From ab6ceb7b47b415abaedb60a5cb5435015fdc2f83 Mon Sep 17 00:00:00 2001 From: Jim Procter Date: Mon, 19 Nov 2018 17:27:22 +0000 Subject: [PATCH] =?utf8?q?JAL-3156=20javadoc=20re=20JAL-3127=20and=20FIXME=20?= =?utf8?q?to=20make=20AlignmentI.getSequences(hidden=20representatives)=20be?= =?utf8?q?have=20like=20SequenceGroup.getSequences(=E2=80=A6).?= MIME-Version: 1.0 Content-Type: text/plain; charset=utf8 Content-Transfer-Encoding: 8bit --- src/jalview/datamodel/SequenceCollectionI.java | 13 +++++++++++++ 1 file changed, 13 insertions(+) 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 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 getSequences( Map hiddenReps); -- 1.7.10.2