SequenceI seq4 = new Sequence("Seq4", "CA--t");
SequenceI[] seqs = new SequenceI[] { seq1, seq2, seq3, seq4 };
int width = seq1.getLength();
- ProfilesI result = AAFrequency.calculate(seqs, width, 0, width,
- false);
+ ProfilesI result = AAFrequency.calculate(seqs, width, 0, width, false);
// col 0 is 100% C
ProfileI col = result.get(0);
SequenceI seq4 = new Sequence("Seq4", "CA-t");
SequenceI[] seqs = new SequenceI[] { seq1, seq2, seq3, seq4 };
int width = seq1.getLength();
- ProfilesI result = AAFrequency.calculate(seqs, width, 0, width,
- true);
+ ProfilesI result = AAFrequency.calculate(seqs, width, 0, width, true);
ProfileI profile = result.get(0);
assertEquals(4, profile.getCounts().getCount('C'));
AlignmentAnnotation consensus = new AlignmentAnnotation("Consensus",
"PID", new Annotation[width]);
- AAFrequency
- .completeConsensus(consensus, profiles, 0, 5, false, true, 4);
+ AAFrequency.completeConsensus(consensus, profiles, 0, 5, false, true,
+ 4);
Annotation ann = consensus.annotations[0];
assertEquals("C 100%", ann.description);
SequenceI[] seqs = new SequenceI[] { seq1, seq2, seq3, seq4 };
int width = seq1.getLength();
ProfilesI profiles = AAFrequency.calculate(seqs, width, 0, width, true);
-
+
AlignmentAnnotation consensus = new AlignmentAnnotation("Consensus",
"PID", new Annotation[width]);
- AAFrequency
- .completeConsensus(consensus, profiles, 0, 5, true, false, 4);
-
+ AAFrequency.completeConsensus(consensus, profiles, 0, 5, true, false,
+ 4);
+
Annotation ann = consensus.annotations[0];
assertEquals("C 100%", ann.description);
assertEquals("C", ann.displayCharacter);
counts.put('L', 38);
counts.put('H', 2);
profile.setCounts(counts);
-
+
/*
* [0, noOfValues, totalPercent, char1, count1, ...]
* G: 70/200 = 35%
*/
int[] extracted = AAFrequency.extractProfile(profile, false);
int[] expected = new int[] { AlignmentAnnotation.SEQUENCE_PROFILE, 4,
- 85, 'G', 35, 'R', 30, 'L', 19, 'H',
- 1 };
+ 85, 'G', 35, 'R', 30, 'L', 19, 'H', 1 };
org.testng.Assert.assertEquals(extracted, expected);
-
+
/*
* add some counts of 1; these round down to 0% and should be discarded
*/
expected = new int[] { AlignmentAnnotation.SEQUENCE_PROFILE, 4, 84, 'G',
34, 'R', 30, 'L', 19, 'H', 1 };
org.testng.Assert.assertEquals(extracted, expected);
-
+
}
@Test(groups = { "Functional" })
codonCounts[0] = 120;
codonCounts[1] = 110;
profile.put(AAFrequency.PROFILE, codonCounts);
-
+
/*
* [0, noOfValues, totalPercent, char1, count1, ...]
* codon1: 30/110 = 27.2 = 27%
* max count 70 for modal residue 'G'
*/
Hashtable profile = new Hashtable();
-
+
/*
* cdna profile is {seqCount, ungappedCount, codonCount1, ...codonCount64}
* where 1..64 positions correspond to encoded codons
codonCounts[0] = 120;
codonCounts[1] = 110;
profile.put(AAFrequency.PROFILE, codonCounts);
-
+
/*
* [0, noOfValues, totalPercent, char1, count1, ...]
* codon1: 30/120 = 25%