X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Fsurfacing%2FSimpleDomain.java;h=2520e6cbe9ec7c8154aeee9baf8b282394a02aeb;hb=9c3a223ef0fd72affdb9f4e40845d1e3ebe52f90;hp=5182865fda898408651e65e13779b2a7cfe412d1;hpb=656be28debec520e0e35a8b311114398a40ea366;p=jalview.git

diff --git a/forester/java/src/org/forester/surfacing/SimpleDomain.java b/forester/java/src/org/forester/surfacing/SimpleDomain.java
index 5182865..2520e6c 100644
--- a/forester/java/src/org/forester/surfacing/SimpleDomain.java
+++ b/forester/java/src/org/forester/surfacing/SimpleDomain.java
@@ -26,9 +26,8 @@
 
 package org.forester.surfacing;
 
-import org.forester.go.GoId;
+import org.forester.protein.BasicDomain;
 import org.forester.protein.Domain;
-import org.forester.protein.DomainId;
 import org.forester.util.ForesterUtil;
 
 /*
@@ -37,18 +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
@@ -60,8 +54,8 @@ public class SimpleDomain implements Domain {
     }
 
     @Override
-    public DomainId getDomainId() {
-        return _id;
+    public String getDomainId() {
+        return BasicDomain.obtainIdFromShort( _id );
     }
 
     @Override
@@ -70,11 +64,6 @@ public class SimpleDomain implements Domain {
     }
 
     @Override
-    public GoId getGoId( final int i ) {
-        throw new RuntimeException( "method not implemented" );
-    }
-
-    @Override
     public int getLength() {
         throw new RuntimeException( "method not implemented" );
     }
@@ -85,11 +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" );
     }
@@ -100,34 +84,27 @@ public class SimpleDomain implements Domain {
     }
 
     @Override
-    public double getPerSequenceEvalue() {
+    public int getTo() {
         throw new RuntimeException( "method not implemented" );
     }
 
     @Override
-    public double getPerSequenceScore() {
-        throw new RuntimeException( "method not implemented" );
-    }
-
-    public String getSearchParameter() {
+    public short getTotalCount() {
         throw new RuntimeException( "method not implemented" );
     }
 
     @Override
-    public int getTo() {
+    public short getHmmLen() {
         throw new RuntimeException( "method not implemented" );
     }
 
     @Override
-    public short getTotalCount() {
+    public short getHmmFrom() {
         throw new RuntimeException( "method not implemented" );
     }
 
-    public boolean isCompleteQueryMatch() {
-        throw new RuntimeException( "method not implemented" );
-    }
-
-    public boolean isCompleteTargetMatch() {
+    @Override
+    public short getHmmTo() {
         throw new RuntimeException( "method not implemented" );
     }
 }