private static boolean testPfamToGoParser( final File test_dir ) {
try {
final PfamToGoParser parser = new PfamToGoParser( new File( test_dir + ForesterUtil.getFileSeparator()
private static boolean testPfamToGoParser( final File test_dir ) {
try {
final PfamToGoParser parser = new PfamToGoParser( new File( test_dir + ForesterUtil.getFileSeparator()
private static boolean testSuperTermCounting( final File test_dir ) {
try {
final OBOparser parser = new OBOparser( new File( test_dir + ForesterUtil.getFileSeparator()
private static boolean testSuperTermCounting( final File test_dir ) {
try {
final OBOparser parser = new OBOparser( new File( test_dir + ForesterUtil.getFileSeparator()
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
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
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
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
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
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
experiment_set.add( new BasicGoTerm( new GoId( "GO:0010658" ),
"striated muscle cell apoptosis",
GoNameSpace.createUnassigned(),
experiment_set.add( new BasicGoTerm( new GoId( "GO:0010658" ),
"striated muscle cell apoptosis",
GoNameSpace.createUnassigned(),
- .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
categories.add( new BasicGoTerm( new GoId( "GO:0006915" ),
"apoptosis",
GoNameSpace.createUnassigned(),
false ) );
categories.add( new BasicGoTerm( new GoId( "GO:0008150" ), "biological_process", GoNameSpace
categories.add( new BasicGoTerm( new GoId( "GO:0010658" ), "striated muscle cell apoptosis", GoNameSpace
categories.add( new BasicGoTerm( new GoId( "GO:0010658" ), "striated muscle cell apoptosis", GoNameSpace
categories.add( new BasicGoTerm( new GoId( "GO:0046242" ), "o-xylene biosynthetic process", GoNameSpace
categories.add( new BasicGoTerm( new GoId( "GO:0046242" ), "o-xylene biosynthetic process", GoNameSpace
categories.add( new BasicGoTerm( new GoId( "GO:0051094" ),
"positive regulation of developmental process",
GoNameSpace.createUnassigned(),
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()
private static boolean testSuperTermGetting( final File test_dir ) {
try {
final OBOparser parser = new OBOparser( new File( test_dir + ForesterUtil.getFileSeparator()