From: amwaterhouse Date: Thu, 16 Mar 2006 15:20:57 +0000 (+0000) Subject: getHiddenSequences X-Git-Tag: Root_VamJalview_2_07b+~50 X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=f14d234620501b7b5024a9f98e94c520641e7a09;p=jalview.git getHiddenSequences --- diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java index b4e2b3f..00d1be8 100755 --- a/src/jalview/datamodel/Alignment.java +++ b/src/jalview/datamodel/Alignment.java @@ -24,7 +24,6 @@ import jalview.util.*; import java.util.*; - /** Data structure to hold and manipulate a multiple sequence alignment */ public class Alignment implements AlignmentI @@ -41,6 +40,9 @@ public class Alignment implements AlignmentI /** DOCUMENT ME!! */ public AlignmentAnnotation[] annotations; + HiddenSequences hiddenSequences = new HiddenSequences(this); + + /** Make an alignment from an array of Sequences. * * @param sequences @@ -823,4 +825,10 @@ public class Alignment implements AlignmentI } return modified; } + + public HiddenSequences getHiddenSequences() + { + return hiddenSequences; + } + } diff --git a/src/jalview/datamodel/AlignmentI.java b/src/jalview/datamodel/AlignmentI.java index 10ea154..7fe4627 100755 --- a/src/jalview/datamodel/AlignmentI.java +++ b/src/jalview/datamodel/AlignmentI.java @@ -292,7 +292,8 @@ public interface AlignmentI */ public boolean padGaps(); - public void adjustSequenceAnnotations(); + public void adjustSequenceAnnotations(); + public HiddenSequences getHiddenSequences(); }