@Test
public void testCreateNamedSequences() {
// A DNA Sequence
ISequence seq = biojava.createSequence("sequence1", "CCCTCGGCTTC");
try {
assertEquals("CCCTCGGCTTC", seq.getPlainSequence().trim().toUpperCase());
// Right now: don't care about name as it is set by BioJava
} catch (IOException e) {
fail(e.getMessage());
}
// A Protein Sequence
seq = biojava.createSequence("sequence2", "SEQUENCE");
try {
assertEquals("SEQUENCE", seq.getPlainSequence().trim().toUpperCase());
} catch (IOException e) {
fail(e.getMessage());
}
/*
//An RNA Sequence
seq=biojava.createSequence("CCCUCGGCUUC");
try {
assertEquals("CCCUCGGCUUC", seq.getPlainSequence());
} catch (IOException e) {
fail(e.getMessage());
}
*/
}
@Test
public void testCreateSequences() {
// A DNA Sequence
ISequence seq = biojava.createSequence("CCCTCGGCTTC");
try {
assertEquals("CCCTCGGCTTC", seq.getPlainSequence().trim().toUpperCase());
} catch (IOException e) {
fail(e.getMessage());
}
// A Protein Sequence
seq = biojava.createSequence("SEQUENCE");
try {
assertEquals("SEQUENCE", seq.getPlainSequence().trim().toUpperCase());
} catch (IOException e) {
fail(e.getMessage());
}
/*
//An RNA Sequence
seq=biojava.createSequence("CCCUCGGCUUC");
try {
assertEquals("CCCUCGGCUUC", seq.getPlainSequence());
} catch (IOException e) {
fail(e.getMessage());
}
*/
}
@Test
public void TestBiolist() {
RecordableList<BiojavaSequence> list = new RecordableList<BiojavaSequence>();
InputStream stream =
getClass().getResourceAsStream("/net/bioclipse/biojava/ui/test/resources/111076.gbk");
BiojavaSequence tseq = biojava.loadSequence(stream);
list.add(tseq);
for (ISequence seq : list) {
System.out.println(seq.getName());
}
stream = getClass().getResourceAsStream("/net/bioclipse/biojava/ui/test/resources/111077.gbk");
System.out.println("--");
tseq = biojava.loadSequence(stream);
list.add(tseq);
for (ISequence seq : list) {
System.out.println(seq.getName());
}
}