X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FFinder.java;h=167d8995453bb8a23d6c355001e23c1868242019;hb=832101caf0bd7b01d0103879875a724078ea118f;hp=4b555743d278ecee0b33720c840e80127949d608;hpb=24de2d6a6f3db1b9d55f367e2bf8ba112e202a8a;p=jalview.git

diff --git a/src/jalview/appletgui/Finder.java b/src/jalview/appletgui/Finder.java
index 4b55574..167d899 100644
--- a/src/jalview/appletgui/Finder.java
+++ b/src/jalview/appletgui/Finder.java
@@ -20,15 +20,6 @@
  */
 package jalview.appletgui;
 
-import jalview.api.AlignViewportI;
-import jalview.api.FinderI;
-import jalview.datamodel.SearchResultMatchI;
-import jalview.datamodel.SearchResultsI;
-import jalview.datamodel.SequenceFeature;
-import jalview.datamodel.SequenceGroup;
-import jalview.datamodel.SequenceI;
-import jalview.util.MessageManager;
-
 import java.awt.Button;
 import java.awt.Checkbox;
 import java.awt.Font;
@@ -48,6 +39,14 @@ import java.util.HashMap;
 import java.util.List;
 import java.util.Map;
 
+import jalview.api.AlignViewportI;
+import jalview.api.FinderI;
+import jalview.datamodel.SearchResultMatchI;
+import jalview.datamodel.SearchResultsI;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceI;
+import jalview.util.MessageManager;
+
 public class Finder extends Panel implements ActionListener
 {
   private AlignViewportI av;
@@ -163,23 +162,22 @@ public class Finder extends Panel implements ActionListener
       /*
        * first time we searched this viewport
        */
-      finder = new jalview.analysis.Finder(av.getAlignment());
+      finder = new jalview.analysis.Finder(av);
       finders.put(av, finder);
     }
 
     String searchString = textfield.getText();
-    SequenceGroup selectionGroup = av.getSelectionGroup();
     boolean isCaseSensitive = caseSensitive.getState();
     boolean doSearchDescription = searchDescription.getState();
     if (doFindAll)
     {
-      finder.findAll(searchString, selectionGroup, isCaseSensitive,
-              doSearchDescription);
+      finder.findAll(searchString, isCaseSensitive, doSearchDescription,
+              false, false);
     }
     else
     {
-      finder.findNext(searchString, selectionGroup, isCaseSensitive,
-              doSearchDescription);
+      finder.findNext(searchString, isCaseSensitive, doSearchDescription,
+              false, false);
     }
 
     searchResults = finder.getSearchResults();
@@ -210,16 +208,17 @@ public class Finder extends Panel implements ActionListener
     {
       if (doFindAll)
       {
-        String message = (idMatches.size() > 0) ? "" + idMatches.size() + " IDs"
+        String message = (idMatches.size() > 0)
+                ? "" + idMatches.size() + " IDs"
                 : "";
         if (idMatches.size() > 0 && searchResults != null
-                && searchResults.getSize() > 0)
+                && searchResults.getCount() > 0)
         {
           message += " and ";
         }
         if (searchResults != null)
         {
-          message += searchResults.getSize() + " subsequence matches.";
+          message += searchResults.getCount() + " subsequence matches.";
         }
         ap.alignFrame.statusBar.setText(MessageManager
                 .formatMessage("label.search_results", new String[]