@Test
public void assertEncodeSequence() {
FastaInput in = new FastaInput();
Sequence seq = null;
long numSeqs = 0;
Assert.assertTrue(in.open("A.fasta"));
try {
while ((seq = in.readNextSequence()) != null) {
String sequence = seq.getSequence();
int seqOldLen = sequence.length();
byte[] comSequence = SequenceUtils.compressSequence(sequence);
int seqNewLen = comSequence.length;
System.out.print(seqOldLen + " : ");
System.out.print(seqNewLen + " = " + ((double) seqNewLen / (double) seqOldLen));
System.out.print(" -> ");
String decomp = SequenceUtils.decompressSequence(comSequence);
System.out.println(decomp.length());
Assert.assertTrue(seq.getAttributes().size() > 0);
Assert.assertTrue(seq.getChunks() != null);
Assert.assertTrue(seq.getChunks().size() > 0);
Assert.assertEquals(sequence, decomp.substring(0, seqOldLen));
++numSeqs;
}
} finally {
in.close();
}
Assert.assertTrue(numSeqs == 6);
}
@Test
public void testReadNextSequence() {
FastaInput in = new FastaInput();
Sequence seq = null;
long numSeqs = 0;
Assert.assertTrue(in.open("A.fasta"));
try {
while ((seq = in.readNextSequence()) != null) {
// System.out.println(seq.getId());
/*for(String key : seq.getAttributes().keySet()) {
System.out.println("key: " + key + ", value = " + seq.getAttributes().get(key));
}*/
Assert.assertTrue(seq.getAttributes().size() > 0);
Assert.assertTrue(seq.getChunks() != null);
Assert.assertTrue(seq.getChunks().size() > 0);
++numSeqs;
}
} finally {
in.close();
}
Assert.assertTrue(numSeqs == 6);
}