inprogress

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

diff --git a/forester/java/src/org/forester/surfacing/SimpleDomain.java b/forester/java/src/org/forester/surfacing/SimpleDomain.java
index 9200eb8..2d1826e 100644 (file)
--- a/forester/java/src/org/forester/surfacing/SimpleDomain.java
+++ b/forester/java/src/org/forester/surfacing/SimpleDomain.java
@@ -22,11 +22,11 @@
 // 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.Domain;
 import org.forester.util.ForesterUtil;
 
 /*
@@ -35,20 +35,19 @@ import org.forester.util.ForesterUtil;
  */
 public class SimpleDomain implements Domain {
 
-    final private DomainId _id;
+    final private String _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 = id;
     }
 
+    // ^^  @Override
+    // ^^  public void addGoId( final GoId go_id ) {
+    // ^^     throw new RuntimeException( "method not implemented" );
+    // ^^ }
     @Override
     public int compareTo( final Domain domain ) {
         if ( this == domain ) {
@@ -58,7 +57,7 @@ public class SimpleDomain implements Domain {
     }
 
     @Override
-    public DomainId getDomainId() {
+    public String getDomainId() {
         return _id;
     }
 
@@ -67,11 +66,11 @@ public class SimpleDomain implements Domain {
         throw new RuntimeException( "method not implemented" );
     }
 
+    // ^^   @Override
+    // ^^   public GoId getGoId( final int i ) {
+    // ^^      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" );
     }
@@ -81,11 +80,10 @@ public class SimpleDomain implements Domain {
         throw new RuntimeException( "method not implemented" );
     }
 
-    @Override
-    public int getNumberOfGoIds() {
-        throw new RuntimeException( "method not implemented" );
-    }
-
+    // ^^   @Override
+    // ^^  public int getNumberOfGoIds() {
+    // ^^      throw new RuntimeException( "method not implemented" );
+    // ^^ }
     @Override
     public double getPerDomainEvalue() {
         throw new RuntimeException( "method not implemented" );