/* * 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.datamodel; import static org.testng.AssertJUnit.assertEquals; import static org.testng.AssertJUnit.assertFalse; import static org.testng.AssertJUnit.assertNotNull; import static org.testng.AssertJUnit.assertNotSame; import static org.testng.AssertJUnit.assertNull; import static org.testng.AssertJUnit.assertSame; import static org.testng.AssertJUnit.assertTrue; import jalview.analysis.AlignmentGenerator; import jalview.commands.EditCommand; import jalview.commands.EditCommand.Action; import jalview.datamodel.PDBEntry.Type; import jalview.gui.JvOptionPane; import jalview.util.MapList; import jalview.ws.params.InvalidArgumentException; import java.io.File; import java.util.ArrayList; import java.util.Arrays; import java.util.BitSet; import java.util.Iterator; import java.util.List; import java.util.Vector; import org.testng.Assert; import org.testng.annotations.BeforeClass; import org.testng.annotations.BeforeMethod; import org.testng.annotations.Test; import junit.extensions.PA; public class SequenceTest { @BeforeClass(alwaysRun = true) public void setUpJvOptionPane() { JvOptionPane.setInteractiveMode(false); JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION); } Sequence seq; @BeforeMethod(alwaysRun = true) public void setUp() { seq = new Sequence("FER1", "AKPNGVL"); } @Test(groups = { "Functional" }) public void testInsertGapsAndGapmaps() { SequenceI aseq = seq.deriveSequence(); aseq.insertCharAt(2, 3, '-'); aseq.insertCharAt(6, 3, '-'); assertEquals("Gap insertions not correct", "AK---P---NGVL", aseq.getSequenceAsString()); List gapInt = aseq.getInsertions(); assertEquals("Gap interval 1 start wrong", 2, gapInt.get(0)[0]); assertEquals("Gap interval 1 end wrong", 4, gapInt.get(0)[1]); assertEquals("Gap interval 2 start wrong", 6, gapInt.get(1)[0]); assertEquals("Gap interval 2 end wrong", 8, gapInt.get(1)[1]); BitSet gapfield = aseq.getInsertionsAsBits(); BitSet expectedgaps = new BitSet(); expectedgaps.set(2, 5); expectedgaps.set(6, 9); assertEquals(6, expectedgaps.cardinality()); assertEquals("getInsertionsAsBits didn't mark expected number of gaps", 6, gapfield.cardinality()); assertEquals("getInsertionsAsBits not correct.", expectedgaps, gapfield); } @Test(groups = ("Functional")) public void testIsProtein() { // test Protein assertTrue(new Sequence("prot", "ASDFASDFASDF").isProtein()); // test DNA assertFalse(new Sequence("prot", "ACGTACGTACGT").isProtein()); // test RNA SequenceI sq = new Sequence("prot", "ACGUACGUACGU"); assertFalse(sq.isProtein()); // change sequence, should trigger an update of cached result sq.setSequence("ASDFASDFADSF"); assertTrue(sq.isProtein()); } @Test(groups = { "Functional" }) public void testGetAnnotation() { // initial state returns null not an empty array assertNull(seq.getAnnotation()); AlignmentAnnotation ann = addAnnotation("label1", "desc1", "calcId1", 1f); AlignmentAnnotation[] anns = seq.getAnnotation(); assertEquals(1, anns.length); assertSame(ann, anns[0]); // removing all annotations reverts array to null seq.removeAlignmentAnnotation(ann); assertNull(seq.getAnnotation()); } @Test(groups = { "Functional" }) public void testGetAnnotation_forLabel() { AlignmentAnnotation ann1 = addAnnotation("label1", "desc1", "calcId1", 1f); addAnnotation("label2", "desc2", "calcId2", 1f); AlignmentAnnotation ann3 = addAnnotation("label1", "desc3", "calcId3", 1f); AlignmentAnnotation[] anns = seq.getAnnotation("label1"); assertEquals(2, anns.length); assertSame(ann1, anns[0]); assertSame(ann3, anns[1]); } private AlignmentAnnotation addAnnotation(String label, String description, String calcId, float value) { final AlignmentAnnotation annotation = new AlignmentAnnotation(label, description, value); annotation.setCalcId(calcId); seq.addAlignmentAnnotation(annotation); return annotation; } @Test(groups = { "Functional" }) public void testGetAlignmentAnnotations_forCalcIdAndLabel() { addAnnotation("label1", "desc1", "calcId1", 1f); AlignmentAnnotation ann2 = addAnnotation("label2", "desc2", "calcId2", 1f); addAnnotation("label2", "desc3", "calcId3", 1f); AlignmentAnnotation ann4 = addAnnotation("label2", "desc3", "calcId2", 1f); addAnnotation("label5", "desc3", null, 1f); addAnnotation(null, "desc3", "calcId3", 1f); List anns = seq.getAlignmentAnnotations("calcId2", "label2"); assertEquals(2, anns.size()); assertSame(ann2, anns.get(0)); assertSame(ann4, anns.get(1)); assertTrue(seq.getAlignmentAnnotations("calcId2", "label3").isEmpty()); assertTrue(seq.getAlignmentAnnotations("calcId3", "label5").isEmpty()); assertTrue(seq.getAlignmentAnnotations("calcId2", null).isEmpty()); assertTrue(seq.getAlignmentAnnotations(null, "label3").isEmpty()); assertTrue(seq.getAlignmentAnnotations(null, null).isEmpty()); } /** * Tests for addAlignmentAnnotation. Note this method has the side-effect of * setting the sequenceRef on the annotation. Adding the same annotation twice * should be ignored. */ @Test(groups = { "Functional" }) public void testAddAlignmentAnnotation() { assertNull(seq.getAnnotation()); final AlignmentAnnotation annotation = new AlignmentAnnotation("a", "b", 2d); assertNull(annotation.sequenceRef); seq.addAlignmentAnnotation(annotation); assertSame(seq, annotation.sequenceRef); AlignmentAnnotation[] anns = seq.getAnnotation(); assertEquals(1, anns.length); assertSame(annotation, anns[0]); // re-adding does nothing seq.addAlignmentAnnotation(annotation); anns = seq.getAnnotation(); assertEquals(1, anns.length); assertSame(annotation, anns[0]); // an identical but different annotation can be added final AlignmentAnnotation annotation2 = new AlignmentAnnotation("a", "b", 2d); seq.addAlignmentAnnotation(annotation2); anns = seq.getAnnotation(); assertEquals(2, anns.length); assertSame(annotation, anns[0]); assertSame(annotation2, anns[1]); } @Test(groups = { "Functional" }) public void testGetStartGetEnd() { SequenceI sq = new Sequence("test", "ABCDEF"); assertEquals(1, sq.getStart()); assertEquals(6, sq.getEnd()); sq = new Sequence("test", "--AB-C-DEF--"); assertEquals(1, sq.getStart()); assertEquals(6, sq.getEnd()); sq = new Sequence("test", "----"); assertEquals(1, sq.getStart()); assertEquals(0, sq.getEnd()); // ?? } /** * Tests for the method that returns an alignment column position (base 1) for * a given sequence position (base 1). */ @Test(groups = { "Functional" }) public void testFindIndex() { /* * call sequenceChanged() after each test to invalidate any cursor, * forcing the 1-arg findIndex to be executed */ SequenceI sq = new Sequence("test", "ABCDEF"); assertEquals(0, sq.findIndex(0)); sq.sequenceChanged(); assertEquals(1, sq.findIndex(1)); sq.sequenceChanged(); assertEquals(5, sq.findIndex(5)); sq.sequenceChanged(); assertEquals(6, sq.findIndex(6)); sq.sequenceChanged(); assertEquals(6, sq.findIndex(9)); final String aligned = "-A--B-C-D-E-F--"; assertEquals(15, aligned.length()); sq = new Sequence("test/8-13", aligned); assertEquals(2, sq.findIndex(8)); sq.sequenceChanged(); assertEquals(5, sq.findIndex(9)); sq.sequenceChanged(); assertEquals(7, sq.findIndex(10)); // before start returns 0 sq.sequenceChanged(); assertEquals(0, sq.findIndex(0)); sq.sequenceChanged(); assertEquals(0, sq.findIndex(-1)); // beyond end returns last residue column sq.sequenceChanged(); assertEquals(13, sq.findIndex(99)); /* * residue before sequence 'end' but beyond end of sequence returns * length of sequence (last column) (rightly or wrongly!) */ sq = new Sequence("test/8-15", "A-B-C-"); // trailing gap case assertEquals(6, sq.getLength()); sq.sequenceChanged(); assertEquals(sq.getLength(), sq.findIndex(14)); sq = new Sequence("test/8-99", "-A--B-C-D"); // trailing residue case sq.sequenceChanged(); assertEquals(sq.getLength(), sq.findIndex(65)); /* * residue after sequence 'start' but before first residue returns * zero (before first column) (rightly or wrongly!) */ sq = new Sequence("test/8-15", "-A-B-C-"); // leading gap case sq.sequenceChanged(); assertEquals(0, sq.findIndex(3)); sq = new Sequence("test/8-15", "A-B-C-"); // leading residue case sq.sequenceChanged(); assertEquals(0, sq.findIndex(2)); } @Test(groups = { "Functional" }) public void testFindPositions() { SequenceI sq = new Sequence("test/8-13", "-ABC---DE-F--"); /* * invalid inputs */ assertNull(sq.findPositions(6, 5)); assertNull(sq.findPositions(0, 5)); assertNull(sq.findPositions(-1, 5)); /* * all gapped ranges */ assertNull(sq.findPositions(1, 1)); // 1-based columns assertNull(sq.findPositions(5, 5)); assertNull(sq.findPositions(5, 6)); assertNull(sq.findPositions(5, 7)); /* * all ungapped ranges */ assertEquals(new Range(8, 8), sq.findPositions(2, 2)); // A assertEquals(new Range(8, 9), sq.findPositions(2, 3)); // AB assertEquals(new Range(8, 10), sq.findPositions(2, 4)); // ABC assertEquals(new Range(9, 10), sq.findPositions(3, 4)); // BC /* * gap to ungapped range */ assertEquals(new Range(8, 10), sq.findPositions(1, 4)); // ABC assertEquals(new Range(11, 12), sq.findPositions(6, 9)); // DE /* * ungapped to gapped range */ assertEquals(new Range(10, 10), sq.findPositions(4, 5)); // C assertEquals(new Range(9, 13), sq.findPositions(3, 11)); // BCDEF /* * ungapped to ungapped enclosing gaps */ assertEquals(new Range(10, 11), sq.findPositions(4, 8)); // CD assertEquals(new Range(8, 13), sq.findPositions(2, 11)); // ABCDEF /* * gapped to gapped enclosing ungapped */ assertEquals(new Range(8, 10), sq.findPositions(1, 5)); // ABC assertEquals(new Range(11, 12), sq.findPositions(5, 10)); // DE assertEquals(new Range(8, 13), sq.findPositions(1, 13)); // the lot assertEquals(new Range(8, 13), sq.findPositions(1, 99)); } /** * Tests for the method that returns a dataset sequence position (start..) for * an aligned column position (base 0). */ @Test(groups = { "Functional" }) public void testFindPosition() { /* * call sequenceChanged() after each test to invalidate any cursor, * forcing the 1-arg findPosition to be executed */ SequenceI sq = new Sequence("test/8-13", "ABCDEF"); assertEquals(8, sq.findPosition(0)); // Sequence should now hold a cursor at [8, 0] assertEquals("test:Pos8:Col1:startCol1:endCol0:tok0", PA.getValue(sq, "cursor").toString()); SequenceCursor cursor = (SequenceCursor) PA.getValue(sq, "cursor"); int token = (int) PA.getValue(sq, "changeCount"); assertEquals(new SequenceCursor(sq, 8, 1, token), cursor); sq.sequenceChanged(); /* * find F13 at column offset 5, cursor should update to [13, 6] * endColumn is found and saved in cursor */ assertEquals(13, sq.findPosition(5)); cursor = (SequenceCursor) PA.getValue(sq, "cursor"); assertEquals(++token, (int) PA.getValue(sq, "changeCount")); assertEquals(new SequenceCursor(sq, 13, 6, token), cursor); assertEquals("test:Pos13:Col6:startCol1:endCol6:tok1", PA.getValue(sq, "cursor").toString()); // assertEquals(-1, seq.findPosition(6)); // fails sq = new Sequence("test/8-11", "AB-C-D--"); token = (int) PA.getValue(sq, "changeCount"); // 0 assertEquals(8, sq.findPosition(0)); cursor = (SequenceCursor) PA.getValue(sq, "cursor"); assertEquals(new SequenceCursor(sq, 8, 1, token), cursor); assertEquals("test:Pos8:Col1:startCol1:endCol0:tok0", PA.getValue(sq, "cursor").toString()); sq.sequenceChanged(); assertEquals(9, sq.findPosition(1)); cursor = (SequenceCursor) PA.getValue(sq, "cursor"); assertEquals(new SequenceCursor(sq, 9, 2, ++token), cursor); assertEquals("test:Pos9:Col2:startCol1:endCol0:tok1", PA.getValue(sq, "cursor").toString()); sq.sequenceChanged(); // gap position 'finds' residue to the right (not the left as per javadoc) // cursor is set to the last residue position found [B 2] assertEquals(10, sq.findPosition(2)); cursor = (SequenceCursor) PA.getValue(sq, "cursor"); assertEquals(new SequenceCursor(sq, 9, 2, ++token), cursor); assertEquals("test:Pos9:Col2:startCol1:endCol0:tok2", PA.getValue(sq, "cursor").toString()); sq.sequenceChanged(); assertEquals(10, sq.findPosition(3)); cursor = (SequenceCursor) PA.getValue(sq, "cursor"); assertEquals(new SequenceCursor(sq, 10, 4, ++token), cursor); assertEquals("test:Pos10:Col4:startCol1:endCol0:tok3", PA.getValue(sq, "cursor").toString()); sq.sequenceChanged(); // column[4] is the gap after C - returns D11 // cursor is set to [C 4] assertEquals(11, sq.findPosition(4)); cursor = (SequenceCursor) PA.getValue(sq, "cursor"); assertEquals(new SequenceCursor(sq, 10, 4, ++token), cursor); assertEquals("test:Pos10:Col4:startCol1:endCol0:tok4", PA.getValue(sq, "cursor").toString()); sq.sequenceChanged(); assertEquals(11, sq.findPosition(5)); // D cursor = (SequenceCursor) PA.getValue(sq, "cursor"); assertEquals(new SequenceCursor(sq, 11, 6, ++token), cursor); // lastCol has been found and saved in the cursor assertEquals("test:Pos11:Col6:startCol1:endCol6:tok5", PA.getValue(sq, "cursor").toString()); sq.sequenceChanged(); // returns 1 more than sequence length if off the end ?!? assertEquals(12, sq.findPosition(6)); sq.sequenceChanged(); assertEquals(12, sq.findPosition(7)); /* * first findPosition should also set firstResCol in cursor */ sq = new Sequence("test/8-13", "--AB-C-DEF--"); assertEquals(8, sq.findPosition(0)); assertNull(PA.getValue(sq, "cursor")); sq.sequenceChanged(); assertEquals(8, sq.findPosition(1)); assertNull(PA.getValue(sq, "cursor")); sq.sequenceChanged(); assertEquals(8, sq.findPosition(2)); assertEquals("test:Pos8:Col3:startCol3:endCol0:tok2", PA.getValue(sq, "cursor").toString()); sq.sequenceChanged(); assertEquals(9, sq.findPosition(3)); assertEquals("test:Pos9:Col4:startCol3:endCol0:tok3", PA.getValue(sq, "cursor").toString()); sq.sequenceChanged(); // column[4] is a gap, returns next residue pos (C10) // cursor is set to last residue found [B] assertEquals(10, sq.findPosition(4)); assertEquals("test:Pos9:Col4:startCol3:endCol0:tok4", PA.getValue(sq, "cursor").toString()); sq.sequenceChanged(); assertEquals(10, sq.findPosition(5)); assertEquals("test:Pos10:Col6:startCol3:endCol0:tok5", PA.getValue(sq, "cursor").toString()); sq.sequenceChanged(); // column[6] is a gap, returns next residue pos (D11) // cursor is set to last residue found [C] assertEquals(11, sq.findPosition(6)); assertEquals("test:Pos10:Col6:startCol3:endCol0:tok6", PA.getValue(sq, "cursor").toString()); sq.sequenceChanged(); assertEquals(11, sq.findPosition(7)); assertEquals("test:Pos11:Col8:startCol3:endCol0:tok7", PA.getValue(sq, "cursor").toString()); sq.sequenceChanged(); assertEquals(12, sq.findPosition(8)); assertEquals("test:Pos12:Col9:startCol3:endCol0:tok8", PA.getValue(sq, "cursor").toString()); /* * when the last residue column is found, it is set in the cursor */ sq.sequenceChanged(); assertEquals(13, sq.findPosition(9)); assertEquals("test:Pos13:Col10:startCol3:endCol10:tok9", PA.getValue(sq, "cursor").toString()); sq.sequenceChanged(); assertEquals(14, sq.findPosition(10)); assertEquals("test:Pos13:Col10:startCol3:endCol10:tok10", PA.getValue(sq, "cursor").toString()); /* * findPosition for column beyond sequence length * returns 1 more than last residue position */ sq.sequenceChanged(); assertEquals(14, sq.findPosition(11)); assertEquals("test:Pos13:Col10:startCol3:endCol10:tok11", PA.getValue(sq, "cursor").toString()); sq.sequenceChanged(); assertEquals(14, sq.findPosition(99)); assertEquals("test:Pos13:Col10:startCol3:endCol10:tok12", PA.getValue(sq, "cursor").toString()); /* * gapped sequence ending in non-gap */ sq = new Sequence("test/8-13", "--AB-C-DEF"); assertEquals(13, sq.findPosition(9)); assertEquals("test:Pos13:Col10:startCol3:endCol10:tok0", PA.getValue(sq, "cursor").toString()); sq.sequenceChanged(); assertEquals(12, sq.findPosition(8)); // E12 // sequenceChanged() invalidates cursor.lastResidueColumn cursor = (SequenceCursor) PA.getValue(sq, "cursor"); assertEquals("test:Pos12:Col9:startCol3:endCol0:tok1", cursor.toString()); // findPosition with cursor accepts base 1 column values assertEquals(13, ((Sequence) sq).findPosition(10, cursor)); assertEquals(13, sq.findPosition(9)); // F13 // lastResidueColumn has now been found and saved in cursor assertEquals("test:Pos13:Col10:startCol3:endCol10:tok1", PA.getValue(sq, "cursor").toString()); } @Test(groups = { "Functional" }) public void testDeleteChars() { /* * internal delete */ SequenceI sq = new Sequence("test", "ABCDEF"); assertNull(PA.getValue(sq, "datasetSequence")); assertEquals(1, sq.getStart()); assertEquals(6, sq.getEnd()); sq.deleteChars(2, 3); assertEquals("ABDEF", sq.getSequenceAsString()); assertEquals(1, sq.getStart()); assertEquals(5, sq.getEnd()); assertNull(PA.getValue(sq, "datasetSequence")); /* * delete at start */ sq = new Sequence("test", "ABCDEF"); sq.deleteChars(0, 2); assertEquals("CDEF", sq.getSequenceAsString()); assertEquals(3, sq.getStart()); assertEquals(6, sq.getEnd()); assertNull(PA.getValue(sq, "datasetSequence")); sq = new Sequence("test", "ABCDE"); sq.deleteChars(0, 3); assertEquals("DE", sq.getSequenceAsString()); assertEquals(4, sq.getStart()); assertEquals(5, sq.getEnd()); assertNull(PA.getValue(sq, "datasetSequence")); /* * delete at end */ sq = new Sequence("test", "ABCDEF"); sq.deleteChars(4, 6); assertEquals("ABCD", sq.getSequenceAsString()); assertEquals(1, sq.getStart()); assertEquals(4, sq.getEnd()); assertNull(PA.getValue(sq, "datasetSequence")); /* * delete more positions than there are */ sq = new Sequence("test/8-11", "ABCD"); sq.deleteChars(0, 99); assertEquals("", sq.getSequenceAsString()); assertEquals(12, sq.getStart()); // = findPosition(99) ?!? assertEquals(11, sq.getEnd()); sq = new Sequence("test/8-11", "----"); sq.deleteChars(0, 99); // ArrayIndexOutOfBoundsException <= 2.10.2 assertEquals("", sq.getSequenceAsString()); assertEquals(8, sq.getStart()); assertEquals(11, sq.getEnd()); } @Test(groups = { "Functional" }) public void testDeleteChars_withDbRefsAndFeatures() { /* * internal delete - new dataset sequence created * gets a copy of any dbrefs */ SequenceI sq = new Sequence("test", "ABCDEF"); sq.createDatasetSequence(); DBRefEntry dbr1 = new DBRefEntry("Uniprot", "0", "a123"); sq.addDBRef(dbr1); Object ds = PA.getValue(sq, "datasetSequence"); assertNotNull(ds); assertEquals(1, sq.getStart()); assertEquals(6, sq.getEnd()); sq.deleteChars(2, 3); assertEquals("ABDEF", sq.getSequenceAsString()); assertEquals(1, sq.getStart()); assertEquals(5, sq.getEnd()); Object newDs = PA.getValue(sq, "datasetSequence"); assertNotNull(newDs); assertNotSame(ds, newDs); assertNotNull(sq.getDBRefs()); assertEquals(1, sq.getDBRefs().size()); assertNotSame(dbr1, sq.getDBRefs().get(0)); assertEquals(dbr1, sq.getDBRefs().get(0)); /* * internal delete with sequence features * (failure case for JAL-2541) */ sq = new Sequence("test", "ABCDEF"); sq.createDatasetSequence(); SequenceFeature sf1 = new SequenceFeature("Cath", "desc", 2, 4, 2f, "CathGroup"); sq.addSequenceFeature(sf1); ds = PA.getValue(sq, "datasetSequence"); assertNotNull(ds); assertEquals(1, sq.getStart()); assertEquals(6, sq.getEnd()); sq.deleteChars(2, 4); assertEquals("ABEF", sq.getSequenceAsString()); assertEquals(1, sq.getStart()); assertEquals(4, sq.getEnd()); newDs = PA.getValue(sq, "datasetSequence"); assertNotNull(newDs); assertNotSame(ds, newDs); List sfs = sq.getSequenceFeatures(); assertEquals(1, sfs.size()); assertNotSame(sf1, sfs.get(0)); assertEquals(sf1, sfs.get(0)); /* * delete at start - no new dataset sequence created * any sequence features remain as before */ sq = new Sequence("test", "ABCDEF"); sq.createDatasetSequence(); ds = PA.getValue(sq, "datasetSequence"); sf1 = new SequenceFeature("Cath", "desc", 2, 4, 2f, "CathGroup"); sq.addSequenceFeature(sf1); sq.deleteChars(0, 2); assertEquals("CDEF", sq.getSequenceAsString()); assertEquals(3, sq.getStart()); assertEquals(6, sq.getEnd()); assertSame(ds, PA.getValue(sq, "datasetSequence")); sfs = sq.getSequenceFeatures(); assertNotNull(sfs); assertEquals(1, sfs.size()); assertSame(sf1, sfs.get(0)); /* * delete at end - no new dataset sequence created * any dbrefs remain as before */ sq = new Sequence("test", "ABCDEF"); sq.createDatasetSequence(); ds = PA.getValue(sq, "datasetSequence"); dbr1 = new DBRefEntry("Uniprot", "0", "a123"); sq.addDBRef(dbr1); sq.deleteChars(4, 6); assertEquals("ABCD", sq.getSequenceAsString()); assertEquals(1, sq.getStart()); assertEquals(4, sq.getEnd()); assertSame(ds, PA.getValue(sq, "datasetSequence")); assertNotNull(sq.getDBRefs()); assertEquals(1, sq.getDBRefs().size()); assertSame(dbr1, sq.getDBRefs().get(0)); } @Test(groups = { "Functional" }) public void testInsertCharAt() { // non-static methods: SequenceI sq = new Sequence("test", "ABCDEF"); sq.insertCharAt(0, 'z'); assertEquals("zABCDEF", sq.getSequenceAsString()); sq.insertCharAt(2, 2, 'x'); assertEquals("zAxxBCDEF", sq.getSequenceAsString()); // for static method see StringUtilsTest } /** * Test the method that returns an array of aligned sequence positions where * the array index is the data sequence position (both base 0). */ @Test(groups = { "Functional" }) public void testGapMap() { SequenceI sq = new Sequence("test", "-A--B-CD-E--F-"); sq.createDatasetSequence(); assertEquals("[1, 4, 6, 7, 9, 12]", Arrays.toString(sq.gapMap())); } /** * Test the method that gets sequence features, either from the sequence or * its dataset. */ @Test(groups = { "Functional" }) public void testGetSequenceFeatures() { SequenceI sq = new Sequence("test", "GATCAT"); sq.createDatasetSequence(); assertTrue(sq.getSequenceFeatures().isEmpty()); /* * SequenceFeature on sequence */ SequenceFeature sf = new SequenceFeature("Cath", "desc", 2, 4, 2f, null); sq.addSequenceFeature(sf); List sfs = sq.getSequenceFeatures(); assertEquals(1, sfs.size()); assertSame(sf, sfs.get(0)); /* * SequenceFeature on sequence and dataset sequence; returns that on * sequence * * Note JAL-2046: spurious: we have no use case for this at the moment. * This test also buggy - as sf2.equals(sf), no new feature is added */ SequenceFeature sf2 = new SequenceFeature("Cath", "desc", 2, 4, 2f, null); sq.getDatasetSequence().addSequenceFeature(sf2); sfs = sq.getSequenceFeatures(); assertEquals(1, sfs.size()); assertSame(sf, sfs.get(0)); /* * SequenceFeature on dataset sequence only * Note JAL-2046: spurious: we have no use case for setting a non-dataset sequence's feature array to null at the moment. */ sq.setSequenceFeatures(null); assertTrue(sq.getDatasetSequence().getSequenceFeatures().isEmpty()); /* * Corrupt case - no SequenceFeature, dataset's dataset is the original * sequence. Test shows no infinite loop results. */ sq.getDatasetSequence().setSequenceFeatures(null); /** * is there a usecase for this ? setDatasetSequence should throw an error if * this actually occurs. */ try { sq.getDatasetSequence().setDatasetSequence(sq); // loop! Assert.fail("Expected Error to be raised when calling setDatasetSequence with self reference"); } catch (IllegalArgumentException e) { // TODO Jalview error/exception class for raising implementation errors assertTrue(e.getMessage().toLowerCase() .contains("implementation error")); } assertTrue(sq.getSequenceFeatures().isEmpty()); } /** * Test the method that returns an array, indexed by sequence position, whose * entries are the residue positions at the sequence position (or to the right * if a gap) */ @Test(groups = { "Functional" }) public void testFindPositionMap() { /* * Note: Javadoc for findPosition says it returns the residue position to * the left of a gapped position; in fact it returns the position to the * right. Also it returns a non-existent residue position for a gap beyond * the sequence. */ Sequence sq = new Sequence("TestSeq", "AB.C-D E."); int[] map = sq.findPositionMap(); assertEquals(Arrays.toString(new int[] { 1, 2, 3, 3, 4, 4, 5, 5, 6 }), Arrays.toString(map)); } /** * Test for getSubsequence */ @Test(groups = { "Functional" }) public void testGetSubsequence() { SequenceI sq = new Sequence("TestSeq", "ABCDEFG"); sq.createDatasetSequence(); // positions are base 0, end position is exclusive SequenceI subseq = sq.getSubSequence(2, 4); assertEquals("CD", subseq.getSequenceAsString()); // start/end are base 1 positions assertEquals(3, subseq.getStart()); assertEquals(4, subseq.getEnd()); // subsequence shares the full dataset sequence assertSame(sq.getDatasetSequence(), subseq.getDatasetSequence()); } /** * test createDatasetSequence behaves to doc */ @Test(groups = { "Functional" }) public void testCreateDatasetSequence() { SequenceI sq = new Sequence("my", "ASDASD"); sq.addSequenceFeature(new SequenceFeature("type", "desc", 1, 10, 1f, "group")); sq.addDBRef(new DBRefEntry("source", "version", "accession")); assertNull(sq.getDatasetSequence()); assertNotNull(PA.getValue(sq, "sequenceFeatureStore")); assertNotNull(PA.getValue(sq, "dbrefs")); SequenceI rds = sq.createDatasetSequence(); assertNotNull(rds); assertNull(rds.getDatasetSequence()); assertSame(sq.getDatasetSequence(), rds); // sequence features and dbrefs transferred to dataset sequence assertNull(PA.getValue(sq, "sequenceFeatureStore")); assertNull(PA.getValue(sq, "dbrefs")); assertNotNull(PA.getValue(rds, "sequenceFeatureStore")); assertNotNull(PA.getValue(rds, "dbrefs")); } /** * Test for deriveSequence applied to a sequence with a dataset */ @Test(groups = { "Functional" }) public void testDeriveSequence_existingDataset() { Sequence sq = new Sequence("Seq1", "CD"); sq.setDatasetSequence(new Sequence("Seq1", "ABCDEF")); sq.getDatasetSequence().addSequenceFeature( new SequenceFeature("", "", 1, 2, 0f, null)); sq.setStart(3); sq.setEnd(4); sq.setDescription("Test sequence description.."); sq.setVamsasId("TestVamsasId"); sq.addDBRef(new DBRefEntry("PDB", "version0", "1TST")); sq.addDBRef(new DBRefEntry("PDB", "version1", "1PDB")); sq.addDBRef(new DBRefEntry("PDB", "version2", "2PDB")); sq.addDBRef(new DBRefEntry("PDB", "version3", "3PDB")); sq.addDBRef(new DBRefEntry("PDB", "version4", "4PDB")); sq.addPDBId(new PDBEntry("1PDB", "A", Type.PDB, "filePath/test1")); sq.addPDBId(new PDBEntry("1PDB", "B", Type.PDB, "filePath/test1")); sq.addPDBId(new PDBEntry("2PDB", "A", Type.MMCIF, "filePath/test2")); sq.addPDBId(new PDBEntry("2PDB", "B", Type.MMCIF, "filePath/test2")); // these are the same as ones already added DBRefEntry pdb1pdb = new DBRefEntry("PDB", "version1", "1PDB"); DBRefEntry pdb2pdb = new DBRefEntry("PDB", "version2", "2PDB"); List primRefs = Arrays.asList(new DBRefEntry[] { pdb1pdb, pdb2pdb }); sq.getDatasetSequence().addDBRef(pdb1pdb); // should do nothing sq.getDatasetSequence().addDBRef(pdb2pdb); // should do nothing sq.getDatasetSequence().addDBRef( new DBRefEntry("PDB", "version3", "3PDB")); // should do nothing sq.getDatasetSequence().addDBRef( new DBRefEntry("PDB", "version4", "4PDB")); // should do nothing PDBEntry pdbe1a = new PDBEntry("1PDB", "A", Type.PDB, "filePath/test1"); PDBEntry pdbe1b = new PDBEntry("1PDB", "B", Type.PDB, "filePath/test1"); PDBEntry pdbe2a = new PDBEntry("2PDB", "A", Type.MMCIF, "filePath/test2"); PDBEntry pdbe2b = new PDBEntry("2PDB", "B", Type.MMCIF, "filePath/test2"); sq.getDatasetSequence().addPDBId(pdbe1a); sq.getDatasetSequence().addPDBId(pdbe1b); sq.getDatasetSequence().addPDBId(pdbe2a); sq.getDatasetSequence().addPDBId(pdbe2b); /* * test we added pdb entries to the dataset sequence */ Assert.assertEquals(sq.getDatasetSequence().getAllPDBEntries(), Arrays .asList(new PDBEntry[] { pdbe1a, pdbe1b, pdbe2a, pdbe2b }), "PDB Entries were not found on dataset sequence."); /* * we should recover a pdb entry that is on the dataset sequence via PDBEntry */ Assert.assertEquals(pdbe1a, sq.getDatasetSequence().getPDBEntry("1PDB"), "PDB Entry '1PDB' not found on dataset sequence via getPDBEntry."); ArrayList annotsList = new ArrayList<>(); System.out.println(">>>>>> " + sq.getSequenceAsString().length()); annotsList.add(new Annotation("A", "A", 'X', 0.1f)); annotsList.add(new Annotation("A", "A", 'X', 0.1f)); Annotation[] annots = annotsList.toArray(new Annotation[0]); sq.addAlignmentAnnotation(new AlignmentAnnotation("Test annot", "Test annot description", annots)); sq.getDatasetSequence().addAlignmentAnnotation( new AlignmentAnnotation("Test annot", "Test annot description", annots)); Assert.assertEquals(sq.getDescription(), "Test sequence description.."); Assert.assertEquals(sq.getDBRefs().size(), 5); // DBRefs are on dataset // sequence Assert.assertEquals(sq.getAllPDBEntries().size(), 4); Assert.assertNotNull(sq.getAnnotation()); Assert.assertEquals(sq.getAnnotation()[0].annotations.length, 2); Assert.assertEquals(sq.getDatasetSequence().getDBRefs().size(), 5); // same // as // sq.getDBRefs() Assert.assertEquals(sq.getDatasetSequence().getAllPDBEntries().size(), 4); Assert.assertNotNull(sq.getDatasetSequence().getAnnotation()); Sequence derived = (Sequence) sq.deriveSequence(); Assert.assertEquals(derived.getDescription(), "Test sequence description.."); Assert.assertEquals(derived.getDBRefs().size(), 5); // come from dataset Assert.assertEquals(derived.getAllPDBEntries().size(), 4); Assert.assertNotNull(derived.getAnnotation()); Assert.assertEquals(derived.getAnnotation()[0].annotations.length, 2); Assert.assertEquals(derived.getDatasetSequence().getDBRefs().size(), 5); Assert.assertEquals(derived.getDatasetSequence().getAllPDBEntries() .size(), 4); Assert.assertNotNull(derived.getDatasetSequence().getAnnotation()); assertEquals("CD", derived.getSequenceAsString()); assertSame(sq.getDatasetSequence(), derived.getDatasetSequence()); // derived sequence should access dataset sequence features assertNotNull(sq.getSequenceFeatures()); assertEquals(sq.getSequenceFeatures(), derived.getSequenceFeatures()); /* * verify we have primary db refs *just* for PDB IDs with associated * PDBEntry objects */ assertEquals(primRefs, sq.getPrimaryDBRefs()); assertEquals(primRefs, sq.getDatasetSequence().getPrimaryDBRefs()); assertEquals(sq.getPrimaryDBRefs(), derived.getPrimaryDBRefs()); } /** * Test for deriveSequence applied to an ungapped sequence with no dataset */ @Test(groups = { "Functional" }) public void testDeriveSequence_noDatasetUngapped() { SequenceI sq = new Sequence("Seq1", "ABCDEF"); assertEquals(1, sq.getStart()); assertEquals(6, sq.getEnd()); SequenceI derived = sq.deriveSequence(); assertEquals("ABCDEF", derived.getSequenceAsString()); assertEquals("ABCDEF", derived.getDatasetSequence() .getSequenceAsString()); } /** * Test for deriveSequence applied to a gapped sequence with no dataset */ @Test(groups = { "Functional" }) public void testDeriveSequence_noDatasetGapped() { SequenceI sq = new Sequence("Seq1", "AB-C.D EF"); assertEquals(1, sq.getStart()); assertEquals(6, sq.getEnd()); assertNull(sq.getDatasetSequence()); SequenceI derived = sq.deriveSequence(); assertEquals("AB-C.D EF", derived.getSequenceAsString()); assertEquals("ABCDEF", derived.getDatasetSequence() .getSequenceAsString()); } @Test(groups = { "Functional" }) public void testCopyConstructor_noDataset() { SequenceI seq1 = new Sequence("Seq1", "AB-C.D EF"); seq1.setDescription("description"); seq1.addAlignmentAnnotation(new AlignmentAnnotation("label", "desc", 1.3d)); seq1.addSequenceFeature(new SequenceFeature("type", "desc", 22, 33, 12.4f, "group")); seq1.addPDBId(new PDBEntry("1A70", "B", Type.PDB, "File")); seq1.addDBRef(new DBRefEntry("EMBL", "1.2", "AZ12345")); SequenceI copy = new Sequence(seq1); assertNull(copy.getDatasetSequence()); verifyCopiedSequence(seq1, copy); // copy has a copy of the DBRefEntry // this is murky - DBrefs are only copied for dataset sequences // where the test for 'dataset sequence' is 'dataset is null' // but that doesn't distinguish it from an aligned sequence // which has not yet generated a dataset sequence // NB getDBRef looks inside dataset sequence if not null List dbrefs = copy.getDBRefs(); assertEquals(1, dbrefs.size()); assertFalse(dbrefs.get(0) == seq1.getDBRefs().get(0)); assertTrue(dbrefs.get(0).equals(seq1.getDBRefs().get(0))); } @Test(groups = { "Functional" }) public void testCopyConstructor_withDataset() { SequenceI seq1 = new Sequence("Seq1", "AB-C.D EF"); seq1.createDatasetSequence(); seq1.setDescription("description"); seq1.addAlignmentAnnotation(new AlignmentAnnotation("label", "desc", 1.3d)); // JAL-2046 - what is the contract for using a derived sequence's // addSequenceFeature ? seq1.addSequenceFeature(new SequenceFeature("type", "desc", 22, 33, 12.4f, "group")); seq1.addPDBId(new PDBEntry("1A70", "B", Type.PDB, "File")); // here we add DBRef to the dataset sequence: seq1.getDatasetSequence().addDBRef( new DBRefEntry("EMBL", "1.2", "AZ12345")); SequenceI copy = new Sequence(seq1); assertNotNull(copy.getDatasetSequence()); assertSame(copy.getDatasetSequence(), seq1.getDatasetSequence()); verifyCopiedSequence(seq1, copy); // getDBRef looks inside dataset sequence and this is shared, // so holds the same dbref objects List dbrefs = copy.getDBRefs(); assertEquals(1, dbrefs.size()); assertSame(dbrefs.get(0), seq1.getDBRefs().get(0)); } /** * Helper to make assertions about a copied sequence * * @param seq1 * @param copy */ protected void verifyCopiedSequence(SequenceI seq1, SequenceI copy) { // verify basic properties: assertEquals(copy.getName(), seq1.getName()); assertEquals(copy.getDescription(), seq1.getDescription()); assertEquals(copy.getStart(), seq1.getStart()); assertEquals(copy.getEnd(), seq1.getEnd()); assertEquals(copy.getSequenceAsString(), seq1.getSequenceAsString()); // copy has a copy of the annotation: AlignmentAnnotation[] anns = copy.getAnnotation(); assertEquals(1, anns.length); assertFalse(anns[0] == seq1.getAnnotation()[0]); assertEquals(anns[0].label, seq1.getAnnotation()[0].label); assertEquals(anns[0].description, seq1.getAnnotation()[0].description); assertEquals(anns[0].score, seq1.getAnnotation()[0].score); // copy has a copy of the sequence feature: List sfs = copy.getSequenceFeatures(); assertEquals(1, sfs.size()); if (seq1.getDatasetSequence() != null && copy.getDatasetSequence() == seq1.getDatasetSequence()) { assertSame(sfs.get(0), seq1.getSequenceFeatures().get(0)); } else { assertNotSame(sfs.get(0), seq1.getSequenceFeatures().get(0)); } assertEquals(sfs.get(0), seq1.getSequenceFeatures().get(0)); // copy has a copy of the PDB entry Vector pdbs = copy.getAllPDBEntries(); assertEquals(1, pdbs.size()); assertFalse(pdbs.get(0) == seq1.getAllPDBEntries().get(0)); assertTrue(pdbs.get(0).equals(seq1.getAllPDBEntries().get(0))); } @Test(groups = "Functional") public void testGetCharAt() { SequenceI sq = new Sequence("", "abcde"); assertEquals('a', sq.getCharAt(0)); assertEquals('e', sq.getCharAt(4)); assertEquals(' ', sq.getCharAt(5)); assertEquals(' ', sq.getCharAt(-1)); } @Test(groups = { "Functional" }) public void testAddSequenceFeatures() { SequenceI sq = new Sequence("", "abcde"); // type may not be null assertFalse(sq.addSequenceFeature(new SequenceFeature(null, "desc", 4, 8, 0f, null))); assertTrue(sq.addSequenceFeature(new SequenceFeature("Cath", "desc", 4, 8, 0f, null))); // can't add a duplicate feature assertFalse(sq.addSequenceFeature(new SequenceFeature("Cath", "desc", 4, 8, 0f, null))); // can add a different feature assertTrue(sq.addSequenceFeature(new SequenceFeature("Scop", "desc", 4, 8, 0f, null))); // different type assertTrue(sq.addSequenceFeature(new SequenceFeature("Cath", "description", 4, 8, 0f, null)));// different description assertTrue(sq.addSequenceFeature(new SequenceFeature("Cath", "desc", 3, 8, 0f, null))); // different start position assertTrue(sq.addSequenceFeature(new SequenceFeature("Cath", "desc", 4, 9, 0f, null))); // different end position assertTrue(sq.addSequenceFeature(new SequenceFeature("Cath", "desc", 4, 8, 1f, null))); // different score assertTrue(sq.addSequenceFeature(new SequenceFeature("Cath", "desc", 4, 8, Float.NaN, null))); // score NaN assertTrue(sq.addSequenceFeature(new SequenceFeature("Cath", "desc", 4, 8, 0f, "Metal"))); // different group assertEquals(8, sq.getFeatures().getAllFeatures().size()); } /** * Tests for adding (or updating) dbrefs * * @see DBRefEntry#updateFrom(DBRefEntry) */ @Test(groups = { "Functional" }) public void testAddDBRef() { SequenceI sq = new Sequence("", "abcde"); assertNull(sq.getDBRefs()); DBRefEntry dbref = new DBRefEntry("Uniprot", "1", "P00340"); sq.addDBRef(dbref); assertEquals(1, sq.getDBRefs().size()); assertSame(dbref, sq.getDBRefs().get(0)); /* * change of version - new entry */ DBRefEntry dbref2 = new DBRefEntry("Uniprot", "2", "P00340"); sq.addDBRef(dbref2); assertEquals(2, sq.getDBRefs().size()); assertSame(dbref, sq.getDBRefs().get(0)); assertSame(dbref2, sq.getDBRefs().get(1)); /* * matches existing entry - not added */ sq.addDBRef(new DBRefEntry("UNIPROT", "1", "p00340")); assertEquals(2, sq.getDBRefs().size()); /* * different source = new entry */ DBRefEntry dbref3 = new DBRefEntry("UniRef", "1", "p00340"); sq.addDBRef(dbref3); assertEquals(3, sq.getDBRefs().size()); assertSame(dbref3, sq.getDBRefs().get(2)); /* * different ref = new entry */ DBRefEntry dbref4 = new DBRefEntry("UniRef", "1", "p00341"); sq.addDBRef(dbref4); assertEquals(4, sq.getDBRefs().size()); assertSame(dbref4, sq.getDBRefs().get(3)); /* * matching ref with a mapping - map updated */ DBRefEntry dbref5 = new DBRefEntry("UniRef", "1", "p00341"); Mapping map = new Mapping(new MapList(new int[] { 1, 3 }, new int[] { 1, 1 }, 3, 1)); dbref5.setMap(map); sq.addDBRef(dbref5); assertEquals(4, sq.getDBRefs().size()); assertSame(dbref4, sq.getDBRefs().get(3)); assertSame(map, dbref4.getMap()); /* * 'real' version replaces "0" version */ dbref2.setVersion("0"); DBRefEntry dbref6 = new DBRefEntry(dbref2.getSource(), "3", dbref2.getAccessionId()); sq.addDBRef(dbref6); assertEquals(4, sq.getDBRefs().size()); assertSame(dbref2, sq.getDBRefs().get(1)); assertEquals("3", dbref2.getVersion()); /* * 'real' version replaces "source:0" version */ dbref3.setVersion("Uniprot:0"); DBRefEntry dbref7 = new DBRefEntry(dbref3.getSource(), "3", dbref3.getAccessionId()); sq.addDBRef(dbref7); assertEquals(4, sq.getDBRefs().size()); assertSame(dbref3, sq.getDBRefs().get(2)); assertEquals("3", dbref2.getVersion()); } @Test(groups = { "Functional" }) public void testGetPrimaryDBRefs_peptide() { SequenceI sq = new Sequence("aseq", "ASDFKYLMQPRST", 10, 22); // no dbrefs List primaryDBRefs = sq.getPrimaryDBRefs(); assertTrue(primaryDBRefs.isEmpty()); // empty dbrefs sq.setDBRefs(null); primaryDBRefs = sq.getPrimaryDBRefs(); assertTrue(primaryDBRefs.isEmpty()); // primary - uniprot DBRefEntry upentry1 = new DBRefEntry("UNIPROT", "0", "Q04760"); sq.addDBRef(upentry1); // primary - uniprot with congruent map DBRefEntry upentry2 = new DBRefEntry("UNIPROT", "0", "Q04762"); upentry2.setMap(new Mapping(null, new MapList(new int[] { 10, 22 }, new int[] { 10, 22 }, 1, 1))); sq.addDBRef(upentry2); // primary - uniprot with map of enclosing sequence DBRefEntry upentry3 = new DBRefEntry("UNIPROT", "0", "Q04763"); upentry3.setMap(new Mapping(null, new MapList(new int[] { 8, 24 }, new int[] { 8, 24 }, 1, 1))); sq.addDBRef(upentry3); // not primary - uniprot with map of sub-sequence (5') DBRefEntry upentry4 = new DBRefEntry("UNIPROT", "0", "Q04764"); upentry4.setMap(new Mapping(null, new MapList(new int[] { 10, 18 }, new int[] { 10, 18 }, 1, 1))); sq.addDBRef(upentry4); // not primary - uniprot with map that overlaps 3' DBRefEntry upentry5 = new DBRefEntry("UNIPROT", "0", "Q04765"); upentry5.setMap(new Mapping(null, new MapList(new int[] { 12, 22 }, new int[] { 12, 22 }, 1, 1))); sq.addDBRef(upentry5); // not primary - uniprot with map to different coordinates frame DBRefEntry upentry6 = new DBRefEntry("UNIPROT", "0", "Q04766"); upentry6.setMap(new Mapping(null, new MapList(new int[] { 12, 18 }, new int[] { 112, 118 }, 1, 1))); sq.addDBRef(upentry6); // not primary - dbref to 'non-core' database DBRefEntry upentry7 = new DBRefEntry("Pfam", "0", "PF00903"); sq.addDBRef(upentry7); // primary - type is PDB DBRefEntry pdbentry = new DBRefEntry("PDB", "0", "1qip"); sq.addDBRef(pdbentry); // not primary - PDBEntry has no file sq.addDBRef(new DBRefEntry("PDB", "0", "1AAA")); // not primary - no PDBEntry sq.addDBRef(new DBRefEntry("PDB", "0", "1DDD")); // add corroborating PDB entry for primary DBref - // needs to have a file as well as matching ID // note PDB ID is not treated as case sensitive sq.addPDBId(new PDBEntry("1QIP", null, Type.PDB, new File("/blah") .toString())); // not valid DBRef - no file.. sq.addPDBId(new PDBEntry("1AAA", null, null, null)); primaryDBRefs = sq.getPrimaryDBRefs(); assertEquals(4, primaryDBRefs.size()); assertTrue("Couldn't find simple primary reference (UNIPROT)", primaryDBRefs.contains(upentry1)); assertTrue("Couldn't find mapped primary reference (UNIPROT)", primaryDBRefs.contains(upentry2)); assertTrue("Couldn't find mapped context reference (UNIPROT)", primaryDBRefs.contains(upentry3)); assertTrue("Couldn't find expected PDB primary reference", primaryDBRefs.contains(pdbentry)); } @Test(groups = { "Functional" }) public void testGetPrimaryDBRefs_nucleotide() { SequenceI sq = new Sequence("aseq", "TGATCACTCGACTAGCATCAGCATA", 10, 34); // primary - Ensembl DBRefEntry dbr1 = new DBRefEntry("ENSEMBL", "0", "ENSG1234"); sq.addDBRef(dbr1); // not primary - Ensembl 'transcript' mapping of sub-sequence DBRefEntry dbr2 = new DBRefEntry("ENSEMBL", "0", "ENST1234"); dbr2.setMap(new Mapping(null, new MapList(new int[] { 15, 25 }, new int[] { 1, 11 }, 1, 1))); sq.addDBRef(dbr2); // primary - EMBL with congruent map DBRefEntry dbr3 = new DBRefEntry("EMBL", "0", "J1234"); dbr3.setMap(new Mapping(null, new MapList(new int[] { 10, 34 }, new int[] { 10, 34 }, 1, 1))); sq.addDBRef(dbr3); // not primary - to non-core database DBRefEntry dbr4 = new DBRefEntry("CCDS", "0", "J1234"); sq.addDBRef(dbr4); // not primary - to protein DBRefEntry dbr5 = new DBRefEntry("UNIPROT", "0", "Q87654"); sq.addDBRef(dbr5); List primaryDBRefs = sq.getPrimaryDBRefs(); assertEquals(2, primaryDBRefs.size()); assertTrue(primaryDBRefs.contains(dbr1)); assertTrue(primaryDBRefs.contains(dbr3)); } /** * Test the method that updates the list of PDBEntry from any new DBRefEntry * for PDB */ @Test(groups = { "Functional" }) public void testUpdatePDBIds() { PDBEntry pdbe1 = new PDBEntry("3A6S", null, null, null); seq.addPDBId(pdbe1); seq.addDBRef(new DBRefEntry("Ensembl", "8", "ENST1234")); seq.addDBRef(new DBRefEntry("PDB", "0", "1A70")); seq.addDBRef(new DBRefEntry("PDB", "0", "4BQGa")); seq.addDBRef(new DBRefEntry("PDB", "0", "3a6sB")); // 7 is not a valid chain code: seq.addDBRef(new DBRefEntry("PDB", "0", "2GIS7")); seq.updatePDBIds(); List pdbIds = seq.getAllPDBEntries(); assertEquals(4, pdbIds.size()); assertSame(pdbe1, pdbIds.get(0)); // chain code got added to 3A6S: assertEquals("B", pdbe1.getChainCode()); assertEquals("1A70", pdbIds.get(1).getId()); // 4BQGA is parsed into id + chain assertEquals("4BQG", pdbIds.get(2).getId()); assertEquals("a", pdbIds.get(2).getChainCode()); assertEquals("2GIS7", pdbIds.get(3).getId()); assertNull(pdbIds.get(3).getChainCode()); } /** * Test the method that either adds a pdbid or updates an existing one */ @Test(groups = { "Functional" }) public void testAddPDBId() { PDBEntry pdbe = new PDBEntry("3A6S", null, null, null); seq.addPDBId(pdbe); assertEquals(1, seq.getAllPDBEntries().size()); assertSame(pdbe, seq.getPDBEntry("3A6S")); assertSame(pdbe, seq.getPDBEntry("3a6s")); // case-insensitive // add the same entry seq.addPDBId(pdbe); assertEquals(1, seq.getAllPDBEntries().size()); assertSame(pdbe, seq.getPDBEntry("3A6S")); // add an identical entry seq.addPDBId(new PDBEntry("3A6S", null, null, null)); assertEquals(1, seq.getAllPDBEntries().size()); assertSame(pdbe, seq.getPDBEntry("3A6S")); // add a different entry PDBEntry pdbe2 = new PDBEntry("1A70", null, null, null); seq.addPDBId(pdbe2); assertEquals(2, seq.getAllPDBEntries().size()); assertSame(pdbe, seq.getAllPDBEntries().get(0)); assertSame(pdbe2, seq.getAllPDBEntries().get(1)); // update pdbe with chain code, file, type PDBEntry pdbe3 = new PDBEntry("3a6s", "A", Type.PDB, "filepath"); seq.addPDBId(pdbe3); assertEquals(2, seq.getAllPDBEntries().size()); assertSame(pdbe, seq.getAllPDBEntries().get(0)); // updated in situ assertEquals("3A6S", pdbe.getId()); // unchanged assertEquals("A", pdbe.getChainCode()); // updated assertEquals(Type.PDB.toString(), pdbe.getType()); // updated assertEquals("filepath", pdbe.getFile()); // updated assertSame(pdbe2, seq.getAllPDBEntries().get(1)); // add with a different file path PDBEntry pdbe4 = new PDBEntry("3a6s", "A", Type.PDB, "filepath2"); seq.addPDBId(pdbe4); assertEquals(3, seq.getAllPDBEntries().size()); assertSame(pdbe4, seq.getAllPDBEntries().get(2)); // add with a different chain code PDBEntry pdbe5 = new PDBEntry("3a6s", "B", Type.PDB, "filepath"); seq.addPDBId(pdbe5); assertEquals(4, seq.getAllPDBEntries().size()); assertSame(pdbe5, seq.getAllPDBEntries().get(3)); } @Test( groups = { "Functional" }, expectedExceptions = { IllegalArgumentException.class }) public void testSetDatasetSequence_toSelf() { seq.setDatasetSequence(seq); } @Test( groups = { "Functional" }, expectedExceptions = { IllegalArgumentException.class }) public void testSetDatasetSequence_cascading() { SequenceI seq2 = new Sequence("Seq2", "xyz"); seq2.createDatasetSequence(); seq.setDatasetSequence(seq2); } @Test(groups = { "Functional" }) public void testFindFeatures() { SequenceI sq = new Sequence("test/8-16", "-ABC--DEF--GHI--"); sq.createDatasetSequence(); assertTrue(sq.findFeatures(1, 99).isEmpty()); // add non-positional feature SequenceFeature sf0 = new SequenceFeature("Cath", "desc", 0, 0, 2f, null); sq.addSequenceFeature(sf0); // add feature on BCD SequenceFeature sfBCD = new SequenceFeature("Cath", "desc", 9, 11, 2f, null); sq.addSequenceFeature(sfBCD); // add feature on DE SequenceFeature sfDE = new SequenceFeature("Cath", "desc", 11, 12, 2f, null); sq.addSequenceFeature(sfDE); // add contact feature at [B, H] SequenceFeature sfContactBH = new SequenceFeature("Disulphide bond", "desc", 9, 15, 2f, null); sq.addSequenceFeature(sfContactBH); // add contact feature at [F, G] SequenceFeature sfContactFG = new SequenceFeature("Disulfide Bond", "desc", 13, 14, 2f, null); sq.addSequenceFeature(sfContactFG); // add single position feature at [I] SequenceFeature sfI = new SequenceFeature("Disulfide Bond", "desc", 16, 16, null); sq.addSequenceFeature(sfI); // no features in columns 1-2 (-A) List found = sq.findFeatures(1, 2); assertTrue(found.isEmpty()); // columns 1-6 (-ABC--) includes BCD and B/H feature but not DE found = sq.findFeatures(1, 6); assertEquals(2, found.size()); assertTrue(found.contains(sfBCD)); assertTrue(found.contains(sfContactBH)); // columns 5-6 (--) includes (enclosing) BCD but not (contact) B/H feature found = sq.findFeatures(5, 6); assertEquals(1, found.size()); assertTrue(found.contains(sfBCD)); // columns 7-10 (DEF-) includes BCD, DE, F/G but not B/H feature found = sq.findFeatures(7, 10); assertEquals(3, found.size()); assertTrue(found.contains(sfBCD)); assertTrue(found.contains(sfDE)); assertTrue(found.contains(sfContactFG)); // columns 10-11 (--) should find nothing found = sq.findFeatures(10, 11); assertEquals(0, found.size()); // columns 14-14 (I) should find variant feature found = sq.findFeatures(14, 14); assertEquals(1, found.size()); assertTrue(found.contains(sfI)); } @Test(groups = { "Functional" }) public void testFindIndex_withCursor() { Sequence sq = new Sequence("test/8-13", "-A--BCD-EF--"); // find F given A, check cursor is now at the found position assertEquals(10, sq.findIndex(13, new SequenceCursor(sq, 8, 2, 0))); SequenceCursor cursor = (SequenceCursor) PA.getValue(sq, "cursor"); assertEquals(13, cursor.residuePosition); assertEquals(10, cursor.columnPosition); // find A given F assertEquals(2, sq.findIndex(8, new SequenceCursor(sq, 13, 10, 0))); cursor = (SequenceCursor) PA.getValue(sq, "cursor"); assertEquals(8, cursor.residuePosition); assertEquals(2, cursor.columnPosition); // find C given C (no cursor update is done for this case) assertEquals(6, sq.findIndex(10, new SequenceCursor(sq, 10, 6, 0))); SequenceCursor cursor2 = (SequenceCursor) PA.getValue(sq, "cursor"); assertSame(cursor2, cursor); /* * sequence 'end' beyond end of sequence returns length of sequence * (for compatibility with pre-cursor code) * - also verify the cursor is left in a valid state */ sq = new Sequence("test/8-99", "-A--B-C-D-E-F--"); // trailing gap case assertEquals(7, sq.findIndex(10)); // establishes a cursor cursor = (SequenceCursor) PA.getValue(sq, "cursor"); assertEquals(10, cursor.residuePosition); assertEquals(7, cursor.columnPosition); assertEquals(sq.getLength(), sq.findIndex(65)); cursor2 = (SequenceCursor) PA.getValue(sq, "cursor"); assertSame(cursor, cursor2); // not updated for this case! sq = new Sequence("test/8-99", "-A--B-C-D-E-F"); // trailing residue case sq.findIndex(10); // establishes a cursor cursor = (SequenceCursor) PA.getValue(sq, "cursor"); assertEquals(sq.getLength(), sq.findIndex(65)); cursor2 = (SequenceCursor) PA.getValue(sq, "cursor"); assertSame(cursor, cursor2); // not updated for this case! /* * residue after sequence 'start' but before first residue should return * zero (for compatibility with pre-cursor code) */ sq = new Sequence("test/8-15", "-A-B-C-"); // leading gap case sq.findIndex(10); // establishes a cursor cursor = (SequenceCursor) PA.getValue(sq, "cursor"); assertEquals(0, sq.findIndex(3)); cursor2 = (SequenceCursor) PA.getValue(sq, "cursor"); assertSame(cursor, cursor2); // not updated for this case! sq = new Sequence("test/8-15", "A-B-C-"); // leading residue case sq.findIndex(10); // establishes a cursor cursor = (SequenceCursor) PA.getValue(sq, "cursor"); assertEquals(0, sq.findIndex(2)); cursor2 = (SequenceCursor) PA.getValue(sq, "cursor"); assertSame(cursor, cursor2); // not updated for this case! } @Test(groups = { "Functional" }) public void testFindPosition_withCursor() { Sequence sq = new Sequence("test/8-13", "-A--BCD-EF--"); // find F pos given A - lastCol gets set in cursor assertEquals(13, sq.findPosition(10, new SequenceCursor(sq, 8, 2, 0))); assertEquals("test:Pos13:Col10:startCol0:endCol10:tok0", PA.getValue(sq, "cursor").toString()); // find A pos given F - first residue column is saved in cursor assertEquals(8, sq.findPosition(2, new SequenceCursor(sq, 13, 10, 0))); assertEquals("test:Pos8:Col2:startCol2:endCol10:tok0", PA.getValue(sq, "cursor").toString()); // find C pos given C (neither startCol nor endCol is set) assertEquals(10, sq.findPosition(6, new SequenceCursor(sq, 10, 6, 0))); assertEquals("test:Pos10:Col6:startCol0:endCol0:tok0", PA.getValue(sq, "cursor").toString()); // now the grey area - what residue position for a gapped column? JAL-2562 // find 'residue' for column 3 given cursor for D (so working left) // returns B9; cursor is updated to [B 5] assertEquals(9, sq.findPosition(3, new SequenceCursor(sq, 11, 7, 0))); assertEquals("test:Pos9:Col5:startCol0:endCol0:tok0", PA.getValue(sq, "cursor").toString()); // find 'residue' for column 8 given cursor for D (so working right) // returns E12; cursor is updated to [D 7] assertEquals(12, sq.findPosition(8, new SequenceCursor(sq, 11, 7, 0))); assertEquals("test:Pos11:Col7:startCol0:endCol0:tok0", PA.getValue(sq, "cursor").toString()); // find 'residue' for column 12 given cursor for B // returns 1 more than last residue position; cursor is updated to [F 10] // lastCol position is saved in cursor assertEquals(14, sq.findPosition(12, new SequenceCursor(sq, 9, 5, 0))); assertEquals("test:Pos13:Col10:startCol0:endCol10:tok0", PA.getValue(sq, "cursor").toString()); /* * findPosition for column beyond length of sequence * returns 1 more than the last residue position * cursor is set to last real residue position [F 10] */ assertEquals(14, sq.findPosition(99, new SequenceCursor(sq, 8, 2, 0))); assertEquals("test:Pos13:Col10:startCol0:endCol10:tok0", PA.getValue(sq, "cursor").toString()); /* * and the case without a trailing gap */ sq = new Sequence("test/8-13", "-A--BCD-EF"); // first find C from A assertEquals(10, sq.findPosition(6, new SequenceCursor(sq, 8, 2, 0))); SequenceCursor cursor = (SequenceCursor) PA.getValue(sq, "cursor"); assertEquals("test:Pos10:Col6:startCol0:endCol0:tok0", cursor.toString()); // now 'find' 99 from C // cursor is set to [F 10] and saved lastCol assertEquals(14, sq.findPosition(99, cursor)); assertEquals("test:Pos13:Col10:startCol0:endCol10:tok0", PA.getValue(sq, "cursor").toString()); } @Test public void testIsValidCursor() { Sequence sq = new Sequence("Seq", "ABC--DE-F", 8, 13); assertFalse(sq.isValidCursor(null)); /* * cursor is valid if it has valid sequence ref and changeCount token * and positions within the range of the sequence */ int changeCount = (int) PA.getValue(sq, "changeCount"); SequenceCursor cursor = new SequenceCursor(sq, 13, 1, changeCount); assertTrue(sq.isValidCursor(cursor)); /* * column position outside [0 - length] is rejected */ cursor = new SequenceCursor(sq, 13, -1, changeCount); assertFalse(sq.isValidCursor(cursor)); cursor = new SequenceCursor(sq, 13, 10, changeCount); assertFalse(sq.isValidCursor(cursor)); cursor = new SequenceCursor(sq, 7, 8, changeCount); assertFalse(sq.isValidCursor(cursor)); cursor = new SequenceCursor(sq, 14, 2, changeCount); assertFalse(sq.isValidCursor(cursor)); /* * wrong sequence is rejected */ cursor = new SequenceCursor(null, 13, 1, changeCount); assertFalse(sq.isValidCursor(cursor)); cursor = new SequenceCursor(new Sequence("Seq", "abc"), 13, 1, changeCount); assertFalse(sq.isValidCursor(cursor)); /* * wrong token value is rejected */ cursor = new SequenceCursor(sq, 13, 1, changeCount + 1); assertFalse(sq.isValidCursor(cursor)); cursor = new SequenceCursor(sq, 13, 1, changeCount - 1); assertFalse(sq.isValidCursor(cursor)); } @Test(groups = { "Functional" }) public void testFindPosition_withCursorAndEdits() { Sequence sq = new Sequence("test/8-13", "-A--BCD-EF--"); // find F pos given A assertEquals(13, sq.findPosition(10, new SequenceCursor(sq, 8, 2, 0))); int token = (int) PA.getValue(sq, "changeCount"); // 0 SequenceCursor cursor = (SequenceCursor) PA.getValue(sq, "cursor"); assertEquals(new SequenceCursor(sq, 13, 10, token), cursor); /* * setSequence should invalidate the cursor cached by the sequence */ sq.setSequence("-A-BCD-EF---"); // one gap removed assertEquals(8, sq.getStart()); // sanity check assertEquals(11, sq.findPosition(5)); // D11 // cursor should now be at [D 6] cursor = (SequenceCursor) PA.getValue(sq, "cursor"); assertEquals(new SequenceCursor(sq, 11, 6, ++token), cursor); assertEquals(0, cursor.lastColumnPosition); // not yet found assertEquals(13, sq.findPosition(8)); // E13 cursor = (SequenceCursor) PA.getValue(sq, "cursor"); assertEquals(9, cursor.lastColumnPosition); // found /* * deleteChars should invalidate the cached cursor */ sq.deleteChars(2, 5); // delete -BC assertEquals("-AD-EF---", sq.getSequenceAsString()); assertEquals(8, sq.getStart()); // sanity check assertEquals(10, sq.findPosition(4)); // E10 // cursor should now be at [E 5] cursor = (SequenceCursor) PA.getValue(sq, "cursor"); assertEquals(new SequenceCursor(sq, 10, 5, ++token), cursor); /* * Edit to insert gaps should invalidate the cached cursor * insert 2 gaps at column[3] to make -AD---EF--- */ SequenceI[] seqs = new SequenceI[] { sq }; AlignmentI al = new Alignment(seqs); new EditCommand().appendEdit(Action.INSERT_GAP, seqs, 3, 2, al, true); assertEquals("-AD---EF---", sq.getSequenceAsString()); assertEquals(10, sq.findPosition(4)); // E10 // cursor should now be at [D 3] cursor = (SequenceCursor) PA.getValue(sq, "cursor"); assertEquals(new SequenceCursor(sq, 9, 3, ++token), cursor); /* * insertCharAt should invalidate the cached cursor * insert CC at column[4] to make -AD-CC--EF--- */ sq.insertCharAt(4, 2, 'C'); assertEquals("-AD-CC--EF---", sq.getSequenceAsString()); assertEquals(13, sq.findPosition(9)); // F13 // cursor should now be at [F 10] cursor = (SequenceCursor) PA.getValue(sq, "cursor"); assertEquals(new SequenceCursor(sq, 13, 10, ++token), cursor); } @Test(groups = { "Functional" }) public void testGetSequence() { String seqstring = "-A--BCD-EF--"; Sequence sq = new Sequence("test/8-13", seqstring); sq.createDatasetSequence(); assertTrue(Arrays.equals(sq.getSequence(), seqstring.toCharArray())); assertTrue(Arrays.equals(sq.getDatasetSequence().getSequence(), "ABCDEF".toCharArray())); // verify a copy of the sequence array is returned char[] theSeq = (char[]) PA.getValue(sq, "sequence"); assertNotSame(theSeq, sq.getSequence()); theSeq = (char[]) PA.getValue(sq.getDatasetSequence(), "sequence"); assertNotSame(theSeq, sq.getDatasetSequence().getSequence()); } @Test(groups = { "Functional" }) public void testReplace() { String seqstring = "-A--BCD-EF--"; SequenceI sq = new Sequence("test/8-13", seqstring); assertEquals(0, PA.getValue(sq, "changeCount")); assertEquals(0, sq.replace('A', 'A')); // same char assertEquals(seqstring, sq.getSequenceAsString()); assertEquals(0, PA.getValue(sq, "changeCount")); assertEquals(0, sq.replace('X', 'Y')); // not there assertEquals(seqstring, sq.getSequenceAsString()); assertEquals(0, PA.getValue(sq, "changeCount")); assertEquals(1, sq.replace('A', 'K')); assertEquals("-K--BCD-EF--", sq.getSequenceAsString()); assertEquals(1, PA.getValue(sq, "changeCount")); assertEquals(6, sq.replace('-', '.')); assertEquals(".K..BCD.EF..", sq.getSequenceAsString()); assertEquals(2, PA.getValue(sq, "changeCount")); } @Test(groups = { "Functional" }) public void testGapBitset() { SequenceI sq = new Sequence("test/8-13", "-ABC---DE-F--"); BitSet bs = sq.gapBitset(); BitSet expected = new BitSet(); expected.set(0); expected.set(4, 7); expected.set(9); expected.set(11, 13); assertTrue(bs.equals(expected)); } public void testFindFeatures_largeEndPos() { /* * imitate a PDB sequence where end is larger than end position */ SequenceI sq = new Sequence("test", "-ABC--DEF--", 1, 20); sq.createDatasetSequence(); assertTrue(sq.findFeatures(1, 9).isEmpty()); // should be no array bounds exception - JAL-2772 assertTrue(sq.findFeatures(1, 15).isEmpty()); // add feature on BCD SequenceFeature sfBCD = new SequenceFeature("Cath", "desc", 2, 4, 2f, null); sq.addSequenceFeature(sfBCD); // no features in columns 1-2 (-A) List found = sq.findFeatures(1, 2); assertTrue(found.isEmpty()); // columns 1-6 (-ABC--) includes BCD found = sq.findFeatures(1, 6); assertEquals(1, found.size()); assertTrue(found.contains(sfBCD)); // columns 10-11 (--) should find nothing found = sq.findFeatures(10, 11); assertEquals(0, found.size()); } @Test(groups = { "Functional" }) public void testSetName() { SequenceI sq = new Sequence("test", "-ABC---DE-F--"); assertEquals("test", sq.getName()); assertEquals(1, sq.getStart()); assertEquals(6, sq.getEnd()); sq.setName("testing"); assertEquals("testing", sq.getName()); sq.setName("test/8-10"); assertEquals("test", sq.getName()); assertEquals(8, sq.getStart()); assertEquals(13, sq.getEnd()); // note end is recomputed sq.setName("testing/7-99"); assertEquals("testing", sq.getName()); assertEquals(7, sq.getStart()); assertEquals(99, sq.getEnd()); // end may be beyond physical end sq.setName("/2-3"); assertEquals("", sq.getName()); assertEquals(2, sq.getStart()); assertEquals(7, sq.getEnd()); sq.setName("test/"); // invalid assertEquals("test/", sq.getName()); assertEquals(2, sq.getStart()); assertEquals(7, sq.getEnd()); sq.setName("test/6-13/7-99"); assertEquals("test/6-13", sq.getName()); assertEquals(7, sq.getStart()); assertEquals(99, sq.getEnd()); sq.setName("test/0-5"); // 0 is invalid - ignored assertEquals("test/0-5", sq.getName()); assertEquals(7, sq.getStart()); assertEquals(99, sq.getEnd()); sq.setName("test/a-5"); // a is invalid - ignored assertEquals("test/a-5", sq.getName()); assertEquals(7, sq.getStart()); assertEquals(99, sq.getEnd()); sq.setName("test/6-5"); // start > end is invalid - ignored assertEquals("test/6-5", sq.getName()); assertEquals(7, sq.getStart()); assertEquals(99, sq.getEnd()); sq.setName("test/5"); // invalid - ignored assertEquals("test/5", sq.getName()); assertEquals(7, sq.getStart()); assertEquals(99, sq.getEnd()); sq.setName("test/-5"); // invalid - ignored assertEquals("test/-5", sq.getName()); assertEquals(7, sq.getStart()); assertEquals(99, sq.getEnd()); sq.setName("test/5-"); // invalid - ignored assertEquals("test/5-", sq.getName()); assertEquals(7, sq.getStart()); assertEquals(99, sq.getEnd()); sq.setName("test/5-6-7"); // invalid - ignored assertEquals("test/5-6-7", sq.getName()); assertEquals(7, sq.getStart()); assertEquals(99, sq.getEnd()); sq.setName(null); // invalid, gets converted to space assertEquals("", sq.getName()); assertEquals(7, sq.getStart()); assertEquals(99, sq.getEnd()); } @Test(groups = { "Functional" }) public void testCheckValidRange() { Sequence sq = new Sequence("test/7-12", "-ABC---DE-F--"); assertEquals(7, sq.getStart()); assertEquals(12, sq.getEnd()); /* * checkValidRange ensures end is at least the last residue position */ PA.setValue(sq, "end", 2); sq.checkValidRange(); assertEquals(12, sq.getEnd()); /* * end may be beyond the last residue position */ PA.setValue(sq, "end", 22); sq.checkValidRange(); assertEquals(22, sq.getEnd()); } @Test(groups = { "Functional" }) public void testDeleteChars_withGaps() { /* * delete gaps only */ SequenceI sq = new Sequence("test/8-10", "A-B-C"); sq.createDatasetSequence(); assertEquals("ABC", sq.getDatasetSequence().getSequenceAsString()); sq.deleteChars(1, 2); // delete first gap assertEquals("AB-C", sq.getSequenceAsString()); assertEquals(8, sq.getStart()); assertEquals(10, sq.getEnd()); assertEquals("ABC", sq.getDatasetSequence().getSequenceAsString()); /* * delete gaps and residues at start (no new dataset sequence) */ sq = new Sequence("test/8-10", "A-B-C"); sq.createDatasetSequence(); sq.deleteChars(0, 3); // delete A-B assertEquals("-C", sq.getSequenceAsString()); assertEquals(10, sq.getStart()); assertEquals(10, sq.getEnd()); assertEquals("ABC", sq.getDatasetSequence().getSequenceAsString()); /* * delete gaps and residues at end (no new dataset sequence) */ sq = new Sequence("test/8-10", "A-B-C"); sq.createDatasetSequence(); sq.deleteChars(2, 5); // delete B-C assertEquals("A-", sq.getSequenceAsString()); assertEquals(8, sq.getStart()); assertEquals(8, sq.getEnd()); assertEquals("ABC", sq.getDatasetSequence().getSequenceAsString()); /* * delete gaps and residues internally (new dataset sequence) * first delete from gap to residue */ sq = new Sequence("test/8-10", "A-B-C"); sq.createDatasetSequence(); sq.deleteChars(1, 3); // delete -B assertEquals("A-C", sq.getSequenceAsString()); assertEquals(8, sq.getStart()); assertEquals(9, sq.getEnd()); assertEquals("AC", sq.getDatasetSequence().getSequenceAsString()); assertEquals(8, sq.getDatasetSequence().getStart()); assertEquals(9, sq.getDatasetSequence().getEnd()); /* * internal delete from gap to gap */ sq = new Sequence("test/8-10", "A-B-C"); sq.createDatasetSequence(); sq.deleteChars(1, 4); // delete -B- assertEquals("AC", sq.getSequenceAsString()); assertEquals(8, sq.getStart()); assertEquals(9, sq.getEnd()); assertEquals("AC", sq.getDatasetSequence().getSequenceAsString()); assertEquals(8, sq.getDatasetSequence().getStart()); assertEquals(9, sq.getDatasetSequence().getEnd()); /* * internal delete from residue to residue */ sq = new Sequence("test/8-10", "A-B-C"); sq.createDatasetSequence(); sq.deleteChars(2, 3); // delete B assertEquals("A--C", sq.getSequenceAsString()); assertEquals(8, sq.getStart()); assertEquals(9, sq.getEnd()); assertEquals("AC", sq.getDatasetSequence().getSequenceAsString()); assertEquals(8, sq.getDatasetSequence().getStart()); assertEquals(9, sq.getDatasetSequence().getEnd()); } /** * Test the code used to locate the reference sequence ruler origin */ @Test(groups = { "Functional" }) public void testLocateVisibleStartofSequence() { // create random alignment AlignmentGenerator gen = new AlignmentGenerator(false); AlignmentI al = gen.generate(50, 20, 123, 5, 5); HiddenColumns cs = al.getHiddenColumns(); ColumnSelection colsel = new ColumnSelection(); SequenceI seq = new Sequence("RefSeq", "-A-SD-ASD--E---"); assertEquals(2, seq.findIndex(seq.getStart())); // no hidden columns assertEquals(seq.findIndex(seq.getStart()) - 1, seq.firstResidueOutsideIterator(cs.iterator())); // hidden column on gap after end of sequence - should not affect bounds colsel.hideSelectedColumns(13, al.getHiddenColumns()); assertEquals(seq.findIndex(seq.getStart()) - 1, seq.firstResidueOutsideIterator(cs.iterator())); cs.revealAllHiddenColumns(colsel); // hidden column on gap before beginning of sequence - should vis bounds by // one colsel.hideSelectedColumns(0, al.getHiddenColumns()); assertEquals(seq.findIndex(seq.getStart()) - 2, cs.absoluteToVisibleColumn( seq.firstResidueOutsideIterator(cs.iterator()))); cs.revealAllHiddenColumns(colsel); // hide columns around most of sequence - leave one residue remaining cs.hideColumns(1, 3); cs.hideColumns(6, 11); Iterator it = cs.getVisContigsIterator(0, 6, false); assertEquals("-D", seq.getSequenceStringFromIterator(it)); // cs.getVisibleSequenceStrings(0, 5, new SequenceI[] // { seq })[0]); assertEquals(4, seq.firstResidueOutsideIterator(cs.iterator())); cs.revealAllHiddenColumns(colsel); // hide whole sequence - should just get location of hidden region // containing sequence cs.hideColumns(1, 11); assertEquals(0, seq.firstResidueOutsideIterator(cs.iterator())); cs.revealAllHiddenColumns(colsel); cs.hideColumns(0, 15); assertEquals(0, seq.firstResidueOutsideIterator(cs.iterator())); SequenceI seq2 = new Sequence("RefSeq2", "-------A-SD-ASD--E---"); cs.revealAllHiddenColumns(colsel); cs.hideColumns(7, 17); assertEquals(0, seq2.firstResidueOutsideIterator(cs.iterator())); cs.revealAllHiddenColumns(colsel); cs.hideColumns(3, 17); assertEquals(0, seq2.firstResidueOutsideIterator(cs.iterator())); cs.revealAllHiddenColumns(colsel); cs.hideColumns(3, 19); assertEquals(0, seq2.firstResidueOutsideIterator(cs.iterator())); cs.revealAllHiddenColumns(colsel); cs.hideColumns(0, 0); assertEquals(1, seq.firstResidueOutsideIterator(cs.iterator())); cs.revealAllHiddenColumns(colsel); cs.hideColumns(0, 1); assertEquals(3, seq.firstResidueOutsideIterator(cs.iterator())); cs.revealAllHiddenColumns(colsel); cs.hideColumns(0, 2); assertEquals(3, seq.firstResidueOutsideIterator(cs.iterator())); cs.revealAllHiddenColumns(colsel); cs.hideColumns(1, 1); assertEquals(3, seq.firstResidueOutsideIterator(cs.iterator())); cs.revealAllHiddenColumns(colsel); cs.hideColumns(1, 2); assertEquals(3, seq.firstResidueOutsideIterator(cs.iterator())); cs.revealAllHiddenColumns(colsel); cs.hideColumns(1, 3); assertEquals(4, seq.firstResidueOutsideIterator(cs.iterator())); cs.revealAllHiddenColumns(colsel); cs.hideColumns(0, 2); cs.hideColumns(5, 6); assertEquals(3, seq.firstResidueOutsideIterator(cs.iterator())); cs.revealAllHiddenColumns(colsel); cs.hideColumns(0, 2); cs.hideColumns(5, 6); cs.hideColumns(9, 10); assertEquals(3, seq.firstResidueOutsideIterator(cs.iterator())); cs.revealAllHiddenColumns(colsel); cs.hideColumns(0, 2); cs.hideColumns(7, 11); assertEquals(3, seq.firstResidueOutsideIterator(cs.iterator())); cs.revealAllHiddenColumns(colsel); cs.hideColumns(2, 4); cs.hideColumns(7, 11); assertEquals(1, seq.firstResidueOutsideIterator(cs.iterator())); cs.revealAllHiddenColumns(colsel); cs.hideColumns(2, 4); cs.hideColumns(7, 12); assertEquals(1, seq.firstResidueOutsideIterator(cs.iterator())); cs.revealAllHiddenColumns(colsel); cs.hideColumns(1, 11); assertEquals(0, seq.firstResidueOutsideIterator(cs.iterator())); cs.revealAllHiddenColumns(colsel); cs.hideColumns(0, 12); assertEquals(0, seq.firstResidueOutsideIterator(cs.iterator())); cs.revealAllHiddenColumns(colsel); cs.hideColumns(0, 4); cs.hideColumns(6, 12); assertEquals(0, seq.firstResidueOutsideIterator(cs.iterator())); cs.revealAllHiddenColumns(colsel); cs.hideColumns(0, 1); cs.hideColumns(3, 12); assertEquals(0, seq.firstResidueOutsideIterator(cs.iterator())); cs.revealAllHiddenColumns(colsel); cs.hideColumns(3, 14); cs.hideColumns(17, 19); assertEquals(0, seq2.firstResidueOutsideIterator(cs.iterator())); cs.revealAllHiddenColumns(colsel); cs.hideColumns(3, 7); cs.hideColumns(9, 14); cs.hideColumns(17, 19); assertEquals(0, seq2.firstResidueOutsideIterator(cs.iterator())); cs.revealAllHiddenColumns(colsel); cs.hideColumns(0, 1); cs.hideColumns(3, 4); cs.hideColumns(6, 8); cs.hideColumns(10, 12); assertEquals(0, seq.firstResidueOutsideIterator(cs.iterator())); } }