Iterator<int[]> contigs = cs.getVisContigsIterator(0, alf.getWidth(),
false);
Dna dna = new Dna(av, contigs);
Iterator<int[]> contigs = cs.getVisContigsIterator(0, alf.getWidth(),
false);
Dna dna = new Dna(av, contigs);
cs.hideColumns(0, ipos - 1);
}
cs.hideColumns(ipos + vwidth, alf.getWidth());
cs.hideColumns(0, ipos - 1);
}
cs.hideColumns(ipos + vwidth, alf.getWidth());
- Iterator<int[]> vcontigs = cs.getVisContigsIterator(0,
- alf.getWidth(), false);
+ Iterator<int[]> vcontigs = cs.getVisContigsIterator(0, alf.getWidth(),
+ false);
AlignViewportI av = new AlignViewport(alf, cs);
Dna dna = new Dna(av, vcontigs);
AlignViewportI av = new AlignViewport(alf, cs);
Dna dna = new Dna(av, vcontigs);
assertTrue("Translation failed (ipos=" + ipos + ") Empty alignment.",
transAlf.getHeight() > 0);
assertTrue("Translation failed (ipos=" + ipos + ") Empty alignment.",
transAlf.getHeight() > 0);
- assertTrue("Translation failed (ipos=" + ipos + ") Translated "
- + transAlf.getHeight() + " sequences from " + alf.getHeight()
- + " sequences", alf.getHeight() == transAlf.getHeight());
+ assertTrue(
+ "Translation failed (ipos=" + ipos + ") Translated "
+ + transAlf.getHeight() + " sequences from "
+ + alf.getHeight() + " sequences",
+ alf.getHeight() == transAlf.getHeight());
Iterator<int[]> contigs = cs.getVisContigsIterator(0, alf.getWidth(),
false);
Dna dna = new Dna(av, contigs);
Iterator<int[]> contigs = cs.getVisContigsIterator(0, alf.getWidth(),
false);
Dna dna = new Dna(av, contigs);
String aa = translated.getSequenceAt(0).getSequenceAsString();
assertEquals(
"AAAACCDDEEFFGGGGHHIIIKKLLLLLLMNNPPPPQQRRRRRRSSSSSSTTTTVVVVWYY***",
String aa = translated.getSequenceAt(0).getSequenceAsString();
assertEquals(
"AAAACCDDEEFFGGGGHHIIIKKLLLLLLMNNPPPPQQRRRRRRSSSSSSTTTTVVVVWYY***",
Iterator<int[]> contigs = cs.getVisContigsIterator(0, alf.getWidth(),
false);
Dna dna = new Dna(av, contigs);
Iterator<int[]> contigs = cs.getVisContigsIterator(0, alf.getWidth(),
false);
Dna dna = new Dna(av, contigs);
- AlignmentI cdna = new AlignmentGenerator(true)
- .generate(12, 8, 97, 5, 5);
+ AlignmentI cdna = new AlignmentGenerator(true).generate(12, 8, 97, 5,
+ 5);
HiddenColumns cs = new HiddenColumns();
AlignViewportI av = new AlignViewport(cdna, cs);
Iterator<int[]> contigs = cs.getVisContigsIterator(0, cdna.getWidth(),
false);
Dna dna = new Dna(av, contigs);
HiddenColumns cs = new HiddenColumns();
AlignViewportI av = new AlignViewport(cdna, cs);
Iterator<int[]> contigs = cs.getVisContigsIterator(0, cdna.getWidth(),
false);
Dna dna = new Dna(av, contigs);
av = new AlignViewport(cdnaReordered, cs);
contigs = cs.getVisContigsIterator(0, cdna.getWidth(), false);
dna = new Dna(av, contigs);
av = new AlignViewport(cdnaReordered, cs);
contigs = cs.getVisContigsIterator(0, cdna.getWidth(), false);
dna = new Dna(av, contigs);
- final String translation1 = translated.getSequenceAt(
- originalSequenceIndex).getSequenceAsString();
- final String translation2 = translated2.getSequenceAt(
- sortedSequenceIndex).getSequenceAsString();
+ final String translation1 = translated
+ .getSequenceAt(originalSequenceIndex).getSequenceAsString();
+ final String translation2 = translated2
+ .getSequenceAt(sortedSequenceIndex).getSequenceAsString();
- assertEquals("Comparison of '" + codon1 + "' and '" + codon2
- + " not symmetric", Integer.signum(compare(codon1, codon2)),
+ assertEquals(
+ "Comparison of '" + codon1 + "' and '" + codon2
+ + " not symmetric",
+ Integer.signum(compare(codon1, codon2)),
- assertEquals("Expected '" + codon1 + "' precedes '" + codon2 + "'",
- -1, compare(codon1, codon2));
+ assertEquals("Expected '" + codon1 + "' precedes '" + codon2 + "'", -1,
+ compare(codon1, codon2));
SequenceI dna = new Sequence("Seq1", seq);
Alignment al = new Alignment(new SequenceI[] { dna });
al.createDatasetAlignment();
SequenceI dna = new Sequence("Seq1", seq);
Alignment al = new Alignment(new SequenceI[] { dna });
al.createDatasetAlignment();
HiddenColumns cs = new HiddenColumns();
AlignViewportI av = new AlignViewport(al, cs);
HiddenColumns cs = new HiddenColumns();
AlignViewportI av = new AlignViewport(al, cs);