X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Fsequence%2FSequence.java;h=cac6bcfe9a6bf50b05ff8f40d4bda20f15ba5d41;hb=90e29ddfe15f6c44f3e3ba419a67c3e267e279bd;hp=3ee58935978fe2e7ff7e666dc80943231962e5f6;hpb=48f7a89be9d34f1930a1f863e608235cc27184c5;p=jalview.git

diff --git a/forester/java/src/org/forester/sequence/Sequence.java b/forester/java/src/org/forester/sequence/Sequence.java
index 3ee5893..cac6bcf 100644
--- a/forester/java/src/org/forester/sequence/Sequence.java
+++ b/forester/java/src/org/forester/sequence/Sequence.java
@@ -6,7 +6,7 @@
 // Copyright (C) 2010 Christian M Zmasek
 // Copyright (C) 2010 Sanford-Burnham Medical Research Institute
 // All rights reserved
-// 
+//
 // This library is free software; you can redistribute it and/or
 // modify it under the terms of the GNU Lesser General Public
 // License as published by the Free Software Foundation; either
@@ -16,13 +16,13 @@
 // but WITHOUT ANY WARRANTY; without even the implied warranty of
 // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
 // Lesser General Public License for more details.
-// 
+//
 // You should have received a copy of the GNU Lesser General Public
 // License along with this library; if not, write to the Free Software
 // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
 //
 // Contact: phylosoft @ gmail . com
-// WWW: www.phylosoft.org/forester
+// WWW: https://sites.google.com/site/cmzmasek/home/software/forester
 
 package org.forester.sequence;
 
@@ -37,14 +37,20 @@ public interface Sequence {
     static final String        DNA_REGEXP      = "[^ACGTRYMKWSN\\-\\*]";
     static final String        RNA_REGEXP      = "[^ACGURYMKWSN\\-\\*]";
 
-    public abstract Object getIdentifier();
+    public abstract String getIdentifier();
 
     public abstract int getLength();
 
+    public abstract int getNumberOfGapResidues();
+
     public abstract char[] getMolecularSequence();
 
+    public abstract String getMolecularSequenceAsString();
+
     public abstract char getResidueAt( final int position );
 
+    public abstract boolean isGapAt( final int position );
+
     public abstract TYPE getType();
 
     public enum TYPE {