*/
package jalview.io;
+import static org.testng.Assert.assertTrue;
import static org.testng.AssertJUnit.assertEquals;
import static org.testng.AssertJUnit.assertNotNull;
import static org.testng.AssertJUnit.assertTrue;
import static org.testng.AssertJUnit.fail;
-import jalview.datamodel.AlignmentAnnotation;
-import jalview.datamodel.AlignmentI;
-import jalview.datamodel.Annotation;
-import jalview.datamodel.SequenceFeature;
-import jalview.datamodel.SequenceI;
-
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;
import org.testng.annotations.Test;
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.Annotation;
+import jalview.datamodel.DBRefEntry;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceI;
+import jalview.gui.JvOptionPane;
+import jalview.util.DBRefUtils;
+
public class StockholmFileTest
{
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
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);
+ 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);
+ }
+
+ /**
+ * JAL-3529 - verify uniprot refs for sequences are output for sequences
+ * retrieved via Pfam
+ */
+ @Test(groups = { "Functional" })
+ public void dbrefOutput() throws Exception
+ {
+ // sequences retrieved in a Pfam domain alignment also have a PFAM database
+ // reference
+ SequenceI sq = new Sequence("FER2_SPIOL", "AASSDDDFFF");
+ sq.addDBRef(new DBRefEntry("UNIPROT", "1", "P00224"));
+ sq.addDBRef(new DBRefEntry("PFAM", "1", "P00224.1"));
+ sq.addDBRef(new DBRefEntry("PFAM", "1", "PF00111"));
+ AppletFormatAdapter af = new AppletFormatAdapter();
+ String toStockholm = af.formatSequences(FileFormat.Stockholm,
+ new Alignment(new SequenceI[]
+ { sq }), false);
+ System.out.println(toStockholm);
+ // bleh - java.util.Regex sucks
+ assertTrue(
+ Pattern.compile(
+ "^#=GS\\s+FER2_SPIOL(/\\d+-\\d+)?\\s+AC\\s+P00224$",
+ Pattern.MULTILINE).matcher(toStockholm).find(),
+ "Couldn't locate UNIPROT Accession in generated Stockholm file.");
+ AlignmentI fromStockholm = af.readFile(toStockholm,
+ DataSourceType.PASTE, FileFormat.Stockholm);
+ SequenceI importedSeq = fromStockholm.getSequenceAt(0);
+ assertTrue(importedSeq.getDBRefs().size() == 1,
+ "Expected just one database reference to be added to sequence.");
+ assertTrue(
+ importedSeq.getDBRefs().get(0).getAccessionId()
+ .indexOf(" ") == -1,
+ "Spaces were found in accession ID.");
+ List<DBRefEntry> dbrefs = DBRefUtils.searchRefs(importedSeq.getDBRefs(),
+ "P00224");
+ assertTrue(dbrefs.size() == 1,
+ "Couldn't find Uniprot DBRef on re-imported sequence.");
+
}
/**
* @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();
al.getSequenceAt(i).createDatasetSequence();
}
String outputfile = rf.formatSequences(ioformat, al, true);
- System.out.println("Output file in '" + ioformat + "':\n"
- + outputfile + "\n<<EOF\n");
+ System.out.println("Output file in '" + ioformat + "':\n" + outputfile
+ + "\n<<EOF\n");
// test for consistency in io
AlignmentI al_input = new AppletFormatAdapter().readFile(outputfile,
DataSourceType.PASTE, ioformat);
"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())
{
assertTrue(
"Number of sequence associated annotations wasn't at least "
- + nminseqann, numsqswithali >= nminseqann);
+ + nminseqann,
+ numsqswithali >= nminseqann);
} catch (Exception e)
{
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);
- assertTrue("Alignment dimension mismatch: original: " + al.getHeight()
- + "x" + al.getWidth() + ", generated: " + al_input.getHeight()
- + "x" + al_input.getWidth(),
+ assertTrue(
+ "Alignment dimension mismatch: original: " + al.getHeight()
+ + "x" + al.getWidth() + ", generated: "
+ + al_input.getHeight() + "x" + al_input.getWidth(),
al.getHeight() == al_input.getHeight()
&& al.getWidth() == al_input.getWidth());
// check Alignment annotation
AlignmentAnnotation[] aa_new = al_input.getAlignmentAnnotation();
AlignmentAnnotation[] aa_original = al.getAlignmentAnnotation();
+ boolean expectProteinSS = !al.isNucleotide();
+ assertTrue(
+ "Alignments not both "
+ + (al.isNucleotide() ? "nucleotide" : "protein"),
+ al_input.isNucleotide() == al.isNucleotide());
// note - at moment we do not distinguish between alignment without any
// annotation rows and alignment with no annotation row vector
// 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)
{
{
if (aa_new.length > i)
{
- assertTrue("Different alignment annotation at position " + i,
- equalss(aa_original[i], aa_new[i]));
+ assertEqualSecondaryStructure(
+ "Different alignment annotation at position " + i,
+ aa_original[i], aa_new[i], allowNullAnnotation);
+ if (aa_original[i].hasIcons)
+ {
+ assertTrue(
+ "Secondary structure expected to be "
+ + (expectProteinSS ? "protein" : "nucleotide"),
+ expectProteinSS == !aa_original[i].isRNA());
+ }
// 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,
- aa_new[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
- Integer o_ggrp = new Integer(aa_original[i].graphGroup + 2);
- Integer n_ggrp = new Integer(aa_new[i].graphGroup + 2);
+ Integer o_ggrp = Integer.valueOf(aa_original[i].graphGroup + 2);
+ Integer n_ggrp = Integer.valueOf(aa_new[i].graphGroup + 2);
BitSet orig_g = orig_groups.get(o_ggrp);
BitSet new_g = new_groups.get(n_ggrp);
if (orig_g == null)
// check sequences, annotation and features
SequenceI[] seq_original = new SequenceI[al.getSequencesArray().length];
seq_original = al.getSequencesArray();
- SequenceI[] seq_new = new SequenceI[al_input.getSequencesArray().length];
+ 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++)
String name = seq_original[i].getName();
int start = seq_original[i].getStart();
int end = seq_original[i].getEnd();
- System.out.println("Check sequence: " + name + "/" + start + "-"
- + end);
+ System.out
+ .println("Check sequence: " + name + "/" + start + "-" + end);
// search equal sequence
for (int in = 0; in < al_input.getSequencesArray().length; in++)
"Sequence Features were not equivalent"
+ (ignoreFeatures ? " ignoring." : ""),
ignoreFeatures
- || (seq_original[i].getSequenceFeatures() == null && seq_new[in]
- .getSequenceFeatures() == null)
- || (seq_original[i].getSequenceFeatures() != null && seq_new[in]
- .getSequenceFeatures() != null));
+ || (seq_original[i].getSequenceFeatures() == null
+ && seq_new[in]
+ .getSequenceFeatures() == null)
+ || (seq_original[i].getSequenceFeatures() != null
+ && seq_new[in]
+ .getSequenceFeatures() != null));
// compare sequence features
if (seq_original[i].getSequenceFeatures() != null
&& 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);
+ 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
if (al.getSequenceAt(i).getAnnotation() != null
&& al_input.getSequenceAt(in).getAnnotation() != null)
{
- for (int j = 0; j < al.getSequenceAt(i).getAnnotation().length; j++)
+ for (int j = 0; j < al.getSequenceAt(i)
+ .getAnnotation().length; j++)
{
- if (al.getSequenceAt(i).getAnnotation()[j] != null
- && al_input.getSequenceAt(in).getAnnotation()[j] != null)
+ if (al.getSequenceAt(i).getAnnotation()[j] != null && al_input
+ .getSequenceAt(in).getAnnotation()[j] != null)
{
annot_original = al.getSequenceAt(i).getAnnotation()[j];
annot_new = al_input.getSequenceAt(in).getAnnotation()[j];
- assertTrue("Different annotation elements",
- equalss(annot_original, annot_new));
+ assertEqualSecondaryStructure(
+ "Different annotation elements", annot_original,
+ annot_new, allowNullAnnotation);
}
}
}
}
}
- /*
- * compare annotations
+ /**
+ * 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 boolean equalss(AlignmentAnnotation annot_or,
- AlignmentAnnotation annot_new)
+ private static void assertEqualSecondaryStructure(String message,
+ 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 (annot_or.annotations.length != annot_new.annotations.length)
{
- System.err.println("Different lengths for annotation row elements: "
+ fail("Different lengths for annotation row elements: "
+ annot_or.annotations.length + "!="
+ annot_new.annotations.length);
- return false;
}
+ boolean isRna = annot_or.isRNA();
+ assertTrue(
+ "Expected " + (isRna ? " valid RNA " : " no RNA ")
+ + " secondary structure in the row.",
+ isRna == annot_new.isRNA());
for (int i = 0; i < annot_or.annotations.length; i++)
{
- Annotation an_or = annot_or.annotations[i], an_new = annot_new.annotations[i];
+ Annotation an_or = annot_or.annotations[i],
+ an_new = annot_new.annotations[i];
if (an_or != null && an_new != null)
{
- if (!an_or.displayCharacter.trim().equals(
- an_new.displayCharacter.trim())
- || !("" + an_or.secondaryStructure).trim().equals(
- ("" + an_new.secondaryStructure).trim())
- || (an_or.description != an_new.description && !((an_or.description == null && an_new.description
- .trim().length() == 0)
- || (an_new.description == null && an_or.description
- .trim().length() == 0) || an_or.description
- .trim().equals(an_new.description.trim()))))
+
+ if (isRna)
{
- System.err.println("Annotation Element Mismatch\nElement " + i
- + " in original: " + annot_or.annotations[i].toString()
- + "\nElement " + i + " in new: "
- + annot_new.annotations[i].toString());
- return false;
+ if (an_or.secondaryStructure != an_new.secondaryStructure
+ || ((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()
+ + "] but got: [" + annot_new.annotations[i].toString()
+ + "]");
+ }
+ }
+ else
+ {
+ // not RNA secondary structure, so expect all elements to match...
+ 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())
+ || (an_or.description != an_new.description
+ && !((an_or.description == null
+ && an_new.description.trim()
+ .length() == 0)
+ || (an_new.description == null
+ && an_or.description.trim()
+ .length() == 0)
+ || an_or.description.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()
+ + "\nElement " + i + " in new: "
+ + annot_new.annotations[i].toString());
+ }
}
}
else if (annot_or.annotations[i] == null
}
else
{
- System.err.println("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()));
- return false;
+ 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);
+ }
}
}
- return 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.RNASS_BRACKETS.indexOf(ch) >= 0,
+ "Didn't recognise '" + ch + "' as a WUSS bracket");
+ }
+ for (char ch : new char[] { '@', '!', '*', ' ', '-', '.' })
+ {
+ Assert.assertFalse(StockholmFile.RNASS_BRACKETS.indexOf(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);
+
+ }
+
+ // 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);
+
}
}
git://source.jalview.org / jalview.git / blobdiff