fixing lining up of domains.

[jalview.git] / forester / java / src / org / forester / protein / BinaryDomainCombination.java

diff --git a/forester/java/src/org/forester/protein/BinaryDomainCombination.java b/forester/java/src/org/forester/protein/BinaryDomainCombination.java
index 02bd7f8..4013904 100644 (file)
--- a/forester/java/src/org/forester/protein/BinaryDomainCombination.java
+++ b/forester/java/src/org/forester/protein/BinaryDomainCombination.java
@@ -21,7 +21,7 @@
 // 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.protein;
 
@@ -29,23 +29,17 @@ public interface BinaryDomainCombination extends Comparable<BinaryDomainCombinat
 
     public static final String SEPARATOR = "=";
 
-    public DomainId getId0();
+    public String getId0();
 
-    public DomainId getId1();
+    public String getId1();
 
-    public abstract StringBuffer toGraphDescribingLanguage( final OutputFormat format,
-                                                            final String node_attribute,
-                                                            String edge_attribute );
+    short getId0Code();
 
-    /**
-     * This has to return a String representation
-     * in the following format:
-     * id0 - id1
-     * 
-     * @return a String representation in the form id0 - id1
-     */
-    @Override
-    public String toString();
+    short getId1Code();
+
+    public StringBuffer toGraphDescribingLanguage( final OutputFormat format,
+                                                   final String node_attribute,
+                                                   String edge_attribute );
 
     public static enum DomainCombinationType {
         BASIC, DIRECTED, DIRECTED_ADJACTANT;