X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FFinder.java;fp=src%2Fjalview%2Fanalysis%2FFinder.java;h=5d42905ba40dad454a23b8c1e2ec0a4219cd6cd7;hb=4016a0a5baf92cea3f1303fdaae3804244857427;hp=fc6537910140ac4c8bfb378f34c1c1c283fc1589;hpb=9d614db4de3b9c8018a42c0c82eedd134af85d6c;p=jalview.git

diff --git a/src/jalview/analysis/Finder.java b/src/jalview/analysis/Finder.java
index fc65379..5d42905 100644
--- a/src/jalview/analysis/Finder.java
+++ b/src/jalview/analysis/Finder.java
@@ -223,6 +223,7 @@ public class Finder implements FinderI
     if (ignoreHidden)
     {
       seqString = getVisibleSequence(seq);
+      this.searchedSequenceStartPosition = 1;
     }
     else
     {
@@ -262,8 +263,12 @@ public class Finder implements FinderI
    */
   private String getVisibleSequence(SequenceI seq)
   {
-    int seqStartCol = seq.findIndex(seq.getStart());
-    int seqEndCol = seq.findIndex(seq.getStart() + seq.getLength() - 1);
+    /*
+     * get start / end columns of sequence and convert to base 0
+     * (so as to match the visible column ranges)
+     */
+    int seqStartCol = seq.findIndex(seq.getStart()) - 1;
+    int seqEndCol = seq.findIndex(seq.getStart() + seq.getLength() - 1) - 1;
     Iterator<int[]> visibleColumns = viewport.getViewAsVisibleContigs(true);
     StringBuilder visibleSeq = new StringBuilder(seqEndCol - seqStartCol);
     List<int[]> fromRanges = new ArrayList<>();
@@ -291,7 +296,7 @@ public class Finder implements FinderI
          * so add the range to the mapping being constructed
          */
         int seqResFrom = seq.findPosition(range[0]);
-        int seqResTo = seq.findPosition(range[1]);
+        int seqResTo = seqResFrom + ungapped.length() - 1;
         fromRanges.add(new int[] { seqResFrom, seqResTo });
       }
     }