearch flag in seqCanvas
+    ap.highlightSearchResults(searchResults);
+
+    if (findAll)
+    {
+      String message = (searchResults == null ? 0 : searchResults.getSize()) +
+          " matches found.";
+      ap.alignFrame.statusBar.setText("Search results: " + searchString + " : " +
+                                      message);
+    }
+
+  }
+
+  Label jLabel1 = new Label();
+  protected TextField textfield = new TextField();
+  protected Button findAll = new Button();
+  protected Button findNext = new Button();
+  Panel jPanel1 = new Panel();
+  GridLayout gridLayout1 = new GridLayout();
+  protected Button createNewGroup = new Button();
+  Checkbox caseSensitive = new Checkbox();
+
+  private void jbInit()
+      throws Exception
+  {
+    jLabel1.setFont(new java.awt.Font("Verdana", 0, 12));
+    jLabel1.setText("Find");
+    jLabel1.setBounds(new Rectangle(3, 30, 34, 15));
+    this.setLayout(null);
+    textfield.setFont(new java.awt.Font("Verdana", Font.PLAIN, 10));
+    textfield.setText("");
+    textfield.setBounds(new Rectangle(40, 27, 133, 21));
+    textfield.addKeyListener(new java.awt.event.KeyAdapter()
+    {
+      public void keyTyped(KeyEvent e)
+      {
+        textfield_keyTyped(e);
+      }
+    });
+    textfield.addActionListener(this);
+    findAll.setFont(new java.awt.Font("Verdana", Font.PLAIN, 10));
+    findAll.setLabel("Find all");
+    findAll.addActionListener(this);
+    findNext.setEnabled(false);
+    findNext.setFont(new java.awt.Font("Verdana", Font.PLAIN, 10));
+    findNext.setLabel("Find Next");
+    findNext.addActionListener(this);
+    jPanel1.setBounds(new Rectangle(180, 5, 141, 64));
+    jPanel1.setLayout(gridLayout1);
+    gridLayout1.setHgap(0);
+    gridLayout1.setRows(3);
+    gridLayout1.setVgap(2);
+    createNewGroup.setEnabled(false);
+    createNewGroup.setFont(new java.awt.Font("Verdana", Font.PLAIN, 10));
+    createNewGroup.setLabel("New Feature");
+    createNewGroup.addActionListener(this);
+    caseSensitive.setLabel("Match Case");
+    caseSensitive.setBounds(new Rectangle(40, 49, 126, 23));
+    jPanel1.add(findNext, null);
+    jPanel1.add(findAll, null);
+    jPanel1.add(createNewGroup, null);
+    this.add(caseSensitive);
+    this.add(textfield, null);
+    this.add(jLabel1, null);
+    this.add(jPanel1, null);
+  }
+
+  void textfield_keyTyped(KeyEvent e)
+  {
+    findNext.setEnabled(true);
+  }
+
+}