X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fanalysis%2FAAFrequencyTest.java;h=1c04b8e936fe84a802a4d4e767e602ee3fbe50f8;hb=494a321d41897be1492b973fdb37fa4ccb0ec94e;hp=77d592adf4283bede2e8093a1d69199e8bfdb2c0;hpb=ab22918ab8fc67d30dad1fb1ae0f37e51f49df95;p=jalview.git diff --git a/test/jalview/analysis/AAFrequencyTest.java b/test/jalview/analysis/AAFrequencyTest.java index 77d592a..1c04b8e 100644 --- a/test/jalview/analysis/AAFrequencyTest.java +++ b/test/jalview/analysis/AAFrequencyTest.java @@ -1,115 +1,130 @@ - +/* + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ The Jalview Authors + * + * This file is part of Jalview. + * + * Jalview is free software: you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation, either version 3 + * of the License, or (at your option) any later version. + * + * Jalview is distributed in the hope that it will be useful, but + * WITHOUT ANY WARRANTY; without even the implied warranty + * of MERCHANTABILITY or FITNESS FOR A PARTICULAR + * PURPOSE. See the GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with Jalview. If not, see . + * The Jalview Authors are detailed in the 'AUTHORS' file. + */ 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.Sequence; import jalview.datamodel.SequenceI; -import java.util.Hashtable; - 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; - - @Test(groups ={ "Functional" }) + @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[] seqs = new SequenceI[] - { seq1, seq2, seq3, seq4 }; - Hashtable[] result = new Hashtable[seq1.getLength()]; - + 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 }; + ProfileI[] result = new ProfileI[seq1.getLength()]; + AAFrequency.calculate(seqs, 0, seq1.getLength(), result, false); // col 0 is 100% C - Hashtable col = result[0]; - assertEquals(100f, (Float) col.get(G), 0.0001f); - assertEquals(100f, (Float) col.get(N), 0.0001f); - assertEquals(4, col.get(C)); - assertEquals("C", col.get(R)); - assertNull(col.get(P)); + ProfileI col = result[0]; + assertEquals(100f, col.getPercentageIdentity(false)); + assertEquals(100f, col.getPercentageIdentity(true)); + assertEquals(4, col.getMaxCount()); + assertEquals("C", col.getModalResidue()); + assertNull(col.getCounts()); // col 1 is 75% A col = result[1]; - assertEquals(75f, (Float) col.get(G), 0.0001f); - assertEquals(100f, (Float) col.get(N), 0.0001f); - assertEquals(3, col.get(C)); - assertEquals("A", col.get(R)); + 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]; - assertEquals(25f, (Float) col.get(G), 0.0001f); - assertEquals(50f, (Float) col.get(N), 0.0001f); - assertEquals(1, col.get(C)); - assertEquals("CG", col.get(R)); + 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 3 is all gaps col = result[3]; - assertEquals(75f, (Float) col.get(G), 0.0001f); - assertEquals(75f, (Float) col.get(N), 0.0001f); - assertEquals(3, col.get(C)); - assertEquals("T", col.get(R)); + 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[4]; + assertEquals(75f, col.getPercentageIdentity(false)); + assertEquals(75f, col.getPercentageIdentity(true)); + assertEquals(3, col.getMaxCount()); + assertEquals("T", col.getModalResidue()); } - @Test(groups ={ "Functional" }) + @Test(groups = { "Functional" }) public void testCalculate_withProfile() { 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[] seqs = new SequenceI[] - { seq1, seq2, seq3, seq4 }; - Hashtable[] result = new Hashtable[seq1.getLength()]; + SequenceI[] seqs = new SequenceI[] { seq1, seq2, seq3, seq4 }; + ProfileI[] result = new ProfileI[seq1.getLength()]; AAFrequency.calculate(seqs, 0, seq1.getLength(), result, true); - int[][] profile = (int[][]) result[0].get(P); - assertEquals(4, profile[0]['C']); - assertEquals(4, profile[1][0]); // no of seqs - assertEquals(4, profile[1][1]); // nongapped in column - - profile = (int[][]) result[1].get(P); - assertEquals(3, profile[0]['A']); - assertEquals(4, profile[1][0]); - assertEquals(3, profile[1][1]); - - profile = (int[][]) result[2].get(P); - assertEquals(1, profile[0]['G']); - assertEquals(1, profile[0]['C']); - assertEquals(4, profile[1][0]); - assertEquals(2, profile[1][1]); - - profile = (int[][]) result[3].get(P); - assertEquals(3, profile[0]['T']); - assertEquals(1, profile[0]['G']); - assertEquals(4, profile[1][0]); - assertEquals(4, profile[1][1]); + ProfileI profile = result[0]; + assertEquals(4, profile.getCounts().getCount('C')); + assertEquals(4, profile.getHeight()); + assertEquals(4, profile.getNonGapped()); + + profile = result[1]; + assertEquals(3, profile.getCounts().getCount('A')); + assertEquals(4, profile.getHeight()); + assertEquals(3, profile.getNonGapped()); + + profile = result[2]; + assertEquals(1, profile.getCounts().getCount('C')); + assertEquals(1, profile.getCounts().getCount('G')); + assertEquals(4, profile.getHeight()); + assertEquals(2, profile.getNonGapped()); + + profile = result[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"); SequenceI seq2 = new Sequence("Seq2", "CACT"); SequenceI seq3 = new Sequence("Seq3", "C--G"); SequenceI seq4 = new Sequence("Seq4", "CA-t"); - SequenceI[] seqs = new SequenceI[] - { seq1, seq2, seq3, seq4 }; - Hashtable[] result = new Hashtable[seq1.getLength()]; + SequenceI[] seqs = new SequenceI[] { seq1, seq2, seq3, seq4 }; + ProfileI[] result = new ProfileI[seq1.getLength()]; // ensure class loaded and initialized AAFrequency.calculate(seqs, 0, seq1.getLength(), result, true); @@ -122,14 +137,86 @@ public class AAFrequencyTest System.out.println(System.currentTimeMillis() - start); } - @Test(groups ={ "Functional" }) - public void testGetPercentageFormat() + /** + * 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 }; + ProfileI[] profiles = new ProfileI[seq1.getLength()]; + AAFrequency.calculate(seqs, 0, seq1.getLength(), profiles, true); + + AlignmentAnnotation consensus = new AlignmentAnnotation("Consensus", + "PID", new Annotation[seq1.getLength()]); + 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() { - assertNull(AAFrequency.getPercentageFormat(0)); - assertNull(AAFrequency.getPercentageFormat(99)); - assertEquals("%3.1f", AAFrequency.getPercentageFormat(100).toString()); - assertEquals("%3.1f", AAFrequency.getPercentageFormat(999).toString()); - assertEquals("%3.2f", AAFrequency.getPercentageFormat(1000).toString()); - assertEquals("%3.2f", AAFrequency.getPercentageFormat(9999).toString()); + /* + * 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 }; + ProfileI[] profiles = new ProfileI[seq1.getLength()]; + AAFrequency.calculate(seqs, 0, seq1.getLength(), profiles, true); + + AlignmentAnnotation consensus = new AlignmentAnnotation("Consensus", + "PID", new Annotation[seq1.getLength()]); + 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); } }