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 jalview.analysis.AlignmentUtils;
24 import jalview.analysis.SequenceIdMatcher;
25 import jalview.api.AlignViewportI;
26 import jalview.api.FeatureColourI;
27 import jalview.api.FeatureRenderer;
28 import jalview.api.FeaturesSourceI;
29 import jalview.datamodel.AlignedCodonFrame;
30 import jalview.datamodel.Alignment;
31 import jalview.datamodel.AlignmentI;
32 import jalview.datamodel.MappedFeatures;
33 import jalview.datamodel.SequenceDummy;
34 import jalview.datamodel.SequenceFeature;
35 import jalview.datamodel.SequenceI;
36 import jalview.datamodel.features.FeatureMatcherSet;
37 import jalview.datamodel.features.FeatureMatcherSetI;
38 import jalview.gui.Desktop;
39 import jalview.io.gff.GffHelperFactory;
40 import jalview.io.gff.GffHelperI;
41 import jalview.schemes.FeatureColour;
42 import jalview.util.ColorUtils;
43 import jalview.util.MapList;
44 import jalview.util.ParseHtmlBodyAndLinks;
45 import jalview.util.StringUtils;
47 import java.awt.Color;
48 import java.io.IOException;
49 import java.util.ArrayList;
50 import java.util.Arrays;
51 import java.util.Collections;
52 import java.util.HashMap;
53 import java.util.LinkedHashMap;
54 import java.util.List;
56 import java.util.Map.Entry;
57 import java.util.TreeMap;
60 * Parses and writes features files, which may be in Jalview, GFF2 or GFF3
61 * format. These are tab-delimited formats but with differences in the use of
64 * A Jalview feature file may define feature colours and then declare that the
65 * remainder of the file is in GFF format with the line 'GFF'.
67 * GFF3 files may include alignment mappings for features, which Jalview will
68 * attempt to model, and may include sequence data following a ##FASTA line.
75 public class FeaturesFile extends AlignFile implements FeaturesSourceI
77 private static final String EQUALS = "=";
79 private static final String TAB_REGEX = "\\t";
81 private static final String STARTGROUP = "STARTGROUP";
83 private static final String ENDGROUP = "ENDGROUP";
85 private static final String STARTFILTERS = "STARTFILTERS";
87 private static final String ENDFILTERS = "ENDFILTERS";
89 private static final String ID_NOT_SPECIFIED = "ID_NOT_SPECIFIED";
91 protected static final String GFF_VERSION = "##gff-version";
93 private AlignmentI lastmatchedAl = null;
95 private SequenceIdMatcher matcher = null;
97 protected AlignmentI dataset;
99 protected int gffVersion;
102 * Creates a new FeaturesFile object.
104 public FeaturesFile()
109 * Constructor which does not parse the file immediately
113 * @throws IOException
115 public FeaturesFile(String file, DataSourceType paste)
118 super(false, file, paste);
123 * @throws IOException
125 public FeaturesFile(FileParse source) throws IOException
131 * Constructor that optionally parses the file immediately
133 * @param parseImmediately
136 * @throws IOException
138 public FeaturesFile(boolean parseImmediately, String file,
139 DataSourceType type) throws IOException
141 super(parseImmediately, file, type);
145 * Parse GFF or sequence features file using case-independent matching,
149 * - alignment/dataset containing sequences that are to be annotated
151 * - hashtable to store feature colour definitions
153 * - process html strings into plain text
154 * @return true if features were added
156 public boolean parse(AlignmentI align,
157 Map<String, FeatureColourI> colours, boolean removeHTML)
159 return parse(align, colours, removeHTML, false);
163 * Extends the default addProperties by also adding peptide-to-cDNA mappings
164 * (if any) derived while parsing a GFF file
167 public void addProperties(AlignmentI al)
169 super.addProperties(al);
170 if (dataset != null && dataset.getCodonFrames() != null)
172 AlignmentI ds = (al.getDataset() == null) ? al : al.getDataset();
173 for (AlignedCodonFrame codons : dataset.getCodonFrames())
175 ds.addCodonFrame(codons);
181 * Parse GFF or Jalview format sequence features file
184 * - alignment/dataset containing sequences that are to be annotated
186 * - map to store feature colour definitions
188 * - process html strings into plain text
189 * @param relaxedIdmatching
190 * - when true, ID matches to compound sequence IDs are allowed
191 * @return true if features were added
193 public boolean parse(AlignmentI align,
194 Map<String, FeatureColourI> colours, boolean removeHTML,
195 boolean relaxedIdmatching)
197 return parse(align, colours, null, removeHTML, relaxedIdmatching);
201 * Parse GFF or Jalview format sequence features file
204 * - alignment/dataset containing sequences that are to be annotated
206 * - map to store feature colour definitions
208 * - map to store feature filter definitions
210 * - process html strings into plain text
211 * @param relaxedIdmatching
212 * - when true, ID matches to compound sequence IDs are allowed
213 * @return true if features were added
215 public boolean parse(AlignmentI align,
216 Map<String, FeatureColourI> colours,
217 Map<String, FeatureMatcherSetI> filters, boolean removeHTML,
218 boolean relaxedIdmatching)
220 Map<String, String> gffProps = new HashMap<>();
222 * keep track of any sequences we try to create from the data
224 List<SequenceI> newseqs = new ArrayList<>();
230 String featureGroup = null;
232 while ((line = nextLine()) != null)
234 // skip comments/process pragmas
235 if (line.length() == 0 || line.startsWith("#"))
237 if (line.toLowerCase().startsWith("##"))
239 processGffPragma(line, gffProps, align, newseqs);
244 gffColumns = line.split(TAB_REGEX);
245 if (gffColumns.length == 1)
247 if (line.trim().equalsIgnoreCase("GFF"))
250 * Jalview features file with appended GFF
251 * assume GFF2 (though it may declare ##gff-version 3)
258 if (gffColumns.length > 0 && gffColumns.length < 4)
261 * if 2 or 3 tokens, we anticipate either 'startgroup', 'endgroup' or
262 * a feature type colour specification
264 String ft = gffColumns[0];
265 if (ft.equalsIgnoreCase(STARTFILTERS))
267 parseFilters(filters);
270 if (ft.equalsIgnoreCase(STARTGROUP))
272 featureGroup = gffColumns[1];
274 else if (ft.equalsIgnoreCase(ENDGROUP))
276 // We should check whether this is the current group,
277 // but at present there's no way of showing more than 1 group
282 String colscheme = gffColumns[1];
283 FeatureColourI colour = FeatureColour
284 .parseJalviewFeatureColour(colscheme);
287 colours.put(ft, colour);
294 * if not a comment, GFF pragma, startgroup, endgroup or feature
295 * colour specification, that just leaves a feature details line
296 * in either Jalview or GFF format
300 parseJalviewFeature(line, gffColumns, align, colours, removeHTML,
301 relaxedIdmatching, featureGroup);
305 parseGff(gffColumns, align, relaxedIdmatching, newseqs);
309 } catch (Exception ex)
311 // should report somewhere useful for UI if necessary
312 warningMessage = ((warningMessage == null) ? "" : warningMessage)
313 + "Parsing error at\n" + line;
314 System.out.println("Error parsing feature file: " + ex + "\n" + line);
315 ex.printStackTrace(System.err);
321 * experimental - add any dummy sequences with features to the alignment
322 * - we need them for Ensembl feature extraction - though maybe not otherwise
324 for (SequenceI newseq : newseqs)
326 if (newseq.getFeatures().hasFeatures())
328 align.addSequence(newseq);
335 * Reads input lines from STARTFILTERS to ENDFILTERS and adds a feature type
336 * filter to the map for each line parsed. After exit from this method,
337 * nextLine() should return the line after ENDFILTERS (or we are already at
338 * end of file if ENDFILTERS was missing).
341 * @throws IOException
343 protected void parseFilters(Map<String, FeatureMatcherSetI> filters)
347 while ((line = nextLine()) != null)
349 if (line.toUpperCase().startsWith(ENDFILTERS))
353 String[] tokens = line.split(TAB_REGEX);
354 if (tokens.length != 2)
356 System.err.println(String.format("Invalid token count %d for %d",
357 tokens.length, line));
361 String featureType = tokens[0];
362 FeatureMatcherSetI fm = FeatureMatcherSet.fromString(tokens[1]);
363 if (fm != null && filters != null)
365 filters.put(featureType, fm);
372 * Try to parse a Jalview format feature specification and add it as a
373 * sequence feature to any matching sequences in the alignment. Returns true
374 * if successful (a feature was added), or false if not.
379 * @param featureColours
381 * @param relaxedIdmatching
382 * @param featureGroup
384 protected boolean parseJalviewFeature(String line, String[] gffColumns,
385 AlignmentI alignment, Map<String, FeatureColourI> featureColours,
386 boolean removeHTML, boolean relaxedIdMatching,
390 * tokens: description seqid seqIndex start end type [score]
392 if (gffColumns.length < 6)
394 System.err.println("Ignoring feature line '" + line
395 + "' with too few columns (" + gffColumns.length + ")");
398 String desc = gffColumns[0];
399 String seqId = gffColumns[1];
400 SequenceI seq = findSequence(seqId, alignment, null, relaxedIdMatching);
402 if (!ID_NOT_SPECIFIED.equals(seqId))
404 seq = findSequence(seqId, alignment, null, relaxedIdMatching);
410 String seqIndex = gffColumns[2];
413 int idx = Integer.parseInt(seqIndex);
414 seq = alignment.getSequenceAt(idx);
415 } catch (NumberFormatException ex)
417 System.err.println("Invalid sequence index: " + seqIndex);
423 System.out.println("Sequence not found: " + line);
427 int startPos = Integer.parseInt(gffColumns[3]);
428 int endPos = Integer.parseInt(gffColumns[4]);
430 String ft = gffColumns[5];
432 if (!featureColours.containsKey(ft))
435 * Perhaps an old style groups file with no colours -
436 * synthesize a colour from the feature type
438 Color colour = ColorUtils.createColourFromName(ft);
439 featureColours.put(ft, new FeatureColour(colour));
441 SequenceFeature sf = null;
442 if (gffColumns.length > 6)
444 float score = Float.NaN;
447 score = Float.valueOf(gffColumns[6]).floatValue();
448 } catch (NumberFormatException ex)
450 sf = new SequenceFeature(ft, desc, startPos, endPos, featureGroup);
452 sf = new SequenceFeature(ft, desc, startPos, endPos, score,
457 sf = new SequenceFeature(ft, desc, startPos, endPos, featureGroup);
460 parseDescriptionHTML(sf, removeHTML);
462 seq.addSequenceFeature(sf);
465 && (seq = alignment.findName(seq, seqId, false)) != null)
467 seq.addSequenceFeature(new SequenceFeature(sf));
473 * clear any temporary handles used to speed up ID matching
475 protected void resetMatcher()
477 lastmatchedAl = null;
482 * Returns a sequence matching the given id, as follows
484 * <li>strict matching is on exact sequence name</li>
485 * <li>relaxed matching allows matching on a token within the sequence name,
487 * <li>first tries to find a match in the alignment sequences</li>
488 * <li>else tries to find a match in the new sequences already generated while
489 * parsing the features file</li>
490 * <li>else creates a new placeholder sequence, adds it to the new sequences
491 * list, and returns it</li>
497 * @param relaxedIdMatching
501 protected SequenceI findSequence(String seqId, AlignmentI align,
502 List<SequenceI> newseqs, boolean relaxedIdMatching)
504 // TODO encapsulate in SequenceIdMatcher, share the matcher
505 // with the GffHelper (removing code duplication)
506 SequenceI match = null;
507 if (relaxedIdMatching)
509 if (lastmatchedAl != align)
511 lastmatchedAl = align;
512 matcher = new SequenceIdMatcher(align.getSequencesArray());
515 matcher.addAll(newseqs);
518 match = matcher.findIdMatch(seqId);
522 match = align.findName(seqId, true);
523 if (match == null && newseqs != null)
525 for (SequenceI m : newseqs)
527 if (seqId.equals(m.getName()))
535 if (match == null && newseqs != null)
537 match = new SequenceDummy(seqId);
538 if (relaxedIdMatching)
540 matcher.addAll(Arrays.asList(new SequenceI[] { match }));
542 // add dummy sequence to the newseqs list
548 public void parseDescriptionHTML(SequenceFeature sf, boolean removeHTML)
550 if (sf.getDescription() == null)
554 ParseHtmlBodyAndLinks parsed = new ParseHtmlBodyAndLinks(
555 sf.getDescription(), removeHTML, newline);
559 sf.setDescription(parsed.getNonHtmlContent());
562 for (String link : parsed.getLinks())
569 * Returns contents of a Jalview format features file, for visible features, as
570 * filtered by type and group. Features with a null group are displayed if their
571 * feature type is visible. Non-positional features may optionally be included
572 * (with no check on type or group).
576 * @param includeNonPositional
577 * if true, include non-positional features
578 * (regardless of group or type)
579 * @param includeComplement
580 * if true, include visible complementary
581 * (CDS/protein) positional features, with
582 * locations converted to local sequence
586 public String printJalviewFormat(SequenceI[] sequences,
587 FeatureRenderer fr, boolean includeNonPositional,
588 boolean includeComplement)
590 Map<String, FeatureColourI> visibleColours = fr
591 .getDisplayedFeatureCols();
592 Map<String, FeatureMatcherSetI> featureFilters = fr.getFeatureFilters();
595 * write out feature colours (if we know them)
597 // TODO: decide if feature links should also be written here ?
598 StringBuilder out = new StringBuilder(256);
599 if (visibleColours != null)
601 for (Entry<String, FeatureColourI> featureColour : visibleColours
604 FeatureColourI colour = featureColour.getValue();
605 out.append(colour.toJalviewFormat(featureColour.getKey())).append(
610 String[] types = visibleColours == null ? new String[0]
611 : visibleColours.keySet()
612 .toArray(new String[visibleColours.keySet().size()]);
615 * feature filters if any
617 outputFeatureFilters(out, visibleColours, featureFilters);
620 * output features within groups
622 int count = outputFeaturesByGroup(out, fr, types, sequences,
623 includeNonPositional);
625 if (includeComplement)
627 count += outputComplementFeatures(out, fr, sequences);
630 return count > 0 ? out.toString() : "No Features Visible";
634 * Outputs any visible complementary (CDS/peptide) positional features as
635 * Jalview format, within feature group. The coordinates of the linked features
636 * are converted to the corresponding positions of the local sequences.
643 private int outputComplementFeatures(StringBuilder out,
644 FeatureRenderer fr, SequenceI[] sequences)
646 AlignViewportI comp = fr.getViewport().getCodingComplement();
647 FeatureRenderer fr2 = Desktop.getAlignFrameFor(comp)
648 .getFeatureRenderer();
651 * bin features by feature group and sequence
653 Map<String, Map<String, List<SequenceFeature>>> map = new TreeMap<>(
654 String.CASE_INSENSITIVE_ORDER);
657 for (SequenceI seq : sequences)
660 * find complementary features
662 List<SequenceFeature> complementary = findComplementaryFeatures(seq,
664 String seqName = seq.getName();
666 for (SequenceFeature sf : complementary)
668 String group = sf.getFeatureGroup();
669 if (!map.containsKey(group))
671 map.put(group, new LinkedHashMap<>()); // preserves sequence order
673 Map<String, List<SequenceFeature>> groupFeatures = map.get(group);
674 if (!groupFeatures.containsKey(seqName))
676 groupFeatures.put(seqName, new ArrayList<>());
678 List<SequenceFeature> foundFeatures = groupFeatures.get(seqName);
679 foundFeatures.add(sf);
685 * output features by group
687 for (Entry<String, Map<String, List<SequenceFeature>>> groupFeatures : map.entrySet())
690 String group = groupFeatures.getKey();
691 if (!"".equals(group))
693 out.append(STARTGROUP).append(TAB).append(group).append(newline);
695 Map<String, List<SequenceFeature>> seqFeaturesMap = groupFeatures
697 for (Entry<String, List<SequenceFeature>> seqFeatures : seqFeaturesMap
700 String sequenceName = seqFeatures.getKey();
701 for (SequenceFeature sf : seqFeatures.getValue())
703 formatJalviewFeature(out, sequenceName, sf);
706 if (!"".equals(group))
708 out.append(ENDGROUP).append(TAB).append(group).append(newline);
716 * Answers a list of mapped features visible in the (CDS/protein) complement,
717 * with feature positions translated to local sequence coordinates
723 protected List<SequenceFeature> findComplementaryFeatures(SequenceI seq,
727 * avoid duplication of features (e.g. peptide feature
728 * at all 3 mapped codon positions)
730 List<SequenceFeature> found = new ArrayList<>();
731 List<SequenceFeature> complementary = new ArrayList<>();
733 for (int pos = seq.getStart(); pos <= seq.getEnd(); pos++)
735 MappedFeatures mf = fr2.findComplementFeaturesAtResidue(seq, pos);
739 MapList mapping = mf.mapping.getMap();
740 for (SequenceFeature sf : mf.features)
743 * make a virtual feature with local coordinates
745 if (!found.contains(sf))
747 String group = sf.getFeatureGroup();
753 int begin = sf.getBegin();
754 int end = sf.getEnd();
755 int[] range = mf.mapping.getTo() == seq.getDatasetSequence()
756 ? mapping.locateInTo(begin, end)
757 : mapping.locateInFrom(begin, end);
758 SequenceFeature sf2 = new SequenceFeature(sf, range[0],
759 range[1], group, sf.getScore());
760 complementary.add(sf2);
766 return complementary;
770 * Outputs any feature filters defined for visible feature types, sandwiched by
771 * STARTFILTERS and ENDFILTERS lines
775 * @param featureFilters
777 void outputFeatureFilters(StringBuilder out,
778 Map<String, FeatureColourI> visible,
779 Map<String, FeatureMatcherSetI> featureFilters)
781 if (visible == null || featureFilters == null
782 || featureFilters.isEmpty())
787 boolean first = true;
788 for (String featureType : visible.keySet())
790 FeatureMatcherSetI filter = featureFilters.get(featureType);
796 out.append(newline).append(STARTFILTERS).append(newline);
798 out.append(featureType).append(TAB).append(filter.toStableString())
804 out.append(ENDFILTERS).append(newline);
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.
816 * @param featureTypes
818 * @param includeNonPositional
821 private int outputFeaturesByGroup(StringBuilder out,
822 FeatureRenderer fr, String[] featureTypes,
823 SequenceI[] sequences, boolean includeNonPositional)
825 List<String> featureGroups = fr.getFeatureGroups();
828 * sort groups alphabetically, and ensure that features with a
829 * null or empty group are output after those in named groups
831 List<String> sortedGroups = new ArrayList<>(featureGroups);
832 sortedGroups.remove(null);
833 sortedGroups.remove("");
834 Collections.sort(sortedGroups);
835 sortedGroups.add(null);
836 sortedGroups.add("");
839 List<String> visibleGroups = fr.getDisplayedFeatureGroups();
842 * loop over all groups (may be visible or not);
843 * non-positional features are output even if group is not visible
845 for (String group : sortedGroups)
847 boolean firstInGroup = true;
848 boolean isNullGroup = group == null || "".equals(group);
850 for (int i = 0; i < sequences.length; i++)
852 String sequenceName = sequences[i].getName();
853 List<SequenceFeature> features = new ArrayList<>();
856 * get any non-positional features in this group, if wanted
857 * (for any feature type, whether visible or not)
859 if (includeNonPositional)
861 features.addAll(sequences[i].getFeatures()
862 .getFeaturesForGroup(false, group));
866 * add positional features for visible feature types, but
867 * (for named groups) only if feature group is visible
869 if (featureTypes.length > 0
870 && (isNullGroup || visibleGroups.contains(group)))
872 features.addAll(sequences[i].getFeatures().getFeaturesForGroup(
873 true, group, featureTypes));
876 for (SequenceFeature sf : features)
878 if (sf.isNonPositional() || fr.isVisible(sf))
886 out.append(STARTGROUP).append(TAB).append(group)
890 firstInGroup = false;
891 formatJalviewFeature(out, sequenceName, sf);
896 if (!isNullGroup && !firstInGroup)
898 out.append(ENDGROUP).append(TAB).append(group).append(newline);
905 * Formats one feature in Jalview format and appends to the string buffer
908 * @param sequenceName
909 * @param sequenceFeature
911 protected void formatJalviewFeature(
912 StringBuilder out, String sequenceName,
913 SequenceFeature sequenceFeature)
915 if (sequenceFeature.description == null
916 || sequenceFeature.description.equals(""))
918 out.append(sequenceFeature.type).append(TAB);
922 if (sequenceFeature.links != null
923 && sequenceFeature.getDescription().indexOf("<html>") == -1)
925 out.append("<html>");
928 out.append(sequenceFeature.description);
929 if (sequenceFeature.links != null)
931 for (int l = 0; l < sequenceFeature.links.size(); l++)
933 String label = sequenceFeature.links.elementAt(l);
934 String href = label.substring(label.indexOf("|") + 1);
935 label = label.substring(0, label.indexOf("|"));
937 if (sequenceFeature.description.indexOf(href) == -1)
939 out.append(" <a href=\"").append(href).append("\">")
940 .append(label).append("</a>");
944 if (sequenceFeature.getDescription().indexOf("</html>") == -1)
946 out.append("</html>");
952 out.append(sequenceName);
953 out.append("\t-1\t");
954 out.append(sequenceFeature.begin);
956 out.append(sequenceFeature.end);
958 out.append(sequenceFeature.type);
959 if (!Float.isNaN(sequenceFeature.score))
962 out.append(sequenceFeature.score);
968 * Parse method that is called when a GFF file is dragged to the desktop
973 AlignViewportI av = getViewport();
976 if (av.getAlignment() != null)
978 dataset = av.getAlignment().getDataset();
982 // working in the applet context ?
983 dataset = av.getAlignment();
988 dataset = new Alignment(new SequenceI[] {});
991 Map<String, FeatureColourI> featureColours = new HashMap<>();
992 boolean parseResult = parse(dataset, featureColours, false, true);
995 // pass error up somehow
999 // update viewport with the dataset data ?
1003 setSeqs(dataset.getSequencesArray());
1008 * Implementation of unused abstract method
1010 * @return error message
1013 public String print(SequenceI[] sqs, boolean jvsuffix)
1015 System.out.println("Use printGffFormat() or printJalviewFormat()");
1020 * Returns features output in GFF2 format
1023 * the sequences whose features are to be
1026 * a map whose keys are the type names of
1028 * @param visibleFeatureGroups
1029 * @param includeNonPositionalFeatures
1030 * @param includeComplement
1033 public String printGffFormat(SequenceI[] sequences,
1034 FeatureRenderer fr, boolean includeNonPositionalFeatures,
1035 boolean includeComplement)
1037 FeatureRenderer fr2 = null;
1038 if (includeComplement)
1040 AlignViewportI comp = fr.getViewport().getCodingComplement();
1041 fr2 = Desktop.getAlignFrameFor(comp).getFeatureRenderer();
1044 Map<String, FeatureColourI> visibleColours = fr.getDisplayedFeatureCols();
1046 StringBuilder out = new StringBuilder(256);
1048 out.append(String.format("%s %d\n", GFF_VERSION, gffVersion == 0 ? 2 : gffVersion));
1050 String[] types = visibleColours == null ? new String[0]
1051 : visibleColours.keySet()
1052 .toArray(new String[visibleColours.keySet().size()]);
1054 for (SequenceI seq : sequences)
1056 List<SequenceFeature> seqFeatures = new ArrayList<>();
1057 List<SequenceFeature> features = new ArrayList<>();
1058 if (includeNonPositionalFeatures)
1060 features.addAll(seq.getFeatures().getNonPositionalFeatures());
1062 if (visibleColours != null && !visibleColours.isEmpty())
1064 features.addAll(seq.getFeatures().getPositionalFeatures(types));
1066 for (SequenceFeature sf : features)
1068 if (sf.isNonPositional() || fr.isVisible(sf))
1071 * drop features hidden by group visibility, colour threshold,
1072 * or feature filter condition
1074 seqFeatures.add(sf);
1078 if (includeComplement)
1080 seqFeatures.addAll(findComplementaryFeatures(seq, fr2));
1084 * sort features here if wanted
1086 for (SequenceFeature sf : seqFeatures)
1088 formatGffFeature(out, seq, sf);
1089 out.append(newline);
1093 return out.toString();
1097 * Formats one feature as GFF and appends to the string buffer
1099 private void formatGffFeature(StringBuilder out, SequenceI seq,
1102 String source = sf.featureGroup;
1105 source = sf.getDescription();
1108 out.append(seq.getName());
1112 out.append(sf.type);
1114 out.append(sf.begin);
1118 out.append(sf.score);
1121 int strand = sf.getStrand();
1122 out.append(strand == 1 ? "+" : (strand == -1 ? "-" : "."));
1125 String phase = sf.getPhase();
1126 out.append(phase == null ? "." : phase);
1128 if (sf.otherDetails != null && !sf.otherDetails.isEmpty())
1130 Map<String, Object> map = sf.otherDetails;
1131 formatAttributes(out, map);
1136 * A helper method that outputs attributes stored in the map as
1137 * semicolon-delimited values e.g.
1140 * AC_Male=0;AF_NFE=0.00000e 00;Hom_FIN=0;GQ_MEDIAN=9
1143 * A map-valued attribute is formatted as a comma-delimited list within braces,
1147 * jvmap_CSQ={ALLELE_NUM=1,UNIPARC=UPI0002841053,Feature=ENST00000585561}
1150 * The {@code jvmap_} prefix designates a values map and is removed if the value
1151 * is parsed when read in. (The GFF3 specification allows 'semi-structured data'
1152 * to be represented provided the attribute name begins with a lower case
1157 * @see http://gmod.org/wiki/GFF3#GFF3_Format
1159 void formatAttributes(StringBuilder sb, Map<String, Object> map)
1162 boolean first = true;
1163 for (String key : map.keySet())
1165 if (SequenceFeature.STRAND.equals(key)
1166 || SequenceFeature.PHASE.equals(key))
1169 * values stashed in map but output to their own columns
1180 Object value = map.get(key);
1181 if (value instanceof Map<?, ?>)
1183 formatMapAttribute(sb, key, (Map<?, ?>) value);
1187 String formatted = StringUtils.urlEncode(value.toString(),
1188 GffHelperI.GFF_ENCODABLE);
1189 sb.append(key).append(EQUALS).append(formatted);
1195 * Formats the map entries as
1198 * key=key1=value1,key2=value2,...
1201 * and appends this to the string buffer
1207 private void formatMapAttribute(StringBuilder sb, String key,
1210 if (map == null || map.isEmpty())
1216 * AbstractMap.toString would be a shortcut here, but more reliable
1217 * to code the required format in case toString changes in future
1219 sb.append(key).append(EQUALS);
1220 boolean first = true;
1221 for (Entry<?, ?> entry : map.entrySet())
1228 sb.append(entry.getKey().toString()).append(EQUALS);
1229 String formatted = StringUtils.urlEncode(entry.getValue().toString(),
1230 GffHelperI.GFF_ENCODABLE);
1231 sb.append(formatted);
1236 * Returns a mapping given list of one or more Align descriptors (exonerate
1239 * @param alignedRegions
1240 * a list of "Align fromStart toStart fromCount"
1241 * @param mapIsFromCdna
1242 * if true, 'from' is dna, else 'from' is protein
1244 * either 1 (forward) or -1 (reverse)
1246 * @throws IOException
1248 protected MapList constructCodonMappingFromAlign(
1249 List<String> alignedRegions, boolean mapIsFromCdna, int strand)
1254 throw new IOException(
1255 "Invalid strand for a codon mapping (cannot be 0)");
1257 int regions = alignedRegions.size();
1258 // arrays to hold [start, end] for each aligned region
1259 int[] fromRanges = new int[regions * 2]; // from dna
1260 int[] toRanges = new int[regions * 2]; // to protein
1261 int fromRangesIndex = 0;
1262 int toRangesIndex = 0;
1264 for (String range : alignedRegions)
1267 * Align mapFromStart mapToStart mapFromCount
1268 * e.g. if mapIsFromCdna
1269 * Align 11270 143 120
1271 * 120 bases from pos 11270 align to pos 143 in peptide
1272 * if !mapIsFromCdna this would instead be
1273 * Align 143 11270 40
1275 String[] tokens = range.split(" ");
1276 if (tokens.length != 3)
1278 throw new IOException("Wrong number of fields for Align");
1285 fromStart = Integer.parseInt(tokens[0]);
1286 toStart = Integer.parseInt(tokens[1]);
1287 fromCount = Integer.parseInt(tokens[2]);
1288 } catch (NumberFormatException nfe)
1290 throw new IOException(
1291 "Invalid number in Align field: " + nfe.getMessage());
1295 * Jalview always models from dna to protein, so adjust values if the
1296 * GFF mapping is from protein to dna
1301 int temp = fromStart;
1302 fromStart = toStart;
1305 fromRanges[fromRangesIndex++] = fromStart;
1306 fromRanges[fromRangesIndex++] = fromStart + strand * (fromCount - 1);
1309 * If a codon has an intron gap, there will be contiguous 'toRanges';
1310 * this is handled for us by the MapList constructor.
1311 * (It is not clear that exonerate ever generates this case)
1313 toRanges[toRangesIndex++] = toStart;
1314 toRanges[toRangesIndex++] = toStart + (fromCount - 1) / 3;
1317 return new MapList(fromRanges, toRanges, 3, 1);
1321 * Parse a GFF format feature. This may include creating a 'dummy' sequence to
1322 * hold the feature, or for its mapped sequence, or both, to be resolved
1323 * either later in the GFF file (##FASTA section), or when the user loads
1324 * additional sequences.
1328 * @param relaxedIdMatching
1332 protected SequenceI parseGff(String[] gffColumns, AlignmentI alignment,
1333 boolean relaxedIdMatching, List<SequenceI> newseqs)
1336 * GFF: seqid source type start end score strand phase [attributes]
1338 if (gffColumns.length < 5)
1340 System.err.println("Ignoring GFF feature line with too few columns ("
1341 + gffColumns.length + ")");
1346 * locate referenced sequence in alignment _or_
1347 * as a forward or external reference (SequenceDummy)
1349 String seqId = gffColumns[0];
1350 SequenceI seq = findSequence(seqId, alignment, newseqs,
1353 SequenceFeature sf = null;
1354 GffHelperI helper = GffHelperFactory.getHelper(gffColumns);
1359 sf = helper.processGff(seq, gffColumns, alignment, newseqs,
1363 seq.addSequenceFeature(sf);
1364 while ((seq = alignment.findName(seq, seqId, true)) != null)
1366 seq.addSequenceFeature(new SequenceFeature(sf));
1369 } catch (IOException e)
1371 System.err.println("GFF parsing failed with: " + e.getMessage());
1380 * After encountering ##fasta in a GFF3 file, process the remainder of the
1381 * file as FAST sequence data. Any placeholder sequences created during
1382 * feature parsing are updated with the actual sequences.
1386 * @throws IOException
1388 protected void processAsFasta(AlignmentI align, List<SequenceI> newseqs)
1394 } catch (IOException q)
1397 FastaFile parser = new FastaFile(this);
1398 List<SequenceI> includedseqs = parser.getSeqs();
1400 SequenceIdMatcher smatcher = new SequenceIdMatcher(newseqs);
1403 * iterate over includedseqs, and replacing matching ones with newseqs
1404 * sequences. Generic iterator not used here because we modify
1405 * includedseqs as we go
1407 for (int p = 0, pSize = includedseqs.size(); p < pSize; p++)
1409 // search for any dummy seqs that this sequence can be used to update
1410 SequenceI includedSeq = includedseqs.get(p);
1411 SequenceI dummyseq = smatcher.findIdMatch(includedSeq);
1412 if (dummyseq != null && dummyseq instanceof SequenceDummy)
1414 // probably have the pattern wrong
1415 // idea is that a flyweight proxy for a sequence ID can be created for
1416 // 1. stable reference creation
1417 // 2. addition of annotation
1418 // 3. future replacement by a real sequence
1419 // current pattern is to create SequenceDummy objects - a convenience
1420 // constructor for a Sequence.
1421 // problem is that when promoted to a real sequence, all references
1422 // need to be updated somehow. We avoid that by keeping the same object.
1423 ((SequenceDummy) dummyseq).become(includedSeq);
1424 dummyseq.createDatasetSequence();
1427 * Update mappings so they are now to the dataset sequence
1429 for (AlignedCodonFrame mapping : align.getCodonFrames())
1431 mapping.updateToDataset(dummyseq);
1435 * replace parsed sequence with the realised forward reference
1437 includedseqs.set(p, dummyseq);
1440 * and remove from the newseqs list
1442 newseqs.remove(dummyseq);
1447 * finally add sequences to the dataset
1449 for (SequenceI seq : includedseqs)
1451 // experimental: mapping-based 'alignment' to query sequence
1452 AlignmentUtils.alignSequenceAs(seq, align,
1453 String.valueOf(align.getGapCharacter()), false, true);
1455 // rename sequences if GFF handler requested this
1456 // TODO a more elegant way e.g. gffHelper.postProcess(newseqs) ?
1457 List<SequenceFeature> sfs = seq.getFeatures().getPositionalFeatures();
1460 String newName = (String) sfs.get(0).getValue(
1461 GffHelperI.RENAME_TOKEN);
1462 if (newName != null)
1464 seq.setName(newName);
1467 align.addSequence(seq);
1472 * Process a ## directive
1478 * @throws IOException
1480 protected void processGffPragma(String line, Map<String, String> gffProps,
1481 AlignmentI align, List<SequenceI> newseqs) throws IOException
1484 if ("###".equals(line))
1486 // close off any open 'forward references'
1490 String[] tokens = line.substring(2).split(" ");
1491 String pragma = tokens[0];
1492 String value = tokens.length == 1 ? null : tokens[1];
1494 if ("gff-version".equalsIgnoreCase(pragma))
1500 // value may be e.g. "3.1.2"
1501 gffVersion = Integer.parseInt(value.split("\\.")[0]);
1502 } catch (NumberFormatException e)
1508 else if ("sequence-region".equalsIgnoreCase(pragma))
1510 // could capture <seqid start end> if wanted here
1512 else if ("feature-ontology".equalsIgnoreCase(pragma))
1514 // should resolve against the specified feature ontology URI
1516 else if ("attribute-ontology".equalsIgnoreCase(pragma))
1518 // URI of attribute ontology - not currently used in GFF3
1520 else if ("source-ontology".equalsIgnoreCase(pragma))
1522 // URI of source ontology - not currently used in GFF3
1524 else if ("species-build".equalsIgnoreCase(pragma))
1526 // save URI of specific NCBI taxon version of annotations
1527 gffProps.put("species-build", value);
1529 else if ("fasta".equalsIgnoreCase(pragma))
1531 // process the rest of the file as a fasta file and replace any dummy
1533 processAsFasta(align, newseqs);
1537 System.err.println("Ignoring unknown pragma: " + line);