X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FFinder.java;h=b1dcb880af79c0b3c422a00fe64709ffc998d039;hb=17e77c3f2949a0729322b4a8d907f3f34b6a9914;hp=ab4cd7ba8c28f7119864208498ff8d11710ae9dd;hpb=5150ffd5baa1f58bb6b4059616bc6b9050326553;p=jalview.git

diff --git a/src/jalview/appletgui/Finder.java b/src/jalview/appletgui/Finder.java
old mode 100755
new mode 100644
index ab4cd7b..b1dcb88
--- a/src/jalview/appletgui/Finder.java
+++ b/src/jalview/appletgui/Finder.java
@@ -1,242 +1,292 @@
-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)
-  {
-    jalview.schemes.UserColourScheme ucs = new jalview.schemes.UserColourScheme();
-   Color [] newColors = new Color[24];
-   for(int i=0; i<24; i++)
-     newColors[i] = new Color(60,160,115);
-
-   ucs.setColourScheme(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 (Version 2.9)
+ * Copyright (C) 2015 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.appletgui;
+
+import jalview.datamodel.SearchResults;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceI;
+import jalview.util.MessageManager;
+import jalview.viewmodel.AlignmentViewport;
+
+import java.awt.Button;
+import java.awt.Checkbox;
+import java.awt.Font;
+import java.awt.Frame;
+import java.awt.GridLayout;
+import java.awt.Label;
+import java.awt.Panel;
+import java.awt.Rectangle;
+import java.awt.TextField;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.KeyEvent;
+import java.awt.event.WindowAdapter;
+import java.awt.event.WindowEvent;
+import java.util.Vector;
+
+public class Finder extends Panel implements ActionListener
+{
+  AlignmentViewport av;
+
+  AlignmentPanel ap;
+
+  Frame frame;
+
+  SearchResults searchResults;
+
+  int seqIndex = 0;
+
+  int resIndex = -1;
+
+  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,
+            MessageManager.getString("action.find"), 340, 120);
+    frame.repaint();
+    frame.addWindowListener(new WindowAdapter()
+    {
+      public void windowClosing(WindowEvent evt)
+      {
+        ap.highlightSearchResults(null);
+      }
+    });
+    textfield.requestFocus();
+  }
+
+  public void actionPerformed(ActionEvent evt)
+  {
+    if (evt.getSource() == textfield)
+    {
+      doSearch(false);
+    }
+
+    else if (evt.getSource() == findNext)
+    {
+      doSearch(false);
+    }
+
+    else if (evt.getSource() == findAll)
+    {
+      resIndex = -1;
+      seqIndex = 0;
+      doSearch(true);
+    }
+    else if (evt.getSource() == createNewGroup)
+    {
+      createNewGroup_actionPerformed();
+    }
+  }
+
+  public void createNewGroup_actionPerformed()
+  {
+    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);
+
+      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.sequenceFeatures.setState(true);
+      av.setShowSequenceFeatures(true);
+      ap.highlightSearchResults(null);
+    }
+  }
+
+  void doSearch(boolean findAll)
+  {
+    if (ap.av.applet.currentAlignFrame != null)
+    {
+      ap = ap.av.applet.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.setIncludeDescription(searchDescription.getState());
+    finder.setFindAll(findAll);
+
+    String searchString = textfield.getText();
+
+    finder.find(searchString);
+    seqIndex = finder.getSeqIndex();
+    resIndex = finder.getResIndex();
+    searchResults = finder.getSearchResults();
+    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)
+    {
+      ap.alignFrame.statusBar.setText(MessageManager
+              .getString("label.finished_searching"));
+      resIndex = -1;
+      seqIndex = 0;
+    }
+    else
+    {
+      if (findAll)
+      {
+        String message = (idMatch.size() > 0) ? "" + idMatch.size()
+                + " IDs" : "";
+        if (idMatch.size() > 0 && searchResults != null
+                && searchResults.getSize() > 0)
+        {
+          message += " and ";
+        }
+        if (searchResults != null)
+        {
+          message += searchResults.getSize() + " subsequence matches.";
+        }
+        ap.alignFrame.statusBar.setText(MessageManager.formatMessage(
+                "label.search_results", new String[] { searchString,
+                    message }));
+
+      }
+      else
+      {
+        // TODO: indicate sequence and matching position in status bar
+        ap.alignFrame.statusBar.setText(MessageManager.formatMessage(
+                "label.found_match_for", new String[] { searchString }));
+      }
+    }
+  }
+
+  Label jLabel1 = new Label();
+
+  protected TextField textfield = new TextField();
+
+  protected Button findAll = new Button();
+
+  protected Button findNext = new Button();
+
+  Panel actionsPanel = new Panel();
+
+  GridLayout gridLayout1 = new GridLayout();
+
+  protected Button createNewGroup = new Button();
+
+  Checkbox caseSensitive = new Checkbox();
+
+  Checkbox searchDescription = new Checkbox();
+
+  private void jbInit() throws Exception
+  {
+    jLabel1.setFont(new java.awt.Font("Verdana", 0, 12));
+    jLabel1.setText(MessageManager.getString("action.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, 17, 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(MessageManager.getString("action.find_all"));
+    findAll.addActionListener(this);
+    findNext.setEnabled(false);
+    findNext.setFont(new java.awt.Font("Verdana", Font.PLAIN, 10));
+    findNext.setLabel(MessageManager.getString("action.find_next"));
+    findNext.addActionListener(this);
+    actionsPanel.setBounds(new Rectangle(195, 5, 141, 64));
+    actionsPanel.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(MessageManager.getString("label.new_feature"));
+    createNewGroup.addActionListener(this);
+    caseSensitive.setLabel(MessageManager.getString("label.match_case"));
+    caseSensitive.setBounds(new Rectangle(30, 39, 126, 23));
+
+    searchDescription.setLabel(MessageManager
+            .getString("label.include_description"));
+    searchDescription.setBounds(new Rectangle(30, 59, 170, 23));
+    actionsPanel.add(findNext, null);
+    actionsPanel.add(findAll, null);
+    actionsPanel.add(createNewGroup, null);
+    this.add(caseSensitive);
+    this.add(textfield, null);
+    this.add(jLabel1, null);
+    this.add(actionsPanel, null);
+    this.add(searchDescription);
+  }
+
+  void textfield_keyTyped(KeyEvent e)
+  {
+    findNext.setEnabled(true);
+  }
+
+}