FileFormat.Fasta);
HiddenColumns cs = new HiddenColumns();
AlignViewportI av = new AlignViewport(alf, cs);
- Iterator<int[]> contigs = cs.getVisContigsIterator(0, alf.getWidth());
+ Iterator<int[]> contigs = cs.getVisContigsIterator(0, alf.getWidth(),
+ false);
Dna dna = new Dna(av, contigs);
- AlignmentI translated = dna.translateCdna();
+ AlignmentI translated = dna
+ .translateCdna(GeneticCodes.getStandardCodeTable());
assertNotNull("Couldn't do a full width translation of test data.",
translated);
}
}
cs.hideColumns(ipos + vwidth, alf.getWidth());
Iterator<int[]> vcontigs = cs.getVisContigsIterator(0,
- alf.getWidth());
+ alf.getWidth(), false);
AlignViewportI av = new AlignViewport(alf, cs);
Dna dna = new Dna(av, vcontigs);
- AlignmentI transAlf = dna.translateCdna();
+ AlignmentI transAlf = dna
+ .translateCdna(GeneticCodes.getStandardCodeTable());
assertTrue("Translation failed (ipos=" + ipos
+ ") No alignment data.", transAlf != null);
DataSourceType.PASTE, FileFormat.Fasta);
HiddenColumns cs = new HiddenColumns();
AlignViewportI av = new AlignViewport(alf, cs);
- Iterator<int[]> contigs = cs.getVisContigsIterator(0, alf.getWidth());
+ Iterator<int[]> contigs = cs.getVisContigsIterator(0, alf.getWidth(),
+ false);
Dna dna = new Dna(av, contigs);
- AlignmentI translated = dna.translateCdna();
+ AlignmentI translated = dna
+ .translateCdna(GeneticCodes.getStandardCodeTable());
String aa = translated.getSequenceAt(0).getSequenceAsString();
assertEquals(
"AAAACCDDEEFFGGGGHHIIIKKLLLLLLMNNPPPPQQRRRRRRSSSSSSTTTTVVVVWYY***",
cs.hideColumns(24, 35); // hide codons 9-12
cs.hideColumns(177, 191); // hide codons 60-64
AlignViewportI av = new AlignViewport(alf, cs);
- Iterator<int[]> contigs = cs.getVisContigsIterator(0, alf.getWidth());
+ Iterator<int[]> contigs = cs.getVisContigsIterator(0, alf.getWidth(),
+ false);
Dna dna = new Dna(av, contigs);
- AlignmentI translated = dna.translateCdna();
+ AlignmentI translated = dna
+ .translateCdna(GeneticCodes.getStandardCodeTable());
String aa = translated.getSequenceAt(0).getSequenceAsString();
assertEquals("AACDDGGGGHHIIIKKLLLLLLMNNPPPPQQRRRRRRSSSSSSTTTTVVVVW", aa);
}
.generate(12, 8, 97, 5, 5);
HiddenColumns cs = new HiddenColumns();
AlignViewportI av = new AlignViewport(cdna, cs);
- Iterator<int[]> contigs = cs.getVisContigsIterator(0, cdna.getWidth());
+ Iterator<int[]> contigs = cs.getVisContigsIterator(0, cdna.getWidth(),
+ false);
Dna dna = new Dna(av, contigs);
- AlignmentI translated = dna.translateCdna();
+ AlignmentI translated = dna
+ .translateCdna(GeneticCodes.getStandardCodeTable());
/*
* Jumble the cDNA sequences and translate.
}
AlignmentI cdnaReordered = new Alignment(sorted);
av = new AlignViewport(cdnaReordered, cs);
- contigs = cs.getVisContigsIterator(0, cdna.getWidth());
+ contigs = cs.getVisContigsIterator(0, cdna.getWidth(), false);
dna = new Dna(av, contigs);
- AlignmentI translated2 = dna.translateCdna();
+ AlignmentI translated2 = dna
+ .translateCdna(GeneticCodes.getStandardCodeTable());
/*
* Check translated sequences are the same in both alignments.
HiddenColumns cs = new HiddenColumns();
AlignViewportI av = new AlignViewport(al, cs);
- Iterator<int[]> contigs = cs.getVisContigsIterator(0, al.getWidth());
+ Iterator<int[]> contigs = cs.getVisContigsIterator(0, al.getWidth(),
+ false);
Dna testee = new Dna(av, contigs);
AlignmentI reversed = testee.reverseCdna(false);
assertEquals(1, reversed.getHeight());