X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FFinder.java;h=2bad00626ed1e0c10fea28ed95c8f77eeea3a8f4;hb=86a9434feba170f5a91b0eb366d152262cc65ff8;hp=1c767a12ea76302ea04d525f8d796a5d1c301e39;hpb=153dd62dc91da13ae732600e6ea55ddbe15eab39;p=jalview.git

diff --git a/src/jalview/gui/Finder.java b/src/jalview/gui/Finder.java
index 1c767a1..2bad006 100755
--- a/src/jalview/gui/Finder.java
+++ b/src/jalview/gui/Finder.java
@@ -1,60 +1,83 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, 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 jalview.datamodel.SearchResultMatchI;
+import jalview.datamodel.SearchResultsI;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceI;
+import jalview.jbgui.GFinder;
+import jalview.util.MessageManager;
+import jalview.viewmodel.AlignmentViewport;
 
-import java.awt.*;
-import java.awt.event.*;
-import javax.swing.*;
+import java.awt.event.ActionEvent;
+import java.awt.event.KeyEvent;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Vector;
+import java.util.regex.Pattern;
+import java.util.regex.PatternSyntaxException;
 
-import jalview.datamodel.*;
-import jalview.jbgui.*;
+import javax.swing.AbstractAction;
+import javax.swing.JComponent;
+import javax.swing.JInternalFrame;
+import javax.swing.JLayeredPane;
+import javax.swing.KeyStroke;
+import javax.swing.event.InternalFrameEvent;
 
 /**
- * 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 MY_HEIGHT = 120;
+
+  private static final int MY_WIDTH = 400;
+
+  AlignmentViewport av;
 
   AlignmentPanel ap;
 
+  private static final int MIN_WIDTH = 350;
+
+  private static final int MIN_HEIGHT = 120;
+
   JInternalFrame frame;
 
   int seqIndex = 0;
 
   int resIndex = -1;
 
-  SearchResults searchResults;
+  SearchResultsI searchResults;
 
   /**
-   * Creates a new Finder object.
-   * 
-   * @param av
-   *          DOCUMENT ME!
-   * @param ap
-   *          DOCUMENT ME!
-   * @param f
-   *          DOCUMENT ME!
+   * Creates a new Finder object with no associated viewport or panel.
    */
   public Finder()
   {
@@ -62,7 +85,14 @@ public class Finder extends GFinder
     focusfixed = false;
   }
 
-  public Finder(AlignViewport viewport, AlignmentPanel alignPanel)
+  /**
+   * 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;
@@ -70,17 +100,44 @@ public class Finder extends GFinder
     frame = new JInternalFrame();
     frame.setContentPane(this);
     frame.setLayer(JLayeredPane.PALETTE_LAYER);
-    Desktop.addInternalFrame(frame, "Find", 340, 110);
+    frame.addInternalFrameListener(
+            new javax.swing.event.InternalFrameAdapter()
+            {
+              @Override
+              public void internalFrameClosing(InternalFrameEvent e)
+              {
+                closeAction();
+              }
+            });
+    addEscapeHandler();
+    Desktop.addInternalFrame(frame, MessageManager.getString("label.find"),
+            true, MY_WIDTH, MY_HEIGHT, true, true);
+    searchBox.getComponent().requestFocus();
+  }
 
-    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()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        closeAction();
+      }
+    });
   }
 
   /**
-   * DOCUMENT ME!
+   * Performs the 'Find Next' action.
    * 
    * @param e
-   *          DOCUMENT ME!
    */
+  @Override
   public void findNext_actionPerformed(ActionEvent e)
   {
     if (getFocusedViewport())
@@ -90,11 +147,11 @@ public class Finder extends GFinder
   }
 
   /**
-   * DOCUMENT ME!
+   * Performs the 'Find All' action.
    * 
    * @param e
-   *          DOCUMENT ME!
    */
+  @Override
   public void findAll_actionPerformed(ActionEvent e)
   {
     if (getFocusedViewport())
@@ -133,11 +190,11 @@ 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)
       {
-        av = ((AlignFrame) frame).viewport;
-        ap = ((AlignFrame) frame).alignPanel;
+        av = ((AlignFrame) alignFrame).viewport;
+        ap = ((AlignFrame) alignFrame).alignPanel;
         return true;
       }
     }
@@ -145,48 +202,49 @@ 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<SequenceI>();
+    List<SequenceFeature> features = new ArrayList<SequenceFeature>();
 
-    if (ap.seqPanel.seqCanvas.getFeatureRenderer().amendFeatures(seqs,
-            features, true, ap))
+    String searchString = searchBox.getUserInput();
+    String desc = "Search Results";
+
+    /*
+     * 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;
     }
@@ -195,9 +253,11 @@ public class Finder extends GFinder
     // TODO: add switches to control what is searched - sequences, IDS,
     // descriptions, features
     jalview.analysis.Finder finder = new jalview.analysis.Finder(
-            av.alignment, av.getSelectionGroup(), seqIndex, resIndex);
+            av.getAlignment(), av.getSelectionGroup(), seqIndex, resIndex);
     finder.setCaseSensitive(caseSensitive.isSelected());
-    finder.setFindAll(findAll);
+    finder.setIncludeDescription(searchDescription.isSelected());
+
+    finder.setFindAll(doFindAll);
 
     finder.find(searchString); // returns true if anything was actually found
 
@@ -206,29 +266,31 @@ public class Finder extends GFinder
 
     searchResults = finder.getSearchResults(); // find(regex,
     // caseSensitive.isSelected(), )
-    Vector idMatch = finder.getIdMatch();
+    Vector<SequenceI> idMatch = finder.getIdMatch();
     boolean haveResults = false;
     // set or reset the GUI
     if ((idMatch.size() > 0))
     {
       haveResults = true;
-      ap.idPanel.highlightSearchResults(idMatch);
+      ap.getIdPanel().highlightSearchResults(idMatch);
     }
     else
     {
-      ap.idPanel.highlightSearchResults(null);
+      ap.getIdPanel().highlightSearchResults(null);
     }
 
     if (searchResults.getSize() > 0)
     {
       haveResults = true;
-      createNewGroup.setEnabled(true);
+      createFeatures.setEnabled(true);
     }
     else
     {
       searchResults = null;
     }
 
+    searchBox.updateCache();
+
     // if allResults is null, this effectively switches displaySearch flag in
     // seqCanvas
     ap.highlightSearchResults(searchResults);
@@ -236,26 +298,94 @@ public class Finder extends GFinder
     // 'SelectRegion' selection
     if (!haveResults)
     {
-      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 (idMatch.size() > 0 && searchResults.getSize() > 0)
+      if (doFindAll)
       {
-        message += " and ";
+        // 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.";
+        }
+        resIndex = -1;
+        seqIndex = 0;
+        JvOptionPane.showInternalMessageDialog(this, message, null,
+                JvOptionPane.PLAIN_MESSAGE);
       }
-      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;
+    }
+    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();
+    }
   }
 }