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;
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'
* @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);
{
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);
annot_new = al_input.getSequenceAt(in).getAnnotation()[j];
assertEqualSecondaryStructure(
"Different annotation elements", annot_original,
- annot_new);
+ annot_new, allowNullAnnotation);
}
}
}
}
}
+ /**
+ * 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
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()
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())
.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()
}
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<AlignmentAnnotation> 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";
// 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);
}
}
git://source.jalview.org / jalview.git / commitdiff