X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FFinder.java;h=5a2271d3ebcb5db5a017afb5e733e13758c9300e;hb=ad15cff29620f960119f80176f1fd443da9f6763;hp=3161271ac7593ba3f7bea5ddcb8d2a0c3504d27a;hpb=b2f9a8d7bce642ff4011bc6d49e02bb0569fbb11;p=jalview.git

diff --git a/src/jalview/gui/Finder.java b/src/jalview/gui/Finder.java
index 3161271..5a2271d 100755
--- a/src/jalview/gui/Finder.java
+++ b/src/jalview/gui/Finder.java
@@ -1,40 +1,57 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
- * Copyright (C) 2014 The Jalview Authors
+ * 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.awt.event.*;
+import jalview.datamodel.SearchResults;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceI;
+import jalview.jbgui.GFinder;
+import jalview.util.MessageManager;
 
-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 jalview.util.MessageManager;
+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
 {
+  private static final int HEIGHT = 110;
+
+  private static final int WIDTH = 340;
+
   AlignViewport av;
 
   AlignmentPanel ap;
@@ -48,14 +65,7 @@ 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()
   {
@@ -63,6 +73,13 @@ public class Finder extends GFinder
     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(AlignViewport viewport, AlignmentPanel alignPanel)
   {
     av = viewport;
@@ -71,16 +88,16 @@ public class Finder extends GFinder
     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)
   {
@@ -91,10 +108,9 @@ public class Finder extends GFinder
   }
 
   /**
-   * DOCUMENT ME!
+   * Performs the 'Find All' action.
    * 
    * @param e
-   *          DOCUMENT ME!
    */
   public void findAll_actionPerformed(ActionEvent e)
   {
@@ -166,7 +182,7 @@ 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);
@@ -176,10 +192,10 @@ 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)
   {
@@ -187,7 +203,7 @@ public class Finder extends GFinder
 
     String searchString = textfield.getText().trim();
 
-    if (searchString.length() < 1)
+    if (isInvalidSearchString(searchString))
     {
       return;
     }
@@ -198,6 +214,8 @@ public class Finder extends GFinder
     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
@@ -213,11 +231,11 @@ public class Finder extends GFinder
     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)
@@ -237,11 +255,14 @@ public class Finder extends GFinder
     // 'SelectRegion' selection
     if (!haveResults)
     {
-      JOptionPane.showInternalMessageDialog(this, MessageManager.getString("label.finished_searching"),
-              null, JOptionPane.INFORMATION_MESSAGE);
+      JOptionPane.showInternalMessageDialog(this,
+              MessageManager.getString("label.finished_searching"), null,
+              JOptionPane.INFORMATION_MESSAGE);
       resIndex = -1;
       seqIndex = 0;
-    } else {
+    }
+    else
+    {
       if (findAll)
       {
         // then we report the matches that were found
@@ -264,4 +285,54 @@ public class Finder extends GFinder
     }
 
   }
+
+  /**
+   * 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;
+  }
 }