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[jalview.git] / src / jalview / appletgui / Finder.java

diff --git a/src/jalview/appletgui/Finder.java b/src/jalview/appletgui/Finder.java
index a3a6124..7cb3763 100755 (executable)
--- a/src/jalview/appletgui/Finder.java
+++ b/src/jalview/appletgui/Finder.java
@@ -113,7 +113,7 @@ public class Finder
 \r
       SequenceGroup sg = new SequenceGroup(searchString, ucs, true, true, false,\r
                                            startRes, endRes);\r
-      sg.addSequence(seq);\r
+      sg.addSequence(seq, false);\r
       av.alignment.addGroup(sg);\r
       searchGroup.addGroup(sg);\r
 \r
@@ -144,18 +144,18 @@ public class Finder
       int res = Integer.parseInt(searchString);\r
       found = true;\r
 \r
-      if (av.getSelectionGroup().getSize() > 0)\r
+      if (av.getSelectionGroup() == null || av.getSelectionGroup().getSize() < 1)\r
       {\r
-        seq = (Sequence) (av.getSelectionGroup().getSequenceAt(0));\r
+        seq = (Sequence) av.getAlignment().getSequenceAt(0);\r
       }\r
       else\r
       {\r
-        seq = (Sequence) av.getAlignment().getSequenceAt(0);\r
+        seq = (Sequence) (av.getSelectionGroup().getSequenceAt(0));\r
       }\r
 \r
       searchResults.addElement(Integer.toString(av.getAlignment().findIndex(seq)));\r
-      searchResults.addElement(Integer.toString(seq.findIndex(res) - 1));\r
-      searchResults.addElement(Integer.toString(seq.findIndex(res) - 1));\r
+      searchResults.addElement(String.valueOf(res));\r
+      searchResults.addElement(String.valueOf(res));\r
 \r
     }\r
     catch (NumberFormatException ex)\r
@@ -246,6 +246,8 @@ public class Finder
 \r
           r = resIndex;\r
         }\r
+        else\r
+          break;\r
       }\r
       if (!found)\r
       {\r