X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FFinder.java;h=909b55df92ad10e3d05ac0f7db7590f7d165d3c8;hb=59d682209891099d46b960509907c79e3fb276fe;hp=b3fad97e370de200057c142eb101ce432960555e;hpb=eae01b09aadd51c1062c67fa66de5636f1854dd2;p=jalview.git

diff --git a/src/jalview/gui/Finder.java b/src/jalview/gui/Finder.java
index b3fad97..909b55d 100755
--- a/src/jalview/gui/Finder.java
+++ b/src/jalview/gui/Finder.java
@@ -1,20 +1,19 @@
 /*
- * 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 2.8)
+ * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, 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 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
+ * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  */
 package jalview.gui;
 
@@ -51,14 +50,23 @@ public class Finder extends GFinder
    * Creates a new Finder object.
    * 
    * @param av
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * @param ap
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * @param f
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   public Finder()
   {
+    this(null, null);
+    focusfixed = false;
+  }
+
+  public Finder(AlignViewport viewport, AlignmentPanel alignPanel)
+  {
+    av = viewport;
+    ap = alignPanel;
+    focusfixed = true;
     frame = new JInternalFrame();
     frame.setContentPane(this);
     frame.setLayer(JLayeredPane.PALETTE_LAYER);
@@ -71,7 +79,7 @@ public class Finder extends GFinder
    * DOCUMENT ME!
    * 
    * @param e
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   public void findNext_actionPerformed(ActionEvent e)
   {
@@ -85,7 +93,7 @@ public class Finder extends GFinder
    * DOCUMENT ME!
    * 
    * @param e
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   public void findAll_actionPerformed(ActionEvent e)
   {
@@ -98,14 +106,33 @@ 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 +148,7 @@ public class Finder extends GFinder
    * DOCUMENT ME!
    * 
    * @param e
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   public void createNewGroup_actionPerformed(ActionEvent e)
   {
@@ -151,7 +178,7 @@ public class Finder extends GFinder
    * incrementally search the alignment
    * 
    * @param findAll
-   *                true means find all results and raise a dialog box
+   *          true means find all results and raise a dialog box
    */
   void doSearch(boolean findAll)
   {
@@ -168,7 +195,7 @@ 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);
 
@@ -178,21 +205,23 @@ 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;
+      haveResults = true;
       ap.idPanel.highlightSearchResults(idMatch);
-    } else {
+    }
+    else
+    {
       ap.idPanel.highlightSearchResults(null);
     }
-    
+
     if (searchResults.getSize() > 0)
     {
-      haveResults=true;
+      haveResults = true;
       createNewGroup.setEnabled(true);
     }
     else
@@ -215,11 +244,16 @@ public class Finder extends GFinder
 
     if (findAll)
     {
-      String message = (idMatch.size()>0) ? ""+idMatch.size()+" IDs" : "";
-      if (idMatch.size()>0 && searchResults.getSize()>0) {
-        message += " and ";
+      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.";
       }
-      message += searchResults.getSize() + " subsequence matches found.";
       JOptionPane.showInternalMessageDialog(this, message, null,
               JOptionPane.INFORMATION_MESSAGE);
       resIndex = -1;