X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FFinder.java;h=358d9a417936c670e7751852b5a187691a1829a1;hb=57738a1f3c19b1c3a00bd3ac5108f8cd0af32f99;hp=3bcb2c003424cb7a046a0f0fa3b5d407093d3119;hpb=d053a3c980cf4318b9a19a255f9fc870e74de989;p=jalview.git

diff --git a/src/jalview/gui/Finder.java b/src/jalview/gui/Finder.java
index 3bcb2c0..358d9a4 100755
--- a/src/jalview/gui/Finder.java
+++ b/src/jalview/gui/Finder.java
@@ -1,87 +1,171 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ * 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.
- * 
+ * 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/>.
+ * 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 java.util.*;
+import java.util.Locale;
+
+import java.awt.Dimension;
+import java.awt.event.ActionEvent;
+import java.awt.event.FocusAdapter;
+import java.awt.event.FocusEvent;
+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 java.awt.*;
-import java.awt.event.*;
-import javax.swing.*;
+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;
 
-import jalview.datamodel.*;
-import jalview.jbgui.*;
+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;
 
 /**
- * DOCUMENT ME!
+ * 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
 {
-  AlignViewport av;
+  private static final int MIN_WIDTH = 350;
+
+  private static final int MIN_HEIGHT = 120;
+
+  private static final int MY_HEIGHT = 150;
 
-  AlignmentPanel ap;
+  private static final int MY_WIDTH = 400;
 
-  JInternalFrame frame;
+  private AlignViewportI av;
 
-  int seqIndex = 0;
+  private AlignmentPanel ap;
 
-  int resIndex = -1;
+  private JInternalFrame frame;
 
-  SearchResults searchResults;
+  /*
+   * Finder agent per viewport searched
+   */
+  private Map<AlignViewportI, FinderI> finders;
+
+  private SearchResultsI searchResults;
+
+  /*
+   * true if Finder always acts on the same alignment,
+   * false if it acts on the alignment with focus
+   */
+  private boolean focusFixed;
 
   /**
-   * Creates a new Finder object.
+   * Constructor given an associated alignment panel. Constructs and displays an
+   * internal frame where the user can enter a search string. The Finder may
+   * have 'fixed focus' (always act the panel for which it is constructed), or
+   * not (acts on the alignment that has focus). An optional 'scope' may be
+   * added to be shown in the title of the Finder frame.
    * 
-   * @param av
-   *          DOCUMENT ME!
-   * @param ap
-   *          DOCUMENT ME!
-   * @param f
-   *          DOCUMENT ME!
+   * @param alignPanel
+   * @param fixedFocus
+   * @param scope
    */
-  public Finder()
+  public Finder(AlignmentPanel alignPanel, boolean fixedFocus, String scope)
   {
-    this(null, null);
-    focusfixed = false;
-  }
-
-  public Finder(AlignViewport viewport, AlignmentPanel alignPanel)
-  {
-    av = viewport;
+    av = alignPanel.getAlignViewport();
     ap = alignPanel;
-    focusfixed = true;
+    focusFixed = fixedFocus;
+    finders = new HashMap<>();
     frame = new JInternalFrame();
     frame.setContentPane(this);
     frame.setLayer(JLayeredPane.PALETTE_LAYER);
-    Desktop.addInternalFrame(frame, "Find", 340, 110);
+    frame.addInternalFrameListener(new InternalFrameAdapter()
+    {
+      @Override
+      public void internalFrameClosing(InternalFrameEvent e)
+      {
+        closeAction();
+      }
+    });
+    frame.addFocusListener(new FocusAdapter()
+    {
+      @Override
+      public void focusGained(FocusEvent e)
+      {
+        /*
+         * ensure 'ignore hidden columns' is only enabled
+         * if the alignment with focus has hidden columns
+         */
+        getFocusedViewport();
+      }
+    });
+
+    addEscapeHandler();
 
-    textfield.requestFocus();
+    String title = MessageManager.getString("label.find");
+    if (scope != null)
+    {
+      title += " " + scope;
+    }
+    Desktop.addInternalFrame(frame, title, MY_WIDTH, MY_HEIGHT);
+    frame.setMinimumSize(new Dimension(MIN_WIDTH, MIN_HEIGHT));
+    searchBox.getComponent().requestFocus();
   }
 
   /**
-   * DOCUMENT ME!
-   * 
-   * @param e
-   *          DOCUMENT ME!
+   * Add a handler for the Escape key when the window has focus
    */
-  public void findNext_actionPerformed(ActionEvent e)
+  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())
     {
@@ -90,39 +174,32 @@ public class Finder extends GFinder
   }
 
   /**
-   * DOCUMENT ME!
-   * 
-   * @param e
-   *          DOCUMENT ME!
+   * Performs the 'Find All' action on the alignment panel with focus
    */
-  public void findAll_actionPerformed(ActionEvent e)
+  @Override
+  public void findAll_actionPerformed()
   {
     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
+   * 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 (focusfixed || Desktop.desktop == null)
+    if (focusFixed || Desktop.desktop == null)
     {
       if (ap != null && av != null)
       {
+        ignoreHidden.setEnabled(av.hasHiddenColumns());
         return true;
       }
       // we aren't in a desktop environment, so give up now.
@@ -133,11 +210,13 @@ public class Finder extends GFinder
     JInternalFrame[] frames = Desktop.desktop.getAllFrames();
     for (int f = 0; f < frames.length; f++)
     {
-      JInternalFrame frame = frames[f];
-      if (frame != null && frame instanceof AlignFrame)
+      JInternalFrame alignFrame = frames[f];
+      if (alignFrame != null && alignFrame instanceof AlignFrame
+              && !alignFrame.isIcon())
       {
-        av = ((AlignFrame) frame).viewport;
-        ap = ((AlignFrame) frame).alignPanel;
+        av = ((AlignFrame) alignFrame).viewport;
+        ap = ((AlignFrame) alignFrame).alignPanel;
+        ignoreHidden.setEnabled(av.hasHiddenColumns());
         return true;
       }
     }
@@ -145,48 +224,49 @@ public class Finder extends GFinder
   }
 
   /**
-   * DOCUMENT ME!
-   * 
-   * @param e
-   *          DOCUMENT ME!
+   * Opens a dialog that allows the user to create sequence features for the
+   * find match results
    */
-  public void createNewGroup_actionPerformed(ActionEvent e)
+  @Override
+  public void createFeatures_actionPerformed()
   {
-    SequenceI[] seqs = new SequenceI[searchResults.getSize()];
-    SequenceFeature[] features = new SequenceFeature[searchResults
-            .getSize()];
-
-    for (int i = 0; i < searchResults.getSize(); i++)
+    if (searchResults.isEmpty())
     {
-      seqs[i] = searchResults.getResultSequence(i).getDatasetSequence();
-
-      features[i] = new SequenceFeature(textfield.getText().trim(),
-              "Search Results", null, searchResults.getResultStart(i),
-              searchResults.getResultEnd(i), "Search Results");
+      return; // shouldn't happen
     }
+    List<SequenceI> seqs = new ArrayList<>();
+    List<SequenceFeature> features = new ArrayList<>();
+
+    String searchString = searchBox.getUserInput();
+    String desc = "Search Results";
 
-    if (ap.seqPanel.seqCanvas.getFeatureRenderer().amendFeatures(seqs,
-            features, true, ap))
+    /*
+     * assemble dataset sequences, and template new sequence features,
+     * for the amend features dialog
+     */
+    for (SearchResultMatchI match : searchResults.getResults())
     {
-      ap.alignFrame.showSeqFeatures.setSelected(true);
-      av.setShowSequenceFeatures(true);
-      ap.highlightSearchResults(null);
+      seqs.add(match.getSequence().getDatasetSequence());
+      features.add(new SequenceFeature(searchString, desc, match.getStart(),
+              match.getEnd(), desc));
     }
+
+    new FeatureEditor(ap, seqs, features, true).showDialog();
   }
 
   /**
-   * incrementally search the alignment
+   * 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
-   *          true means find all results and raise a dialog box
+   * @param doFindAll
    */
-  void doSearch(boolean findAll)
+  void doSearch(boolean doFindAll)
   {
-    createNewGroup.setEnabled(false);
+    createFeatures.setEnabled(false);
 
-    String searchString = textfield.getText().trim();
+    String searchString = searchBox.getUserInput();
 
-    if (searchString.length() < 1)
+    if (isInvalidSearchString(searchString))
     {
       return;
     }
@@ -194,71 +274,139 @@ public class Finder extends GFinder
     // 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))
+    FinderI finder = finders.get(av);
+    if (finder == null)
     {
-      haveResults = true;
-      ap.idPanel.highlightSearchResults(idMatch);
+      /*
+       * 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
     {
-      ap.idPanel.highlightSearchResults(null);
+      finder.findNext(searchString, isCaseSensitive, doSearchDescription,
+              skipHidden);
     }
 
-    if (searchResults.getSize() > 0)
+    searchResults = finder.getSearchResults();
+    List<SequenceI> idMatch = finder.getIdMatches();
+    ap.getIdPanel().highlightSearchResults(idMatch);
+
+    if (searchResults.isEmpty())
     {
-      haveResults = true;
-      createNewGroup.setEnabled(true);
+      searchResults = null;
     }
     else
     {
-      searchResults = null;
+      createFeatures.setEnabled(true);
     }
 
-    // if allResults is null, this effectively switches displaySearch flag in
-    // seqCanvas
+    searchBox.updateCache();
+
     ap.highlightSearchResults(searchResults);
     // TODO: add enablers for 'SelectSequences' or 'SelectColumns' or
     // 'SelectRegion' selection
-    if (!haveResults)
+    if (idMatch.isEmpty() && searchResults == null)
     {
-      JOptionPane.showInternalMessageDialog(this, "Finished searching",
-              null, JOptionPane.INFORMATION_MESSAGE);
-      resIndex = -1;
-      seqIndex = 0;
+      JvOptionPane.showInternalMessageDialog(this,
+              MessageManager.getString("label.finished_searching"), null,
+              JvOptionPane.PLAIN_MESSAGE);
     }
-
-    if (findAll)
+    else
     {
-      String message = (idMatch.size() > 0) ? "" + idMatch.size() + " IDs"
-              : "";
-      if (searchResults != null)
+      if (doFindAll)
       {
-        if (idMatch.size() > 0 && searchResults.getSize() > 0)
+        // then we report the matches that were found
+        StringBuilder message = new StringBuilder();
+        if (idMatch.size() > 0)
         {
-          message += " and ";
+          message.append(idMatch.size()).append(" IDs");
         }
-        message += searchResults.getSize() + " subsequence matches found.";
+        if (searchResults != null)
+        {
+          if (idMatch.size() > 0 && searchResults.getCount() > 0)
+          {
+            message.append(" ").append(MessageManager.getString("label.and")
+                    .toLowerCase(Locale.ROOT)).append(" ");
+          }
+          message.append(MessageManager.formatMessage(
+                  "label.subsequence_matches_found",
+                  searchResults.getCount()));
+        }
+        JvOptionPane.showInternalMessageDialog(this, message.toString(),
+                null, JvOptionPane.INFORMATION_MESSAGE);
       }
-      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;
+    }
+    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();
+    }
   }
 }