X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FFinder.java;h=c385ac8f8e254cf4042f80887a5c8b67d34060b9;hb=0452450533728e478ef8c893ea2cb3483c740fb3;hp=e24a6c059c69119154e8e53bf1948954cc702f82;hpb=dbcfef03ad3d2853eda62c727978a160fc347f58;p=jalview.git

diff --git a/src/jalview/analysis/Finder.java b/src/jalview/analysis/Finder.java
index e24a6c0..c385ac8 100644
--- a/src/jalview/analysis/Finder.java
+++ b/src/jalview/analysis/Finder.java
@@ -22,7 +22,7 @@ public class Finder {
         this.alignment=alignment;
         this.selection = selection;
     }
-    
+
     public Finder(AlignmentI alignment, SequenceGroup selectionGroup, int seqIndex, int resIndex) {
         this(alignment, selectionGroup);
         this.seqIndex=seqIndex;
@@ -45,7 +45,7 @@ public class Finder {
         {
             int res = Integer.parseInt(searchString);
             found = true;
-            if (selection == null || selection.getSize(false) < 1)
+            if (selection == null || selection.getSize() < 1)
             {
               seq = (Sequence) alignment.getSequenceAt(0);
             }
@@ -65,10 +65,10 @@ public class Finder {
 
         int end = alignment.getHeight();
 
-        
+
         if (selection != null)
         {
-            if ((selection.getSize(false) < 1) ||
+            if ((selection.getSize() < 1) ||
                     ((selection.getEndRes() - selection.getStartRes()) < 2))
             {
                 selection = null;
@@ -79,7 +79,7 @@ public class Finder {
         {
             seq = (Sequence) alignment.getSequenceAt(seqIndex);
 
-            if ((selection != null) && !selection.getSequences(false).contains(seq))
+            if ((selection != null) && !selection.getSequences(null).contains(seq))
             {
                 seqIndex++;
                 resIndex = 0;
@@ -97,7 +97,7 @@ public class Finder {
             {
                 item = item.substring(0, selection.getEndRes() + 1);
             }
-            
+
             ///Shall we ignore gaps???? - JBPNote: Add Flag for forcing this or not
             StringBuffer noGapsSB = new StringBuffer();
             int insertCount = 0;