X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Fgo%2FTestGo.java;h=9d5f0c7a45a8a66fb5bbbed2e43146a6fe886305;hb=41ea5973f93687513d29e5b7cad1abff8f3adb4b;hp=4fdcd297d6175655be4230853563c1827a14d8fc;hpb=48f7a89be9d34f1930a1f863e608235cc27184c5;p=jalview.git

diff --git a/forester/java/src/org/forester/go/TestGo.java b/forester/java/src/org/forester/go/TestGo.java
index 4fdcd29..9d5f0c7 100644
--- a/forester/java/src/org/forester/go/TestGo.java
+++ b/forester/java/src/org/forester/go/TestGo.java
@@ -5,7 +5,7 @@
 // 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
@@ -15,13 +15,13 @@
 // 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.go;
 
@@ -31,7 +31,6 @@ import java.util.List;
 import java.util.Map;
 import java.util.SortedSet;
 
-import org.forester.surfacing.DomainId;
 import org.forester.util.ForesterUtil;
 
 public class TestGo {
@@ -212,8 +211,7 @@ public class TestGo {
             if ( !g0.getComment().equals( "" ) ) {
                 return false;
             }
-            if ( !g0
-                    .getDefinition()
+            if ( !g0.getDefinition()
                     .equals( "\"The distribution of mitochondria, including the mitochondrial genome, into daughter cells after mitosis or meiosis, mediated by interactions between mitochondria and the cytoskeleton.\" [GOC:mcc, PMID:10873824, PMID:11389764]" ) ) {
                 return false;
             }
@@ -244,8 +242,7 @@ public class TestGo {
             if ( !g1.getComment().equals( "comment" ) ) {
                 return false;
             }
-            if ( !g1
-                    .getDefinition()
+            if ( !g1.getDefinition()
                     .equals( "\"The maintenance of the structure and integrity of the mitochondrial genome.\" [GOC:ai]" ) ) {
                 return false;
             }
@@ -358,11 +355,11 @@ public class TestGo {
 
     private static boolean testPfamToGoMapping() {
         try {
-            final PfamToGoMapping pg0 = new PfamToGoMapping( new DomainId( "A" ), new GoId( "GO:0000001" ) );
-            final PfamToGoMapping pg1 = new PfamToGoMapping( new DomainId( "A" ), new GoId( "GO:0000001" ) );
-            final PfamToGoMapping pg2 = new PfamToGoMapping( new DomainId( "B" ), new GoId( "GO:0000001" ) );
-            final PfamToGoMapping pg3 = new PfamToGoMapping( new DomainId( "A" ), new GoId( "GO:0000002" ) );
-            final PfamToGoMapping pg4 = new PfamToGoMapping( new DomainId( "B" ), new GoId( "GO:0000002" ) );
+            final PfamToGoMapping pg0 = new PfamToGoMapping( "A", new GoId( "GO:0000001" ) );
+            final PfamToGoMapping pg1 = new PfamToGoMapping( "A", new GoId( "GO:0000001" ) );
+            final PfamToGoMapping pg2 = new PfamToGoMapping( "B", new GoId( "GO:0000001" ) );
+            final PfamToGoMapping pg3 = new PfamToGoMapping( "A", new GoId( "GO:0000002" ) );
+            final PfamToGoMapping pg4 = new PfamToGoMapping( "B", new GoId( "GO:0000002" ) );
             if ( !pg0.equals( pg0 ) ) {
                 return false;
             }
@@ -414,55 +411,55 @@ public class TestGo {
             final PfamToGoMapping m5 = mappings.get( 5 );
             final PfamToGoMapping m424 = mappings.get( 424 );
             final PfamToGoMapping m425 = mappings.get( 425 );
-            if ( !m0.getKey().equals( new DomainId( "7tm_1" ) ) ) {
+            if ( !m0.getKey().equals( "7tm_1" ) ) {
                 return false;
             }
             if ( !m0.getValue().equals( new GoId( "GO:0001584" ) ) ) {
                 return false;
             }
-            if ( m0.getKey().equals( new DomainId( "7tm_x" ) ) ) {
+            if ( m0.getKey().equals( "7tm_x" ) ) {
                 return false;
             }
             if ( m0.getValue().equals( new GoId( "GO:0001585" ) ) ) {
                 return false;
             }
-            if ( !m1.getKey().equals( new DomainId( "7tm_1" ) ) ) {
+            if ( !m1.getKey().equals( "7tm_1" ) ) {
                 return false;
             }
             if ( !m1.getValue().equals( new GoId( "GO:0007186" ) ) ) {
                 return false;
             }
-            if ( !m2.getKey().equals( new DomainId( "7tm_1" ) ) ) {
+            if ( !m2.getKey().equals( "7tm_1" ) ) {
                 return false;
             }
             if ( !m2.getValue().equals( new GoId( "GO:0016021" ) ) ) {
                 return false;
             }
-            if ( !m3.getKey().equals( new DomainId( "7tm_2" ) ) ) {
+            if ( !m3.getKey().equals( "7tm_2" ) ) {
                 return false;
             }
             if ( !m3.getValue().equals( new GoId( "GO:0004930" ) ) ) {
                 return false;
             }
-            if ( !m4.getKey().equals( new DomainId( "7tm_2" ) ) ) {
+            if ( !m4.getKey().equals( "7tm_2" ) ) {
                 return false;
             }
             if ( !m4.getValue().equals( new GoId( "GO:0016020" ) ) ) {
                 return false;
             }
-            if ( !m5.getKey().equals( new DomainId( "7tm_3" ) ) ) {
+            if ( !m5.getKey().equals( "7tm_3" ) ) {
                 return false;
             }
             if ( !m5.getValue().equals( new GoId( "GO:0008067" ) ) ) {
                 return false;
             }
-            if ( !m424.getKey().equals( new DomainId( "OMPdecase" ) ) ) {
+            if ( !m424.getKey().equals( "OMPdecase" ) ) {
                 return false;
             }
             if ( !m424.getValue().equals( new GoId( "GO:0006207" ) ) ) {
                 return false;
             }
-            if ( !m425.getKey().equals( new DomainId( "Bac_DNA_binding" ) ) ) {
+            if ( !m425.getKey().equals( "Bac_DNA_binding" ) ) {
                 return false;
             }
             if ( !m425.getValue().equals( new GoId( "GO:0003677" ) ) ) {