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;
}
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,
- false);
+ false, false, false);
}
@Test(groups = { "Functional" })
public void rfamFileIO() throws Exception
{
testFileIOwithFormat(new File(RfamFile), FileFormat.Stockholm, 2, 1,
- false);
+ 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, boolean ignoreRowVisibility)
+ 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
+ * 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);
// 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);
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";
{
for (char ch : new char[] { '{', '}', '[', ']', '(', ')', '<', '>' })
{
- Assert.assertTrue(StockholmFile.DETECT_BRACKETS.matchAt("" + ch, 0),
- "Didn't recognise " + ch + " as a WUSS bracket");
+ Assert.assertTrue(StockholmFile.RNASS_BRACKETS.indexOf(ch) >= 0,
+ "Didn't recognise '" + ch + "' as a WUSS bracket");
}
- for (char ch : new char[] { '@', '!', 'V', 'Q', '*', ' ', '-', '.' })
+ for (char ch : new char[] { '@', '!', '*', ' ', '-', '.' })
{
- Assert.assertFalse(StockholmFile.DETECT_BRACKETS.matchAt("" + ch, 0),
- "Shouldn't recognise " + ch + " as a WUSS bracket");
+ Assert.assertFalse(StockholmFile.RNASS_BRACKETS.indexOf(ch) >= 0,
+ "Shouldn't recognise '" + ch + "' as a WUSS bracket");
}
}
private static void roundTripSSForRNA(String aliFile, String annFile)
// 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);
+
+ }
+
+ // 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<AlignmentAnnotation> 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<AlignmentAnnotation> 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 <format>' 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);
}
}