X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fanalysis%2FAAFrequencyTest.java;h=75fb39e4e047ed509cca488204747547dfbdb26f;hb=567c2595554096f10feab130153f97286f3f7d80;hp=ecddad1e6cfd9dc4963dbf7f0f4b16776e99fcfb;hpb=1c757dc1e6ee864277825c1ebd9c6a9fbe0da7b2;p=jalview.git diff --git a/test/jalview/analysis/AAFrequencyTest.java b/test/jalview/analysis/AAFrequencyTest.java index ecddad1..75fb39e 100644 --- a/test/jalview/analysis/AAFrequencyTest.java +++ b/test/jalview/analysis/AAFrequencyTest.java @@ -23,37 +23,41 @@ package jalview.analysis; import static org.testng.AssertJUnit.assertEquals; import static org.testng.AssertJUnit.assertNull; +import jalview.datamodel.AlignmentAnnotation; +import jalview.datamodel.Annotation; +import jalview.datamodel.ProfileI; +import jalview.datamodel.ProfilesI; import jalview.datamodel.Sequence; import jalview.datamodel.SequenceI; +import jalview.gui.JvOptionPane; +import org.testng.annotations.BeforeClass; import org.testng.annotations.Test; public class AAFrequencyTest { - private static final String C = AAFrequency.MAXCOUNT; - private static final String R = AAFrequency.MAXRESIDUE; - - private static final String G = AAFrequency.PID_GAPS; - - private static final String N = AAFrequency.PID_NOGAPS; - - private static final String P = AAFrequency.PROFILE; + @BeforeClass(alwaysRun = true) + public void setUpJvOptionPane() + { + JvOptionPane.setInteractiveMode(false); + JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION); + } @Test(groups = { "Functional" }) public void testCalculate_noProfile() { - SequenceI seq1 = new Sequence("Seq1", "CAGT"); - SequenceI seq2 = new Sequence("Seq2", "CACT"); - SequenceI seq3 = new Sequence("Seq3", "C--G"); - SequenceI seq4 = new Sequence("Seq4", "CA-t"); + SequenceI seq1 = new Sequence("Seq1", "CAG-T"); + SequenceI seq2 = new Sequence("Seq2", "CAC-T"); + 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()]; - - AAFrequency.calculate(seqs, 0, seq1.getLength(), result, false); + int width = seq1.getLength(); + ProfilesI result = AAFrequency.calculate(seqs, width, 0, width, + false); // col 0 is 100% C - Profile col = result[0]; + ProfileI col = result.get(0); assertEquals(100f, col.getPercentageIdentity(false)); assertEquals(100f, col.getPercentageIdentity(true)); assertEquals(4, col.getMaxCount()); @@ -61,21 +65,28 @@ public class AAFrequencyTest assertNull(col.getCounts()); // col 1 is 75% A - col = result[1]; + col = result.get(1); assertEquals(75f, col.getPercentageIdentity(false)); assertEquals(100f, col.getPercentageIdentity(true)); assertEquals(3, col.getMaxCount()); assertEquals("A", col.getModalResidue()); // col 2 is 50% G 50% C or 25/25 counting gaps - col = result[2]; + col = result.get(2); assertEquals(25f, col.getPercentageIdentity(false)); assertEquals(50f, col.getPercentageIdentity(true)); assertEquals(1, col.getMaxCount()); assertEquals("CG", col.getModalResidue()); - // col 3 is 75% T 25% G - col = result[3]; + // col 3 is all gaps + col = result.get(3); + assertEquals(0f, col.getPercentageIdentity(false)); + assertEquals(0f, col.getPercentageIdentity(true)); + assertEquals(0, col.getMaxCount()); + assertEquals("", col.getModalResidue()); + + // col 4 is 75% T 25% G + col = result.get(4); assertEquals(75f, col.getPercentageIdentity(false)); assertEquals(75f, col.getPercentageIdentity(true)); assertEquals(3, col.getMaxCount()); @@ -90,33 +101,34 @@ public class AAFrequencyTest 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()]; + int width = seq1.getLength(); + ProfilesI result = AAFrequency.calculate(seqs, width, 0, width, + true); - AAFrequency.calculate(seqs, 0, seq1.getLength(), result, true); - Profile profile = result[0]; + ProfileI profile = result.get(0); assertEquals(4, profile.getCounts().getCount('C')); assertEquals(4, profile.getHeight()); assertEquals(4, profile.getNonGapped()); - profile = result[1]; + profile = result.get(1); assertEquals(3, profile.getCounts().getCount('A')); assertEquals(4, profile.getHeight()); assertEquals(3, profile.getNonGapped()); - profile = result[2]; + profile = result.get(2); assertEquals(1, profile.getCounts().getCount('C')); assertEquals(1, profile.getCounts().getCount('G')); assertEquals(4, profile.getHeight()); assertEquals(2, profile.getNonGapped()); - profile = result[3]; + profile = result.get(3); assertEquals(3, profile.getCounts().getCount('T')); assertEquals(1, profile.getCounts().getCount('G')); assertEquals(4, profile.getHeight()); assertEquals(4, profile.getNonGapped()); } - @Test(groups = { "Functional" }) + @Test(groups = { "Functional" }, enabled = false) public void testCalculate_withProfileTiming() { SequenceI seq1 = new Sequence("Seq1", "CAGT"); @@ -124,16 +136,100 @@ public class AAFrequencyTest 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()]; - // ensure class loaded and initialized - AAFrequency.calculate(seqs, 0, seq1.getLength(), result, true); + // ensure class loaded and initialised + int width = seq1.getLength(); + AAFrequency.calculate(seqs, width, 0, width, true); + int reps = 100000; long start = System.currentTimeMillis(); for (int i = 0; i < reps; i++) { - AAFrequency.calculate(seqs, 0, seq1.getLength(), result, true); + AAFrequency.calculate(seqs, width, 0, width, true); } System.out.println(System.currentTimeMillis() - start); } + + /** + * Test generation of consensus annotation with options 'include gaps' + * (profile percentages are of all sequences, whether gapped or not), and + * 'show logo' (the full profile with all residue percentages is reported in + * the description for the tooltip) + */ + @Test(groups = { "Functional" }) + public void testCompleteConsensus_includeGaps_showLogo() + { + /* + * first compute the profiles + */ + SequenceI seq1 = new Sequence("Seq1", "CAG-T"); + SequenceI seq2 = new Sequence("Seq2", "CAC-T"); + SequenceI seq3 = new Sequence("Seq3", "C---G"); + SequenceI seq4 = new Sequence("Seq4", "CA--t"); + 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, false, true, 4); + + Annotation ann = consensus.annotations[0]; + assertEquals("C 100%", ann.description); + assertEquals("C", ann.displayCharacter); + ann = consensus.annotations[1]; + assertEquals("A 75%", ann.description); + assertEquals("A", ann.displayCharacter); + ann = consensus.annotations[2]; + assertEquals("C 25%; G 25%", ann.description); + assertEquals("+", ann.displayCharacter); + ann = consensus.annotations[3]; + assertEquals("", ann.description); + assertEquals("-", ann.displayCharacter); + ann = consensus.annotations[4]; + assertEquals("T 75%; G 25%", ann.description); + assertEquals("T", ann.displayCharacter); + } + + /** + * Test generation of consensus annotation with options 'ignore gaps' (profile + * percentages are of the non-gapped sequences) and 'no logo' (only the modal + * residue[s] percentage is reported in the description for the tooltip) + */ + @Test(groups = { "Functional" }) + public void testCompleteConsensus_ignoreGaps_noLogo() + { + /* + * first compute the profiles + */ + SequenceI seq1 = new Sequence("Seq1", "CAG-T"); + SequenceI seq2 = new Sequence("Seq2", "CAC-T"); + SequenceI seq3 = new Sequence("Seq3", "C---G"); + SequenceI seq4 = new Sequence("Seq4", "CA--t"); + 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); + + Annotation ann = consensus.annotations[0]; + assertEquals("C 100%", ann.description); + assertEquals("C", ann.displayCharacter); + ann = consensus.annotations[1]; + assertEquals("A 100%", ann.description); + assertEquals("A", ann.displayCharacter); + ann = consensus.annotations[2]; + assertEquals("[CG] 50%", ann.description); + assertEquals("+", ann.displayCharacter); + ann = consensus.annotations[3]; + assertEquals("", ann.description); + assertEquals("-", ann.displayCharacter); + ann = consensus.annotations[4]; + assertEquals("T 75%", ann.description); + assertEquals("T", ann.displayCharacter); + } }