import static org.testng.AssertJUnit.assertEquals;
import static org.testng.AssertJUnit.assertNotNull;
+import static org.testng.AssertJUnit.assertNull;
import static org.testng.AssertJUnit.assertTrue;
import static org.testng.AssertJUnit.fail;
+import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.Annotation;
+import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
import jalview.gui.JvOptionPane;
import java.io.File;
+import java.io.IOException;
+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;
@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" })
@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);
}
/**
* @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();
"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())
{
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);
// 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<Integer, BitSet> orig_groups = new HashMap<Integer, BitSet>();
- Map<Integer, BitSet> new_groups = new HashMap<Integer, BitSet>();
+ Map<Integer, BitSet> orig_groups = new HashMap<>();
+ Map<Integer, BitSet> new_groups = new HashMap<>();
if (aa_new != null && aa_original != null)
{
{
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
seq_original = al.getSequencesArray();
SequenceI[] seq_new = new SequenceI[al_input.getSequencesArray().length];
seq_new = al_input.getSequencesArray();
- SequenceFeature[] sequenceFeatures_original, sequenceFeatures_new;
+ List<SequenceFeature> sequenceFeatures_original;
+ List<SequenceFeature> sequenceFeatures_new;
AlignmentAnnotation annot_original, annot_new;
//
for (int i = 0; i < al.getSequencesArray().length; i++)
&& 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
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";
+ 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 <format>' 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);
+
+ }
+
+ @Test(groups = "Functional")
+ public void testType2id()
+ {
+ assertEquals("OS", StockholmFile.type2id("organism"));
+ // not case-sensitive:
+ assertEquals("OS", StockholmFile.type2id("Organism"));
+ // is space-sensitive:
+ assertNull(StockholmFile.type2id("Organism "));
+ assertNull(StockholmFile.type2id("orgasm"));
+ }
+
+ @Test(groups = "Functional")
+ public void testGetAnnotationCharacter()
+ {
+ SequenceI seq = new Sequence("seq", "abc--def-");
+
+ Annotation[] ann = new Annotation[8];
+ ann[1] = new Annotation("Z", "desc", 'E', 1f);
+ ann[2] = new Annotation("Q", "desc", ' ', 1f);
+ ann[4] = new Annotation("", "desc", 'E', 1f);
+ ann[6] = new Annotation("ZH", "desc", 'E', 1f);
+
+ /*
+ * null annotation in column (not Secondary Structure annotation)
+ * should answer sequence character, or '-' if null sequence
+ */
+ assertEquals('-', StockholmFile.outputCharacter("RF", 0, ann, null));
+ assertEquals('d', StockholmFile.outputCharacter("RF", 5, ann, seq));
+ assertEquals('-', StockholmFile.outputCharacter("RF", 8, ann, seq));
+
+ /*
+ * null annotation in column (SS annotation) should answer underscore
+ */
+ assertEquals('_', StockholmFile.outputCharacter("SS", 0, ann, seq));
+
+ /*
+ * SS secondary structure symbol
+ */
+ assertEquals('E', StockholmFile.outputCharacter("SS", 1, ann, seq));
+
+ /*
+ * no SS symbol, use label instead
+ */
+ assertEquals('Q', StockholmFile.outputCharacter("SS", 2, ann, seq));
+
+ /*
+ * SS with 2 character label - second character overrides SS symbol
+ */
+ assertEquals('H', StockholmFile.outputCharacter("SS", 6, ann, seq));
+
+ /*
+ * empty display character, not SS - answers '.'
+ */
+ assertEquals('.', StockholmFile.outputCharacter("RF", 4, ann, seq));
+ }
+
+ /**
+ * Test to verify that gaps are input/output as underscore in STO annotation
+ *
+ * @throws IOException
+ */
+ @Test(groups = "Functional")
+ public void testRoundtripWithGaps() throws IOException
+ {
+ /*
+ * small extract from RF00031_folded.stk
+ */
+ // @formatter:off
+ String stoData =
+ "# STOCKHOLM 1.0\n" +
+ "#=GR B.taurus.4 SS .._((.))_\n" +
+ "B.taurus.4 AC.UGCGU.\n" +
+ "#=GR B.taurus.5 SS ..((_._))\n" +
+ "B.taurus.5 ACUU.G.CG\n" +
+ "//\n";
+ // @formatter:on
+ StockholmFile parser = new StockholmFile(stoData, DataSourceType.PASTE);
+ SequenceI[] seqs = parser.getSeqsAsArray();
+ assertEquals(2, seqs.length);
+
+ /*
+ * B.taurus.4 has a trailing gap
+ * rendered as underscore in Stockholm annotation
+ */
+ assertEquals("AC.UGCGU.", seqs[0].getSequenceAsString());
+ AlignmentAnnotation[] anns = seqs[0].getAnnotation();
+ assertEquals(1, anns.length);
+ AlignmentAnnotation taurus4SS = anns[0];
+ assertEquals(9, taurus4SS.annotations.length);
+ assertEquals(" .", taurus4SS.annotations[0].displayCharacter);
+ assertNull(taurus4SS.annotations[2]); // gapped position
+ assertNull(taurus4SS.annotations[8]); // gapped position
+ assertEquals('(', taurus4SS.annotations[3].secondaryStructure);
+ assertEquals("(", taurus4SS.annotations[3].displayCharacter);
+ assertEquals(')', taurus4SS.annotations[7].secondaryStructure);
+
+ /*
+ * output as Stockholm and verify it matches the original input
+ * (gaps output as underscore in annotation lines)
+ * note: roundtrip test works with the input lines ordered as above;
+ * can also parse in other orders, but then input doesn't match output
+ */
+ AlignmentFileWriterI afile = FileFormat.Stockholm
+ .getWriter(new Alignment(seqs));
+ String output = afile.print(seqs, false);
+ assertEquals(stoData, output);
+ }
}
git://source.jalview.org / jalview.git / blobdiff