X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fio%2FStockholmFileTest.java;h=e86c8ad79f8852be2aa0ecb0a2a4208eaf546928;hb=483abbfd34bb2e47698f4cb04e21531c2b11924a;hp=86ab0b2ad98c1d142910f493c78b4606ed2e0fa3;hpb=a3ada1606e51721c83f4b271539bf8d443443ff5;p=jalview.git diff --git a/test/jalview/io/StockholmFileTest.java b/test/jalview/io/StockholmFileTest.java index 86ab0b2..e86c8ad 100644 --- a/test/jalview/io/StockholmFileTest.java +++ b/test/jalview/io/StockholmFileTest.java @@ -1,213 +1,455 @@ +/* + * 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.io; -import static org.junit.Assert.*; -import jalview.datamodel.Alignment; +import static org.testng.AssertJUnit.assertEquals; +import static org.testng.AssertJUnit.assertNotNull; +import static org.testng.AssertJUnit.assertTrue; +import static org.testng.AssertJUnit.fail; + import jalview.datamodel.AlignmentAnnotation; import jalview.datamodel.AlignmentI; +import jalview.datamodel.Annotation; import jalview.datamodel.SequenceFeature; import jalview.datamodel.SequenceI; +import jalview.gui.JvOptionPane; import java.io.File; -import java.io.IOException; -import java.io.InputStream; +import java.util.Arrays; +import java.util.BitSet; +import java.util.HashMap; +import java.util.List; +import java.util.Map; +import java.util.regex.Matcher; +import java.util.regex.Pattern; -import org.junit.Test; +import org.testng.Assert; +import org.testng.annotations.BeforeClass; +import org.testng.annotations.Test; public class StockholmFileTest { - public static void main(String argv[]) + @BeforeClass(alwaysRun = true) + public void setUpJvOptionPane() { - try { - new StockholmFileTest().pfamFileIO(); - - } catch (Exception x) - { - x.printStackTrace(); - } + JvOptionPane.setInteractiveMode(false); + JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION); } - static String PfamFile = "examples/PF00111_seed.stk", RfamFile="examples/RF00031_folded.stk"; - @Test + static String PfamFile = "examples/PF00111_seed.stk", + RfamFile = "examples/RF00031_folded.stk", + RnaSSTestFile = "examples/rna_ss_test.stk"; + + @Test(groups = { "Functional" }) public void pfamFileIO() throws Exception { - test(new File(PfamFile)); - AppletFormatAdapter af = new AppletFormatAdapter(); - AlignmentI al = af.readFile(PfamFile, af.FILE, new IdentifyFile().Identify(PfamFile, af.FILE)); - int numpdb=0; - for (SequenceI sq:al.getSequences()) + testFileIOwithFormat(new File(PfamFile), FileFormat.Stockholm, -1, 0, + false, false, false); + } + + @Test(groups = { "Functional" }) + public void pfamFileDataExtraction() throws Exception + { + AppletFormatAdapter af = new AppletFormatAdapter(); + AlignmentI al = af.readFile(PfamFile, DataSourceType.FILE, + new IdentifyFile().identify(PfamFile, DataSourceType.FILE)); + int numpdb = 0; + for (SequenceI sq : al.getSequences()) + { + if (sq.getAllPDBEntries() != null) { - if (sq.getPDBId()!=null) - { - numpdb+=sq.getPDBId().size(); - } + numpdb += sq.getAllPDBEntries().size(); } - assertTrue("PF00111 seed alignment has at least 1 PDB file, but the reader found none.",numpdb>0); + } + assertTrue( + "PF00111 seed alignment has at least 1 PDB file, but the reader found none.", + numpdb > 0); } - @Test + + @Test(groups = { "Functional" }) public void rfamFileIO() throws Exception { - test(new File(RfamFile)); + testFileIOwithFormat(new File(RfamFile), FileFormat.Stockholm, 2, 1, + false, false, false); } - private void test(File f) + /** + * test alignment data in given file can be imported, exported and reimported + * with no dataloss + * + * @param f + * - source datafile (IdentifyFile.identify() should work with it) + * @param ioformat + * - label for IO class used to write and read back in the data from + * f + * @param ignoreFeatures + * @param ignoreRowVisibility + * @param allowNullAnnotations + */ + + public static void testFileIOwithFormat(File f, FileFormatI ioformat, + int naliannot, int nminseqann, boolean ignoreFeatures, + boolean ignoreRowVisibility, boolean allowNullAnnotations) { System.out.println("Reading file: " + f); String ff = f.getPath(); try { - Alignment al = new AppletFormatAdapter().readFile(ff, AppletFormatAdapter.FILE, - new IdentifyFile().Identify(ff, AppletFormatAdapter.FILE)); - + AppletFormatAdapter rf = new AppletFormatAdapter(); + + AlignmentI al = rf.readFile(ff, DataSourceType.FILE, + new IdentifyFile().identify(ff, DataSourceType.FILE)); + + assertNotNull("Couldn't read supplied alignment data.", al); + + // make sure dataset is initialised ? not sure about this for (int i = 0; i < al.getSequencesArray().length; ++i) { - al.getSequenceAt(i).setDatasetSequence(al.getSequenceAt(i)); + al.getSequenceAt(i).createDatasetSequence(); + } + String outputfile = rf.formatSequences(ioformat, al, true); + System.out.println("Output file in '" + ioformat + "':\n" + + outputfile + "\n< -1) + { + assertEquals("Number of alignment annotations", naliannot, + numaliannot); } - AlignFile stFile = new StockholmFile(al); - stFile.setSeqs(al.getSequencesArray()); - String stockholmoutput = stFile.print(); - Alignment al_input = new AppletFormatAdapter().readFile(stockholmoutput, - AppletFormatAdapter.PASTE, "STH"); - if (al != null && al_input != null) + assertTrue( + "Number of sequence associated annotations wasn't at least " + + nminseqann, numsqswithali >= nminseqann); + + } catch (Exception e) + { + e.printStackTrace(); + assertTrue("Couln't format the alignment for output file.", false); + } + } + + /** + * assert alignment equivalence + * + * @param al + * 'original' + * @param al_input + * 'secondary' or generated alignment from some datapreserving + * transformation + * @param ignoreFeatures + * when true, differences in sequence feature annotation are ignored + */ + public static void testAlignmentEquivalence(AlignmentI al, + AlignmentI al_input, boolean ignoreFeatures) + { + testAlignmentEquivalence(al, al_input, ignoreFeatures, false, false); + } + + /** + * assert alignment equivalence - uses special comparators for RNA structure + * annotation rows. + * + * @param al + * 'original' + * @param al_input + * 'secondary' or generated alignment from some datapreserving + * transformation + * @param ignoreFeatures + * when true, differences in sequence feature annotation are ignored + * + * @param ignoreRowVisibility + * when true, do not fail if there are differences in the visibility + * of annotation rows + * @param allowNullAnnotation + * when true, positions in alignment annotation that are null will be + * considered equal to positions containing annotation where + * Annotation.isWhitespace() returns true. + * + */ + public static void testAlignmentEquivalence(AlignmentI al, + AlignmentI al_input, boolean ignoreFeatures, + boolean ignoreRowVisibility, boolean allowNullAnnotation) + { + assertNotNull("Original alignment was null", al); + assertNotNull("Generated alignment was null", al_input); + + assertTrue("Alignment dimension mismatch: original: " + al.getHeight() + + "x" + al.getWidth() + ", generated: " + al_input.getHeight() + + "x" + al_input.getWidth(), + al.getHeight() == al_input.getHeight() + && al.getWidth() == al_input.getWidth()); + + // check Alignment annotation + AlignmentAnnotation[] aa_new = al_input.getAlignmentAnnotation(); + AlignmentAnnotation[] aa_original = al.getAlignmentAnnotation(); + + // note - at moment we do not distinguish between alignment without any + // annotation rows and alignment with no annotation row vector + // we might want to revise this in future + int aa_new_size = (aa_new == null ? 0 : aa_new.length); + int aa_original_size = (aa_original == null ? 0 : aa_original.length); + Map orig_groups = new HashMap<>(); + Map new_groups = new HashMap<>(); + + if (aa_new != null && aa_original != null) + { + for (int i = 0; i < aa_original.length; i++) { - System.out.println("Alignment contains: " + al.getHeight() - + " and " + al_input.getHeight() + " sequences; " - + al.getWidth() + " and " + al_input.getWidth() - + " columns."); - AlignmentAnnotation[] aa_new = al_input.getAlignmentAnnotation(); - AlignmentAnnotation[] aa_original = al.getAlignmentAnnotation(); - - // check Alignment annotation - if (aa_new != null && aa_original != null) + if (aa_new.length > i) { - System.out.println("Alignment contains: " + aa_new.length - + " and " + aa_original.length - + " alignment annotation(s)"); - for (int i = 0; i < aa_original.length; i++) + assertEqualSecondaryStructure( + "Different alignment annotation at position " + i, + aa_original[i], aa_new[i], allowNullAnnotation); + // compare graphGroup or graph properties - needed to verify JAL-1299 + assertEquals("Graph type not identical.", aa_original[i].graph, + aa_new[i].graph); + if (!ignoreRowVisibility) + { + assertEquals("Visibility not identical.", + aa_original[i].visible, + aa_new[i].visible); + } + assertEquals("Threshold line not identical.", + aa_original[i].threshold, aa_new[i].threshold); + // graphGroup may differ, but pattern should be the same + Integer o_ggrp = new Integer(aa_original[i].graphGroup + 2); + Integer n_ggrp = new Integer(aa_new[i].graphGroup + 2); + BitSet orig_g = orig_groups.get(o_ggrp); + BitSet new_g = new_groups.get(n_ggrp); + if (orig_g == null) + { + orig_groups.put(o_ggrp, orig_g = new BitSet()); + } + if (new_g == null) { - assertTrue("Different alignment annotation",equalss(aa_original[i], aa_new[i])); - + new_groups.put(n_ggrp, new_g = new BitSet()); } + assertEquals("Graph Group pattern differs at annotation " + i, + orig_g, new_g); + orig_g.set(i); + new_g.set(i); } + else + { + System.err.println("No matching annotation row for " + + aa_original[i].toString()); + } + } + } + assertEquals( + "Generated and imported alignment have different annotation sets", + aa_original_size, aa_new_size); + + // check sequences, annotation and features + SequenceI[] seq_original = new SequenceI[al.getSequencesArray().length]; + seq_original = al.getSequencesArray(); + SequenceI[] seq_new = new SequenceI[al_input.getSequencesArray().length]; + seq_new = al_input.getSequencesArray(); + List sequenceFeatures_original; + List sequenceFeatures_new; + AlignmentAnnotation annot_original, annot_new; + // + for (int i = 0; i < al.getSequencesArray().length; i++) + { + String name = seq_original[i].getName(); + int start = seq_original[i].getStart(); + int end = seq_original[i].getEnd(); + System.out.println("Check sequence: " + name + "/" + start + "-" + + end); - // check sequences, annotation and features - SequenceI[] seq_original = new SequenceI[al.getSequencesArray().length]; - seq_original = al.getSequencesArray(); - SequenceI[] seq_new = new SequenceI[al_input.getSequencesArray().length]; - seq_new = al_input.getSequencesArray(); - SequenceFeature[] sequenceFeatures_original, sequenceFeatures_new; - AlignmentAnnotation annot_original, annot_new; - // - for (int i = 0; i < al.getSequencesArray().length; i++) + // search equal sequence + for (int in = 0; in < al_input.getSequencesArray().length; in++) + { + if (name.equals(seq_new[in].getName()) + && start == seq_new[in].getStart() + && end == seq_new[in].getEnd()) { - String name = seq_original[i].getName(); - int start = seq_original[i].getStart(); - int end = seq_original[i].getEnd(); - System.out.println("Check sequence: " + name + "/" + start + "-" - + end); - - // search equal sequence - for (int in = 0; in < al_input.getSequencesArray().length; in++) + String ss_original = seq_original[i].getSequenceAsString(); + String ss_new = seq_new[in].getSequenceAsString(); + assertEquals("The sequences " + name + "/" + start + "-" + end + + " are not equal", ss_original, ss_new); + + assertTrue( + "Sequence Features were not equivalent" + + (ignoreFeatures ? " ignoring." : ""), + ignoreFeatures + || (seq_original[i].getSequenceFeatures() == null && seq_new[in] + .getSequenceFeatures() == null) + || (seq_original[i].getSequenceFeatures() != null && seq_new[in] + .getSequenceFeatures() != null)); + // compare sequence features + if (seq_original[i].getSequenceFeatures() != null + && seq_new[in].getSequenceFeatures() != null) { - if (name.equals(seq_new[in].getName()) - && start == seq_new[in].getStart() - && end == seq_new[in].getEnd()) - { - String ss_original = seq_original[i].getSequenceAsString(); - String ss_new = seq_new[in].getSequenceAsString(); - assertTrue("The sequences " + name + "/" + start - + "-" + end + " are not equal", ss_original.equals(ss_new)); - - assertTrue("Sequence Features were not equivalent", (seq_original[i].getSequenceFeatures()==null && seq_new[in].getSequenceFeatures()==null) || (seq_original[i].getSequenceFeatures()!=null && seq_new[in].getSequenceFeatures()!=null)); - // compare sequence features - if (seq_original[i].getSequenceFeatures() != null - && seq_new[in].getSequenceFeatures() != null) - { - System.out.println("There are feature!!!"); - sequenceFeatures_original = new SequenceFeature[seq_original[i] - .getSequenceFeatures().length]; - sequenceFeatures_original = seq_original[i] - .getSequenceFeatures(); - sequenceFeatures_new = new SequenceFeature[seq_new[in] - .getSequenceFeatures().length]; - sequenceFeatures_new = seq_new[in].getSequenceFeatures(); - - assertTrue("different number of features", seq_original[i].getSequenceFeatures().length == seq_new[in] - .getSequenceFeatures().length); - - for (int feat = 0; feat < seq_original[i] - .getSequenceFeatures().length; feat++) - { - assertTrue("Different features",sequenceFeatures_original[feat] - .equals(sequenceFeatures_new[feat])); - } - } + System.out.println("There are feature!!!"); + sequenceFeatures_original = seq_original[i] + .getSequenceFeatures(); + sequenceFeatures_new = seq_new[in].getSequenceFeatures(); - // compare alignment annotation - if (al.getSequenceAt(i).getAnnotation() != null - && al_input.getSequenceAt(in).getAnnotation() != null) - { - for (int j = 0; j < al.getSequenceAt(i).getAnnotation().length; j++) - { - if (al.getSequenceAt(i).getAnnotation()[j] != null - && al_input.getSequenceAt(in).getAnnotation()[j] != null) - { - annot_original = al.getSequenceAt(i).getAnnotation()[j]; - annot_new = al_input.getSequenceAt(in).getAnnotation()[j]; - assertTrue("Different annotation", equalss(annot_original, annot_new)); - } - } - } - else if (al.getSequenceAt(i).getAnnotation() == null - && al_input.getSequenceAt(in).getAnnotation() == null) - { - System.out.println("No annotations"); - } - else if (al.getSequenceAt(i).getAnnotation() != null - && al_input.getSequenceAt(in).getAnnotation() == null) + assertEquals("different number of features", seq_original[i] + .getSequenceFeatures().size(), seq_new[in] + .getSequenceFeatures().size()); + + for (int feat = 0; feat < seq_original[i].getSequenceFeatures() + .size(); feat++) + { + assertEquals("Different features", + sequenceFeatures_original.get(feat), + sequenceFeatures_new.get(feat)); + } + } + // compare alignment annotation + if (al.getSequenceAt(i).getAnnotation() != null + && al_input.getSequenceAt(in).getAnnotation() != null) + { + for (int j = 0; j < al.getSequenceAt(i).getAnnotation().length; j++) + { + if (al.getSequenceAt(i).getAnnotation()[j] != null + && al_input.getSequenceAt(in).getAnnotation()[j] != null) { - assertTrue("Annotations differed between sequences ("+al.getSequenceAt(i).getName()+") and ("+al_input.getSequenceAt(i).getName()+")", false); + annot_original = al.getSequenceAt(i).getAnnotation()[j]; + annot_new = al_input.getSequenceAt(in).getAnnotation()[j]; + assertEqualSecondaryStructure( + "Different annotation elements", annot_original, + annot_new, allowNullAnnotation); } - break; } } + else if (al.getSequenceAt(i).getAnnotation() == null + && al_input.getSequenceAt(in).getAnnotation() == null) + { + System.out.println("No annotations"); + } + else if (al.getSequenceAt(i).getAnnotation() != null + && al_input.getSequenceAt(in).getAnnotation() == null) + { + fail("Annotations differed between sequences (" + + al.getSequenceAt(i).getName() + ") and (" + + al_input.getSequenceAt(i).getName() + ")"); + } + break; } } - else - { - assertTrue("Couldn't read alignment", false); - } - } catch (Exception e) - { - e.printStackTrace(); - assertTrue("Couln't format the alignment for output file.", false); } } - /* - * compare annotations + /** + * compare two annotation rows, with special support for secondary structure + * comparison. With RNA, only the value and the secondaryStructure symbols are + * compared, displayCharacter and description are ignored. Annotations where + * Annotation.isWhitespace() is true are always considered equal. + * + * @param message + * - not actually used yet.. + * @param annot_or + * - the original annotation + * @param annot_new + * - the one compared to the original annotation + * @param allowNullEquivalence + * when true, positions in alignment annotation that are null will be + * considered equal to non-null positions for which + * Annotation.isWhitespace() is true. */ - private boolean equalss(AlignmentAnnotation annot_or, - AlignmentAnnotation annot_new) + private static void assertEqualSecondaryStructure(String message, + AlignmentAnnotation annot_or, AlignmentAnnotation annot_new, + boolean allowNullEqivalence) { + // TODO: test to cover this assert behaves correctly for all allowed + // variations of secondary structure annotation row equivalence if (annot_or.annotations.length != annot_new.annotations.length) { - return false; + fail("Different lengths for annotation row elements: " + + annot_or.annotations.length + "!=" + + annot_new.annotations.length); } + boolean isRna = annot_or.isRNA(); + assertTrue("Expected " + (isRna ? " valid RNA " : " no RNA ") + + " secondary structure in the row.", + isRna == annot_new.isRNA()); for (int i = 0; i < annot_or.annotations.length; i++) { - if (annot_or.annotations[i] != null - && annot_new.annotations[i] != null) + Annotation an_or = annot_or.annotations[i], an_new = annot_new.annotations[i]; + if (an_or != null && an_new != null) { - // Jim's comment - shouldn't the conditional here be using || not && for all these clauses ? - if (!annot_or.annotations[i].displayCharacter - .equals(annot_new.annotations[i].displayCharacter) - && annot_or.annotations[i].secondaryStructure != annot_new.annotations[i].secondaryStructure - && !annot_or.annotations[i].description - .equals(annot_new.annotations[i].description)) + + if (isRna) { - return false; + if (an_or.secondaryStructure != an_new.secondaryStructure + || ((Float.isNaN(an_or.value) != Float + .isNaN(an_new.value)) || an_or.value != an_new.value)) + { + fail("Different RNA secondary structure at column " + i + + " expected: [" + annot_or.annotations[i].toString() + + "] but got: [" + annot_new.annotations[i].toString() + + "]"); + } + } + else + { + // not RNA secondary structure, so expect all elements to match... + if ((an_or.isWhitespace() != an_new.isWhitespace()) + || !an_or.displayCharacter.trim().equals( + an_new.displayCharacter.trim()) + || !("" + an_or.secondaryStructure).trim().equals( + ("" + an_new.secondaryStructure).trim()) + || (an_or.description != an_new.description && !((an_or.description == null && an_new.description + .trim().length() == 0) + || (an_new.description == null && an_or.description + .trim().length() == 0) || an_or.description + .trim().equals(an_new.description.trim()))) + || !((Float.isNaN(an_or.value) && Float + .isNaN(an_new.value)) || an_or.value == an_new.value)) + { + fail("Annotation Element Mismatch\nElement " + i + + " in original: " + annot_or.annotations[i].toString() + + "\nElement " + i + " in new: " + + annot_new.annotations[i].toString()); + } } } else if (annot_or.annotations[i] == null @@ -217,9 +459,389 @@ public class StockholmFileTest } else { - return false; + if (allowNullEqivalence) + { + if (an_or != null && an_or.isWhitespace()) + + { + continue; + } + if (an_new != null && an_new.isWhitespace()) + { + continue; + } + } + // need also to test for null in one, non-SS annotation in other... + fail("Annotation Element Mismatch\nElement " + i + " in original: " + + (an_or == null ? "is null" : an_or.toString()) + + "\nElement " + i + " in new: " + + (an_new == null ? "is null" : an_new.toString())); + } + } + } + + /** + * @see assertEqualSecondaryStructure - test if two secondary structure + * annotations are not equal + * @param message + * @param an_orig + * @param an_new + * @param allowNullEquivalence + */ + public static void assertNotEqualSecondaryStructure(String message, + AlignmentAnnotation an_orig, AlignmentAnnotation an_new, + boolean allowNullEquivalence) + { + boolean thrown = false; + try + { + assertEqualSecondaryStructure("", an_orig, an_new, + allowNullEquivalence); + } catch (AssertionError af) + { + thrown = true; + } + if (!thrown) + { + fail("Expected difference for [" + an_orig + "] and [" + an_new + "]"); + } + } + private AlignmentAnnotation makeAnnot(Annotation ae) + { + return new AlignmentAnnotation("label", "description", new Annotation[] + { ae }); + } + + @Test(groups={"Functional"}) + public void testAnnotationEquivalence() + { + AlignmentAnnotation one = makeAnnot(new Annotation("", "", ' ', 1)); + AlignmentAnnotation anotherOne = makeAnnot(new Annotation("", "", ' ', + 1)); + AlignmentAnnotation sheet = makeAnnot(new Annotation("","",'E',0f)); + AlignmentAnnotation anotherSheet = makeAnnot(new Annotation("","",'E',0f)); + AlignmentAnnotation sheetWithLabel = makeAnnot(new Annotation("1", "", + 'E', 0f)); + AlignmentAnnotation anotherSheetWithLabel = makeAnnot(new Annotation( + "1", "", 'E', 0f)); + AlignmentAnnotation rnaNoDC = makeAnnot(new Annotation("","",'<',0f)); + AlignmentAnnotation anotherRnaNoDC = makeAnnot(new Annotation("","",'<',0f)); + AlignmentAnnotation rnaWithDC = makeAnnot(new Annotation("B", "", '<', + 0f)); + AlignmentAnnotation anotherRnaWithDC = makeAnnot(new Annotation("B", + "", '<', 0f)); + + // check self equivalence + for (boolean allowNull : new boolean[] { true, false }) + { + assertEqualSecondaryStructure("Should be equal", one, anotherOne, + allowNull); + assertEqualSecondaryStructure("Should be equal", sheet, anotherSheet, + allowNull); + assertEqualSecondaryStructure("Should be equal", sheetWithLabel, + anotherSheetWithLabel, allowNull); + assertEqualSecondaryStructure("Should be equal", rnaNoDC, + anotherRnaNoDC, allowNull); + assertEqualSecondaryStructure("Should be equal", rnaWithDC, + anotherRnaWithDC, allowNull); + // display character doesn't matter for RNA structure (for 2.10.2) + assertEqualSecondaryStructure("Should be equal", rnaWithDC, rnaNoDC, + allowNull); + assertEqualSecondaryStructure("Should be equal", rnaNoDC, rnaWithDC, + allowNull); + } + + // verify others are different + List aaSet = Arrays.asList(one, sheet, + sheetWithLabel, rnaWithDC); + for (int p = 0; p < aaSet.size(); p++) + { + for (int q = 0; q < aaSet.size(); q++) + { + if (p != q) + { + assertNotEqualSecondaryStructure("Should be different", + aaSet.get(p), aaSet.get(q), false); + } + else + { + assertEqualSecondaryStructure("Should be same", aaSet.get(p), + aaSet.get(q), false); + assertEqualSecondaryStructure("Should be same", aaSet.get(p), + aaSet.get(q), true); + assertNotEqualSecondaryStructure( + "Should be different to empty anot", aaSet.get(p), + makeAnnot(Annotation.EMPTY_ANNOTATION), false); + assertNotEqualSecondaryStructure( + "Should be different to empty annot", + makeAnnot(Annotation.EMPTY_ANNOTATION), aaSet.get(q), + true); + assertNotEqualSecondaryStructure("Should be different to null", + aaSet.get(p), makeAnnot(null), false); + assertNotEqualSecondaryStructure("Should be different to null", + makeAnnot(null), aaSet.get(q), true); + } } } - return true; + + // test null + + } + + String aliFile = ">Dm\nAAACCCUUUUACACACGGGAAAGGG"; + String annFile = "JALVIEW_ANNOTATION\n# Created: Thu May 04 11:16:52 BST 2017\n\n" + + "SEQUENCE_REF\tDm\nNO_GRAPH\tsecondary structure\tsecondary structure\t" + + "(|(|(|(|, .|, .|, .|, .|)|)|)|)|\t0.0\nROWPROPERTIES\t" + + "secondary structure\tscaletofit=true\tshowalllabs=true\tcentrelabs=false"; + + String annFileCurlyWuss = "JALVIEW_ANNOTATION\n# Created: Thu May 04 11:16:52 BST 2017\n\n" + + "SEQUENCE_REF\tDm\nNO_GRAPH\tsecondary structure\tsecondary structure\t" + + "(|(|(|(||{|{||{|{||)|)|)|)||}|}|}|}|\t0.0\nROWPROPERTIES\t" + + "secondary structure\tscaletofit=true\tshowalllabs=true\tcentrelabs=false"; + String annFileFullWuss = "JALVIEW_ANNOTATION\n# Created: Thu May 04 11:16:52 BST 2017\n\n" + + "SEQUENCE_REF\tDm\nNO_GRAPH\tsecondary structure\tsecondary structure\t" + + "(|(|(|(||{|{||[|[||)|)|)|)||}|}|]|]|\t0.0\nROWPROPERTIES\t" + + "secondary structure\tscaletofit=true\tshowalllabs=true\tcentrelabs=false"; + + @Test(groups = { "Functional" }) + public void secondaryStructureForRNASequence() throws Exception + { + roundTripSSForRNA(aliFile, annFile); + } + + @Test(groups = { "Functional" }) + public void curlyWUSSsecondaryStructureForRNASequence() throws Exception + { + roundTripSSForRNA(aliFile, annFileCurlyWuss); + } + + @Test(groups = { "Functional" }) + public void fullWUSSsecondaryStructureForRNASequence() throws Exception + { + roundTripSSForRNA(aliFile, annFileFullWuss); + } + + @Test(groups = { "Functional" }) + public void detectWussBrackets() + { + for (char ch : new char[] { '{', '}', '[', ']', '(', ')', '<', '>' }) + { + Assert.assertTrue(StockholmFile.RNASS_BRACKETS.indexOf(ch) >= 0, + "Didn't recognise '" + ch + "' as a WUSS bracket"); + } + for (char ch : new char[] { '@', '!', '*', ' ', '-', '.' }) + { + Assert.assertFalse(StockholmFile.RNASS_BRACKETS.indexOf(ch) >= 0, + "Shouldn't recognise '" + ch + "' as a WUSS bracket"); + } + } + private static void roundTripSSForRNA(String aliFile, String annFile) + throws Exception + { + AlignmentI al = new AppletFormatAdapter().readFile(aliFile, + DataSourceType.PASTE, jalview.io.FileFormat.Fasta); + AnnotationFile aaf = new AnnotationFile(); + aaf.readAnnotationFile(al, annFile, DataSourceType.PASTE); + al.getAlignmentAnnotation()[0].visible = true; + + // TODO: create a better 'save as ' pattern + StockholmFile sf = new StockholmFile(al); + + String stockholmFile = sf.print(al.getSequencesArray(), true); + + AlignmentI newAl = new AppletFormatAdapter().readFile(stockholmFile, + DataSourceType.PASTE, jalview.io.FileFormat.Stockholm); + // AlignmentUtils.showOrHideSequenceAnnotations(newAl.getViewport() + // .getAlignment(), Arrays.asList("Secondary Structure"), newAl + // .getViewport().getAlignment().getSequences(), true, true); + testAlignmentEquivalence(al, newAl, true, true, true); + + } + + // this is the single sequence alignment and the SS annotations equivalent to + // the ones in file RnaSSTestFile + String aliFileRnaSS = ">Test.sequence/1-14\n" + + "GUACAAAAAAAAAA"; + String annFileRnaSSAlphaChars = "JALVIEW_ANNOTATION\n" + + "# Created: Thu Aug 02 14:54:57 BST 2018\n" + "\n" + + "NO_GRAPH\tSecondary Structure\tSecondary Structure\t<,<|(,(|E,E|H,H|B,B|h,h|e,e|b,b|(,(|E,E|),)|e,e|),)|>,>|\t2.0\n" + + "\n" + + "ROWPROPERTIES\tSecondary Structure\tscaletofit=true\tshowalllabs=true\tcentrelabs=false\n" + + "\n" + "\n" + "ALIGNMENT\tID=RNA.SS.TEST\tTP=RNA;"; + String wrongAnnFileRnaSSAlphaChars = "JALVIEW_ANNOTATION\n" + + "# Created: Thu Aug 02 14:54:57 BST 2018\n" + "\n" + + "NO_GRAPH\tSecondary Structure\tSecondary Structure\t<,<|(,(|H,H|E,E|B,B|h,h|e,e|b,b|(,(|E,E|),)|e,e|),)|>,>|\t2.0\n" + + "\n" + + "ROWPROPERTIES\tSecondary Structure\tscaletofit=true\tshowalllabs=true\tcentrelabs=false\n" + + "\n" + "\n" + "ALIGNMENT\tID=RNA.SS.TEST\tTP=RNA;"; + @Test(groups = { "Functional" }) + public void stockholmFileRnaSSAlphaChars() throws Exception + { + AppletFormatAdapter af = new AppletFormatAdapter(); + AlignmentI al = af.readFile(RnaSSTestFile, DataSourceType.FILE, + jalview.io.FileFormat.Stockholm); + Iterable aai = al.findAnnotations(null, null, + "Secondary Structure"); + AlignmentAnnotation aa = aai.iterator().next(); + Assert.assertTrue(aa.isRNA(), + "'" + RnaSSTestFile + "' not recognised as RNA SS"); + Assert.assertTrue(aa.isValidStruc(), + "'" + RnaSSTestFile + "' not recognised as valid structure"); + Annotation[] as = aa.annotations; + char[] As = new char[as.length]; + for (int i = 0; i < as.length; i++) + { + As[i] = as[i].secondaryStructure; + } + char[] shouldBe = { '<', '(', 'E', 'H', 'B', 'h', 'e', 'b', '(', 'E', + ')', 'e', ')', '>' }; + Assert.assertTrue( + Arrays.equals(As, shouldBe), + "Annotation is " + new String(As) + " but should be " + + new String(shouldBe)); + + // this should result in the same RNA SS Annotations + AlignmentI newAl = new AppletFormatAdapter().readFile( + aliFileRnaSS, + DataSourceType.PASTE, jalview.io.FileFormat.Fasta); + AnnotationFile aaf = new AnnotationFile(); + aaf.readAnnotationFile(newAl, annFileRnaSSAlphaChars, + DataSourceType.PASTE); + + Assert.assertTrue( + testRnaSSAnnotationsEquivalent(al.getAlignmentAnnotation()[0], + newAl.getAlignmentAnnotation()[0]), + "RNA SS Annotations SHOULD be pair-wise equivalent (but apparently aren't): \n" + + "RNA SS A 1:" + al.getAlignmentAnnotation()[0] + "\n" + + "RNA SS A 2:" + newAl.getAlignmentAnnotation()[0]); + + // this should NOT result in the same RNA SS Annotations + newAl = new AppletFormatAdapter().readFile( + aliFileRnaSS, DataSourceType.PASTE, + jalview.io.FileFormat.Fasta); + aaf = new AnnotationFile(); + aaf.readAnnotationFile(newAl, wrongAnnFileRnaSSAlphaChars, + DataSourceType.PASTE); + + boolean mismatch = testRnaSSAnnotationsEquivalent(al.getAlignmentAnnotation()[0], + newAl.getAlignmentAnnotation()[0]); + Assert.assertFalse(mismatch, + "RNA SS Annotations SHOULD NOT be pair-wise equivalent (but apparently are): \n" + + "RNA SS A 1:" + al.getAlignmentAnnotation()[0] + "\n" + + "RNA SS A 2:" + newAl.getAlignmentAnnotation()[0]); + } + + private static boolean testRnaSSAnnotationsEquivalent( + AlignmentAnnotation a1, + AlignmentAnnotation a2) + { + return a1.rnaSecondaryStructureEquivalent(a2); + } + + String annFileRnaSSWithSpaceChars = "JALVIEW_ANNOTATION\n" + + "# Created: Thu Aug 02 14:54:57 BST 2018\n" + "\n" + + "NO_GRAPH\tSecondary Structure\tSecondary Structure\t<,<|.,.|H,H| , |B,B|h,h| , |b,b|(,(|E,E|.,.|e,e|),)|>,>|\t2.0\n" + + "\n" + + "ROWPROPERTIES\tSecondary Structure\tscaletofit=true\tshowalllabs=true\tcentrelabs=false\n" + + "\n" + "\n" + "ALIGNMENT\tID=RNA.SS.TEST\tTP=RNA;"; + String annFileRnaSSWithoutSpaceChars = "JALVIEW_ANNOTATION\n" + + "# Created: Thu Aug 02 14:54:57 BST 2018\n" + "\n" + + "NO_GRAPH\tSecondary Structure\tSecondary Structure\t<,<|.,.|H,H|.,.|B,B|h,h|.,.|b,b|(,(|E,E|.,.|e,e|),)|>,>|\t2.0\n" + + "\n" + + "ROWPROPERTIES\tSecondary Structure\tscaletofit=true\tshowalllabs=true\tcentrelabs=false\n" + + "\n" + "\n" + "ALIGNMENT\tID=RNA.SS.TEST\tTP=RNA;"; + + String wrongAnnFileRnaSSWithoutSpaceChars = "JALVIEW_ANNOTATION\n" + + "# Created: Thu Aug 02 14:54:57 BST 2018\n" + "\n" + + "NO_GRAPH\tSecondary Structure\tSecondary Structure\t<,<|.,.|H,H|Z,Z|B,B|h,h|z,z|b,b|(,(|E,E|.,.|e,e|),)|>,>|\t2.0\n" + + "\n" + + "ROWPROPERTIES\tSecondary Structure\tscaletofit=true\tshowalllabs=true\tcentrelabs=false\n" + + "\n" + "\n" + "ALIGNMENT\tID=RNA.SS.TEST\tTP=RNA;"; + + @Test(groups = { "Functional" }) + public void stockholmFileRnaSSSpaceChars() throws Exception + { + AlignmentI alWithSpaces = new AppletFormatAdapter().readFile( + aliFileRnaSS, DataSourceType.PASTE, + jalview.io.FileFormat.Fasta); + AnnotationFile afWithSpaces = new AnnotationFile(); + afWithSpaces.readAnnotationFile(alWithSpaces, + annFileRnaSSWithSpaceChars, DataSourceType.PASTE); + + Iterable aaiWithSpaces = alWithSpaces + .findAnnotations(null, null, "Secondary Structure"); + AlignmentAnnotation aaWithSpaces = aaiWithSpaces.iterator().next(); + Assert.assertTrue(aaWithSpaces.isRNA(), + "'" + aaWithSpaces + "' not recognised as RNA SS"); + Assert.assertTrue(aaWithSpaces.isValidStruc(), + "'" + aaWithSpaces + "' not recognised as valid structure"); + Annotation[] annWithSpaces = aaWithSpaces.annotations; + char[] As = new char[annWithSpaces.length]; + for (int i = 0; i < annWithSpaces.length; i++) + { + As[i] = annWithSpaces[i].secondaryStructure; + } + // check all spaces and dots are spaces in the internal representation + char[] shouldBe = { '<', ' ', 'H', ' ', 'B', 'h', ' ', 'b', '(', 'E', + ' ', 'e', ')', '>' }; + Assert.assertTrue(Arrays.equals(As, shouldBe), "Annotation is " + + new String(As) + " but should be " + new String(shouldBe)); + + // this should result in the same RNA SS Annotations + AlignmentI alWithoutSpaces = new AppletFormatAdapter().readFile( + aliFileRnaSS, DataSourceType.PASTE, + jalview.io.FileFormat.Fasta); + AnnotationFile afWithoutSpaces = new AnnotationFile(); + afWithoutSpaces.readAnnotationFile(alWithoutSpaces, + annFileRnaSSWithoutSpaceChars, + DataSourceType.PASTE); + + Assert.assertTrue( + testRnaSSAnnotationsEquivalent( + alWithSpaces.getAlignmentAnnotation()[0], + alWithoutSpaces.getAlignmentAnnotation()[0]), + "RNA SS Annotations SHOULD be pair-wise equivalent (but apparently aren't): \n" + + "RNA SS A 1:" + + alWithSpaces.getAlignmentAnnotation()[0] + .getRnaSecondaryStructure() + + "\n" + "RNA SS A 2:" + + alWithoutSpaces.getAlignmentAnnotation()[0] + .getRnaSecondaryStructure()); + + // this should NOT result in the same RNA SS Annotations + AlignmentI wrongAlWithoutSpaces = new AppletFormatAdapter().readFile( + aliFileRnaSS, DataSourceType.PASTE, + jalview.io.FileFormat.Fasta); + AnnotationFile wrongAfWithoutSpaces = new AnnotationFile(); + wrongAfWithoutSpaces.readAnnotationFile(wrongAlWithoutSpaces, + wrongAnnFileRnaSSWithoutSpaceChars, + DataSourceType.PASTE); + + Assert.assertFalse( + testRnaSSAnnotationsEquivalent( + alWithSpaces.getAlignmentAnnotation()[0], + wrongAlWithoutSpaces.getAlignmentAnnotation()[0]), + "RNA SS Annotations SHOULD NOT be pair-wise equivalent (but apparently are): \n" + + "RNA SS A 1:" + + alWithSpaces.getAlignmentAnnotation()[0] + .getRnaSecondaryStructure() + + "\n" + "RNA SS A 2:" + + wrongAlWithoutSpaces.getAlignmentAnnotation()[0] + .getRnaSecondaryStructure()); + + // check no spaces in the output + // TODO: create a better 'save as ' pattern + alWithSpaces.getAlignmentAnnotation()[0].visible = true; + StockholmFile sf = new StockholmFile(alWithSpaces); + + String stockholmFile = sf.print(alWithSpaces.getSequencesArray(), true); + Pattern noSpacesInRnaSSAnnotation = Pattern + .compile("\\n#=GC SS_cons\\s+\\S{14}\\n"); + Matcher m = noSpacesInRnaSSAnnotation.matcher(stockholmFile); + boolean matches = m.find(); + Assert.assertTrue(matches, + "StockholmFile output does not contain expected output (may contain spaces):\n" + + stockholmFile); + } }