X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FFinder.java;h=772246161658062aa3dce56b100caa447ecdd28c;hb=fdf3e97f5e1100fcd499f76023bb5d293ff10d5e;hp=945e900fbd8544f8bdffe352a4f222f811d272fd;hpb=eae01b09aadd51c1062c67fa66de5636f1854dd2;p=jalview.git

diff --git a/src/jalview/appletgui/Finder.java b/src/jalview/appletgui/Finder.java
index 945e900..7722461 100755
--- a/src/jalview/appletgui/Finder.java
+++ b/src/jalview/appletgui/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.appletgui;
 
@@ -116,14 +115,14 @@ public class Finder extends Panel implements ActionListener
 
   void doSearch(boolean findAll)
   {
-    if (jalview.bin.JalviewLite.currentAlignFrame != null)
+    if (ap.av.applet.currentAlignFrame != null)
     {
-      ap = jalview.bin.JalviewLite.currentAlignFrame.alignPanel;
+      ap = ap.av.applet.currentAlignFrame.alignPanel;
       av = ap.av;
     }
     createNewGroup.setEnabled(false);
-    jalview.analysis.Finder finder = new jalview.analysis.Finder(av
-            .getAlignment(), av.getSelectionGroup(), seqIndex, resIndex);
+    jalview.analysis.Finder finder = new jalview.analysis.Finder(
+            av.getAlignment(), av.getSelectionGroup(), seqIndex, resIndex);
     finder.setCaseSensitive(caseSensitive.getState());
     finder.setFindAll(findAll);
 
@@ -134,19 +133,21 @@ public class Finder extends Panel implements ActionListener
     resIndex = finder.getResIndex();
     searchResults = finder.getSearchResults();
     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);
 
     }
@@ -162,24 +163,35 @@ public class Finder extends Panel implements ActionListener
     // 'SelectRegion' selection
     if (!haveResults)
     {
-    ap.alignFrame.statusBar.setText("Finished searching.");
-    resIndex = -1;
-    seqIndex = 0;
+      ap.alignFrame.statusBar.setText("Finished searching.");
+      resIndex = -1;
+      seqIndex = 0;
     }
-    if (findAll)
+    else
     {
-      String message = (idMatch.size()>0) ? ""+idMatch.size()+" IDs" : "";
-      if (idMatch.size()>0 && searchResults!=null && searchResults.getSize()>0) {
-        message += " and ";
+      if (findAll)
+      {
+        String message = (idMatch.size() > 0) ? "" + idMatch.size()
+                + " IDs" : "";
+        if (idMatch.size() > 0 && searchResults != null
+                && searchResults.getSize() > 0)
+        {
+          message += " and ";
+        }
+        if (searchResults != null)
+        {
+          message += searchResults.getSize() + " subsequence matches.";
+        }
+        ap.alignFrame.statusBar.setText("Search results: " + searchString
+                + " : " + message);
+
       }
-      if (searchResults!=null) {
-        message += searchResults.getSize() + " subsequence matches.";
+      else
+      {
+        // TODO: indicate sequence and matching position in status bar
+        ap.alignFrame.statusBar.setText("Found match for " + searchString);
       }
-      ap.alignFrame.statusBar.setText("Search results: " + searchString
-              + " : " + message);
-              
     }
-
   }
 
   Label jLabel1 = new Label();