Iterator<int[]> contigs = cs.getVisContigsIterator(0, alf.getWidth(),
false);
Dna dna = new Dna(av, contigs);
- AlignmentI translated = dna.translateCdna();
+ AlignmentI translated = dna.translateCdna(GeneticCodes.getInstance()
+ .getStandardCodeTable());
assertNotNull("Couldn't do a full width translation of test data.",
translated);
}
alf.getWidth(), false);
AlignViewportI av = new AlignViewport(alf, cs);
Dna dna = new Dna(av, vcontigs);
- AlignmentI transAlf = dna.translateCdna();
+ AlignmentI transAlf = dna.translateCdna(GeneticCodes.getInstance()
+ .getStandardCodeTable());
assertTrue("Translation failed (ipos=" + ipos
+ ") No alignment data.", transAlf != null);
Iterator<int[]> contigs = cs.getVisContigsIterator(0, alf.getWidth(),
false);
Dna dna = new Dna(av, contigs);
- AlignmentI translated = dna.translateCdna();
+ AlignmentI translated = dna.translateCdna(GeneticCodes.getInstance()
+ .getStandardCodeTable());
String aa = translated.getSequenceAt(0).getSequenceAsString();
assertEquals(
"AAAACCDDEEFFGGGGHHIIIKKLLLLLLMNNPPPPQQRRRRRRSSSSSSTTTTVVVVWYY***",
Iterator<int[]> contigs = cs.getVisContigsIterator(0, alf.getWidth(),
false);
Dna dna = new Dna(av, contigs);
- AlignmentI translated = dna.translateCdna();
+ AlignmentI translated = dna.translateCdna(GeneticCodes.getInstance()
+ .getStandardCodeTable());
String aa = translated.getSequenceAt(0).getSequenceAsString();
assertEquals("AACDDGGGGHHIIIKKLLLLLLMNNPPPPQQRRRRRRSSSSSSTTTTVVVVW", aa);
}
Iterator<int[]> contigs = cs.getVisContigsIterator(0, cdna.getWidth(),
false);
Dna dna = new Dna(av, contigs);
- AlignmentI translated = dna.translateCdna();
+ AlignmentI translated = dna.translateCdna(GeneticCodes.getInstance()
+ .getStandardCodeTable());
/*
* Jumble the cDNA sequences and translate.
av = new AlignViewport(cdnaReordered, cs);
contigs = cs.getVisContigsIterator(0, cdna.getWidth(), false);
dna = new Dna(av, contigs);
- AlignmentI translated2 = dna.translateCdna();
+ AlignmentI translated2 = dna.translateCdna(GeneticCodes.getInstance()
+ .getStandardCodeTable());
/*
* Check translated sequences are the same in both alignments.