From: Jim Procter <jprocter@issues.jalview.org>
Date: Wed, 15 Feb 2017 15:41:58 +0000 (+0000)
Subject: JAL-2374 new contains methods for seq and seq,apos
X-Git-Tag: Release_2_10_3b1~344^2~5
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=0585c8478eccc42896dbd1a4d365ecdc913551f2;p=jalview.git

JAL-2374 new contains methods for seq and seq,apos
---

diff --git a/src/jalview/datamodel/SequenceGroup.java b/src/jalview/datamodel/SequenceGroup.java
index 4f9d530..e37c55e 100755
--- a/src/jalview/datamodel/SequenceGroup.java
+++ b/src/jalview/datamodel/SequenceGroup.java
@@ -1411,4 +1411,24 @@ public class SequenceGroup implements AnnotatedCollectionI
     }
     return false;
   }
+
+  /**
+   * @param seq
+   * @return true if seq is a member of the group
+   */
+
+  public boolean contains(SequenceI seq1)
+  {
+    return sequences.contains(seq1);
+  }
+
+  /**
+   * @param seq
+   * @param apos
+   * @return true if startRes<=apos and endRes>=apos and seq is in the group
+   */
+  public boolean contains(SequenceI seq, int apos)
+  {
+    return (startRes <= apos && endRes >= apos) && sequences.contains(seq);
+  }
 }