JAL-2388 Missed commit

[jalview.git] / src / jalview / datamodel / HiddenSequences.java

diff --git a/src/jalview/datamodel/HiddenSequences.java b/src/jalview/datamodel/HiddenSequences.java
index 8ca3c5a..588e5ed 100755 (executable)
--- 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)
@@ -296,6 +308,7 @@ public class HiddenSequences
    * makes a copy of the alignment with hidden sequences included. Using the
    * copy for anything other than simple output is not recommended. Note - this
    * method DOES NOT USE THE AlignmentI COPY CONSTRUCTOR!
+   * 
    * @return
    */
   public AlignmentI getFullAlignment()