X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FFinder.java;h=537c323fa4b259f13ba80b6211bffe64245a2b30;hb=3d2750d886f1b6015b2fc3f8671a6cf3e32bb07a;hp=594baf8ac358b897891fd157255a73d06ecd87e7;hpb=5150ffd5baa1f58bb6b4059616bc6b9050326553;p=jalview.git

diff --git a/src/jalview/gui/Finder.java b/src/jalview/gui/Finder.java
index 594baf8..537c323 100755
--- a/src/jalview/gui/Finder.java
+++ b/src/jalview/gui/Finder.java
@@ -1,269 +1,392 @@
-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)
-  {
-    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.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){}
-    ///////////////////////////////////////////////
-
-
-    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);
-
-    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 ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ 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.api.AlignViewportI;
+import jalview.api.FinderI;
+import jalview.datamodel.SearchResultMatchI;
+import jalview.datamodel.SearchResultsI;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceI;
+import jalview.jbgui.GFinder;
+import jalview.util.MessageManager;
+
+import java.awt.Dimension;
+import java.awt.Graphics;
+import java.awt.event.ActionEvent;
+import java.awt.event.KeyEvent;
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.regex.Pattern;
+import java.util.regex.PatternSyntaxException;
+
+import javax.swing.AbstractAction;
+import javax.swing.JComponent;
+import javax.swing.JInternalFrame;
+import javax.swing.JLayeredPane;
+import javax.swing.KeyStroke;
+import javax.swing.event.InternalFrameAdapter;
+import javax.swing.event.InternalFrameEvent;
+
+/**
+ * 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 MIN_WIDTH = 350;
+
+  private static final int MIN_HEIGHT = 120;
+
+  private static final int MY_HEIGHT = 150;
+
+  private static final int MY_WIDTH = 400;
+
+  private AlignViewportI av;
+
+  private AlignmentPanel ap;
+
+  private JInternalFrame frame;
+
+  /*
+   * Finder agent per viewport searched
+   */
+  private Map<AlignViewportI, FinderI> finders;
+
+  private SearchResultsI searchResults;
+
+  /**
+   * Constructor given an associated alignment panel. Constructs and displays an
+   * internal frame where the user can enter a search string.
+   * 
+   * @param alignPanel
+   */
+  public Finder(AlignmentPanel alignPanel)
+  {
+    av = alignPanel.getAlignViewport();
+    ap = alignPanel;
+    finders = new HashMap<>();
+    frame = new JInternalFrame();
+    frame.setContentPane(this);
+    frame.setLayer(JLayeredPane.PALETTE_LAYER);
+    frame.addInternalFrameListener(
+            new InternalFrameAdapter()
+            {
+              @Override
+              public void internalFrameClosing(InternalFrameEvent e)
+              {
+                closeAction();
+              }
+            });
+    addEscapeHandler();
+
+    Desktop.addInternalFrame(frame, MessageManager.getString("label.find"),
+            MY_WIDTH, MY_HEIGHT);
+    frame.setMinimumSize(new Dimension(MIN_WIDTH, MIN_HEIGHT));
+    searchBox.requestFocus();
+  }
+
+  /**
+   * Add a handler for the Escape key when the window has focus
+   */
+  private void addEscapeHandler()
+  {
+    getRootPane().getInputMap(JComponent.WHEN_IN_FOCUSED_WINDOW)
+            .put(KeyStroke.getKeyStroke(KeyEvent.VK_ESCAPE, 0), "Cancel");
+    getRootPane().getActionMap().put("Cancel", new AbstractAction()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        closeAction();
+      }
+    });
+  }
+
+  /**
+   * Performs the 'Find Next' action on the alignment panel with focus
+   */
+  @Override
+  public void findNext_actionPerformed()
+  {
+    if (getFocusedViewport())
+    {
+      doSearch(false);
+    }
+  }
+
+  /**
+   * Performs the 'Find All' action on the alignment panel with focus
+   */
+  @Override
+  public void findAll_actionPerformed()
+  {
+    if (getFocusedViewport())
+    {
+      doSearch(true);
+    }
+  }
+
+  /**
+   * 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. Also sets the 'ignore hidden' checkbox disabled if the viewport
+   * has no hidden columns.
+   * 
+   * @return false if no alignment window was found
+   */
+  boolean getFocusedViewport()
+  {
+    if (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 alignFrame = frames[f];
+      if (alignFrame != null && alignFrame instanceof AlignFrame
+              && !alignFrame.isIcon())
+      {
+        av = ((AlignFrame) alignFrame).viewport;
+        ap = ((AlignFrame) alignFrame).alignPanel;
+        ignoreHidden.setEnabled(av.hasHiddenColumns());
+        return true;
+      }
+    }
+    return false;
+  }
+
+  /**
+   * Opens a dialog that allows the user to create sequence features for the
+   * find match results.
+   */
+  @Override
+  public void createFeatures_actionPerformed()
+  {
+    List<SequenceI> seqs = new ArrayList<>();
+    List<SequenceFeature> features = new ArrayList<>();
+
+    String searchString = searchBox.getEditor().getItem().toString().trim();
+    String desc = "Search Results";
+
+    /*
+     * assemble dataset sequences, and template new sequence features,
+     * for the amend features dialog
+     */
+    for (SearchResultMatchI match : searchResults.getResults())
+    {
+      seqs.add(match.getSequence().getDatasetSequence());
+      features.add(new SequenceFeature(searchString, desc,
+              match
+              .getStart(), match.getEnd(), desc));
+    }
+
+    if (ap.getSeqPanel().seqCanvas.getFeatureRenderer().amendFeatures(seqs,
+            features, true, ap))
+    {
+      /*
+       * ensure feature display is turned on to show the new features,
+       * and remove them as highlighted regions
+       */
+      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 doFindAll
+   */
+  void doSearch(boolean doFindAll)
+  {
+    createFeatures.setEnabled(false);
+
+    String searchString = searchBox.getUserInput().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
+    FinderI finder = finders.get(av);
+    if (finder == null)
+    {
+      /*
+       * first time we've searched this viewport
+       */
+      finder = new jalview.analysis.Finder(av);
+      finders.put(av, finder);
+    }
+
+    boolean isCaseSensitive = caseSensitive.isSelected();
+    boolean doSearchDescription = searchDescription.isSelected();
+    boolean skipHidden = ignoreHidden.isSelected();
+    if (doFindAll)
+    {
+      finder.findAll(searchString, isCaseSensitive, doSearchDescription,
+              skipHidden);
+    }
+    else
+    {
+      finder.findNext(searchString, isCaseSensitive, doSearchDescription,
+              skipHidden);
+    }
+
+    searchResults = finder.getSearchResults();
+    List<SequenceI> idMatch = finder.getIdMatches();
+    ap.getIdPanel().highlightSearchResults(idMatch);
+
+    if (searchResults.isEmpty())
+    {
+      searchResults = null;
+    }
+    else
+    {
+      createFeatures.setEnabled(true);
+    }
+
+    ap.highlightSearchResults(searchResults);
+    // TODO: add enablers for 'SelectSequences' or 'SelectColumns' or
+    // 'SelectRegion' selection
+    if (idMatch.isEmpty() && searchResults == null)
+    {
+      JvOptionPane.showInternalMessageDialog(this,
+              MessageManager.getString("label.finished_searching"), null,
+              JvOptionPane.INFORMATION_MESSAGE);
+    }
+    else
+    {
+      if (doFindAll)
+      {
+        // then we report the matches that were found
+        String message = (idMatch.size() > 0) ? "" + idMatch.size() + " IDs"
+                : "";
+        if (searchResults != null)
+        {
+          if (idMatch.size() > 0 && searchResults.getCount() > 0)
+          {
+            message += " and ";
+          }
+          message += searchResults.getCount()
+                  + " subsequence matches found.";
+        }
+        JvOptionPane.showInternalMessageDialog(this, message, null,
+                JvOptionPane.INFORMATION_MESSAGE);
+      }
+    }
+    searchBox.updateCache();
+  }
+
+  /**
+   * 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;
+    }
+    JvOptionPane.showInternalMessageDialog(this, error,
+            MessageManager.getString("label.invalid_search"), // $NON-NLS-1$
+            JvOptionPane.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;
+  }
+
+  protected void closeAction()
+  {
+    frame.setVisible(false);
+    frame.dispose();
+    searchBox.persistCache();
+    if (getFocusedViewport())
+    {
+      ap.alignFrame.requestFocus();
+    }
+  }
+
+  @Override
+  protected void paintComponent(Graphics g)
+  {
+    /*
+     * enable 'hidden regions' option only if
+     * 'top' viewport has hidden columns
+     */
+    getFocusedViewport();
+    super.paintComponent(g);
+  }
+}