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.DBRefEntry;
+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;
// 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)
{
testAlignmentEquivalence(al, newAl, true, true, true);
}
+
+ @Test(groups = { "Functional" })
+ public void testTypeToDescription()
+ {
+ assertEquals("Secondary Structure",
+ StockholmFile.typeToDescription("SS"));
+ assertEquals("Surface Accessibility",
+ StockholmFile.typeToDescription("SA"));
+ assertEquals("transmembrane", StockholmFile.typeToDescription("TM"));
+ assertEquals("Posterior Probability",
+ StockholmFile.typeToDescription("PP"));
+ assertEquals("ligand binding", StockholmFile.typeToDescription("LI"));
+ assertEquals("active site", StockholmFile.typeToDescription("AS"));
+ assertEquals("intron", StockholmFile.typeToDescription("IN"));
+ assertEquals("interacting residue",
+ StockholmFile.typeToDescription("IR"));
+ assertEquals("accession", StockholmFile.typeToDescription("AC"));
+ assertEquals("organism", StockholmFile.typeToDescription("OS"));
+ assertEquals("class", StockholmFile.typeToDescription("CL"));
+ assertEquals("description", StockholmFile.typeToDescription("DE"));
+ assertEquals("reference", StockholmFile.typeToDescription("DR"));
+ assertEquals("look", StockholmFile.typeToDescription("LO"));
+ assertEquals("Reference Positions",
+ StockholmFile.typeToDescription("RF"));
+
+ // case-sensitive:
+ assertEquals("Rf", StockholmFile.typeToDescription("Rf"));
+ assertEquals("junk", StockholmFile.typeToDescription("junk"));
+ assertEquals("", StockholmFile.typeToDescription(""));
+ assertNull(StockholmFile.typeToDescription(null));
+ }
+
+ @Test(groups = { "Functional" })
+ public void testDescriptionToType()
+ {
+ assertEquals("SS",
+ StockholmFile.descriptionToType("Secondary Structure"));
+ assertEquals("SA",
+ StockholmFile.descriptionToType("Surface Accessibility"));
+ assertEquals("TM", StockholmFile.descriptionToType("transmembrane"));
+
+ // test is not case-sensitive:
+ assertEquals("SS",
+ StockholmFile.descriptionToType("secondary structure"));
+
+ // test is white-space sensitive:
+ assertNull(StockholmFile.descriptionToType("secondary structure "));
+
+ assertNull(StockholmFile.descriptionToType("any old junk"));
+ assertNull(StockholmFile.descriptionToType(""));
+ assertNull(StockholmFile.descriptionToType(null));
+ }
+
+ @Test(groups = { "Functional" })
+ public void testPrint()
+ {
+ SequenceI seq1 = new Sequence("seq1", "LKMF-RS-Q");
+ SequenceI seq2 = new Sequence("seq2/10-15", "RRS-LIP-");
+ SequenceI[] seqs = new SequenceI[] { seq1, seq2 };
+ AlignmentI al = new Alignment(seqs);
+
+ StockholmFile testee = new StockholmFile(al);
+
+ /*
+ * basic output (sequences only):
+ * sequence ids are padded with 9 spaces more than the widest id
+ */
+ String output = testee.print(seqs, true);
+ String expected = "# STOCKHOLM 1.0\n" + "seq1/1-7 LKMF-RS-Q\n"
+ + "seq2/10-15 RRS-LIP-\n//\n";
+ assertEquals(expected, output);
+
+ /*
+ * add some dbrefs
+ */
+ seq1.addDBRef(new DBRefEntry("PFAM", "1", "PF00111"));
+ seq1.addDBRef(new DBRefEntry("UNIPROT", "1", "P83527"));
+ seq2.addDBRef(new DBRefEntry("RFAM", "1", "AY119185.1"));
+ seq2.addDBRef(new DBRefEntry("EMBL", "1", "AF125575"));
+ output = testee.print(seqs, true);
+ // PFAM and RFAM dbrefs should be output as AC, others as DR
+ expected = "# STOCKHOLM 1.0\n" + "#=GS seq1/1-7 AC PF00111\n"
+ + "#=GS seq1/1-7 DR UNIPROT ; P83527\n"
+ + "#=GS seq2/10-15 AC AY119185.1\n"
+ + "#=GS seq2/10-15 DR EMBL ; AF125575\n"
+ + "seq1/1-7 LKMF-RS-Q\n"
+ + "seq2/10-15 RRS-LIP-\n//\n";
+ assertEquals(expected, output);
+
+ /*
+ * add some sequence and alignment annotation
+ */
+ Annotation[] anns = new Annotation[5];
+ for (int i = 0; i < anns.length; i++)
+ {
+ anns[i] = new Annotation(String.valueOf((char) ('B' + i)),
+ "Desc " + i,
+ (char) ('C' + i), i + 3);
+ }
+
+ // expect "secondary structure" to be output as #=GR seqid SS
+ // using the secondary structure character (CDEFG) not display char (BCDEF)
+ AlignmentAnnotation aa1 = new AlignmentAnnotation("secondary structure",
+ "ssdesc", anns);
+ aa1.sequenceRef = seq1;
+ seq1.addAlignmentAnnotation(aa1);
+ al.addAnnotation(aa1);
+
+ // "sec structure" should not be output as no corresponding feature id
+ AlignmentAnnotation aa2 = new AlignmentAnnotation("sec structure",
+ "ssdesc", anns);
+ aa2.sequenceRef = seq2;
+ seq2.addAlignmentAnnotation(aa2);
+ al.addAnnotation(aa2);
+
+ // alignment annotation for Reference Positions: output as #=GC RF
+ AlignmentAnnotation aa3 = new AlignmentAnnotation("reference positions",
+ "refpos", anns);
+ al.addAnnotation(aa3);
+
+ // 'seq' annotation: output as seq_cons
+ AlignmentAnnotation aa4 = new AlignmentAnnotation("seq", "seqdesc",
+ anns);
+ al.addAnnotation(aa4);
+
+ // 'intron' annotation: output as IN_cons
+ AlignmentAnnotation aa5 = new AlignmentAnnotation("intron",
+ "introndesc", anns);
+ al.addAnnotation(aa5);
+
+ // 'binding site' annotation: output as binding_site
+ AlignmentAnnotation aa6 = new AlignmentAnnotation("binding site",
+ "bindingdesc", anns);
+ al.addAnnotation(aa6);
+
+ // 'autocalc' annotation should not be output
+ AlignmentAnnotation aa7 = new AlignmentAnnotation("Consensus",
+ "consensusdesc", anns);
+ aa7.autoCalculated = true;
+ al.addAnnotation(aa7);
+
+ // hidden annotation should not be output
+ AlignmentAnnotation aa8 = new AlignmentAnnotation("domains",
+ "domaindesc", anns);
+ aa8.visible = false;
+ al.addAnnotation(aa8);
+
+ output = testee.print(seqs, true);
+ //@formatter:off
+ expected =
+ "# STOCKHOLM 1.0\n"
+ + "#=GS seq1/1-7 AC PF00111\n"
+ + "#=GS seq1/1-7 DR UNIPROT ; P83527\n"
+ + "#=GS seq2/10-15 AC AY119185.1\n"
+ + "#=GS seq2/10-15 DR EMBL ; AF125575\n"
+ + "#=GR seq1/1-7 SS CDEFG\n"
+ + "seq1/1-7 LKMF-RS-Q\n"
+ + "seq2/10-15 RRS-LIP-\n"
+ + "#=GC RF BCDEF\n" + "#=GC seq_cons BCDEF\n"
+ + "#=GC IN_cons BCDEF\n" + "#=GC binding_site BCDEF\n"
+ + "//\n";
+ //@formatter:on
+ assertEquals(expected, output);
+ }
+
+ @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.getAnnotationCharacter("RF", 0, ann[0], null));
+ assertEquals('d',
+ StockholmFile.getAnnotationCharacter("RF", 5, ann[5], seq));
+ assertEquals('-',
+ StockholmFile.getAnnotationCharacter("RF", 8, null, seq));
+
+ /*
+ * null annotation in column (SS annotation) should answer underscore
+ */
+ assertEquals('_',
+ StockholmFile.getAnnotationCharacter("SS", 0, ann[0], seq));
+
+ /*
+ * SS secondary structure symbol
+ */
+ assertEquals('E',
+ StockholmFile.getAnnotationCharacter("SS", 1, ann[1], seq));
+
+ /*
+ * no SS symbol, use label instead
+ */
+ assertEquals('Q',
+ StockholmFile.getAnnotationCharacter("SS", 2, ann[2], seq));
+
+ /*
+ * SS with 2 character label - second character overrides SS symbol
+ */
+ assertEquals('H',
+ StockholmFile.getAnnotationCharacter("SS", 6, ann[6], seq));
+
+ /*
+ * empty display character, not SS - answers '.'
+ */
+ assertEquals('.',
+ StockholmFile.getAnnotationCharacter("RF", 4, ann[4], 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