From: Jim Procter <jprocter@issues.jalview.org>
Date: Mon, 19 Nov 2018 17:27:22 +0000 (+0000)
Subject: JAL-3156 javadoc re JAL-3127 and FIXME to make AlignmentI.getSequences(hidden represe... 
X-Git-Tag: Release_2_11_0~17^2~46^2~5
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=ab6ceb7b47b415abaedb60a5cb5435015fdc2f83;p=jalview.git

JAL-3156 javadoc re JAL-3127 and FIXME to make AlignmentI.getSequences(hidden representatives) behave like SequenceGroup.getSequences(…).
---

diff --git a/src/jalview/datamodel/SequenceCollectionI.java b/src/jalview/datamodel/SequenceCollectionI.java
index f681f11..e2bb5a6 100644
--- a/src/jalview/datamodel/SequenceCollectionI.java
+++ b/src/jalview/datamodel/SequenceCollectionI.java
@@ -25,8 +25,21 @@ import java.util.Map;
 
 public interface SequenceCollectionI
 {
+  /**
+   * 
+   * @return (visible) sequences in this collection. This may be a direct
+   *         reference to the collection so not thread safe
+   */
   List<SequenceI> getSequences();
 
+  /**
+   * FIXME: AlignmentI.getSequences(hiddenReps) doesn't actually obey this
+   * contract!
+   * 
+   * @param hiddenReps
+   * @return the full set of sequences in this collection, including any
+   *         sequences represented by sequences in the collection.
+   */
   List<SequenceI> getSequences(
           Map<SequenceI, SequenceCollectionI> hiddenReps);