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=9200eb887d3b4f6d9d115eb687c11d1c4c9f3049;hpb=eee996a6476a1e3d84c07f8f690dcde3ff4b2ef5;p=jalview.git

diff --git a/forester/java/src/org/forester/surfacing/SimpleDomain.java b/forester/java/src/org/forester/surfacing/SimpleDomain.java
index 9200eb8..782ce20 100644
--- a/forester/java/src/org/forester/surfacing/SimpleDomain.java
+++ b/forester/java/src/org/forester/surfacing/SimpleDomain.java
@@ -22,11 +22,12 @@
 // 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;
 
 /*
@@ -35,18 +36,13 @@ 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 );
-    }
-
-    @Override
-    public void addGoId( final GoId go_id ) {
-        throw new RuntimeException( "method not implemented" );
+        _id = BasicDomain.obtainIdAsShort( id );
     }
 
     @Override
@@ -58,8 +54,8 @@ public class SimpleDomain implements Domain {
     }
 
     @Override
-    public DomainId getDomainId() {
-        return _id;
+    public String getDomainId() {
+        return BasicDomain.obtainIdFromShort( _id );
     }
 
     @Override
@@ -68,10 +64,6 @@ public class SimpleDomain implements Domain {
     }
 
     @Override
-    public GoId getGoId( final int i ) {
-        throw new RuntimeException( "method not implemented" );
-    }
-
     public int getLength() {
         throw new RuntimeException( "method not implemented" );
     }
@@ -82,11 +74,6 @@ public class SimpleDomain implements Domain {
     }
 
     @Override
-    public int getNumberOfGoIds() {
-        throw new RuntimeException( "method not implemented" );
-    }
-
-    @Override
     public double getPerDomainEvalue() {
         throw new RuntimeException( "method not implemented" );
     }
@@ -97,20 +84,6 @@ public class SimpleDomain implements Domain {
     }
 
     @Override
-    public double getPerSequenceEvalue() {
-        throw new RuntimeException( "method not implemented" );
-    }
-
-    @Override
-    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" );
     }
@@ -119,12 +92,4 @@ public class SimpleDomain implements Domain {
     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" );
-    }
 }