X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Fsurfacing%2FSimpleDomain.java;h=782ce20691ae0ff63e4aad6f33fa1f00cfb7d1fb;hb=665e671efec73fcb36a9aac45f119330f290fa81;hp=76d73bf9bb381f76a0316a3d3add3aa1f48c2bd8;hpb=48f7a89be9d34f1930a1f863e608235cc27184c5;p=jalview.git

diff --git a/forester/java/src/org/forester/surfacing/SimpleDomain.java b/forester/java/src/org/forester/surfacing/SimpleDomain.java
index 76d73bf..782ce20 100644
--- a/forester/java/src/org/forester/surfacing/SimpleDomain.java
+++ b/forester/java/src/org/forester/surfacing/SimpleDomain.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
@@ -16,17 +16,18 @@
 // 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.go.GoId;
+import org.forester.protein.BasicDomain;
+import org.forester.protein.Domain;
 import org.forester.util.ForesterUtil;
 
 /*
@@ -35,20 +36,16 @@ import org.forester.util.ForesterUtil;
  */
 public class SimpleDomain implements Domain {
 
-    final private DomainId _id;
+    final private short _id;
 
-    public SimpleDomain( final String id_str ) {
-        if ( ForesterUtil.isEmpty( id_str ) ) {
+    public SimpleDomain( final String id ) {
+        if ( ForesterUtil.isEmpty( id ) ) {
             throw new IllegalArgumentException( "attempt to create protein domain with null or empty id" );
         }
-        _id = new DomainId( id_str );
+        _id = BasicDomain.obtainIdAsShort( id );
     }
 
     @Override
-    public void addGoId( final GoId go_id ) {
-        throw new RuntimeException( "method not implemented" );
-    }
-
     public int compareTo( final Domain domain ) {
         if ( this == domain ) {
             return 0;
@@ -56,29 +53,23 @@ public class SimpleDomain implements Domain {
         return getDomainId().compareTo( domain.getDomainId() );
     }
 
-    public DomainId getDomainId() {
-        return _id;
+    @Override
+    public String getDomainId() {
+        return BasicDomain.obtainIdFromShort( _id );
     }
 
+    @Override
     public int getFrom() {
         throw new RuntimeException( "method not implemented" );
     }
 
     @Override
-    public GoId getGoId( final int i ) {
-        throw new RuntimeException( "method not implemented" );
-    }
-
     public int getLength() {
         throw new RuntimeException( "method not implemented" );
     }
 
-    public short getNumber() {
-        throw new RuntimeException( "method not implemented" );
-    }
-
     @Override
-    public int getNumberOfGoIds() {
+    public short getNumber() {
         throw new RuntimeException( "method not implemented" );
     }
 
@@ -92,31 +83,13 @@ public class SimpleDomain implements Domain {
         throw new RuntimeException( "method not implemented" );
     }
 
-    public double getPerSequenceEvalue() {
-        throw new RuntimeException( "method not implemented" );
-    }
-
-    public double getPerSequenceScore() {
-        throw new RuntimeException( "method not implemented" );
-    }
-
-    public String getSearchParameter() {
-        throw new RuntimeException( "method not implemented" );
-    }
-
+    @Override
     public int getTo() {
         throw new RuntimeException( "method not implemented" );
     }
 
+    @Override
     public short getTotalCount() {
         throw new RuntimeException( "method not implemented" );
     }
-
-    public boolean isCompleteQueryMatch() {
-        throw new RuntimeException( "method not implemented" );
-    }
-
-    public boolean isCompleteTargetMatch() {
-        throw new RuntimeException( "method not implemented" );
-    }
 }