X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FFinder.java;h=cc91ebfbecd90eeebbf3ffc6e74486c61302f5b5;hb=ab43013b7e357b84b4abade0dba949668dfb2a0e;hp=1ff31fe25eddb2c68b36d2c1b79968e8adf794c8;hpb=1f183a4e9d63b2af6cf7184274affc80e11ef344;p=jalview.git

diff --git a/src/jalview/gui/Finder.java b/src/jalview/gui/Finder.java
index 1ff31fe..cc91ebf 100755
--- a/src/jalview/gui/Finder.java
+++ b/src/jalview/gui/Finder.java
@@ -1,222 +1,336 @@
-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.util.regex.*;
-import java.awt.*;
-
-public class Finder extends GFinder
-{
-  AlignViewport av;
-  AlignmentPanel ap;
-  JInternalFrame frame;
-  String searchString;
-  SuperGroup searchGroup;
-
-  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 );
-     // frame.setClosed(true);
-    }catch(Exception ex){ }
-  }
-
-
-  public void createNewGroup_actionPerformed(ActionEvent e)
-  {
-    for(int i=0; i<searchGroup.getSize(); i++)
-      av.alignment.addGroup( searchGroup.getGroupeAt(i));
-
-    ap.av.alignment.addSuperGroup(searchGroup);
-    ap.highlightSearchResults( null );
-  }
-
-
-  void doSearch(boolean findAll)
-  {
-    createNewGroup.setEnabled(false);
-    searchString = textfield.getText().toUpperCase();
-
-    ArrayList searchResults = new ArrayList();
-    int [] allResults = null;
-
-    Sequence seq;
-    String item;
-    boolean found = false;
-
-    /// is the searchString a residue number?
-    try{
-      int res = Integer.parseInt(searchString);
-      found = true;
-
-      if(av.getSelection().size()>0)
-        seq = (Sequence)(av.getSelection().sequenceAt(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 ) );
-
-
-      //av.getAlignment().getSequenceAt(seq).findPosition(res)
-    }catch(NumberFormatException ex){}
-
-    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);
-
-    searchGroup = new SuperGroup(searchString, ucs , true, true, false);
-
-    while( !found && seqIndex<av.getAlignment().getHeight())
-    {
-      seq = (Sequence)av.getAlignment().getSequenceAt(seqIndex);
-      if(av.getSelection().size()>0 && !av.getSelection().contains(seq))
-      {
-        // if a selection has been made, only search within that selection
-        seqIndex++;
-        resIndex=0;
-        continue;
-      }
-
-      item = seq.getSequence();
-
-      ///Shall we ignore gaps????
-      StringBuffer noGaps = new StringBuffer();
-      int insertCount=0;
-      ArrayList spaces = new ArrayList();
-
-      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++;
-      }
-
-
-      Pattern pattern = Pattern.compile(searchString);
-      Matcher matcher = pattern.matcher(noGaps);
-
-      for(int r = resIndex; r<noGaps.length(); r++)
-      {
-
-       if( matcher.find( r ) )
-       {
-         resIndex = matcher.start();
-
-         searchResults.add( Integer.toString( seqIndex) );
-         searchResults.add( Integer.toString( resIndex+ Integer.parseInt(spaces.get(resIndex).toString()) ) );
-         searchResults.add( Integer.toString( matcher.end()-1 + Integer.parseInt(spaces.get(matcher.end()-1).toString()) ) );
-
-         SequenceGroup sg = new SequenceGroup(searchString, ucs, true, true, false,
-                                             resIndex+ Integer.parseInt(spaces.get(resIndex).toString()) ,
-                                      matcher.end()-1 + Integer.parseInt(spaces.get(matcher.end()-1).toString())
-            );
-         sg.addSequence((Sequence)av.getAlignment().getSequenceAt(seqIndex));
-         searchGroup.addGroup( sg );
-
-         if(!findAll)
-         {
-           // thats enough, break and display the result
-           found = true;
-           resIndex++;
-           break;
-         }
-
-         r=resIndex+1;
-       }
-      }
-      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());
-
-      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 2.8.2b1)
+ * 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 jalview.datamodel.SearchResults;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceI;
+import jalview.jbgui.GFinder;
+import jalview.util.MessageManager;
+
+import java.awt.event.ActionEvent;
+import java.util.Vector;
+import java.util.regex.Pattern;
+import java.util.regex.PatternSyntaxException;
+
+import javax.swing.JInternalFrame;
+import javax.swing.JLayeredPane;
+import javax.swing.JOptionPane;
+
+/**
+ * Performs the menu option for searching the alignment, for the next or all
+ * matches. If matches are found, they are highlighted, and the user has the
+ * option to create a new feature on the alignment for the matched positions.
+ * 
+ * Searches can be for a simple base sequence, or may use a regular expression.
+ * Any gaps are ignored.
+ * 
+ * @author $author$
+ * @version $Revision$
+ */
+public class Finder extends GFinder
+{
+  private static final int HEIGHT = 110;
+
+  private static final int WIDTH = 340;
+
+  AlignViewport av;
+
+  AlignmentPanel ap;
+
+  JInternalFrame frame;
+
+  int seqIndex = 0;
+
+  int resIndex = -1;
+
+  SearchResults searchResults;
+
+  /**
+   * Creates a new Finder object with no associated viewport or panel.
+   */
+  public Finder()
+  {
+    this(null, null);
+    focusfixed = false;
+  }
+
+  /**
+   * Constructor given an associated viewport and alignment panel. Constructs
+   * and displays an internal frame where the user can enter a search string.
+   * 
+   * @param viewport
+   * @param alignPanel
+   */
+  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, MessageManager.getString("label.find"),
+            WIDTH, HEIGHT);
+
+    textfield.requestFocus();
+  }
+
+  /**
+   * Performs the 'Find Next' action.
+   * 
+   * @param e
+   */
+  public void findNext_actionPerformed(ActionEvent e)
+  {
+    if (getFocusedViewport())
+    {
+      doSearch(false);
+    }
+  }
+
+  /**
+   * Performs the 'Find All' action.
+   * 
+   * @param e
+   */
+  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);
+    }
+  }
+
+  /**
+   * Search the alignment for the next or all matches. If 'all matches', a
+   * dialog is shown with the number of sequence ids and subsequences matched.
+   * 
+   * @param findAll
+   */
+  void doSearch(boolean findAll)
+  {
+    createNewGroup.setEnabled(false);
+
+    String searchString = textfield.getText().trim();
+
+    if (isInvalidSearchString(searchString))
+    {
+      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;
+      }
+    }
+
+  }
+
+  /**
+   * Displays an error dialog, and answers false, if the search string is
+   * invalid, else answers true.
+   * 
+   * @param searchString
+   * @return
+   */
+  protected boolean isInvalidSearchString(String searchString)
+  {
+    String error = getSearchValidationError(searchString);
+    if (error == null)
+    {
+      return false;
+    }
+    JOptionPane.showInternalMessageDialog(this, error,
+            MessageManager.getString("label.invalid_search"), // $NON-NLS-1$
+            JOptionPane.ERROR_MESSAGE);
+    return true;
+  }
+
+  /**
+   * Returns an error message string if the search string is invalid, else
+   * returns null.
+   * 
+   * Currently validation is limited to checking the string is not empty, and is
+   * a valid regular expression (simple searches for base sub-sequences will
+   * pass this test). Additional validations may be added in future if the
+   * search syntax is expanded.
+   * 
+   * @param searchString
+   * @return
+   */
+  protected String getSearchValidationError(String searchString)
+  {
+    String error = null;
+    if (searchString == null || searchString.length() == 0)
+    {
+      error = MessageManager.getString("label.invalid_search");
+    }
+    try
+    {
+      Pattern.compile(searchString);
+    } catch (PatternSyntaxException e)
+    {
+      error = MessageManager.getString("error.invalid_regex") + ": "
+              + e.getDescription();
+    }
+    return error;
+  }
+}