2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3
10 * of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License
18 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 * The Jalview Authors are detailed in the 'AUTHORS' file.
23 import static org.testng.AssertJUnit.assertEquals;
24 import static org.testng.AssertJUnit.assertNotNull;
25 import static org.testng.AssertJUnit.assertTrue;
26 import static org.testng.AssertJUnit.fail;
28 import jalview.datamodel.AlignmentAnnotation;
29 import jalview.datamodel.AlignmentI;
30 import jalview.datamodel.Annotation;
31 import jalview.datamodel.SequenceFeature;
32 import jalview.datamodel.SequenceI;
33 import jalview.gui.JvOptionPane;
36 import java.util.Arrays;
37 import java.util.BitSet;
38 import java.util.HashMap;
39 import java.util.List;
41 import java.util.regex.Matcher;
42 import java.util.regex.Pattern;
44 import org.testng.Assert;
45 import org.testng.annotations.BeforeClass;
46 import org.testng.annotations.Test;
48 public class StockholmFileTest
51 @BeforeClass(alwaysRun = true)
52 public void setUpJvOptionPane()
54 JvOptionPane.setInteractiveMode(false);
55 JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
58 static String PfamFile = "examples/PF00111_seed.stk",
59 RfamFile = "examples/RF00031_folded.stk",
60 RnaSSTestFile = "examples/rna_ss_test.stk";
62 @Test(groups = { "Functional" })
63 public void pfamFileIO() throws Exception
65 testFileIOwithFormat(new File(PfamFile), FileFormat.Stockholm, -1, 0,
69 @Test(groups = { "Functional" })
70 public void pfamFileDataExtraction() throws Exception
72 AppletFormatAdapter af = new AppletFormatAdapter();
73 AlignmentI al = af.readFile(PfamFile, DataSourceType.FILE,
74 new IdentifyFile().identify(PfamFile, DataSourceType.FILE));
76 for (SequenceI sq : al.getSequences())
78 if (sq.getAllPDBEntries() != null)
80 numpdb += sq.getAllPDBEntries().size();
84 "PF00111 seed alignment has at least 1 PDB file, but the reader found none.",
88 @Test(groups = { "Functional" })
89 public void rfamFileIO() throws Exception
91 testFileIOwithFormat(new File(RfamFile), FileFormat.Stockholm, 2, 1,
96 * test alignment data in given file can be imported, exported and reimported
100 * - source datafile (IdentifyFile.identify() should work with it)
102 * - label for IO class used to write and read back in the data from
104 * @param ignoreFeatures
105 * @param ignoreRowVisibility
106 * @param allowNullAnnotations
109 public static void testFileIOwithFormat(File f, FileFormatI ioformat,
110 int naliannot, int nminseqann, boolean ignoreFeatures,
111 boolean ignoreRowVisibility, boolean allowNullAnnotations)
113 System.out.println("Reading file: " + f);
114 String ff = f.getPath();
117 AppletFormatAdapter rf = new AppletFormatAdapter();
119 AlignmentI al = rf.readFile(ff, DataSourceType.FILE,
120 new IdentifyFile().identify(ff, DataSourceType.FILE));
122 assertNotNull("Couldn't read supplied alignment data.", al);
124 // make sure dataset is initialised ? not sure about this
125 for (int i = 0; i < al.getSequencesArray().length; ++i)
127 al.getSequenceAt(i).createDatasetSequence();
129 String outputfile = rf.formatSequences(ioformat, al, true);
130 System.out.println("Output file in '" + ioformat + "':\n"
131 + outputfile + "\n<<EOF\n");
132 // test for consistency in io
133 AlignmentI al_input = new AppletFormatAdapter().readFile(outputfile,
134 DataSourceType.PASTE, ioformat);
135 assertNotNull("Couldn't parse reimported alignment data.", al_input);
137 FileFormatI identifyoutput = new IdentifyFile().identify(outputfile,
138 DataSourceType.PASTE);
139 assertNotNull("Identify routine failed for outputformat " + ioformat,
142 "Identify routine could not recognise output generated by '"
143 + ioformat + "' writer",
144 ioformat.equals(identifyoutput));
145 testAlignmentEquivalence(al, al_input, ignoreFeatures,
146 ignoreRowVisibility, allowNullAnnotations);
147 int numaliannot = 0, numsqswithali = 0;
148 for (AlignmentAnnotation ala : al_input.getAlignmentAnnotation())
150 if (ala.sequenceRef == null)
161 assertEquals("Number of alignment annotations", naliannot,
166 "Number of sequence associated annotations wasn't at least "
167 + nminseqann, numsqswithali >= nminseqann);
169 } catch (Exception e)
172 assertTrue("Couln't format the alignment for output file.", false);
177 * assert alignment equivalence
182 * 'secondary' or generated alignment from some datapreserving
184 * @param ignoreFeatures
185 * when true, differences in sequence feature annotation are ignored
187 public static void testAlignmentEquivalence(AlignmentI al,
188 AlignmentI al_input, boolean ignoreFeatures)
190 testAlignmentEquivalence(al, al_input, ignoreFeatures, false, false);
194 * assert alignment equivalence - uses special comparators for RNA structure
200 * 'secondary' or generated alignment from some datapreserving
202 * @param ignoreFeatures
203 * when true, differences in sequence feature annotation are ignored
205 * @param ignoreRowVisibility
206 * when true, do not fail if there are differences in the visibility
208 * @param allowNullAnnotation
209 * when true, positions in alignment annotation that are null will be
210 * considered equal to positions containing annotation where
211 * Annotation.isWhitespace() returns true.
214 public static void testAlignmentEquivalence(AlignmentI al,
215 AlignmentI al_input, boolean ignoreFeatures,
216 boolean ignoreRowVisibility, boolean allowNullAnnotation)
218 assertNotNull("Original alignment was null", al);
219 assertNotNull("Generated alignment was null", al_input);
221 assertTrue("Alignment dimension mismatch: original: " + al.getHeight()
222 + "x" + al.getWidth() + ", generated: " + al_input.getHeight()
223 + "x" + al_input.getWidth(),
224 al.getHeight() == al_input.getHeight()
225 && al.getWidth() == al_input.getWidth());
227 // check Alignment annotation
228 AlignmentAnnotation[] aa_new = al_input.getAlignmentAnnotation();
229 AlignmentAnnotation[] aa_original = al.getAlignmentAnnotation();
231 // note - at moment we do not distinguish between alignment without any
232 // annotation rows and alignment with no annotation row vector
233 // we might want to revise this in future
234 int aa_new_size = (aa_new == null ? 0 : aa_new.length);
235 int aa_original_size = (aa_original == null ? 0 : aa_original.length);
236 Map<Integer, BitSet> orig_groups = new HashMap<>();
237 Map<Integer, BitSet> new_groups = new HashMap<>();
239 if (aa_new != null && aa_original != null)
241 for (int i = 0; i < aa_original.length; i++)
243 if (aa_new.length > i)
245 assertEqualSecondaryStructure(
246 "Different alignment annotation at position " + i,
247 aa_original[i], aa_new[i], allowNullAnnotation);
248 // compare graphGroup or graph properties - needed to verify JAL-1299
249 assertEquals("Graph type not identical.", aa_original[i].graph,
251 if (!ignoreRowVisibility)
253 assertEquals("Visibility not identical.",
254 aa_original[i].visible,
257 assertEquals("Threshold line not identical.",
258 aa_original[i].threshold, aa_new[i].threshold);
259 // graphGroup may differ, but pattern should be the same
260 Integer o_ggrp = Integer.valueOf(aa_original[i].graphGroup + 2);
261 Integer n_ggrp = Integer.valueOf(aa_new[i].graphGroup + 2);
262 BitSet orig_g = orig_groups.get(o_ggrp);
263 BitSet new_g = new_groups.get(n_ggrp);
266 orig_groups.put(o_ggrp, orig_g = new BitSet());
270 new_groups.put(n_ggrp, new_g = new BitSet());
272 assertEquals("Graph Group pattern differs at annotation " + i,
279 System.err.println("No matching annotation row for "
280 + aa_original[i].toString());
285 "Generated and imported alignment have different annotation sets",
286 aa_original_size, aa_new_size);
288 // check sequences, annotation and features
289 SequenceI[] seq_original = new SequenceI[al.getSequencesArray().length];
290 seq_original = al.getSequencesArray();
291 SequenceI[] seq_new = new SequenceI[al_input.getSequencesArray().length];
292 seq_new = al_input.getSequencesArray();
293 List<SequenceFeature> sequenceFeatures_original;
294 List<SequenceFeature> sequenceFeatures_new;
295 AlignmentAnnotation annot_original, annot_new;
297 for (int i = 0; i < al.getSequencesArray().length; i++)
299 String name = seq_original[i].getName();
300 int start = seq_original[i].getStart();
301 int end = seq_original[i].getEnd();
302 System.out.println("Check sequence: " + name + "/" + start + "-"
305 // search equal sequence
306 for (int in = 0; in < al_input.getSequencesArray().length; in++)
308 if (name.equals(seq_new[in].getName())
309 && start == seq_new[in].getStart()
310 && end == seq_new[in].getEnd())
312 String ss_original = seq_original[i].getSequenceAsString();
313 String ss_new = seq_new[in].getSequenceAsString();
314 assertEquals("The sequences " + name + "/" + start + "-" + end
315 + " are not equal", ss_original, ss_new);
318 "Sequence Features were not equivalent"
319 + (ignoreFeatures ? " ignoring." : ""),
321 || (seq_original[i].getSequenceFeatures() == null && seq_new[in]
322 .getSequenceFeatures() == null)
323 || (seq_original[i].getSequenceFeatures() != null && seq_new[in]
324 .getSequenceFeatures() != null));
325 // compare sequence features
327 && seq_original[i].getSequenceFeatures() != null
328 && seq_new[in].getSequenceFeatures() != null)
330 System.out.println("Checking feature equivalence.");
331 sequenceFeatures_original = seq_original[i]
332 .getSequenceFeatures();
333 sequenceFeatures_new = seq_new[in].getSequenceFeatures();
335 assertEquals("different number of features", seq_original[i]
336 .getSequenceFeatures().size(), seq_new[in]
337 .getSequenceFeatures().size());
339 for (int feat = 0; feat < seq_original[i].getSequenceFeatures()
342 assertEquals("Different features",
343 sequenceFeatures_original.get(feat),
344 sequenceFeatures_new.get(feat));
347 // compare alignment annotation
348 if (al.getSequenceAt(i).getAnnotation() != null
349 && al_input.getSequenceAt(in).getAnnotation() != null)
351 for (int j = 0; j < al.getSequenceAt(i).getAnnotation().length; j++)
353 if (al.getSequenceAt(i).getAnnotation()[j] != null
354 && al_input.getSequenceAt(in).getAnnotation()[j] != null)
356 annot_original = al.getSequenceAt(i).getAnnotation()[j];
357 annot_new = al_input.getSequenceAt(in).getAnnotation()[j];
358 assertEqualSecondaryStructure(
359 "Different annotation elements", annot_original,
360 annot_new, allowNullAnnotation);
364 else if (al.getSequenceAt(i).getAnnotation() == null
365 && al_input.getSequenceAt(in).getAnnotation() == null)
367 System.out.println("No annotations");
369 else if (al.getSequenceAt(i).getAnnotation() != null
370 && al_input.getSequenceAt(in).getAnnotation() == null)
372 fail("Annotations differed between sequences ("
373 + al.getSequenceAt(i).getName() + ") and ("
374 + al_input.getSequenceAt(i).getName() + ")");
383 * compare two annotation rows, with special support for secondary structure
384 * comparison. With RNA, only the value and the secondaryStructure symbols are
385 * compared, displayCharacter and description are ignored. Annotations where
386 * Annotation.isWhitespace() is true are always considered equal.
389 * - not actually used yet..
391 * - the original annotation
393 * - the one compared to the original annotation
394 * @param allowNullEquivalence
395 * when true, positions in alignment annotation that are null will be
396 * considered equal to non-null positions for which
397 * Annotation.isWhitespace() is true.
399 private static void assertEqualSecondaryStructure(String message,
400 AlignmentAnnotation annot_or, AlignmentAnnotation annot_new,
401 boolean allowNullEqivalence)
403 // TODO: test to cover this assert behaves correctly for all allowed
404 // variations of secondary structure annotation row equivalence
405 if (annot_or.annotations.length != annot_new.annotations.length)
407 fail("Different lengths for annotation row elements: "
408 + annot_or.annotations.length + "!="
409 + annot_new.annotations.length);
411 boolean isRna = annot_or.isRNA();
412 assertTrue("Expected " + (isRna ? " valid RNA " : " no RNA ")
413 + " secondary structure in the row.",
414 isRna == annot_new.isRNA());
415 for (int i = 0; i < annot_or.annotations.length; i++)
417 Annotation an_or = annot_or.annotations[i], an_new = annot_new.annotations[i];
418 if (an_or != null && an_new != null)
423 if (an_or.secondaryStructure != an_new.secondaryStructure
424 || ((Float.isNaN(an_or.value) != Float
425 .isNaN(an_new.value)) || an_or.value != an_new.value))
427 fail("Different RNA secondary structure at column " + i
428 + " expected: [" + annot_or.annotations[i].toString()
429 + "] but got: [" + annot_new.annotations[i].toString()
435 // not RNA secondary structure, so expect all elements to match...
436 if ((an_or.isWhitespace() != an_new.isWhitespace())
437 || !an_or.displayCharacter.trim().equals(
438 an_new.displayCharacter.trim())
439 || !("" + an_or.secondaryStructure).trim().equals(
440 ("" + an_new.secondaryStructure).trim())
441 || (an_or.description != an_new.description && !((an_or.description == null && an_new.description
442 .trim().length() == 0)
443 || (an_new.description == null && an_or.description
444 .trim().length() == 0) || an_or.description
445 .trim().equals(an_new.description.trim())))
446 || !((Float.isNaN(an_or.value) && Float
447 .isNaN(an_new.value)) || an_or.value == an_new.value))
449 fail("Annotation Element Mismatch\nElement " + i
450 + " in original: " + annot_or.annotations[i].toString()
451 + "\nElement " + i + " in new: "
452 + annot_new.annotations[i].toString());
456 else if (annot_or.annotations[i] == null
457 && annot_new.annotations[i] == null)
463 if (allowNullEqivalence)
465 if (an_or != null && an_or.isWhitespace())
470 if (an_new != null && an_new.isWhitespace())
475 // need also to test for null in one, non-SS annotation in other...
476 fail("Annotation Element Mismatch\nElement " + i + " in original: "
477 + (an_or == null ? "is null" : an_or.toString())
478 + "\nElement " + i + " in new: "
479 + (an_new == null ? "is null" : an_new.toString()));
485 * @see assertEqualSecondaryStructure - test if two secondary structure
486 * annotations are not equal
490 * @param allowNullEquivalence
492 public static void assertNotEqualSecondaryStructure(String message,
493 AlignmentAnnotation an_orig, AlignmentAnnotation an_new,
494 boolean allowNullEquivalence)
496 boolean thrown = false;
499 assertEqualSecondaryStructure("", an_orig, an_new,
500 allowNullEquivalence);
501 } catch (AssertionError af)
507 fail("Expected difference for [" + an_orig + "] and [" + an_new + "]");
510 private AlignmentAnnotation makeAnnot(Annotation ae)
512 return new AlignmentAnnotation("label", "description", new Annotation[]
516 @Test(groups={"Functional"})
517 public void testAnnotationEquivalence()
519 AlignmentAnnotation one = makeAnnot(new Annotation("", "", ' ', 1));
520 AlignmentAnnotation anotherOne = makeAnnot(new Annotation("", "", ' ',
522 AlignmentAnnotation sheet = makeAnnot(new Annotation("","",'E',0f));
523 AlignmentAnnotation anotherSheet = makeAnnot(new Annotation("","",'E',0f));
524 AlignmentAnnotation sheetWithLabel = makeAnnot(new Annotation("1", "",
526 AlignmentAnnotation anotherSheetWithLabel = makeAnnot(new Annotation(
528 AlignmentAnnotation rnaNoDC = makeAnnot(new Annotation("","",'<',0f));
529 AlignmentAnnotation anotherRnaNoDC = makeAnnot(new Annotation("","",'<',0f));
530 AlignmentAnnotation rnaWithDC = makeAnnot(new Annotation("B", "", '<',
532 AlignmentAnnotation anotherRnaWithDC = makeAnnot(new Annotation("B",
535 // check self equivalence
536 for (boolean allowNull : new boolean[] { true, false })
538 assertEqualSecondaryStructure("Should be equal", one, anotherOne,
540 assertEqualSecondaryStructure("Should be equal", sheet, anotherSheet,
542 assertEqualSecondaryStructure("Should be equal", sheetWithLabel,
543 anotherSheetWithLabel, allowNull);
544 assertEqualSecondaryStructure("Should be equal", rnaNoDC,
545 anotherRnaNoDC, allowNull);
546 assertEqualSecondaryStructure("Should be equal", rnaWithDC,
547 anotherRnaWithDC, allowNull);
548 // display character doesn't matter for RNA structure (for 2.10.2)
549 assertEqualSecondaryStructure("Should be equal", rnaWithDC, rnaNoDC,
551 assertEqualSecondaryStructure("Should be equal", rnaNoDC, rnaWithDC,
555 // verify others are different
556 List<AlignmentAnnotation> aaSet = Arrays.asList(one, sheet,
557 sheetWithLabel, rnaWithDC);
558 for (int p = 0; p < aaSet.size(); p++)
560 for (int q = 0; q < aaSet.size(); q++)
564 assertNotEqualSecondaryStructure("Should be different",
565 aaSet.get(p), aaSet.get(q), false);
569 assertEqualSecondaryStructure("Should be same", aaSet.get(p),
570 aaSet.get(q), false);
571 assertEqualSecondaryStructure("Should be same", aaSet.get(p),
573 assertNotEqualSecondaryStructure(
574 "Should be different to empty anot", aaSet.get(p),
575 makeAnnot(Annotation.EMPTY_ANNOTATION), false);
576 assertNotEqualSecondaryStructure(
577 "Should be different to empty annot",
578 makeAnnot(Annotation.EMPTY_ANNOTATION), aaSet.get(q),
580 assertNotEqualSecondaryStructure("Should be different to null",
581 aaSet.get(p), makeAnnot(null), false);
582 assertNotEqualSecondaryStructure("Should be different to null",
583 makeAnnot(null), aaSet.get(q), true);
592 String aliFile = ">Dm\nAAACCCUUUUACACACGGGAAAGGG";
593 String annFile = "JALVIEW_ANNOTATION\n# Created: Thu May 04 11:16:52 BST 2017\n\n"
594 + "SEQUENCE_REF\tDm\nNO_GRAPH\tsecondary structure\tsecondary structure\t"
595 + "(|(|(|(|, .|, .|, .|, .|)|)|)|)|\t0.0\nROWPROPERTIES\t"
596 + "secondary structure\tscaletofit=true\tshowalllabs=true\tcentrelabs=false";
598 String annFileCurlyWuss = "JALVIEW_ANNOTATION\n# Created: Thu May 04 11:16:52 BST 2017\n\n"
599 + "SEQUENCE_REF\tDm\nNO_GRAPH\tsecondary structure\tsecondary structure\t"
600 + "(|(|(|(||{|{||{|{||)|)|)|)||}|}|}|}|\t0.0\nROWPROPERTIES\t"
601 + "secondary structure\tscaletofit=true\tshowalllabs=true\tcentrelabs=false";
602 String annFileFullWuss = "JALVIEW_ANNOTATION\n# Created: Thu May 04 11:16:52 BST 2017\n\n"
603 + "SEQUENCE_REF\tDm\nNO_GRAPH\tsecondary structure\tsecondary structure\t"
604 + "(|(|(|(||{|{||[|[||)|)|)|)||}|}|]|]|\t0.0\nROWPROPERTIES\t"
605 + "secondary structure\tscaletofit=true\tshowalllabs=true\tcentrelabs=false";
607 @Test(groups = { "Functional" })
608 public void secondaryStructureForRNASequence() throws Exception
610 roundTripSSForRNA(aliFile, annFile);
613 @Test(groups = { "Functional" })
614 public void curlyWUSSsecondaryStructureForRNASequence() throws Exception
616 roundTripSSForRNA(aliFile, annFileCurlyWuss);
619 @Test(groups = { "Functional" })
620 public void fullWUSSsecondaryStructureForRNASequence() throws Exception
622 roundTripSSForRNA(aliFile, annFileFullWuss);
625 @Test(groups = { "Functional" })
626 public void detectWussBrackets()
628 for (char ch : new char[] { '{', '}', '[', ']', '(', ')', '<', '>' })
630 Assert.assertTrue(StockholmFile.RNASS_BRACKETS.indexOf(ch) >= 0,
631 "Didn't recognise '" + ch + "' as a WUSS bracket");
633 for (char ch : new char[] { '@', '!', '*', ' ', '-', '.' })
635 Assert.assertFalse(StockholmFile.RNASS_BRACKETS.indexOf(ch) >= 0,
636 "Shouldn't recognise '" + ch + "' as a WUSS bracket");
639 private static void roundTripSSForRNA(String aliFile, String annFile)
642 AlignmentI al = new AppletFormatAdapter().readFile(aliFile,
643 DataSourceType.PASTE, jalview.io.FileFormat.Fasta);
644 AnnotationFile aaf = new AnnotationFile();
645 aaf.readAnnotationFile(al, annFile, DataSourceType.PASTE);
646 al.getAlignmentAnnotation()[0].visible = true;
648 // TODO: create a better 'save as <format>' pattern
649 StockholmFile sf = new StockholmFile(al);
651 String stockholmFile = sf.print(al.getSequencesArray(), true);
653 AlignmentI newAl = new AppletFormatAdapter().readFile(stockholmFile,
654 DataSourceType.PASTE, jalview.io.FileFormat.Stockholm);
655 // AlignmentUtils.showOrHideSequenceAnnotations(newAl.getViewport()
656 // .getAlignment(), Arrays.asList("Secondary Structure"), newAl
657 // .getViewport().getAlignment().getSequences(), true, true);
658 testAlignmentEquivalence(al, newAl, true, true, true);
662 // this is the single sequence alignment and the SS annotations equivalent to
663 // the ones in file RnaSSTestFile
664 String aliFileRnaSS = ">Test.sequence/1-14\n"
666 String annFileRnaSSAlphaChars = "JALVIEW_ANNOTATION\n"
667 + "# Created: Thu Aug 02 14:54:57 BST 2018\n" + "\n"
668 + "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"
670 + "ROWPROPERTIES\tSecondary Structure\tscaletofit=true\tshowalllabs=true\tcentrelabs=false\n"
671 + "\n" + "\n" + "ALIGNMENT\tID=RNA.SS.TEST\tTP=RNA;";
672 String wrongAnnFileRnaSSAlphaChars = "JALVIEW_ANNOTATION\n"
673 + "# Created: Thu Aug 02 14:54:57 BST 2018\n" + "\n"
674 + "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"
676 + "ROWPROPERTIES\tSecondary Structure\tscaletofit=true\tshowalllabs=true\tcentrelabs=false\n"
677 + "\n" + "\n" + "ALIGNMENT\tID=RNA.SS.TEST\tTP=RNA;";
678 @Test(groups = { "Functional" })
679 public void stockholmFileRnaSSAlphaChars() throws Exception
681 AppletFormatAdapter af = new AppletFormatAdapter();
682 AlignmentI al = af.readFile(RnaSSTestFile, DataSourceType.FILE,
683 jalview.io.FileFormat.Stockholm);
684 Iterable<AlignmentAnnotation> aai = al.findAnnotations(null, null,
685 "Secondary Structure");
686 AlignmentAnnotation aa = aai.iterator().next();
687 Assert.assertTrue(aa.isRNA(),
688 "'" + RnaSSTestFile + "' not recognised as RNA SS");
689 Assert.assertTrue(aa.isValidStruc(),
690 "'" + RnaSSTestFile + "' not recognised as valid structure");
691 Annotation[] as = aa.annotations;
692 char[] As = new char[as.length];
693 for (int i = 0; i < as.length; i++)
695 As[i] = as[i].secondaryStructure;
697 char[] shouldBe = { '<', '(', 'E', 'H', 'B', 'h', 'e', 'b', '(', 'E',
698 ')', 'e', ')', '>' };
700 Arrays.equals(As, shouldBe),
701 "Annotation is " + new String(As) + " but should be "
702 + new String(shouldBe));
704 // this should result in the same RNA SS Annotations
705 AlignmentI newAl = new AppletFormatAdapter().readFile(
707 DataSourceType.PASTE, jalview.io.FileFormat.Fasta);
708 AnnotationFile aaf = new AnnotationFile();
709 aaf.readAnnotationFile(newAl, annFileRnaSSAlphaChars,
710 DataSourceType.PASTE);
713 testRnaSSAnnotationsEquivalent(al.getAlignmentAnnotation()[0],
714 newAl.getAlignmentAnnotation()[0]),
715 "RNA SS Annotations SHOULD be pair-wise equivalent (but apparently aren't): \n"
716 + "RNA SS A 1:" + al.getAlignmentAnnotation()[0] + "\n"
717 + "RNA SS A 2:" + newAl.getAlignmentAnnotation()[0]);
719 // this should NOT result in the same RNA SS Annotations
720 newAl = new AppletFormatAdapter().readFile(
721 aliFileRnaSS, DataSourceType.PASTE,
722 jalview.io.FileFormat.Fasta);
723 aaf = new AnnotationFile();
724 aaf.readAnnotationFile(newAl, wrongAnnFileRnaSSAlphaChars,
725 DataSourceType.PASTE);
727 boolean mismatch = testRnaSSAnnotationsEquivalent(al.getAlignmentAnnotation()[0],
728 newAl.getAlignmentAnnotation()[0]);
729 Assert.assertFalse(mismatch,
730 "RNA SS Annotations SHOULD NOT be pair-wise equivalent (but apparently are): \n"
731 + "RNA SS A 1:" + al.getAlignmentAnnotation()[0] + "\n"
732 + "RNA SS A 2:" + newAl.getAlignmentAnnotation()[0]);
735 private static boolean testRnaSSAnnotationsEquivalent(
736 AlignmentAnnotation a1,
737 AlignmentAnnotation a2)
739 return a1.rnaSecondaryStructureEquivalent(a2);
742 String annFileRnaSSWithSpaceChars = "JALVIEW_ANNOTATION\n"
743 + "# Created: Thu Aug 02 14:54:57 BST 2018\n" + "\n"
744 + "NO_GRAPH\tSecondary Structure\tSecondary Structure\t<,<|.,.|H,H| , |B,B|h,h| , |b,b|(,(|E,E|.,.|e,e|),)|>,>|\t2.0\n"
746 + "ROWPROPERTIES\tSecondary Structure\tscaletofit=true\tshowalllabs=true\tcentrelabs=false\n"
747 + "\n" + "\n" + "ALIGNMENT\tID=RNA.SS.TEST\tTP=RNA;";
748 String annFileRnaSSWithoutSpaceChars = "JALVIEW_ANNOTATION\n"
749 + "# Created: Thu Aug 02 14:54:57 BST 2018\n" + "\n"
750 + "NO_GRAPH\tSecondary Structure\tSecondary Structure\t<,<|.,.|H,H|.,.|B,B|h,h|.,.|b,b|(,(|E,E|.,.|e,e|),)|>,>|\t2.0\n"
752 + "ROWPROPERTIES\tSecondary Structure\tscaletofit=true\tshowalllabs=true\tcentrelabs=false\n"
753 + "\n" + "\n" + "ALIGNMENT\tID=RNA.SS.TEST\tTP=RNA;";
755 String wrongAnnFileRnaSSWithoutSpaceChars = "JALVIEW_ANNOTATION\n"
756 + "# Created: Thu Aug 02 14:54:57 BST 2018\n" + "\n"
757 + "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"
759 + "ROWPROPERTIES\tSecondary Structure\tscaletofit=true\tshowalllabs=true\tcentrelabs=false\n"
760 + "\n" + "\n" + "ALIGNMENT\tID=RNA.SS.TEST\tTP=RNA;";
762 @Test(groups = { "Functional" })
763 public void stockholmFileRnaSSSpaceChars() throws Exception
765 AlignmentI alWithSpaces = new AppletFormatAdapter().readFile(
766 aliFileRnaSS, DataSourceType.PASTE,
767 jalview.io.FileFormat.Fasta);
768 AnnotationFile afWithSpaces = new AnnotationFile();
769 afWithSpaces.readAnnotationFile(alWithSpaces,
770 annFileRnaSSWithSpaceChars, DataSourceType.PASTE);
772 Iterable<AlignmentAnnotation> aaiWithSpaces = alWithSpaces
773 .findAnnotations(null, null, "Secondary Structure");
774 AlignmentAnnotation aaWithSpaces = aaiWithSpaces.iterator().next();
775 Assert.assertTrue(aaWithSpaces.isRNA(),
776 "'" + aaWithSpaces + "' not recognised as RNA SS");
777 Assert.assertTrue(aaWithSpaces.isValidStruc(),
778 "'" + aaWithSpaces + "' not recognised as valid structure");
779 Annotation[] annWithSpaces = aaWithSpaces.annotations;
780 char[] As = new char[annWithSpaces.length];
781 for (int i = 0; i < annWithSpaces.length; i++)
783 As[i] = annWithSpaces[i].secondaryStructure;
785 // check all spaces and dots are spaces in the internal representation
786 char[] shouldBe = { '<', ' ', 'H', ' ', 'B', 'h', ' ', 'b', '(', 'E',
787 ' ', 'e', ')', '>' };
788 Assert.assertTrue(Arrays.equals(As, shouldBe), "Annotation is "
789 + new String(As) + " but should be " + new String(shouldBe));
791 // this should result in the same RNA SS Annotations
792 AlignmentI alWithoutSpaces = new AppletFormatAdapter().readFile(
793 aliFileRnaSS, DataSourceType.PASTE,
794 jalview.io.FileFormat.Fasta);
795 AnnotationFile afWithoutSpaces = new AnnotationFile();
796 afWithoutSpaces.readAnnotationFile(alWithoutSpaces,
797 annFileRnaSSWithoutSpaceChars,
798 DataSourceType.PASTE);
801 testRnaSSAnnotationsEquivalent(
802 alWithSpaces.getAlignmentAnnotation()[0],
803 alWithoutSpaces.getAlignmentAnnotation()[0]),
804 "RNA SS Annotations SHOULD be pair-wise equivalent (but apparently aren't): \n"
806 + alWithSpaces.getAlignmentAnnotation()[0]
807 .getRnaSecondaryStructure()
808 + "\n" + "RNA SS A 2:"
809 + alWithoutSpaces.getAlignmentAnnotation()[0]
810 .getRnaSecondaryStructure());
812 // this should NOT result in the same RNA SS Annotations
813 AlignmentI wrongAlWithoutSpaces = new AppletFormatAdapter().readFile(
814 aliFileRnaSS, DataSourceType.PASTE,
815 jalview.io.FileFormat.Fasta);
816 AnnotationFile wrongAfWithoutSpaces = new AnnotationFile();
817 wrongAfWithoutSpaces.readAnnotationFile(wrongAlWithoutSpaces,
818 wrongAnnFileRnaSSWithoutSpaceChars,
819 DataSourceType.PASTE);
822 testRnaSSAnnotationsEquivalent(
823 alWithSpaces.getAlignmentAnnotation()[0],
824 wrongAlWithoutSpaces.getAlignmentAnnotation()[0]),
825 "RNA SS Annotations SHOULD NOT be pair-wise equivalent (but apparently are): \n"
827 + alWithSpaces.getAlignmentAnnotation()[0]
828 .getRnaSecondaryStructure()
829 + "\n" + "RNA SS A 2:"
830 + wrongAlWithoutSpaces.getAlignmentAnnotation()[0]
831 .getRnaSecondaryStructure());
833 // check no spaces in the output
834 // TODO: create a better 'save as <format>' pattern
835 alWithSpaces.getAlignmentAnnotation()[0].visible = true;
836 StockholmFile sf = new StockholmFile(alWithSpaces);
838 String stockholmFile = sf.print(alWithSpaces.getSequencesArray(), true);
839 Pattern noSpacesInRnaSSAnnotation = Pattern
840 .compile("\\n#=GC SS_cons\\s+\\S{14}\\n");
841 Matcher m = noSpacesInRnaSSAnnotation.matcher(stockholmFile);
842 boolean matches = m.find();
843 Assert.assertTrue(matches,
844 "StockholmFile output does not contain expected output (may contain spaces):\n"