From: Jim Procter <jprocter@issues.jalview.org>
Date: Tue, 12 Jul 2016 16:12:10 +0000 (+0100)
Subject: JAL-2110 javadoc
X-Git-Tag: Release_2_10_0~140^2~5^2~7
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=5dd0323d078fc1f0bab425fcbd4d8bcf1528eb14;p=jalview.git

JAL-2110 javadoc
---

diff --git a/src/jalview/analysis/AlignmentUtils.java b/src/jalview/analysis/AlignmentUtils.java
index e2f6749..7264cd2 100644
--- a/src/jalview/analysis/AlignmentUtils.java
+++ b/src/jalview/analysis/AlignmentUtils.java
@@ -2606,7 +2606,10 @@ public class AlignmentUtils
    * true; else returns false
    * 
    * @param unaligned
+   *          - sequences to be aligned based on aligned
    * @param aligned
+   *          - 'guide' alignment containing sequences derived from same dataset
+   *          as unaligned
    * @return
    */
   static boolean alignAsSameSequences(AlignmentI unaligned,
@@ -2617,6 +2620,7 @@ public class AlignmentUtils
       return false; // should only pass alignments with datasets here
     }
 
+    // map from dataset sequence to alignment sequence
     Map<SequenceI, SequenceI> alignedDatasets = new HashMap<SequenceI, SequenceI>();
     for (SequenceI seq : aligned.getSequences())
     {
diff --git a/src/jalview/datamodel/SequenceI.java b/src/jalview/datamodel/SequenceI.java
index 355e271..45a767c 100755
--- a/src/jalview/datamodel/SequenceI.java
+++ b/src/jalview/datamodel/SequenceI.java
@@ -239,19 +239,21 @@ public interface SequenceI extends ASequenceI
    * DOCUMENT ME!
    * 
    * @param i
-   *          DOCUMENT ME!
+   *          alignment column number
    * @param c
-   *          DOCUMENT ME!
+   *          character to insert
    */
   public void insertCharAt(int i, char c);
 
   /**
-   * DOCUMENT ME!
+   * insert given character at alignment column position
    * 
    * @param position
-   *          DOCUMENT ME!
+   *          alignment column number
+   * @param count
+   *          length of insert
    * @param ch
-   *          DOCUMENT ME!
+   *          character to insert
    */
   public void insertCharAt(int position, int count, char ch);