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=fd13abfe62bfb72e00cc5711b8b19a4e21e4bf59;hpb=045ed0731ed1997f6ccf41b2a7688d028ea73a0a;p=jalview.git

diff --git a/forester/java/src/org/forester/sequence/Sequence.java b/forester/java/src/org/forester/sequence/Sequence.java
index fd13abf..cac6bcf 100644
--- a/forester/java/src/org/forester/sequence/Sequence.java
+++ b/forester/java/src/org/forester/sequence/Sequence.java
@@ -22,7 +22,7 @@
 // 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;
 
@@ -37,7 +37,7 @@ 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();
 
@@ -45,8 +45,12 @@ public interface Sequence {
 
     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 {