X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=test%2Fjalview%2Fio%2FStockholmFileTest.java;h=bb822a06cabf7b70ab54d9d7540e4281d35e2dcf;hb=c87a31d2275d86ec5d64cc20844c6cd626037737;hp=a6ae6307b005e0a16ee18943d9364771c95ec152;hpb=bab4b08733a9543bdce5c0b9d1c32ca7d18ad9e3;p=jalview.git diff --git a/test/jalview/io/StockholmFileTest.java b/test/jalview/io/StockholmFileTest.java index a6ae630..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 { @@ -91,14 +98,57 @@ public class StockholmFileTest } /** + * 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."); + + } + + /** * test alignment data in given file can be imported, exported and reimported * 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 @@ -255,8 +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) @@ -321,10 +371,11 @@ 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!!!"); + System.out.println("Checking feature equivalence."); sequenceFeatures_original = seq_original[i] .getSequenceFeatures(); sequenceFeatures_new = seq_new[in].getSequenceFeatures(); @@ -658,7 +709,7 @@ public class StockholmFileTest // this is the single sequence alignment and the SS annotations equivalent to // the ones in file RnaSSTestFile - String aliFileRnaSSAlphaChars = ">Test.sequence/1-14\n" + String aliFileRnaSS = ">Test.sequence/1-14\n" + "GUACAAAAAAAAAA"; String annFileRnaSSAlphaChars = "JALVIEW_ANNOTATION\n" + "# Created: Thu Aug 02 14:54:57 BST 2018\n" + "\n" @@ -700,7 +751,7 @@ public class StockholmFileTest // this should result in the same RNA SS Annotations AlignmentI newAl = new AppletFormatAdapter().readFile( - aliFileRnaSSAlphaChars, + aliFileRnaSS, DataSourceType.PASTE, jalview.io.FileFormat.Fasta); AnnotationFile aaf = new AnnotationFile(); aaf.readAnnotationFile(newAl, annFileRnaSSAlphaChars, @@ -708,11 +759,14 @@ public class StockholmFileTest Assert.assertTrue( testRnaSSAnnotationsEquivalent(al.getAlignmentAnnotation()[0], - newAl.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( - aliFileRnaSSAlphaChars, DataSourceType.PASTE, + aliFileRnaSS, DataSourceType.PASTE, jalview.io.FileFormat.Fasta); aaf = new AnnotationFile(); aaf.readAnnotationFile(newAl, wrongAnnFileRnaSSAlphaChars, @@ -720,7 +774,10 @@ public class StockholmFileTest boolean mismatch = testRnaSSAnnotationsEquivalent(al.getAlignmentAnnotation()[0], newAl.getAlignmentAnnotation()[0]); - Assert.assertFalse( mismatch ); + 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( @@ -730,4 +787,110 @@ public class StockholmFileTest 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); + + } }