in progress

[jalview.git] / forester / java / src / org / forester / surfacing / BasicBinaryDomainCombination.java

diff --git a/forester/java/src/org/forester/surfacing/BasicBinaryDomainCombination.java b/forester/java/src/org/forester/surfacing/BasicBinaryDomainCombination.java
index 9436ce9..3f799d1 100644 (file)
--- a/forester/java/src/org/forester/surfacing/BasicBinaryDomainCombination.java
+++ b/forester/java/src/org/forester/surfacing/BasicBinaryDomainCombination.java
@@ -6,7 +6,7 @@
 // Copyright (C) 2008-2009 Christian M. Zmasek
 // Copyright (C) 2008-2009 Burnham Institute for Medical Research
 // 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
@@ -16,46 +16,48 @@
 // 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.surfacing;
 
+import org.forester.protein.BinaryDomainCombination;
 import org.forester.util.ForesterUtil;
 
 public class BasicBinaryDomainCombination implements BinaryDomainCombination {
 
-    DomainId _id_0;
-    DomainId _id_1;
+    String _id0;
+    String _id1;
+    String _str;
 
     BasicBinaryDomainCombination() {
-        _id_0 = null;
-        _id_1 = null;
+        _id0 = null;
+        _id1 = null;
     }
 
-    public BasicBinaryDomainCombination( final DomainId id_0, final DomainId id_1 ) {
-        if ( ( id_0 == null ) || ( id_1 == null ) ) {
+    private String getAsStr() {
+        return _id0 + SEPARATOR + _id1;
+    }
+
+    public BasicBinaryDomainCombination( final String id0, final String id1 ) {
+        if ( ( id0 == null ) || ( id1 == null ) ) {
             throw new IllegalArgumentException( "attempt to create binary domain combination using null" );
         }
-        if ( id_0.compareTo( id_1 ) < 0 ) {
-            _id_0 = id_0;
-            _id_1 = id_1;
+        if ( id0.toLowerCase().compareTo( id1.toLowerCase() ) < 0 ) {
+            _id0 = id0;
+            _id1 = id1;
         }
         else {
-            _id_0 = id_1;
-            _id_1 = id_0;
+            _id0 = id1;
+            _id1 = id0;
         }
     }
 
-    public BasicBinaryDomainCombination( final String id_0, final String id_1 ) {
-        this( new DomainId( id_0 ), new DomainId( id_1 ) );
-    }
-
     @Override
     public int compareTo( final BinaryDomainCombination binary_domain_combination ) {
         if ( binary_domain_combination.getClass() != this.getClass() ) {
@@ -92,19 +94,22 @@ public class BasicBinaryDomainCombination implements BinaryDomainCombination {
         }
     }
 
-    public DomainId getId0() {
-        return _id_0;
+    @Override
+    public String getId0() {
+        return _id0;
     }
 
-    public DomainId getId1() {
-        return _id_1;
+    @Override
+    public String getId1() {
+        return _id1;
     }
 
     @Override
     public int hashCode() {
-        return getId0().hashCode() + ( 19 * getId1().hashCode() );
+        return getAsStr().hashCode();
     }
 
+    @Override
     public StringBuffer toGraphDescribingLanguage( final OutputFormat format,
                                                    final String node_attribute,
                                                    final String edge_attribute ) {
@@ -150,11 +155,7 @@ public class BasicBinaryDomainCombination implements BinaryDomainCombination {
 
     @Override
     public String toString() {
-        final StringBuffer sb = new StringBuffer();
-        sb.append( getId0() );
-        sb.append( BinaryDomainCombination.SEPARATOR );
-        sb.append( getId1() );
-        return sb.toString();
+        return getAsStr();
     }
 
     public static BinaryDomainCombination createInstance( final String ids ) {