// make sure dataset is initialised ? not sure about this
for (int i = 0; i < al.getSequencesArray().length; ++i)
{
- al.getSequenceAt(i).setDatasetSequence(al.getSequenceAt(i));
+ al.getSequenceAt(i).createDatasetSequence();
}
String outputfile = rf.formatSequences(ioformat, al, true);
System.out.println("Output file in '" + ioformat + "':\n"
}
assertEquals(
"Generated and imported alignment have different annotation sets",
- aa_new_size, aa_original_size);
+ aa_original_size, aa_new_size);
// check sequences, annotation and features
SequenceI[] seq_original = new SequenceI[al.getSequencesArray().length];
assertEquals("different number of features",
seq_original[i].getSequenceFeatures().length,
- seq_new[in]
- .getSequenceFeatures().length);
+ seq_new[in].getSequenceFeatures().length);
for (int feat = 0; feat < seq_original[i].getSequenceFeatures().length; feat++)
{