From: James Procter <j.procter@dundee.ac.uk>
Date: Thu, 22 Jun 2023 15:38:07 +0000 (+0200)
Subject: JAL-4213 - document the addReferenceAnnotations method’s behaviour when given a selection
X-Git-Tag: Release_2_11_4_0~254^2~1
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=eb64fc14cebadcfbb286bd4865d9df66e428a5d8;p=jalview.git

JAL-4213 - document the addReferenceAnnotations method’s behaviour when given a selection
---

diff --git a/src/jalview/analysis/AlignmentUtils.java b/src/jalview/analysis/AlignmentUtils.java
index 1158c53..6ab49b2 100644
--- a/src/jalview/analysis/AlignmentUtils.java
+++ b/src/jalview/analysis/AlignmentUtils.java
@@ -1512,7 +1512,7 @@ public class AlignmentUtils
    * @param alignment
    *          the alignment to add them to
    * @param selectionGroup
-   *          current selection group (or null if none)
+   *          current selection group - may be null, if provided then any added annotation will be trimmed to just those columns in the selection group
    */
   public static void addReferenceAnnotations(
           Map<SequenceI, List<AlignmentAnnotation>> annotations,
@@ -1536,7 +1536,7 @@ public class AlignmentUtils
    * @param seq
    * @param ann
    * @param selectionGroup
-   *          - may be null
+   *          current selection group - may be null, if provided then any added annotation will be trimmed to just those columns in the selection group
    * @return annotation added to {@code seq and {@code alignment}
    */
   public static AlignmentAnnotation addReferenceAnnotationTo(