X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FHiddenSequences.java;fp=src%2Fjalview%2Fdatamodel%2FHiddenSequences.java;h=588e5ed3bba68390712572c460478c8b5c369812;hb=7c19c72efd3433b14f845c265747010d9dc596cc;hp=9e2cf72b416d1d5a69f3945305d55ce1b12ee7ae;hpb=14a3cc9277d30d14bec559a12d9af72bd2955aff;p=jalview.git

diff --git a/src/jalview/datamodel/HiddenSequences.java b/src/jalview/datamodel/HiddenSequences.java
index 9e2cf72..588e5ed 100755
--- a/src/jalview/datamodel/HiddenSequences.java
+++ b/src/jalview/datamodel/HiddenSequences.java
@@ -246,6 +246,12 @@ public class HiddenSequences
     return hiddenSequences == null ? null : hiddenSequences[alignmentIndex];
   }
 
+  /**
+   * Convert absolute alignment index to visible alignment index
+   * 
+   * @param alignmentIndex
+   * @return
+   */
   public int findIndexWithoutHiddenSeqs(int alignmentIndex)
   {
     if (hiddenSequences == null)
@@ -271,6 +277,12 @@ public class HiddenSequences
     return (alignmentIndex - hiddenSeqs);
   }
 
+  /**
+   * Convert alignment index from visible alignment to absolute alignment
+   * 
+   * @param alignmentIndex
+   * @return
+   */
   public int adjustForHiddenSeqs(int alignmentIndex)
   {
     if (hiddenSequences == null)