// 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
// 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;
import java.util.Map;
import java.util.SortedSet;
-import org.forester.surfacing.DomainId;
import org.forester.util.ForesterUtil;
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;
}
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;
}
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;
}
private static boolean testPfamToGoParser( final File test_dir ) {
try {
final PfamToGoParser parser = new PfamToGoParser( new File( test_dir + ForesterUtil.getFileSeparator()
- + "pfam_to_go_test" ) );
+ + "pfam_to_go_test" ) );
final List<PfamToGoMapping> mappings = parser.parse();
if ( parser.getMappingCount() != 426 ) {
return false;
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" ) ) ) {
private static boolean testSuperTermCounting( final File test_dir ) {
try {
final OBOparser parser = new OBOparser( new File( test_dir + ForesterUtil.getFileSeparator()
- + "gene_ontology_edit.obo" ), OBOparser.ReturnType.BASIC_GO_TERM );
+ + "gene_ontology_edit.obo" ), OBOparser.ReturnType.BASIC_GO_TERM );
final List<GoTerm> all_go_terms = parser.parse();
if ( parser.getGoTermCount() != 27748 ) {
return false;
final List<GoTerm> categories = new ArrayList<GoTerm>();
final List<GoTerm> experiment_set = new ArrayList<GoTerm>();
experiment_set.add( new BasicGoTerm( new GoId( "GO:0005690" ), "snRNP U4atac", GoNameSpace
- .createUnassigned(), false ) );
+ .createUnassigned(), false ) );
experiment_set.add( new BasicGoTerm( new GoId( "GO:0009698" ),
"phenylpropanoid metabolic process",
GoNameSpace.createUnassigned(),
false ) );
experiment_set.add( new BasicGoTerm( new GoId( "GO:0008150" ), "biological_process", GoNameSpace
- .createUnassigned(), false ) );
+ .createUnassigned(), false ) );
experiment_set.add( new BasicGoTerm( new GoId( "GO:0006915" ),
"apoptosis",
GoNameSpace.createUnassigned(),
false ) );
experiment_set.add( new BasicGoTerm( new GoId( "GO:0001783" ), "B cell apoptosis", GoNameSpace
- .createUnassigned(), false ) );
+ .createUnassigned(), false ) );
experiment_set.add( new BasicGoTerm( new GoId( "GO:0010657" ), "muscle cell apoptosis", GoNameSpace
- .createUnassigned(), false ) );
+ .createUnassigned(), false ) );
experiment_set.add( new BasicGoTerm( new GoId( "GO:0010657" ), "muscle cell apoptosis", GoNameSpace
- .createUnassigned(), false ) );
+ .createUnassigned(), false ) );
experiment_set.add( new BasicGoTerm( new GoId( "GO:0010658" ),
"striated muscle cell apoptosis",
GoNameSpace.createUnassigned(),
GoNameSpace.createUnassigned(),
false ) );
categories
- .add( new BasicGoTerm( new GoId( "GO:0016265" ), "death", GoNameSpace.createUnassigned(), false ) );
+ .add( new BasicGoTerm( new GoId( "GO:0016265" ), "death", GoNameSpace.createUnassigned(), false ) );
categories.add( new BasicGoTerm( new GoId( "GO:0006915" ),
"apoptosis",
GoNameSpace.createUnassigned(),
false ) );
categories.add( new BasicGoTerm( new GoId( "GO:0008150" ), "biological_process", GoNameSpace
- .createUnassigned(), false ) );
+ .createUnassigned(), false ) );
categories.add( new BasicGoTerm( new GoId( "GO:0010657" ), "muscle cell apoptosis", GoNameSpace
- .createUnassigned(), false ) );
+ .createUnassigned(), false ) );
categories.add( new BasicGoTerm( new GoId( "GO:0010658" ), "striated muscle cell apoptosis", GoNameSpace
- .createUnassigned(), false ) );
+ .createUnassigned(), false ) );
categories.add( new BasicGoTerm( new GoId( "GO:0046242" ), "o-xylene biosynthetic process", GoNameSpace
- .createUnassigned(), false ) );
+ .createUnassigned(), false ) );
categories.add( new BasicGoTerm( new GoId( "GO:0016326" ), "kinesin motor activity", GoNameSpace
- .createUnassigned(), false ) );
+ .createUnassigned(), false ) );
categories.add( new BasicGoTerm( new GoId( "GO:0005575" ), "cellular_component", GoNameSpace
- .createUnassigned(), false ) );
+ .createUnassigned(), false ) );
categories.add( new BasicGoTerm( new GoId( "GO:0032502" ), "developmental process", GoNameSpace
- .createUnassigned(), false ) );
+ .createUnassigned(), false ) );
categories.add( new BasicGoTerm( new GoId( "GO:0051094" ),
"positive regulation of developmental process",
GoNameSpace.createUnassigned(),
private static boolean testSuperTermGetting( final File test_dir ) {
try {
final OBOparser parser = new OBOparser( new File( test_dir + ForesterUtil.getFileSeparator()
- + "gene_ontology_edit.obo" ), OBOparser.ReturnType.BASIC_GO_TERM );
+ + "gene_ontology_edit.obo" ), OBOparser.ReturnType.BASIC_GO_TERM );
final List<GoTerm> go_terms = parser.parse();
if ( parser.getGoTermCount() != 27748 ) {
return false;
git://source.jalview.org / jalview.git / blobdiff