X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FFinder.java;h=3cce82c1b046b8f37c8aaf71dc91acb2794d59cf;hb=be32c14cd8e48fe0a207cd7030cb9cd46f894678;hp=b3fad97e370de200057c142eb101ce432960555e;hpb=eae01b09aadd51c1062c67fa66de5636f1854dd2;p=jalview.git

diff --git a/src/jalview/gui/Finder.java b/src/jalview/gui/Finder.java
index b3fad97..3cce82c 100755
--- a/src/jalview/gui/Finder.java
+++ b/src/jalview/gui/Finder.java
@@ -1,41 +1,59 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
- * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
- * 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 file is part of Jalview.
  * 
- * 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.
+ * 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 this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ * 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.SearchResults;
+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.util.Vector;
+import java.util.regex.Pattern;
+import java.util.regex.PatternSyntaxException;
 
-import jalview.datamodel.*;
-import jalview.jbgui.*;
+import javax.swing.JInternalFrame;
+import javax.swing.JLayeredPane;
+import javax.swing.JOptionPane;
 
 /**
- * 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 HEIGHT = 110;
+
+  private static final int WIDTH = 340;
+
+  AlignmentViewport av;
 
   AlignmentPanel ap;
 
@@ -48,30 +66,39 @@ public class Finder extends GFinder
   SearchResults 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()
   {
+    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);
-    Desktop.addInternalFrame(frame, "Find", 340, 110);
+    Desktop.addInternalFrame(frame, MessageManager.getString("label.find"),
+            WIDTH, HEIGHT);
 
     textfield.requestFocus();
   }
 
   /**
-   * DOCUMENT ME!
+   * Performs the 'Find Next' action.
    * 
    * @param e
-   *                DOCUMENT ME!
    */
   public void findNext_actionPerformed(ActionEvent e)
   {
@@ -82,10 +109,9 @@ public class Finder extends GFinder
   }
 
   /**
-   * DOCUMENT ME!
+   * Performs the 'Find All' action.
    * 
    * @param e
-   *                DOCUMENT ME!
    */
   public void findAll_actionPerformed(ActionEvent e)
   {
@@ -98,14 +124,33 @@ public class Finder extends GFinder
   }
 
   /**
-   * gets the topmost alignment window and sets av and ap accordingly
+   * 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()
   {
-    // now checks further down the window stack to fix bug https://mantis.lifesci.dundee.ac.uk/view.php?id=36008
+    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++) {
+    for (int f = 0; f < frames.length; f++)
+    {
       JInternalFrame frame = frames[f];
       if (frame != null && frame instanceof AlignFrame)
       {
@@ -121,7 +166,7 @@ public class Finder extends GFinder
    * DOCUMENT ME!
    * 
    * @param e
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   public void createNewGroup_actionPerformed(ActionEvent e)
   {
@@ -138,7 +183,7 @@ public class Finder extends GFinder
               searchResults.getResultEnd(i), "Search Results");
     }
 
-    if (ap.seqPanel.seqCanvas.getFeatureRenderer().amendFeatures(seqs,
+    if (ap.getSeqPanel().seqCanvas.getFeatureRenderer().amendFeatures(seqs,
             features, true, ap))
     {
       ap.alignFrame.showSeqFeatures.setSelected(true);
@@ -148,10 +193,10 @@ public class Finder extends GFinder
   }
 
   /**
-   * 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
    */
   void doSearch(boolean findAll)
   {
@@ -159,7 +204,7 @@ public class Finder extends GFinder
 
     String searchString = textfield.getText().trim();
 
-    if (searchString.length() < 1)
+    if (isInvalidSearchString(searchString))
     {
       return;
     }
@@ -168,8 +213,10 @@ 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.setIncludeDescription(searchDescription.isSelected());
+
     finder.setFindAll(findAll);
 
     finder.find(searchString); // returns true if anything was actually found
@@ -178,21 +225,23 @@ public class Finder extends GFinder
     resIndex = finder.getResIndex();
 
     searchResults = finder.getSearchResults(); // find(regex,
-                                                // caseSensitive.isSelected(), )
+    // caseSensitive.isSelected(), )
     Vector idMatch = finder.getIdMatch();
-    boolean haveResults=false;
+    boolean haveResults = false;
     // set or reset the GUI
     if ((idMatch.size() > 0))
     {
-      haveResults=true;
-      ap.idPanel.highlightSearchResults(idMatch);
-    } else {
-      ap.idPanel.highlightSearchResults(null);
+      haveResults = true;
+      ap.getIdPanel().highlightSearchResults(idMatch);
+    }
+    else
+    {
+      ap.getIdPanel().highlightSearchResults(null);
     }
-    
+
     if (searchResults.getSize() > 0)
     {
-      haveResults=true;
+      haveResults = true;
       createNewGroup.setEnabled(true);
     }
     else
@@ -207,24 +256,84 @@ public class Finder extends GFinder
     // 'SelectRegion' selection
     if (!haveResults)
     {
-      JOptionPane.showInternalMessageDialog(this, "Finished searching",
-              null, JOptionPane.INFORMATION_MESSAGE);
+      JOptionPane.showInternalMessageDialog(this,
+              MessageManager.getString("label.finished_searching"), null,
+              JOptionPane.INFORMATION_MESSAGE);
       resIndex = -1;
       seqIndex = 0;
     }
-
-    if (findAll)
+    else
     {
-      String message = (idMatch.size()>0) ? ""+idMatch.size()+" IDs" : "";
-      if (idMatch.size()>0 && searchResults.getSize()>0) {
-        message += " and ";
+      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;
       }
-      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;
+  }
 }