X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=blobdiff_plain;f=test%2Fjalview%2Fio%2FStockholmFileTest.java;h=b1995ab5945b4d1d99ff1df0b135d5aacd9483b1;hp=e9edd1bd5aeb2013b173853659d630a230cd44fa;hb=0ae965fc73680bdc69b06986c060ff17342c4787;hpb=c784b1b825eada577c28a1ce0c807e6fed1fb392 diff --git a/test/jalview/io/StockholmFileTest.java b/test/jalview/io/StockholmFileTest.java index e9edd1b..b1995ab 100644 --- a/test/jalview/io/StockholmFileTest.java +++ b/test/jalview/io/StockholmFileTest.java @@ -20,26 +20,36 @@ */ package jalview.io; +import static org.testng.Assert.assertTrue; 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.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.testng.Assert; import org.testng.annotations.BeforeClass; import org.testng.annotations.Test; +import jalview.datamodel.Alignment; +import jalview.datamodel.AlignmentAnnotation; +import jalview.datamodel.AlignmentI; +import jalview.datamodel.Annotation; +import jalview.datamodel.DBRefEntry; +import jalview.datamodel.Sequence; +import jalview.datamodel.SequenceFeature; +import jalview.datamodel.SequenceI; +import jalview.gui.JvOptionPane; +import jalview.util.DBRefUtils; + public class StockholmFileTest { @@ -51,12 +61,14 @@ public class StockholmFileTest } static String PfamFile = "examples/PF00111_seed.stk", - RfamFile = "examples/RF00031_folded.stk"; + RfamFile = "examples/RF00031_folded.stk", + RnaSSTestFile = "examples/rna_ss_test.stk"; @Test(groups = { "Functional" }) public void pfamFileIO() throws Exception { - testFileIOwithFormat(new File(PfamFile), FileFormat.Stockholm, -1, 0); + testFileIOwithFormat(new File(PfamFile), FileFormat.Stockholm, -1, 0, + false, false, false); } @Test(groups = { "Functional" }) @@ -81,7 +93,48 @@ public class StockholmFileTest @Test(groups = { "Functional" }) public void rfamFileIO() throws Exception { - testFileIOwithFormat(new File(RfamFile), FileFormat.Stockholm, 2, 1); + testFileIOwithFormat(new File(RfamFile), FileFormat.Stockholm, 2, 1, + false, false, false); + } + + /** + * JAL-3529 - verify uniprot refs for sequences are output for sequences + * retrieved via Pfam + */ + @Test(groups = { "Functional" }) + public void dbrefOutput() throws Exception + { + // sequences retrieved in a Pfam domain alignment also have a PFAM database + // reference + SequenceI sq = new Sequence("FER2_SPIOL", "AASSDDDFFF"); + sq.addDBRef(new DBRefEntry("UNIPROT", "1", "P00224")); + sq.addDBRef(new DBRefEntry("PFAM", "1", "P00224.1")); + sq.addDBRef(new DBRefEntry("PFAM", "1", "PF00111")); + AppletFormatAdapter af = new AppletFormatAdapter(); + String toStockholm = af.formatSequences(FileFormat.Stockholm, + new Alignment(new SequenceI[] + { sq }), false); + System.out.println(toStockholm); + // bleh - java.util.Regex sucks + assertTrue( + Pattern.compile( + "^#=GS\\s+FER2_SPIOL(/\\d+-\\d+)?\\s+AC\\s+P00224$", + Pattern.MULTILINE).matcher(toStockholm).find(), + "Couldn't locate UNIPROT Accession in generated Stockholm file."); + AlignmentI fromStockholm = af.readFile(toStockholm, + DataSourceType.PASTE, FileFormat.Stockholm); + SequenceI importedSeq = fromStockholm.getSequenceAt(0); + assertTrue(importedSeq.getDBRefs().size() == 1, + "Expected just one database reference to be added to sequence."); + assertTrue( + importedSeq.getDBRefs().get(0).getAccessionId() + .indexOf(" ") == -1, + "Spaces were found in accession ID."); + List dbrefs = DBRefUtils.searchRefs(importedSeq.getDBRefs(), + "P00224"); + assertTrue(dbrefs.size() == 1, + "Couldn't find Uniprot DBRef on re-imported sequence."); + } /** @@ -93,10 +146,14 @@ public class StockholmFileTest * @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) + int naliannot, int nminseqann, boolean ignoreFeatures, + boolean ignoreRowVisibility, boolean allowNullAnnotations) { System.out.println("Reading file: " + f); String ff = f.getPath(); @@ -115,8 +172,8 @@ public class StockholmFileTest al.getSequenceAt(i).createDatasetSequence(); } String outputfile = rf.formatSequences(ioformat, al, true); - System.out.println("Output file in '" + ioformat + "':\n" - + outputfile + "\n<= nminseqann); + + nminseqann, + numsqswithali >= nminseqann); } catch (Exception e) { @@ -174,26 +233,60 @@ public class StockholmFileTest 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(), + 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(); + boolean expectProteinSS = !al.isNucleotide(); + assertTrue( + "Alignments not both " + + (al.isNucleotide() ? "nucleotide" : "protein"), + al_input.isNucleotide() == al.isNucleotide()); // 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(); + Map orig_groups = new HashMap<>(); + Map new_groups = new HashMap<>(); if (aa_new != null && aa_original != null) { @@ -203,17 +296,27 @@ public class StockholmFileTest { assertEqualSecondaryStructure( "Different alignment annotation at position " + i, - aa_original[i], aa_new[i]); + aa_original[i], aa_new[i], allowNullAnnotation); + if (aa_original[i].hasIcons) + { + assertTrue( + "Secondary structure expected to be " + + (expectProteinSS ? "protein" : "nucleotide"), + expectProteinSS == !aa_original[i].isRNA()); + } // compare graphGroup or graph properties - needed to verify JAL-1299 assertEquals("Graph type not identical.", aa_original[i].graph, aa_new[i].graph); - assertEquals("Visibility not identical.", aa_original[i].visible, - aa_new[i].visible); + 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); + Integer o_ggrp = Integer.valueOf(aa_original[i].graphGroup + 2); + Integer n_ggrp = Integer.valueOf(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) @@ -243,9 +346,11 @@ public class StockholmFileTest // 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]; + SequenceI[] seq_new = new SequenceI[al_input + .getSequencesArray().length]; seq_new = al_input.getSequencesArray(); - SequenceFeature[] sequenceFeatures_original, sequenceFeatures_new; + List sequenceFeatures_original; + List sequenceFeatures_new; AlignmentAnnotation annot_original, annot_new; // for (int i = 0; i < al.getSequencesArray().length; i++) @@ -253,8 +358,8 @@ public class StockholmFileTest 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); + System.out + .println("Check sequence: " + name + "/" + start + "-" + end); // search equal sequence for (int in = 0; in < al_input.getSequencesArray().length; in++) @@ -272,48 +377,48 @@ public class StockholmFileTest "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)); + || (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(); assertEquals("different number of features", - seq_original[i].getSequenceFeatures().length, - seq_new[in].getSequenceFeatures().length); + seq_original[i].getSequenceFeatures().size(), + seq_new[in].getSequenceFeatures().size()); - for (int feat = 0; feat < seq_original[i].getSequenceFeatures().length; feat++) + for (int feat = 0; feat < seq_original[i].getSequenceFeatures() + .size(); feat++) { assertEquals("Different features", - sequenceFeatures_original[feat], - sequenceFeatures_new[feat]); + 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++) + 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) + 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]; assertEqualSecondaryStructure( "Different annotation elements", annot_original, - annot_new); + annot_new, allowNullAnnotation); } } } @@ -335,9 +440,26 @@ public class StockholmFileTest } } + /** + * 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 static void assertEqualSecondaryStructure(String message, - AlignmentAnnotation annot_or, - AlignmentAnnotation annot_new) + 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 @@ -348,19 +470,23 @@ public class StockholmFileTest + annot_new.annotations.length); } boolean isRna = annot_or.isRNA(); - assertTrue("Expected " + (isRna ? " valid RNA " : " no RNA ") - + " secondary structure in the row.", + 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++) { - Annotation an_or = annot_or.annotations[i], an_new = annot_new.annotations[i]; + Annotation an_or = annot_or.annotations[i], + an_new = annot_new.annotations[i]; if (an_or != null && an_new != null) { if (isRna) { if (an_or.secondaryStructure != an_new.secondaryStructure - || an_or.value != an_new.value) + || ((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() @@ -371,15 +497,23 @@ public class StockholmFileTest else { // not RNA secondary structure, so expect all elements to match... - if (!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())))) + 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() @@ -395,17 +529,395 @@ public class StockholmFileTest } else { - fail("Annotation Element Mismatch\nElement " - + i - + " in original: " - + (annot_or.annotations[i] == null ? "is null" - : annot_or.annotations[i].toString()) - + "\nElement " - + i - + " in new: " - + (annot_new.annotations[i] == null ? "is null" - : annot_new.annotations[i].toString())); + 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); + } } } + + // 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); + } }