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Coverage Report

  1. Project Clover database Mon Nov 11 2024 17:27:16 GMT
  2. Package jalview.io

File FeaturesFile.java

 

Coverage histogram

../../img/srcFileCovDistChart8.png
20% of files have more coverage

Code metrics

214
431
29
1
1,543
951
164
0.38
14.86
29
5.66

Classes

Class Line # Actions
FeaturesFile 76 431 164
0.719584672%
 

Contributing tests

This file is covered by 16 tests. .

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1    /*
2    * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3    * Copyright (C) $$Year-Rel$$ The Jalview Authors
4    *
5    * This file is part of Jalview.
6    *
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.
11    *
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.
16    *
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.
20    */
21    package jalview.io;
22   
23    import java.awt.Color;
24    import java.io.IOException;
25    import java.util.ArrayList;
26    import java.util.Arrays;
27    import java.util.Collections;
28    import java.util.HashMap;
29    import java.util.LinkedHashMap;
30    import java.util.List;
31    import java.util.Locale;
32    import java.util.Map;
33    import java.util.Map.Entry;
34    import java.util.TreeMap;
35   
36    import jalview.analysis.AlignmentUtils;
37    import jalview.analysis.SequenceIdMatcher;
38    import jalview.api.AlignViewportI;
39    import jalview.api.FeatureColourI;
40    import jalview.api.FeatureRenderer;
41    import jalview.api.FeaturesSourceI;
42    import jalview.datamodel.AlignedCodonFrame;
43    import jalview.datamodel.Alignment;
44    import jalview.datamodel.AlignmentI;
45    import jalview.datamodel.MappedFeatures;
46    import jalview.datamodel.SequenceDummy;
47    import jalview.datamodel.SequenceFeature;
48    import jalview.datamodel.SequenceI;
49    import jalview.datamodel.features.FeatureMatcherSet;
50    import jalview.datamodel.features.FeatureMatcherSetI;
51    import jalview.gui.Desktop;
52    import jalview.io.gff.GffHelperFactory;
53    import jalview.io.gff.GffHelperI;
54    import jalview.schemes.FeatureColour;
55    import jalview.util.ColorUtils;
56    import jalview.util.MapList;
57    import jalview.util.ParseHtmlBodyAndLinks;
58    import jalview.util.StringUtils;
59   
60    /**
61    * Parses and writes features files, which may be in Jalview, GFF2 or GFF3
62    * format. These are tab-delimited formats but with differences in the use of
63    * columns.
64    *
65    * A Jalview feature file may define feature colours and then declare that the
66    * remainder of the file is in GFF format with the line 'GFF'.
67    *
68    * GFF3 files may include alignment mappings for features, which Jalview will
69    * attempt to model, and may include sequence data following a ##FASTA line.
70    *
71    *
72    * @author AMW
73    * @author jbprocter
74    * @author gmcarstairs
75    */
 
76    public class FeaturesFile extends AlignFile implements FeaturesSourceI
77    {
78    private static final String EQUALS = "=";
79   
80    private static final String TAB_REGEX = "\\t";
81   
82    private static final String STARTGROUP = "STARTGROUP";
83   
84    private static final String ENDGROUP = "ENDGROUP";
85   
86    private static final String STARTFILTERS = "STARTFILTERS";
87   
88    private static final String ENDFILTERS = "ENDFILTERS";
89   
90    private static final String ID_NOT_SPECIFIED = "ID_NOT_SPECIFIED";
91   
92    protected static final String GFF_VERSION = "##gff-version";
93   
94    private AlignmentI lastmatchedAl = null;
95   
96    private SequenceIdMatcher matcher = null;
97   
98    protected AlignmentI dataset;
99   
100    protected int gffVersion;
101   
102    /**
103    * Creates a new FeaturesFile object.
104    */
 
105  4 toggle public FeaturesFile()
106    {
107    }
108   
109    /**
110    * Constructor which does not parse the file immediately
111    *
112    * @param file
113    * File or String filename
114    * @param paste
115    * @throws IOException
116    */
 
117  8 toggle public FeaturesFile(Object file, DataSourceType paste) throws IOException
118    {
119  8 super(false, file, paste);
120    }
121   
122    /**
123    * @param source
124    * @throws IOException
125    */
 
126  1 toggle public FeaturesFile(FileParse source) throws IOException
127    {
128  1 super(source);
129    }
130   
131    /**
132    * Constructor that optionally parses the file immediately
133    *
134    * @param parseImmediately
135    * @param file
136    * @param type
137    * @throws IOException
138    */
 
139  5 toggle public FeaturesFile(boolean parseImmediately, Object file,
140    DataSourceType type) throws IOException
141    {
142  5 super(parseImmediately, file, type);
143    }
144   
145    /**
146    * Parse GFF or sequence features file using case-independent matching,
147    * discarding URLs
148    *
149    * @param align
150    * - alignment/dataset containing sequences that are to be annotated
151    * @param colours
152    * - hashtable to store feature colour definitions
153    * @param removeHTML
154    * - process html strings into plain text
155    * @return true if features were added
156    */
 
157  5 toggle public boolean parse(AlignmentI align,
158    Map<String, FeatureColourI> colours, boolean removeHTML)
159    {
160  5 return parse(align, colours, removeHTML, false);
161    }
162   
163    /**
164    * Extends the default addProperties by also adding peptide-to-cDNA mappings
165    * (if any) derived while parsing a GFF file
166    */
 
167  2 toggle @Override
168    public void addProperties(AlignmentI al)
169    {
170  2 super.addProperties(al);
171  2 if (dataset != null && dataset.getCodonFrames() != null)
172    {
173  2 AlignmentI ds = (al.getDataset() == null) ? al : al.getDataset();
174  2 for (AlignedCodonFrame codons : dataset.getCodonFrames())
175    {
176  2 ds.addCodonFrame(codons);
177    }
178    }
179    }
180   
181    /**
182    * Parse GFF or Jalview format sequence features file
183    *
184    * @param align
185    * - alignment/dataset containing sequences that are to be annotated
186    * @param colours
187    * - map to store feature colour definitions
188    * @param removeHTML
189    * - process html strings into plain text
190    * @param relaxedIdmatching
191    * - when true, ID matches to compound sequence IDs are allowed
192    * @return true if features were added
193    */
 
194  9 toggle public boolean parse(AlignmentI align,
195    Map<String, FeatureColourI> colours, boolean removeHTML,
196    boolean relaxedIdmatching)
197    {
198  9 return parse(align, colours, null, removeHTML, relaxedIdmatching);
199    }
200   
201    /**
202    * Parse GFF or Jalview format sequence features file
203    *
204    * @param align
205    * - alignment/dataset containing sequences that are to be annotated
206    * @param colours
207    * - map to store feature colour definitions
208    * @param filters
209    * - map to store feature filter definitions
210    * @param removeHTML
211    * - process html strings into plain text
212    * @param relaxedIdmatching
213    * - when true, ID matches to compound sequence IDs are allowed
214    * @return true if features were added
215    */
 
216  13 toggle public boolean parse(AlignmentI align,
217    Map<String, FeatureColourI> colours,
218    Map<String, FeatureMatcherSetI> filters, boolean removeHTML,
219    boolean relaxedIdmatching)
220    {
221  13 Map<String, String> gffProps = new HashMap<>();
222    /*
223    * keep track of any sequences we try to create from the data
224    */
225  13 List<SequenceI> newseqs = new ArrayList<>();
226   
227  13 String line = null;
228  13 try
229    {
230  13 String[] gffColumns;
231  13 String featureGroup = null;
232   
233  ? while ((line = nextLine()) != null)
234    {
235    // skip comments/process pragmas
236  730 if (line.length() == 0 || line.startsWith("#"))
237    {
238  97 if (line.toLowerCase(Locale.ROOT).startsWith("##"))
239    {
240  26 processGffPragma(line, gffProps, align, newseqs);
241    }
242  97 continue;
243    }
244   
245  633 gffColumns = line.split(TAB_REGEX);
246  633 if (gffColumns.length == 1)
247    {
248  2 if (line.trim().equalsIgnoreCase("GFF"))
249    {
250    /*
251    * Jalview features file with appended GFF
252    * assume GFF2 (though it may declare ##gff-version 3)
253    */
254  1 gffVersion = 2;
255  1 continue;
256    }
257    }
258   
259  632 if (gffColumns.length > 0 && gffColumns.length < 4)
260    {
261    /*
262    * if 2 or 3 tokens, we anticipate either 'startgroup', 'endgroup' or
263    * a feature type colour specification
264    */
265  66 String ft = gffColumns[0];
266  66 if (ft.equalsIgnoreCase(STARTFILTERS))
267    {
268  1 parseFilters(filters);
269  1 continue;
270    }
271  65 if (ft.equalsIgnoreCase(STARTGROUP))
272    {
273  7 featureGroup = gffColumns[1];
274    }
275  58 else if (ft.equalsIgnoreCase(ENDGROUP))
276    {
277    // We should check whether this is the current group,
278    // but at present there's no way of showing more than 1 group
279  7 featureGroup = null;
280    }
281    else
282    {
283  51 String colscheme = gffColumns[1];
284  51 FeatureColourI colour = FeatureColour
285    .parseJalviewFeatureColour(colscheme);
286  51 if (colour != null)
287    {
288  51 colours.put(ft, colour);
289    }
290    }
291  65 continue;
292    }
293   
294    /*
295    * if not a comment, GFF pragma, startgroup, endgroup or feature
296    * colour specification, that just leaves a feature details line
297    * in either Jalview or GFF format
298    */
299  566 if (gffVersion == 0)
300    {
301  540 parseJalviewFeature(line, gffColumns, align, colours, removeHTML,
302    relaxedIdmatching, featureGroup);
303    }
304    else
305    {
306  26 parseGff(gffColumns, align, relaxedIdmatching, newseqs);
307    }
308    }
309  13 resetMatcher();
310    } catch (Exception ex)
311    {
312    // should report somewhere useful for UI if necessary
313  0 warningMessage = ((warningMessage == null) ? "" : warningMessage)
314    + "Parsing error at\n" + line;
315  0 jalview.bin.Console.outPrintln(
316    "Error parsing feature file: " + ex + "\n" + line);
317  0 ex.printStackTrace(System.err);
318  0 resetMatcher();
319  0 return false;
320    }
321   
322    /*
323    * experimental - add any dummy sequences with features to the alignment
324    * - we need them for Ensembl feature extraction - though maybe not otherwise
325    */
326  13 for (SequenceI newseq : newseqs)
327    {
328  3 if (newseq.getFeatures().hasFeatures())
329    {
330  1 align.addSequence(newseq);
331    }
332    }
333  13 return true;
334    }
335   
336    /**
337    * Reads input lines from STARTFILTERS to ENDFILTERS and adds a feature type
338    * filter to the map for each line parsed. After exit from this method,
339    * nextLine() should return the line after ENDFILTERS (or we are already at
340    * end of file if ENDFILTERS was missing).
341    *
342    * @param filters
343    * @throws IOException
344    */
 
345  2 toggle protected void parseFilters(Map<String, FeatureMatcherSetI> filters)
346    throws IOException
347    {
348  2 String line;
349  ? while ((line = nextLine()) != null)
350    {
351  5 if (line.toUpperCase(Locale.ROOT).startsWith(ENDFILTERS))
352    {
353  1 return;
354    }
355  4 String[] tokens = line.split(TAB_REGEX);
356  4 if (tokens.length != 2)
357    {
358  0 jalview.bin.Console.errPrintln(String.format(
359    "Invalid token count %d for %d", tokens.length, line));
360    }
361    else
362    {
363  4 String featureType = tokens[0];
364  4 FeatureMatcherSetI fm = FeatureMatcherSet.fromString(tokens[1]);
365  4 if (fm != null && filters != null)
366    {
367  2 filters.put(featureType, fm);
368    }
369    }
370    }
371    }
372   
373    /**
374    * Try to parse a Jalview format feature specification and add it as a
375    * sequence feature to any matching sequences in the alignment. Returns true
376    * if successful (a feature was added), or false if not.
377    *
378    * @param line
379    * @param gffColumns
380    * @param alignment
381    * @param featureColours
382    * @param removeHTML
383    * @param relaxedIdmatching
384    * @param featureGroup
385    */
 
386  540 toggle protected boolean parseJalviewFeature(String line, String[] gffColumns,
387    AlignmentI alignment, Map<String, FeatureColourI> featureColours,
388    boolean removeHTML, boolean relaxedIdMatching,
389    String featureGroup)
390    {
391    /*
392    * tokens: description seqid seqIndex start end type [score]
393    */
394  540 if (gffColumns.length < 6)
395    {
396  0 jalview.bin.Console.errPrintln("Ignoring feature line '" + line
397    + "' with too few columns (" + gffColumns.length + ")");
398  0 return false;
399    }
400  540 String desc = gffColumns[0];
401  540 String seqId = gffColumns[1];
402  540 SequenceI seq = findSequence(seqId, alignment, null, relaxedIdMatching);
403   
404  540 if (!ID_NOT_SPECIFIED.equals(seqId))
405    {
406  539 seq = findSequence(seqId, alignment, null, relaxedIdMatching);
407    }
408    else
409    {
410  1 seqId = null;
411  1 seq = null;
412  1 String seqIndex = gffColumns[2];
413  1 try
414    {
415  1 int idx = Integer.parseInt(seqIndex);
416  1 seq = alignment.getSequenceAt(idx);
417    } catch (NumberFormatException ex)
418    {
419  0 jalview.bin.Console
420    .errPrintln("Invalid sequence index: " + seqIndex);
421    }
422    }
423   
424  540 if (seq == null)
425    {
426  0 jalview.bin.Console.outPrintln("Sequence not found: " + line);
427  0 return false;
428    }
429   
430  540 int startPos = Integer.parseInt(gffColumns[3]);
431  540 int endPos = Integer.parseInt(gffColumns[4]);
432   
433  540 String ft = gffColumns[5];
434   
435  540 if (!featureColours.containsKey(ft))
436    {
437    /*
438    * Perhaps an old style groups file with no colours -
439    * synthesize a colour from the feature type
440    */
441  3 Color colour = ColorUtils.createColourFromName(ft);
442  3 featureColours.put(ft, new FeatureColour(colour));
443    }
444  540 SequenceFeature sf = null;
445  540 if (gffColumns.length > 6)
446    {
447  48 float score = Float.NaN;
448  48 try
449    {
450  48 score = Float.valueOf(gffColumns[6]).floatValue();
451    } catch (NumberFormatException ex)
452    {
453  0 sf = new SequenceFeature(ft, desc, startPos, endPos, featureGroup);
454    }
455  48 sf = new SequenceFeature(ft, desc, startPos, endPos, score,
456    featureGroup);
457    }
458    else
459    {
460  492 sf = new SequenceFeature(ft, desc, startPos, endPos, featureGroup);
461    }
462   
463  540 parseDescriptionHTML(sf, removeHTML);
464   
465  540 seq.addSequenceFeature(sf);
466   
467  ? while (seqId != null
468    && (seq = alignment.findName(seq, seqId, false)) != null)
469    {
470  0 seq.addSequenceFeature(new SequenceFeature(sf));
471    }
472  540 return true;
473    }
474   
475    /**
476    * clear any temporary handles used to speed up ID matching
477    */
 
478  13 toggle protected void resetMatcher()
479    {
480  13 lastmatchedAl = null;
481  13 matcher = null;
482    }
483   
484    /**
485    * Returns a sequence matching the given id, as follows
486    * <ul>
487    * <li>strict matching is on exact sequence name</li>
488    * <li>relaxed matching allows matching on a token within the sequence name,
489    * or a dbxref</li>
490    * <li>first tries to find a match in the alignment sequences</li>
491    * <li>else tries to find a match in the new sequences already generated while
492    * parsing the features file</li>
493    * <li>else creates a new placeholder sequence, adds it to the new sequences
494    * list, and returns it</li>
495    * </ul>
496    *
497    * @param seqId
498    * @param align
499    * @param newseqs
500    * @param relaxedIdMatching
501    *
502    * @return
503    */
 
504  1105 toggle protected SequenceI findSequence(String seqId, AlignmentI align,
505    List<SequenceI> newseqs, boolean relaxedIdMatching)
506    {
507    // TODO encapsulate in SequenceIdMatcher, share the matcher
508    // with the GffHelper (removing code duplication)
509  1105 SequenceI match = null;
510  1105 if (relaxedIdMatching)
511    {
512  12 if (lastmatchedAl != align)
513    {
514  3 lastmatchedAl = align;
515  3 matcher = new SequenceIdMatcher(align.getSequencesArray());
516  3 if (newseqs != null)
517    {
518  3 matcher.addAll(newseqs);
519    }
520    }
521  12 match = matcher.findIdMatch(seqId);
522    }
523    else
524    {
525  1093 match = align.findName(seqId, true);
526  1093 if (match == null && newseqs != null)
527    {
528  9 for (SequenceI m : newseqs)
529    {
530  7 if (seqId.equals(m.getName()))
531    {
532  7 return m;
533    }
534    }
535    }
536   
537    }
538  1098 if (match == null && newseqs != null)
539    {
540  5 match = new SequenceDummy(seqId);
541  5 if (relaxedIdMatching)
542    {
543  3 matcher.addAll(Arrays.asList(new SequenceI[] { match }));
544    }
545    // add dummy sequence to the newseqs list
546  5 newseqs.add(match);
547    }
548  1098 return match;
549    }
550   
 
551  540 toggle public void parseDescriptionHTML(SequenceFeature sf, boolean removeHTML)
552    {
553  540 if (sf.getDescription() == null)
554    {
555  0 return;
556    }
557  540 ParseHtmlBodyAndLinks parsed = new ParseHtmlBodyAndLinks(
558    sf.getDescription(), removeHTML, newline);
559   
560  540 if (removeHTML)
561    {
562  326 sf.setDescription(parsed.getNonHtmlContent());
563    }
564   
565  540 for (String link : parsed.getLinks())
566    {
567  136 sf.addLink(link);
568    }
569    }
570   
571    /**
572    * Returns contents of a Jalview format features file, for visible features,
573    * as filtered by type and group. Features with a null group are displayed if
574    * their feature type is visible. Non-positional features may optionally be
575    * included (with no check on type or group).
576    *
577    * @param sequences
578    * @param fr
579    * @param includeNonPositional
580    * if true, include non-positional features (regardless of group or
581    * type)
582    * @param includeComplement
583    * if true, include visible complementary (CDS/protein) positional
584    * features, with locations converted to local sequence coordinates
585    * @return
586    */
 
587  10 toggle public String printJalviewFormat(SequenceI[] sequences,
588    FeatureRenderer fr, boolean includeNonPositional,
589    boolean includeComplement)
590    {
591  10 Map<String, FeatureColourI> visibleColours = fr
592    .getDisplayedFeatureCols();
593  10 Map<String, FeatureMatcherSetI> featureFilters = fr.getFeatureFilters();
594   
595    /*
596    * write out feature colours (if we know them)
597    */
598    // TODO: decide if feature links should also be written here ?
599  10 StringBuilder out = new StringBuilder(256);
600  10 if (visibleColours != null)
601    {
602  10 for (Entry<String, FeatureColourI> featureColour : visibleColours
603    .entrySet())
604    {
605  15 FeatureColourI colour = featureColour.getValue();
606  15 out.append(colour.toJalviewFormat(featureColour.getKey()))
607    .append(newline);
608    }
609    }
610   
611  10 String[] types = visibleColours == null ? new String[0]
612    : visibleColours.keySet()
613    .toArray(new String[visibleColours.keySet().size()]);
614   
615    /*
616    * feature filters if any
617    */
618  10 outputFeatureFilters(out, visibleColours, featureFilters);
619   
620    /*
621    * output features within groups
622    */
623  10 int count = outputFeaturesByGroup(out, fr, types, sequences,
624    includeNonPositional);
625   
626  10 if (includeComplement)
627    {
628  0 count += outputComplementFeatures(out, fr, sequences);
629    }
630   
631  10 return count > 0 ? out.toString() : "No Features Visible";
632    }
633   
634    /**
635    * Outputs any visible complementary (CDS/peptide) positional features as
636    * Jalview format, within feature group. The coordinates of the linked
637    * features are converted to the corresponding positions of the local
638    * sequences.
639    *
640    * @param out
641    * @param fr
642    * @param sequences
643    * @return
644    */
 
645  0 toggle private int outputComplementFeatures(StringBuilder out,
646    FeatureRenderer fr, SequenceI[] sequences)
647    {
648  0 AlignViewportI comp = fr.getViewport().getCodingComplement();
649  0 FeatureRenderer fr2 = Desktop.getAlignFrameFor(comp)
650    .getFeatureRenderer();
651   
652    /*
653    * bin features by feature group and sequence
654    */
655  0 Map<String, Map<String, List<SequenceFeature>>> map = new TreeMap<>(
656    String.CASE_INSENSITIVE_ORDER);
657  0 int count = 0;
658   
659  0 for (SequenceI seq : sequences)
660    {
661    /*
662    * find complementary features
663    */
664  0 List<SequenceFeature> complementary = findComplementaryFeatures(seq,
665    fr2);
666  0 String seqName = seq.getName();
667   
668  0 for (SequenceFeature sf : complementary)
669    {
670  0 String group = sf.getFeatureGroup();
671  0 if (!map.containsKey(group))
672    {
673  0 map.put(group, new LinkedHashMap<>()); // preserves sequence order
674    }
675  0 Map<String, List<SequenceFeature>> groupFeatures = map.get(group);
676  0 if (!groupFeatures.containsKey(seqName))
677    {
678  0 groupFeatures.put(seqName, new ArrayList<>());
679    }
680  0 List<SequenceFeature> foundFeatures = groupFeatures.get(seqName);
681  0 foundFeatures.add(sf);
682  0 count++;
683    }
684    }
685   
686    /*
687    * output features by group
688    */
689  0 for (Entry<String, Map<String, List<SequenceFeature>>> groupFeatures : map
690    .entrySet())
691    {
692  0 out.append(newline);
693  0 String group = groupFeatures.getKey();
694  0 if (!"".equals(group))
695    {
696  0 out.append(STARTGROUP).append(TAB).append(group).append(newline);
697    }
698  0 Map<String, List<SequenceFeature>> seqFeaturesMap = groupFeatures
699    .getValue();
700  0 for (Entry<String, List<SequenceFeature>> seqFeatures : seqFeaturesMap
701    .entrySet())
702    {
703  0 String sequenceName = seqFeatures.getKey();
704  0 for (SequenceFeature sf : seqFeatures.getValue())
705    {
706  0 formatJalviewFeature(out, sequenceName, sf);
707    }
708    }
709  0 if (!"".equals(group))
710    {
711  0 out.append(ENDGROUP).append(TAB).append(group).append(newline);
712    }
713    }
714   
715  0 return count;
716    }
717   
718    /**
719    * Answers a list of mapped features visible in the (CDS/protein) complement,
720    * with feature positions translated to local sequence coordinates
721    *
722    * @param seq
723    * @param fr2
724    * @return
725    */
 
726  0 toggle protected List<SequenceFeature> findComplementaryFeatures(SequenceI seq,
727    FeatureRenderer fr2)
728    {
729    /*
730    * avoid duplication of features (e.g. peptide feature
731    * at all 3 mapped codon positions)
732    */
733  0 List<SequenceFeature> found = new ArrayList<>();
734  0 List<SequenceFeature> complementary = new ArrayList<>();
735   
736  0 for (int pos = seq.getStart(); pos <= seq.getEnd(); pos++)
737    {
738  0 MappedFeatures mf = fr2.findComplementFeaturesAtResidue(seq, pos);
739   
740  0 if (mf != null)
741    {
742  0 for (SequenceFeature sf : mf.features)
743    {
744    /*
745    * make a virtual feature with local coordinates
746    */
747  0 if (!found.contains(sf))
748    {
749  0 String group = sf.getFeatureGroup();
750  0 if (group == null)
751    {
752  0 group = "";
753    }
754  0 found.add(sf);
755  0 int begin = sf.getBegin();
756  0 int end = sf.getEnd();
757  0 int[] range = mf.getMappedPositions(begin, end);
758  0 SequenceFeature sf2 = new SequenceFeature(sf, range[0],
759    range[1], group, sf.getScore());
760  0 complementary.add(sf2);
761    }
762    }
763    }
764    }
765   
766  0 return complementary;
767    }
768   
769    /**
770    * Outputs any feature filters defined for visible feature types, sandwiched
771    * by STARTFILTERS and ENDFILTERS lines
772    *
773    * @param out
774    * @param visible
775    * @param featureFilters
776    */
 
777  13 toggle void outputFeatureFilters(StringBuilder out,
778    Map<String, FeatureColourI> visible,
779    Map<String, FeatureMatcherSetI> featureFilters)
780    {
781  13 if (visible == null || featureFilters == null
782    || featureFilters.isEmpty())
783    {
784  10 return;
785    }
786   
787  3 boolean first = true;
788  3 for (String featureType : visible.keySet())
789    {
790  4 FeatureMatcherSetI filter = featureFilters.get(featureType);
791  4 if (filter != null)
792    {
793  3 if (first)
794    {
795  2 first = false;
796  2 out.append(newline).append(STARTFILTERS).append(newline);
797    }
798  3 out.append(featureType).append(TAB).append(filter.toStableString())
799    .append(newline);
800    }
801    }
802  3 if (!first)
803    {
804  2 out.append(ENDFILTERS).append(newline);
805    }
806   
807    }
808   
809    /**
810    * Appends output of visible sequence features within feature groups to the
811    * output buffer. Groups other than the null or empty group are sandwiched by
812    * STARTGROUP and ENDGROUP lines. Answers the number of features written.
813    *
814    * @param out
815    * @param fr
816    * @param featureTypes
817    * @param sequences
818    * @param includeNonPositional
819    * @return
820    */
 
821  10 toggle private int outputFeaturesByGroup(StringBuilder out, FeatureRenderer fr,
822    String[] featureTypes, SequenceI[] sequences,
823    boolean includeNonPositional)
824    {
825  10 List<String> featureGroups = fr.getFeatureGroups();
826   
827    /*
828    * sort groups alphabetically, and ensure that features with a
829    * null or empty group are output after those in named groups
830    */
831  10 List<String> sortedGroups = new ArrayList<>(featureGroups);
832  10 sortedGroups.remove(null);
833  10 sortedGroups.remove("");
834  10 Collections.sort(sortedGroups);
835  10 sortedGroups.add(null);
836  10 sortedGroups.add("");
837   
838  10 int count = 0;
839  10 List<String> visibleGroups = fr.getDisplayedFeatureGroups();
840   
841    /*
842    * loop over all groups (may be visible or not);
843    * non-positional features are output even if group is not visible
844    */
845  10 for (String group : sortedGroups)
846    {
847  33 boolean firstInGroup = true;
848  33 boolean isNullGroup = group == null || "".equals(group);
849   
850  528 for (int i = 0; i < sequences.length; i++)
851    {
852  495 String sequenceName = sequences[i].getName();
853  495 List<SequenceFeature> features = new ArrayList<>();
854   
855    /*
856    * get any non-positional features in this group, if wanted
857    * (for any feature type, whether visible or not)
858    */
859  495 if (includeNonPositional)
860    {
861  90 features.addAll(sequences[i].getFeatures()
862    .getFeaturesForGroup(false, group));
863    }
864   
865    /*
866    * add positional features for visible feature types, but
867    * (for named groups) only if feature group is visible
868    */
869  495 if (featureTypes.length > 0
870    && (isNullGroup || visibleGroups.contains(group)))
871    {
872  390 features.addAll(sequences[i].getFeatures()
873    .getFeaturesForGroup(true, group, featureTypes));
874    }
875   
876  495 for (SequenceFeature sf : features)
877    {
878  25 if (sf.isNonPositional() || fr.isVisible(sf))
879    {
880  23 count++;
881  23 if (firstInGroup)
882    {
883  18 out.append(newline);
884  18 if (!isNullGroup)
885    {
886  10 out.append(STARTGROUP).append(TAB).append(group)
887    .append(newline);
888    }
889    }
890  23 firstInGroup = false;
891  23 formatJalviewFeature(out, sequenceName, sf);
892    }
893    }
894    }
895   
896  33 if (!isNullGroup && !firstInGroup)
897    {
898  10 out.append(ENDGROUP).append(TAB).append(group).append(newline);
899    }
900    }
901  10 return count;
902    }
903   
904    /**
905    * Formats one feature in Jalview format and appends to the string buffer
906    *
907    * @param out
908    * @param sequenceName
909    * @param sequenceFeature
910    */
 
911  23 toggle protected void formatJalviewFeature(StringBuilder out,
912    String sequenceName, SequenceFeature sequenceFeature)
913    {
914  23 if (sequenceFeature.description == null
915    || sequenceFeature.description.equals(""))
916    {
917  0 out.append(sequenceFeature.type).append(TAB);
918    }
919    else
920    {
921  23 if (sequenceFeature.links != null
922    && sequenceFeature.getDescription().indexOf("<html>") == -1)
923    {
924  0 out.append("<html>");
925    }
926   
927  23 out.append(sequenceFeature.description);
928  23 if (sequenceFeature.links != null)
929    {
930  2 for (int l = 0; l < sequenceFeature.links.size(); l++)
931    {
932  1 String label = sequenceFeature.links.elementAt(l);
933  1 String href = label.substring(label.indexOf("|") + 1);
934  1 label = label.substring(0, label.indexOf("|"));
935   
936  1 if (sequenceFeature.description.indexOf(href) == -1)
937    {
938  0 out.append(" <a href=\"").append(href).append("\">")
939    .append(label).append("</a>");
940    }
941    }
942   
943  1 if (sequenceFeature.getDescription().indexOf("</html>") == -1)
944    {
945  0 out.append("</html>");
946    }
947    }
948   
949  23 out.append(TAB);
950    }
951  23 out.append(sequenceName);
952  23 out.append("\t-1\t");
953  23 out.append(sequenceFeature.begin);
954  23 out.append(TAB);
955  23 out.append(sequenceFeature.end);
956  23 out.append(TAB);
957  23 out.append(sequenceFeature.type);
958  23 if (!Float.isNaN(sequenceFeature.score))
959    {
960  18 out.append(TAB);
961  18 out.append(sequenceFeature.score);
962    }
963  23 out.append(newline);
964    }
965   
966    /**
967    * Parse method that is called when a GFF file is dragged to the desktop
968    */
 
969  2 toggle @Override
970    public void parse()
971    {
972  2 AlignViewportI av = getViewport();
973  2 if (av != null)
974    {
975  0 if (av.getAlignment() != null)
976    {
977  0 dataset = av.getAlignment().getDataset();
978    }
979  0 if (dataset == null)
980    {
981    // working in the applet context ?
982  0 dataset = av.getAlignment();
983    }
984    }
985    else
986    {
987  2 dataset = new Alignment(new SequenceI[] {});
988    }
989   
990  2 Map<String, FeatureColourI> featureColours = new HashMap<>();
991  2 boolean parseResult = parse(dataset, featureColours, false, true);
992  2 if (!parseResult)
993    {
994    // pass error up somehow
995    }
996  2 if (av != null)
997    {
998    // update viewport with the dataset data ?
999    }
1000    else
1001    {
1002  2 setSeqs(dataset.getSequencesArray());
1003    }
1004    }
1005   
1006    /**
1007    * Implementation of unused abstract method
1008    *
1009    * @return error message
1010    */
 
1011  0 toggle @Override
1012    public String print(SequenceI[] sqs, boolean jvsuffix)
1013    {
1014  0 jalview.bin.Console
1015    .outPrintln("Use printGffFormat() or printJalviewFormat()");
1016  0 return null;
1017    }
1018   
1019    /**
1020    * Returns features output in GFF2 format
1021    *
1022    * @param sequences
1023    * the sequences whose features are to be output
1024    * @param visible
1025    * a map whose keys are the type names of visible features
1026    * @param visibleFeatureGroups
1027    * @param includeNonPositionalFeatures
1028    * @param includeComplement
1029    * @return
1030    */
 
1031  11 toggle public String printGffFormat(SequenceI[] sequences, FeatureRenderer fr,
1032    boolean includeNonPositionalFeatures, boolean includeComplement)
1033    {
1034  11 FeatureRenderer fr2 = null;
1035  11 if (includeComplement)
1036    {
1037  0 AlignViewportI comp = fr.getViewport().getCodingComplement();
1038  0 fr2 = Desktop.getAlignFrameFor(comp).getFeatureRenderer();
1039    }
1040   
1041  11 Map<String, FeatureColourI> visibleColours = fr
1042    .getDisplayedFeatureCols();
1043   
1044  11 StringBuilder out = new StringBuilder(256);
1045   
1046  11 out.append(String.format("%s %d\n", GFF_VERSION,
1047  11 gffVersion == 0 ? 2 : gffVersion));
1048   
1049  11 String[] types = visibleColours == null ? new String[0]
1050    : visibleColours.keySet()
1051    .toArray(new String[visibleColours.keySet().size()]);
1052   
1053  11 for (SequenceI seq : sequences)
1054    {
1055  165 List<SequenceFeature> seqFeatures = new ArrayList<>();
1056  165 List<SequenceFeature> features = new ArrayList<>();
1057  165 if (includeNonPositionalFeatures)
1058    {
1059  30 features.addAll(seq.getFeatures().getNonPositionalFeatures());
1060    }
1061  165 if (visibleColours != null && !visibleColours.isEmpty())
1062    {
1063  105 features.addAll(seq.getFeatures().getPositionalFeatures(types));
1064    }
1065  165 for (SequenceFeature sf : features)
1066    {
1067  16 if (sf.isNonPositional() || fr.isVisible(sf))
1068    {
1069    /*
1070    * drop features hidden by group visibility, colour threshold,
1071    * or feature filter condition
1072    */
1073  13 seqFeatures.add(sf);
1074    }
1075    }
1076   
1077  165 if (includeComplement)
1078    {
1079  0 seqFeatures.addAll(findComplementaryFeatures(seq, fr2));
1080    }
1081   
1082    /*
1083    * sort features here if wanted
1084    */
1085  165 for (SequenceFeature sf : seqFeatures)
1086    {
1087  13 formatGffFeature(out, seq, sf);
1088  13 out.append(newline);
1089    }
1090    }
1091   
1092  11 return out.toString();
1093    }
1094   
1095    /**
1096    * Formats one feature as GFF and appends to the string buffer
1097    */
 
1098  13 toggle private void formatGffFeature(StringBuilder out, SequenceI seq,
1099    SequenceFeature sf)
1100    {
1101  13 String source = sf.featureGroup;
1102  13 if (source == null)
1103    {
1104  9 source = sf.getDescription();
1105    }
1106   
1107  13 out.append(seq.getName());
1108  13 out.append(TAB);
1109  13 out.append(source);
1110  13 out.append(TAB);
1111  13 out.append(sf.type);
1112  13 out.append(TAB);
1113  13 out.append(sf.begin);
1114  13 out.append(TAB);
1115  13 out.append(sf.end);
1116  13 out.append(TAB);
1117  13 out.append(sf.score);
1118  13 out.append(TAB);
1119   
1120  13 int strand = sf.getStrand();
1121  12 out.append(strand == 1 ? "+" : (strand == -1 ? "-" : "."));
1122  13 out.append(TAB);
1123   
1124  13 String phase = sf.getPhase();
1125  13 out.append(phase == null ? "." : phase);
1126   
1127  13 if (sf.otherDetails != null && !sf.otherDetails.isEmpty())
1128    {
1129  7 Map<String, Object> map = sf.otherDetails;
1130  7 formatAttributes(out, map);
1131    }
1132    }
1133   
1134    /**
1135    * A helper method that outputs attributes stored in the map as
1136    * semicolon-delimited values e.g.
1137    *
1138    * <pre>
1139    * AC_Male=0;AF_NFE=0.00000e 00;Hom_FIN=0;GQ_MEDIAN=9
1140    * </pre>
1141    *
1142    * A map-valued attribute is formatted as a comma-delimited list within
1143    * braces, for example
1144    *
1145    * <pre>
1146    * jvmap_CSQ={ALLELE_NUM=1,UNIPARC=UPI0002841053,Feature=ENST00000585561}
1147    * </pre>
1148    *
1149    * The {@code jvmap_} prefix designates a values map and is removed if the
1150    * value is parsed when read in. (The GFF3 specification allows
1151    * 'semi-structured data' to be represented provided the attribute name begins
1152    * with a lower case letter.)
1153    *
1154    * @param sb
1155    * @param map
1156    * @see http://gmod.org/wiki/GFF3#GFF3_Format
1157    */
 
1158  7 toggle void formatAttributes(StringBuilder sb, Map<String, Object> map)
1159    {
1160  7 sb.append(TAB);
1161  7 boolean first = true;
1162  7 for (String key : map.keySet())
1163    {
1164  17 if (SequenceFeature.STRAND.equals(key)
1165    || SequenceFeature.PHASE.equals(key))
1166    {
1167    /*
1168    * values stashed in map but output to their own columns
1169    */
1170  2 continue;
1171    }
1172    {
1173  15 if (!first)
1174    {
1175  8 sb.append(";");
1176    }
1177    }
1178  15 first = false;
1179  15 Object value = map.get(key);
1180  15 if (value instanceof Map<?, ?>)
1181    {
1182  1 formatMapAttribute(sb, key, (Map<?, ?>) value);
1183    }
1184    else
1185    {
1186  14 String formatted = StringUtils.urlEncode(value.toString(),
1187    GffHelperI.GFF_ENCODABLE);
1188  14 sb.append(key).append(EQUALS).append(formatted);
1189    }
1190    }
1191    }
1192   
1193    /**
1194    * Formats the map entries as
1195    *
1196    * <pre>
1197    * key=key1=value1,key2=value2,...
1198    * </pre>
1199    *
1200    * and appends this to the string buffer
1201    *
1202    * @param sb
1203    * @param key
1204    * @param map
1205    */
 
1206  1 toggle private void formatMapAttribute(StringBuilder sb, String key,
1207    Map<?, ?> map)
1208    {
1209  1 if (map == null || map.isEmpty())
1210    {
1211  0 return;
1212    }
1213   
1214    /*
1215    * AbstractMap.toString would be a shortcut here, but more reliable
1216    * to code the required format in case toString changes in future
1217    */
1218  1 sb.append(key).append(EQUALS);
1219  1 boolean first = true;
1220  1 for (Entry<?, ?> entry : map.entrySet())
1221    {
1222  2 if (!first)
1223    {
1224  1 sb.append(",");
1225    }
1226  2 first = false;
1227  2 sb.append(entry.getKey().toString()).append(EQUALS);
1228  2 String formatted = StringUtils.urlEncode(entry.getValue().toString(),
1229    GffHelperI.GFF_ENCODABLE);
1230  2 sb.append(formatted);
1231    }
1232    }
1233   
1234    /**
1235    * Returns a mapping given list of one or more Align descriptors (exonerate
1236    * format)
1237    *
1238    * @param alignedRegions
1239    * a list of "Align fromStart toStart fromCount"
1240    * @param mapIsFromCdna
1241    * if true, 'from' is dna, else 'from' is protein
1242    * @param strand
1243    * either 1 (forward) or -1 (reverse)
1244    * @return
1245    * @throws IOException
1246    */
 
1247  0 toggle protected MapList constructCodonMappingFromAlign(
1248    List<String> alignedRegions, boolean mapIsFromCdna, int strand)
1249    throws IOException
1250    {
1251  0 if (strand == 0)
1252    {
1253  0 throw new IOException(
1254    "Invalid strand for a codon mapping (cannot be 0)");
1255    }
1256  0 int regions = alignedRegions.size();
1257    // arrays to hold [start, end] for each aligned region
1258  0 int[] fromRanges = new int[regions * 2]; // from dna
1259  0 int[] toRanges = new int[regions * 2]; // to protein
1260  0 int fromRangesIndex = 0;
1261  0 int toRangesIndex = 0;
1262   
1263  0 for (String range : alignedRegions)
1264    {
1265    /*
1266    * Align mapFromStart mapToStart mapFromCount
1267    * e.g. if mapIsFromCdna
1268    * Align 11270 143 120
1269    * means:
1270    * 120 bases from pos 11270 align to pos 143 in peptide
1271    * if !mapIsFromCdna this would instead be
1272    * Align 143 11270 40
1273    */
1274  0 String[] tokens = range.split(" ");
1275  0 if (tokens.length != 3)
1276    {
1277  0 throw new IOException("Wrong number of fields for Align");
1278    }
1279  0 int fromStart = 0;
1280  0 int toStart = 0;
1281  0 int fromCount = 0;
1282  0 try
1283    {
1284  0 fromStart = Integer.parseInt(tokens[0]);
1285  0 toStart = Integer.parseInt(tokens[1]);
1286  0 fromCount = Integer.parseInt(tokens[2]);
1287    } catch (NumberFormatException nfe)
1288    {
1289  0 throw new IOException(
1290    "Invalid number in Align field: " + nfe.getMessage());
1291    }
1292   
1293    /*
1294    * Jalview always models from dna to protein, so adjust values if the
1295    * GFF mapping is from protein to dna
1296    */
1297  0 if (!mapIsFromCdna)
1298    {
1299  0 fromCount *= 3;
1300  0 int temp = fromStart;
1301  0 fromStart = toStart;
1302  0 toStart = temp;
1303    }
1304  0 fromRanges[fromRangesIndex++] = fromStart;
1305  0 fromRanges[fromRangesIndex++] = fromStart + strand * (fromCount - 1);
1306   
1307    /*
1308    * If a codon has an intron gap, there will be contiguous 'toRanges';
1309    * this is handled for us by the MapList constructor.
1310    * (It is not clear that exonerate ever generates this case)
1311    */
1312  0 toRanges[toRangesIndex++] = toStart;
1313  0 toRanges[toRangesIndex++] = toStart + (fromCount - 1) / 3;
1314    }
1315   
1316  0 return new MapList(fromRanges, toRanges, 3, 1);
1317    }
1318   
1319    /**
1320    * Parse a GFF format feature. This may include creating a 'dummy' sequence to
1321    * hold the feature, or for its mapped sequence, or both, to be resolved
1322    * either later in the GFF file (##FASTA section), or when the user loads
1323    * additional sequences.
1324    *
1325    * @param gffColumns
1326    * @param alignment
1327    * @param relaxedIdMatching
1328    * @param newseqs
1329    * @return
1330    */
 
1331  26 toggle protected SequenceI parseGff(String[] gffColumns, AlignmentI alignment,
1332    boolean relaxedIdMatching, List<SequenceI> newseqs)
1333    {
1334    /*
1335    * GFF: seqid source type start end score strand phase [attributes]
1336    */
1337  26 if (gffColumns.length < 5)
1338    {
1339  0 jalview.bin.Console
1340    .errPrintln("Ignoring GFF feature line with too few columns ("
1341    + gffColumns.length + ")");
1342  0 return null;
1343    }
1344   
1345    /*
1346    * locate referenced sequence in alignment _or_
1347    * as a forward or external reference (SequenceDummy)
1348    */
1349  26 String seqId = gffColumns[0];
1350  26 SequenceI seq = findSequence(seqId, alignment, newseqs,
1351    relaxedIdMatching);
1352   
1353  26 SequenceFeature sf = null;
1354  26 GffHelperI helper = GffHelperFactory.getHelper(gffColumns);
1355  26 if (helper != null)
1356    {
1357  26 try
1358    {
1359  26 sf = helper.processGff(seq, gffColumns, alignment, newseqs,
1360    relaxedIdMatching);
1361  26 if (sf != null)
1362    {
1363  19 seq.addSequenceFeature(sf);
1364  ? while ((seq = alignment.findName(seq, seqId, true)) != null)
1365    {
1366  0 seq.addSequenceFeature(new SequenceFeature(sf));
1367    }
1368    }
1369    } catch (IOException e)
1370    {
1371  0 jalview.bin.Console
1372    .errPrintln("GFF parsing failed with: " + e.getMessage());
1373  0 return null;
1374    }
1375    }
1376   
1377  26 return seq;
1378    }
1379   
1380    /**
1381    * After encountering ##fasta in a GFF3 file, process the remainder of the
1382    * file as FAST sequence data. Any placeholder sequences created during
1383    * feature parsing are updated with the actual sequences.
1384    *
1385    * @param align
1386    * @param newseqs
1387    * @throws IOException
1388    */
 
1389  4 toggle protected void processAsFasta(AlignmentI align, List<SequenceI> newseqs)
1390    throws IOException
1391    {
1392  4 try
1393    {
1394  4 mark();
1395    } catch (IOException q)
1396    {
1397    }
1398    // Opening a FastaFile object with the remainder of this object's dataIn.
1399    // Tell the constructor to NOT close the dataIn when finished.
1400  4 FastaFile parser = new FastaFile(this, false);
1401  4 List<SequenceI> includedseqs = parser.getSeqs();
1402   
1403  4 SequenceIdMatcher smatcher = new SequenceIdMatcher(newseqs);
1404   
1405    /*
1406    * iterate over includedseqs, and replacing matching ones with newseqs
1407    * sequences. Generic iterator not used here because we modify
1408    * includedseqs as we go
1409    */
1410  12 for (int p = 0, pSize = includedseqs.size(); p < pSize; p++)
1411    {
1412    // search for any dummy seqs that this sequence can be used to update
1413  8 SequenceI includedSeq = includedseqs.get(p);
1414  8 SequenceI dummyseq = smatcher.findIdMatch(includedSeq);
1415  8 if (dummyseq != null && dummyseq instanceof SequenceDummy)
1416    {
1417    // probably have the pattern wrong
1418    // idea is that a flyweight proxy for a sequence ID can be created for
1419    // 1. stable reference creation
1420    // 2. addition of annotation
1421    // 3. future replacement by a real sequence
1422    // current pattern is to create SequenceDummy objects - a convenience
1423    // constructor for a Sequence.
1424    // problem is that when promoted to a real sequence, all references
1425    // need to be updated somehow. We avoid that by keeping the same object.
1426  8 ((SequenceDummy) dummyseq).become(includedSeq);
1427  8 dummyseq.createDatasetSequence();
1428   
1429    /*
1430    * Update mappings so they are now to the dataset sequence
1431    */
1432  8 for (AlignedCodonFrame mapping : align.getCodonFrames())
1433    {
1434  8 mapping.updateToDataset(dummyseq);
1435    }
1436   
1437    /*
1438    * replace parsed sequence with the realised forward reference
1439    */
1440  8 includedseqs.set(p, dummyseq);
1441   
1442    /*
1443    * and remove from the newseqs list
1444    */
1445  8 newseqs.remove(dummyseq);
1446    }
1447    }
1448   
1449    /*
1450    * finally add sequences to the dataset
1451    */
1452  4 for (SequenceI seq : includedseqs)
1453    {
1454    // experimental: mapping-based 'alignment' to query sequence
1455  8 AlignmentUtils.alignSequenceAs(seq, align,
1456    String.valueOf(align.getGapCharacter()), false, true);
1457   
1458    // rename sequences if GFF handler requested this
1459    // TODO a more elegant way e.g. gffHelper.postProcess(newseqs) ?
1460  8 List<SequenceFeature> sfs = seq.getFeatures().getPositionalFeatures();
1461  8 if (!sfs.isEmpty())
1462    {
1463  4 String newName = (String) sfs.get(0)
1464    .getValue(GffHelperI.RENAME_TOKEN);
1465  4 if (newName != null)
1466    {
1467  0 seq.setName(newName);
1468    }
1469    }
1470  8 align.addSequence(seq);
1471    }
1472    }
1473   
1474    /**
1475    * Process a ## directive
1476    *
1477    * @param line
1478    * @param gffProps
1479    * @param align
1480    * @param newseqs
1481    * @throws IOException
1482    */
 
1483  26 toggle protected void processGffPragma(String line, Map<String, String> gffProps,
1484    AlignmentI align, List<SequenceI> newseqs) throws IOException
1485    {
1486  26 line = line.trim();
1487  26 if ("###".equals(line))
1488    {
1489    // close off any open 'forward references'
1490  0 return;
1491    }
1492   
1493  26 String[] tokens = line.substring(2).split(" ");
1494  26 String pragma = tokens[0];
1495  26 String value = tokens.length == 1 ? null : tokens[1];
1496   
1497  26 if ("gff-version".equalsIgnoreCase(pragma))
1498    {
1499  7 if (value != null)
1500    {
1501  7 try
1502    {
1503    // value may be e.g. "3.1.2"
1504  7 gffVersion = Integer.parseInt(value.split("\\.")[0]);
1505    } catch (NumberFormatException e)
1506    {
1507    // ignore
1508    }
1509    }
1510    }
1511  19 else if ("sequence-region".equalsIgnoreCase(pragma))
1512    {
1513    // could capture <seqid start end> if wanted here
1514    }
1515  19 else if ("feature-ontology".equalsIgnoreCase(pragma))
1516    {
1517    // should resolve against the specified feature ontology URI
1518    }
1519  19 else if ("attribute-ontology".equalsIgnoreCase(pragma))
1520    {
1521    // URI of attribute ontology - not currently used in GFF3
1522    }
1523  19 else if ("source-ontology".equalsIgnoreCase(pragma))
1524    {
1525    // URI of source ontology - not currently used in GFF3
1526    }
1527  19 else if ("species-build".equalsIgnoreCase(pragma))
1528    {
1529    // save URI of specific NCBI taxon version of annotations
1530  0 gffProps.put("species-build", value);
1531    }
1532  19 else if ("fasta".equalsIgnoreCase(pragma))
1533    {
1534    // process the rest of the file as a fasta file and replace any dummy
1535    // sequence IDs
1536  4 processAsFasta(align, newseqs);
1537    }
1538    else
1539    {
1540  15 jalview.bin.Console.errPrintln("Ignoring unknown pragma: " + line);
1541    }
1542    }
1543    }
  • Report generated by OpenClover v 4.4.1 on Mon Nov 11 2024 17:34:35 GMT using coverage data from Mon Nov 11 2024 17:34:16 GMT.
  • OpenClover is free and open-source software.