import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.Annotation;
-import jalview.datamodel.Profile;
+import jalview.datamodel.ProfileI;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceI;
SequenceI seq3 = new Sequence("Seq3", "C---G");
SequenceI seq4 = new Sequence("Seq4", "CA--t");
SequenceI[] seqs = new SequenceI[] { seq1, seq2, seq3, seq4 };
- Profile[] result = new Profile[seq1.getLength()];
+ ProfileI[] result = new ProfileI[seq1.getLength()];
AAFrequency.calculate(seqs, 0, seq1.getLength(), result, false);
// col 0 is 100% C
- Profile col = result[0];
+ ProfileI col = result[0];
assertEquals(100f, col.getPercentageIdentity(false));
assertEquals(100f, col.getPercentageIdentity(true));
assertEquals(4, col.getMaxCount());
SequenceI seq3 = new Sequence("Seq3", "C--G");
SequenceI seq4 = new Sequence("Seq4", "CA-t");
SequenceI[] seqs = new SequenceI[] { seq1, seq2, seq3, seq4 };
- Profile[] result = new Profile[seq1.getLength()];
+ ProfileI[] result = new ProfileI[seq1.getLength()];
AAFrequency.calculate(seqs, 0, seq1.getLength(), result, true);
- Profile profile = result[0];
+ ProfileI profile = result[0];
assertEquals(4, profile.getCounts().getCount('C'));
assertEquals(4, profile.getHeight());
assertEquals(4, profile.getNonGapped());
SequenceI seq3 = new Sequence("Seq3", "C--G");
SequenceI seq4 = new Sequence("Seq4", "CA-t");
SequenceI[] seqs = new SequenceI[] { seq1, seq2, seq3, seq4 };
- Profile[] result = new Profile[seq1.getLength()];
+ ProfileI[] result = new ProfileI[seq1.getLength()];
// ensure class loaded and initialized
AAFrequency.calculate(seqs, 0, seq1.getLength(), result, true);
SequenceI seq3 = new Sequence("Seq3", "C---G");
SequenceI seq4 = new Sequence("Seq4", "CA--t");
SequenceI[] seqs = new SequenceI[] { seq1, seq2, seq3, seq4 };
- Profile[] profiles = new Profile[seq1.getLength()];
+ ProfileI[] profiles = new ProfileI[seq1.getLength()];
AAFrequency.calculate(seqs, 0, seq1.getLength(), profiles, true);
AlignmentAnnotation consensus = new AlignmentAnnotation("Consensus",
SequenceI seq3 = new Sequence("Seq3", "C---G");
SequenceI seq4 = new Sequence("Seq4", "CA--t");
SequenceI[] seqs = new SequenceI[] { seq1, seq2, seq3, seq4 };
- Profile[] profiles = new Profile[seq1.getLength()];
+ ProfileI[] profiles = new ProfileI[seq1.getLength()];
AAFrequency.calculate(seqs, 0, seq1.getLength(), profiles, true);
AlignmentAnnotation consensus = new AlignmentAnnotation("Consensus",