From 7d23674eeb527b78e8024c82f01faee7dadced9f Mon Sep 17 00:00:00 2001 From: Jim Procter Date: Thu, 11 May 2017 16:17:29 +0100 Subject: [PATCH] JAL-2507 JAL-2509 allow whitespace==null for annotation row comparison, and test coverage for Annotation equivalence asserts --- test/jalview/io/StockholmFileTest.java | 185 ++++++++++++++++++++++++++++---- 1 file changed, 165 insertions(+), 20 deletions(-) diff --git a/test/jalview/io/StockholmFileTest.java b/test/jalview/io/StockholmFileTest.java index 19df525..1a18fb9 100644 --- a/test/jalview/io/StockholmFileTest.java +++ b/test/jalview/io/StockholmFileTest.java @@ -33,8 +33,10 @@ 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; @@ -178,10 +180,12 @@ public class StockholmFileTest public static void testAlignmentEquivalence(AlignmentI al, AlignmentI al_input, boolean ignoreFeatures) { + testAlignmentEquivalence(al, al_input, ignoreFeatures, false, false); } /** - * assert alignment equivalence + * assert alignment equivalence - uses special comparators for RNA structure + * annotation rows. * * @param al * 'original' @@ -194,10 +198,15 @@ public class StockholmFileTest * @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 ignoreRowVisibility, boolean allowNullAnnotation) { assertNotNull("Original alignment was null", al); assertNotNull("Generated alignment was null", al_input); @@ -228,7 +237,7 @@ 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); @@ -342,7 +351,7 @@ public class StockholmFileTest annot_new = al_input.getSequenceAt(in).getAnnotation()[j]; assertEqualSecondaryStructure( "Different annotation elements", annot_original, - annot_new); + annot_new, allowNullAnnotation); } } } @@ -364,9 +373,26 @@ 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 @@ -389,7 +415,8 @@ 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() @@ -400,7 +427,8 @@ 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()) @@ -408,7 +436,9 @@ 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() @@ -424,18 +454,133 @@ 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"; @@ -504,7 +649,7 @@ public class StockholmFileTest // AlignmentUtils.showOrHideSequenceAnnotations(newAl.getViewport() // .getAlignment(), Arrays.asList("Secondary Structure"), newAl // .getViewport().getAlignment().getSequences(), true, true); - testAlignmentEquivalence(al, newAl, true, true); + testAlignmentEquivalence(al, newAl, true, true, true); } } -- 1.7.10.2