X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fio%2FStockholmFileTest.java;h=bb822a06cabf7b70ab54d9d7540e4281d35e2dcf;hb=c794c5033adeee182b03a5ea92c0a7495a29661f;hp=1a18fb908871ff87f96055b85bf178dde04e8860;hpb=7d23674eeb527b78e8024c82f01faee7dadced9f;p=jalview.git diff --git a/test/jalview/io/StockholmFileTest.java b/test/jalview/io/StockholmFileTest.java index 1a18fb9..bb822a0 100644 --- a/test/jalview/io/StockholmFileTest.java +++ b/test/jalview/io/StockholmFileTest.java @@ -20,29 +20,36 @@ */ 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 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; 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 { @@ -54,13 +61,14 @@ public class StockholmFileTest } 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" }) @@ -86,7 +94,49 @@ public class StockholmFileTest public void rfamFileIO() throws Exception { testFileIOwithFormat(new File(RfamFile), FileFormat.Stockholm, 2, 1, - false); + 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 dbrefs = DBRefUtils.searchRefs(importedSeq.getDBRefs(), + "P00224"); + assertTrue(dbrefs.size() == 1, + "Couldn't find Uniprot DBRef on re-imported sequence."); + } /** @@ -94,15 +144,19 @@ public class StockholmFileTest * with no dataloss * * @param f - * - source datafile (IdentifyFile.identify() should work with it) + * - source datafile (IdentifyFile.identify() + * should work with it) * @param ioformat - * - label for IO class used to write and read back in the data from - * f + * - 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(); @@ -136,7 +190,8 @@ public class StockholmFileTest "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()) { @@ -226,8 +281,8 @@ public class StockholmFileTest // 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 orig_groups = new HashMap(); - Map new_groups = new HashMap(); + Map orig_groups = new HashMap<>(); + Map new_groups = new HashMap<>(); if (aa_new != null && aa_original != null) { @@ -250,8 +305,8 @@ public class StockholmFileTest 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) @@ -283,7 +338,8 @@ public class StockholmFileTest seq_original = al.getSequencesArray(); SequenceI[] seq_new = new SequenceI[al_input.getSequencesArray().length]; seq_new = al_input.getSequencesArray(); - SequenceFeature[] sequenceFeatures_original, sequenceFeatures_new; + List sequenceFeatures_original; + List sequenceFeatures_new; AlignmentAnnotation annot_original, annot_new; // for (int i = 0; i < al.getSequencesArray().length; i++) @@ -315,27 +371,25 @@ public class StockholmFileTest || (seq_original[i].getSequenceFeatures() != null && seq_new[in] .getSequenceFeatures() != null)); // compare sequence features - if (seq_original[i].getSequenceFeatures() != null + if (!ignoreFeatures + && 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]; + System.out.println("Checking feature equivalence."); 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 @@ -621,13 +675,13 @@ public class StockholmFileTest { 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) @@ -652,4 +706,191 @@ public class StockholmFileTest 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 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 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 ' 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); + + } }