X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FFinder.java;h=6bff69a5905dad0a97c3f232a3a13945cedcec54;hb=37de9310bec3501cbc6381e0c3dcb282fcaad812;hp=af1888cdd28274e22d58edbe10b6d488f159c76a;hpb=588042b69abf8e60bcc950b24c283933c7dd422f;p=jalview.git

diff --git a/src/jalview/gui/Finder.java b/src/jalview/gui/Finder.java
index af1888c..6bff69a 100755
--- a/src/jalview/gui/Finder.java
+++ b/src/jalview/gui/Finder.java
@@ -1,335 +1,369 @@
-/*
- * 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 java.util.*;
-
-import java.awt.*;
-import java.awt.event.*;
-import javax.swing.*;
-import javax.swing.event.*;
-
-import jalview.datamodel.*;
-import jalview.jbgui.*;
-
-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 ($$Version-Rel$$)
+ * 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.datamodel.SearchResults;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceI;
+import jalview.jbgui.GFinder;
+import jalview.util.MessageManager;
+import jalview.viewmodel.AlignmentViewport;
+
+import java.awt.event.ActionEvent;
+import java.awt.event.KeyEvent;
+import java.util.Vector;
+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.JOptionPane;
+import javax.swing.KeyStroke;
+
+/**
+ * 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;
+
+  AlignmentViewport 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(AlignmentViewport viewport, AlignmentPanel alignPanel)
+  {
+    av = viewport;
+    ap = alignPanel;
+    focusfixed = true;
+    frame = new JInternalFrame();
+    frame.setContentPane(this);
+    frame.setLayer(JLayeredPane.PALETTE_LAYER);
+    addEscapeHandler();
+    Desktop.addInternalFrame(frame, MessageManager.getString("label.find"),
+            WIDTH, HEIGHT);
+
+    textfield.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()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        escapeActionPerformed();
+      }
+    });
+  }
+
+  /**
+   * Close the panel on Escape key press
+   */
+  protected void escapeActionPerformed()
+  {
+    setVisible(false);
+    frame.dispose();
+  }
+
+  /**
+   * 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.getSeqPanel().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.setIncludeDescription(searchDescription.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.getIdPanel().highlightSearchResults(idMatch);
+    }
+    else
+    {
+      ap.getIdPanel().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;
+  }
+}