X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FFinder.java;h=11bf1ac22b43bb8d649d4879382b8a0834f6fc3e;hb=865a855a4ca87eadb3e5ff284ed32ed307d9c34b;hp=f9962a6e3d9fb345171946358ab6b7b77ad7cc82;hpb=2de8acfae59aced665e4c37ad0f7dcc2ed68818e;p=jalview.git

diff --git a/src/jalview/appletgui/Finder.java b/src/jalview/appletgui/Finder.java
index f9962a6..11bf1ac 100755
--- a/src/jalview/appletgui/Finder.java
+++ b/src/jalview/appletgui/Finder.java
@@ -1,20 +1,20 @@
 /*
- * 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 2.8.0b1)
+ * Copyright (C) 2014 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
+ * 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.appletgui;
 
@@ -37,7 +37,7 @@ public class Finder extends Panel implements ActionListener
 
   int seqIndex = 0;
 
-  int resIndex = 0;
+  int resIndex = -1;
 
   public Finder(final AlignmentPanel ap)
   {
@@ -80,7 +80,7 @@ public class Finder extends Panel implements ActionListener
 
     else if (evt.getSource() == findAll)
     {
-      resIndex = 0;
+      resIndex = -1;
       seqIndex = 0;
       doSearch(true);
     }
@@ -116,14 +116,14 @@ 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);
 
@@ -134,36 +134,65 @@ public class Finder extends Panel implements ActionListener
     resIndex = finder.getResIndex();
     searchResults = finder.getSearchResults();
     Vector idMatch = finder.getIdMatch();
-
-    if (searchResults.getSize() == 0 && idMatch.size() > 0)
+    boolean haveResults = false;
+    // set or reset the GUI
+    if ((idMatch.size() > 0))
     {
+      haveResults = true;
       ap.idPanel.highlightSearchResults(idMatch);
     }
+    else
+    {
+      ap.idPanel.highlightSearchResults(null);
+    }
 
     if (searchResults.getSize() > 0)
     {
+      haveResults = true;
       createNewGroup.setEnabled(true);
 
     }
     else
     {
       searchResults = null;
-      resIndex = 0;
-      seqIndex = 0;
     }
 
     // if allResults is null, this effectively switches displaySearch flag in
     // seqCanvas
     ap.highlightSearchResults(searchResults);
-
-    if (findAll)
+    // TODO: add enablers for 'SelectSequences' or 'SelectColumns' or
+    // 'SelectRegion' selection
+    if (!haveResults)
     {
-      String message = (searchResults == null ? 0 : searchResults.getSize())
-              + " matches found.";
-      ap.alignFrame.statusBar.setText("Search results: " + searchString
-              + " : " + message);
+      ap.alignFrame.statusBar.setText("Finished searching.");
+      resIndex = -1;
+      seqIndex = 0;
     }
+    else
+    {
+      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);
 
+      }
+      else
+      {
+        // TODO: indicate sequence and matching position in status bar
+        ap.alignFrame.statusBar.setText("Found match for " + searchString);
+      }
+    }
   }
 
   Label jLabel1 = new Label();