X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FFinder.java;h=31c914ac53dcff78d7469ab34b6760306d2f1180;hb=74755239a1beeeaba47c0fee8bfc14f8395e65ac;hp=2fc34412e01012d9cb7aff1a5955a98f7231719c;hpb=9b5106c49c8fa0a7269f38ad1825851eb8ba5b85;p=jalview.git

diff --git a/src/jalview/appletgui/Finder.java b/src/jalview/appletgui/Finder.java
index 2fc3441..31c914a 100644
--- a/src/jalview/appletgui/Finder.java
+++ b/src/jalview/appletgui/Finder.java
@@ -171,11 +171,13 @@ public class Finder extends Panel implements ActionListener
     boolean doSearchDescription = searchDescription.getState();
     if (doFindAll)
     {
-      finder.findAll(searchString, isCaseSensitive, doSearchDescription);
+      finder.findAll(searchString, isCaseSensitive, doSearchDescription,
+              false);
     }
     else
     {
-      finder.findNext(searchString, isCaseSensitive, doSearchDescription);
+      finder.findNext(searchString, isCaseSensitive, doSearchDescription,
+              false);
     }
 
     searchResults = finder.getSearchResults();
@@ -206,16 +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[]