X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fio%2FStockholmFileTest.java;h=4273e6ce0dc88888a27ac965cac61e2c8a96650c;hb=ffa5c07d90b4a933762a5d9faa0578c11693d63a;hp=e9edd1bd5aeb2013b173853659d630a230cd44fa;hpb=c784b1b825eada577c28a1ce0c807e6fed1fb392;p=jalview.git diff --git a/test/jalview/io/StockholmFileTest.java b/test/jalview/io/StockholmFileTest.java index e9edd1b..4273e6c 100644 --- a/test/jalview/io/StockholmFileTest.java +++ b/test/jalview/io/StockholmFileTest.java @@ -33,10 +33,13 @@ 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 org.testng.Assert; import org.testng.annotations.BeforeClass; import org.testng.annotations.Test; @@ -56,7 +59,8 @@ public class StockholmFileTest @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 +85,8 @@ 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); } /** @@ -93,10 +98,14 @@ 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(); @@ -130,7 +139,8 @@ public class StockholmFileTest "Identify routine could not recognise output generated by '" + ioformat + "' writer", ioformat.equals(identifyoutput)); - testAlignmentEquivalence(al, al_input, false); + testAlignmentEquivalence(al, al_input, ignoreFeatures, + ignoreRowVisibility, allowNullAnnotations); int numaliannot = 0, numsqswithali = 0; for (AlignmentAnnotation ala : al_input.getAlignmentAnnotation()) { @@ -174,6 +184,34 @@ 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); @@ -203,12 +241,16 @@ public class StockholmFileTest { assertEqualSecondaryStructure( "Different alignment annotation at position " + i, - aa_original[i], aa_new[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); - assertEquals("Visibility not identical.", aa_original[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 @@ -245,7 +287,8 @@ public class StockholmFileTest seq_original = al.getSequencesArray(); 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++) @@ -281,23 +324,20 @@ public class StockholmFileTest && 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); + assertEquals("different number of features", 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 @@ -313,7 +353,7 @@ public class StockholmFileTest annot_new = al_input.getSequenceAt(in).getAnnotation()[j]; assertEqualSecondaryStructure( "Different annotation elements", annot_original, - annot_new); + annot_new, allowNullAnnotation); } } } @@ -335,9 +375,26 @@ 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 @@ -360,7 +417,8 @@ public class StockholmFileTest 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() @@ -371,7 +429,8 @@ public class StockholmFileTest else { // not RNA secondary structure, so expect all elements to match... - if (!an_or.displayCharacter.trim().equals( + 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()) @@ -379,7 +438,9 @@ public class StockholmFileTest .trim().length() == 0) || (an_new.description == null && an_or.description .trim().length() == 0) || an_or.description - .trim().equals(an_new.description.trim())))) + .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 +456,202 @@ 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.DETECT_BRACKETS.matchAt("" + ch, 0), + "Didn't recognise " + ch + " as a WUSS bracket"); + } + for (char ch : new char[] { '@', '!', 'V', 'Q', '*', ' ', '-', '.' }) + { + Assert.assertFalse(StockholmFile.DETECT_BRACKETS.matchAt("" + 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); + + } }