X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FFeaturesFile.java;h=c08c84e32771b43dd0e02e04ddd8e2e9a833852d;hb=39f35c9fc1fb8270d93ba06aa83f3dfbd18dd4a2;hp=ada414021361d6e288a56dd1d7db148ed5a37b16;hpb=3595f261bc6f18dd8a4780976716bea81bd4fae4;p=jalview.git diff --git a/src/jalview/io/FeaturesFile.java b/src/jalview/io/FeaturesFile.java index ada4140..c08c84e 100755 --- a/src/jalview/io/FeaturesFile.java +++ b/src/jalview/io/FeaturesFile.java @@ -20,6 +20,18 @@ */ package jalview.io; +import java.awt.Color; +import java.io.IOException; +import java.util.ArrayList; +import java.util.Arrays; +import java.util.Collections; +import java.util.HashMap; +import java.util.LinkedHashMap; +import java.util.List; +import java.util.Map; +import java.util.Map.Entry; +import java.util.TreeMap; + import jalview.analysis.AlignmentUtils; import jalview.analysis.SequenceIdMatcher; import jalview.api.AlignViewportI; @@ -36,7 +48,6 @@ import jalview.datamodel.SequenceI; import jalview.datamodel.features.FeatureMatcherSet; import jalview.datamodel.features.FeatureMatcherSetI; import jalview.gui.Desktop; -import jalview.io.gff.GffHelperBase; import jalview.io.gff.GffHelperFactory; import jalview.io.gff.GffHelperI; import jalview.schemes.FeatureColour; @@ -45,18 +56,6 @@ import jalview.util.MapList; import jalview.util.ParseHtmlBodyAndLinks; import jalview.util.StringUtils; -import java.awt.Color; -import java.io.IOException; -import java.util.ArrayList; -import java.util.Arrays; -import java.util.Collections; -import java.util.HashMap; -import java.util.LinkedHashMap; -import java.util.List; -import java.util.Map; -import java.util.Map.Entry; -import java.util.TreeMap; - /** * Parses and writes features files, which may be in Jalview, GFF2 or GFF3 * format. These are tab-delimited formats but with differences in the use of @@ -75,6 +74,8 @@ import java.util.TreeMap; */ public class FeaturesFile extends AlignFile implements FeaturesSourceI { + private static final String EQUALS = "="; + private static final String TAB_REGEX = "\\t"; private static final String STARTGROUP = "STARTGROUP"; @@ -87,8 +88,6 @@ public class FeaturesFile extends AlignFile implements FeaturesSourceI private static final String ID_NOT_SPECIFIED = "ID_NOT_SPECIFIED"; - private static final String NOTE = "Note"; - protected static final String GFF_VERSION = "##gff-version"; private AlignmentI lastmatchedAl = null; @@ -109,11 +108,11 @@ public class FeaturesFile extends AlignFile implements FeaturesSourceI /** * Constructor which does not parse the file immediately * - * @param file + * @param file File or String filename * @param paste * @throws IOException */ - public FeaturesFile(String file, DataSourceType paste) + public FeaturesFile(Object file, DataSourceType paste) throws IOException { super(false, file, paste); @@ -136,7 +135,7 @@ public class FeaturesFile extends AlignFile implements FeaturesSourceI * @param type * @throws IOException */ - public FeaturesFile(boolean parseImmediately, String file, + public FeaturesFile(boolean parseImmediately, Object file, DataSourceType type) throws IOException { super(parseImmediately, file, type); @@ -632,7 +631,9 @@ public class FeaturesFile extends AlignFile implements FeaturesSourceI } /** - * Outputs any visible complementary positional features, within feature group + * Outputs any visible complementary (CDS/peptide) positional features as + * Jalview format, within feature group. The coordinates of the linked features + * are converted to the corresponding positions of the local sequences. * * @param out * @param fr @@ -647,66 +648,36 @@ public class FeaturesFile extends AlignFile implements FeaturesSourceI .getFeatureRenderer(); /* - * build a map of {group, {seqName, List}} + * bin features by feature group and sequence */ - Map>> map = new TreeMap<>(); + Map>> map = new TreeMap<>( + String.CASE_INSENSITIVE_ORDER); int count = 0; for (SequenceI seq : sequences) { /* - * avoid duplication of features (e.g. peptide feature - * at all 3 mapped codon positions) + * find complementary features */ - List found = new ArrayList<>(); + List complementary = findComplementaryFeatures(seq, + fr2); String seqName = seq.getName(); - for (int pos = seq.getStart(); pos <= seq.getEnd(); pos++) + for (SequenceFeature sf : complementary) { - MappedFeatures mf = fr2.findComplementFeaturesAtResidue(seq, pos); - - if (mf != null) + String group = sf.getFeatureGroup(); + if (!map.containsKey(group)) { - MapList mapping = mf.mapping.getMap(); - for (SequenceFeature sf : mf.features) - { - String group = sf.getFeatureGroup(); - if (group == null) - { - group = ""; - } - if (!map.containsKey(group)) - { - map.put(group, new LinkedHashMap<>()); - } - Map> groupFeatures = map - .get(group); - if (!groupFeatures.containsKey(seqName)) - { - groupFeatures.put(seqName, new ArrayList<>()); - } - List foundFeatures = groupFeatures - .get(seqName); - - /* - * make a virtual feature with local coordinates - */ - if (!found.contains(sf)) - { - found.add(sf); - int begin = sf.getBegin(); - int end = sf.getEnd(); - int[] range = mf.mapping.getTo() == seq.getDatasetSequence() - ? mapping.locateInTo(begin, end) - : mapping.locateInFrom(begin, end); - SequenceFeature sf2 = new SequenceFeature(sf, range[0], - range[1], group, - sf.getScore()); - foundFeatures.add(sf2); - count++; - } - } + map.put(group, new LinkedHashMap<>()); // preserves sequence order } + Map> groupFeatures = map.get(group); + if (!groupFeatures.containsKey(seqName)) + { + groupFeatures.put(seqName, new ArrayList<>()); + } + List foundFeatures = groupFeatures.get(seqName); + foundFeatures.add(sf); + count++; } } @@ -729,7 +700,7 @@ public class FeaturesFile extends AlignFile implements FeaturesSourceI String sequenceName = seqFeatures.getKey(); for (SequenceFeature sf : seqFeatures.getValue()) { - out.append(formatJalviewFeature(sequenceName, sf)); + formatJalviewFeature(out, sequenceName, sf); } } if (!"".equals(group)) @@ -742,6 +713,57 @@ public class FeaturesFile extends AlignFile implements FeaturesSourceI } /** + * Answers a list of mapped features visible in the (CDS/protein) complement, + * with feature positions translated to local sequence coordinates + * + * @param seq + * @param fr2 + * @return + */ + protected List findComplementaryFeatures(SequenceI seq, + FeatureRenderer fr2) + { + /* + * avoid duplication of features (e.g. peptide feature + * at all 3 mapped codon positions) + */ + List found = new ArrayList<>(); + List complementary = new ArrayList<>(); + + for (int pos = seq.getStart(); pos <= seq.getEnd(); pos++) + { + MappedFeatures mf = fr2.findComplementFeaturesAtResidue(seq, pos); + + if (mf != null) + { + for (SequenceFeature sf : mf.features) + { + /* + * make a virtual feature with local coordinates + */ + if (!found.contains(sf)) + { + String group = sf.getFeatureGroup(); + if (group == null) + { + group = ""; + } + found.add(sf); + int begin = sf.getBegin(); + int end = sf.getEnd(); + int[] range = mf.getMappedPositions(begin, end); + SequenceFeature sf2 = new SequenceFeature(sf, range[0], + range[1], group, sf.getScore()); + complementary.add(sf2); + } + } + } + } + + return complementary; + } + + /** * Outputs any feature filters defined for visible feature types, sandwiched by * STARTFILTERS and ENDFILTERS lines * @@ -863,7 +885,7 @@ public class FeaturesFile extends AlignFile implements FeaturesSourceI } } firstInGroup = false; - out.append(formatJalviewFeature(sequenceName, sf)); + formatJalviewFeature(out, sequenceName, sf); } } } @@ -877,14 +899,16 @@ public class FeaturesFile extends AlignFile implements FeaturesSourceI } /** + * Formats one feature in Jalview format and appends to the string buffer + * * @param out * @param sequenceName * @param sequenceFeature */ - protected String formatJalviewFeature( - String sequenceName, SequenceFeature sequenceFeature) + protected void formatJalviewFeature( + StringBuilder out, String sequenceName, + SequenceFeature sequenceFeature) { - StringBuilder out = new StringBuilder(64); if (sequenceFeature.description == null || sequenceFeature.description.equals("")) { @@ -909,7 +933,8 @@ public class FeaturesFile extends AlignFile implements FeaturesSourceI if (sequenceFeature.description.indexOf(href) == -1) { - out.append(" " + label + ""); + out.append(" ") + .append(label).append(""); } } @@ -934,8 +959,6 @@ public class FeaturesFile extends AlignFile implements FeaturesSourceI out.append(sequenceFeature.score); } out.append(newline); - - return out.toString(); } /** @@ -1008,24 +1031,26 @@ public class FeaturesFile extends AlignFile implements FeaturesSourceI FeatureRenderer fr, boolean includeNonPositionalFeatures, boolean includeComplement) { + FeatureRenderer fr2 = null; + if (includeComplement) + { + AlignViewportI comp = fr.getViewport().getCodingComplement(); + fr2 = Desktop.getAlignFrameFor(comp).getFeatureRenderer(); + } + Map visibleColours = fr.getDisplayedFeatureCols(); StringBuilder out = new StringBuilder(256); out.append(String.format("%s %d\n", GFF_VERSION, gffVersion == 0 ? 2 : gffVersion)); - if (!includeNonPositionalFeatures - && (visibleColours == null || visibleColours.isEmpty())) - { - return out.toString(); - } - String[] types = visibleColours == null ? new String[0] : visibleColours.keySet() .toArray(new String[visibleColours.keySet().size()]); for (SequenceI seq : sequences) { + List seqFeatures = new ArrayList<>(); List features = new ArrayList<>(); if (includeNonPositionalFeatures) { @@ -1035,51 +1060,29 @@ public class FeaturesFile extends AlignFile implements FeaturesSourceI { features.addAll(seq.getFeatures().getPositionalFeatures(types)); } - for (SequenceFeature sf : features) { - if (!sf.isNonPositional() && !fr.isVisible(sf)) + if (sf.isNonPositional() || fr.isVisible(sf)) { /* - * feature hidden by group visibility, colour threshold, + * drop features hidden by group visibility, colour threshold, * or feature filter condition */ - continue; - } - - String source = sf.featureGroup; - if (source == null) - { - source = sf.getDescription(); + seqFeatures.add(sf); } + } - out.append(seq.getName()); - out.append(TAB); - out.append(source); - out.append(TAB); - out.append(sf.type); - out.append(TAB); - out.append(sf.begin); - out.append(TAB); - out.append(sf.end); - out.append(TAB); - out.append(sf.score); - out.append(TAB); - - int strand = sf.getStrand(); - out.append(strand == 1 ? "+" : (strand == -1 ? "-" : ".")); - out.append(TAB); - - String phase = sf.getPhase(); - out.append(phase == null ? "." : phase); - - // miscellaneous key-values (GFF column 9) - String attributes = sf.getAttributes(); - if (attributes != null) - { - out.append(TAB).append(attributes); - } + if (includeComplement) + { + seqFeatures.addAll(findComplementaryFeatures(seq, fr2)); + } + /* + * sort features here if wanted + */ + for (SequenceFeature sf : seqFeatures) + { + formatGffFeature(out, seq, sf); out.append(newline); } } @@ -1088,15 +1091,154 @@ public class FeaturesFile extends AlignFile implements FeaturesSourceI } /** + * Formats one feature as GFF and appends to the string buffer + */ + private void formatGffFeature(StringBuilder out, SequenceI seq, + SequenceFeature sf) + { + String source = sf.featureGroup; + if (source == null) + { + source = sf.getDescription(); + } + + out.append(seq.getName()); + out.append(TAB); + out.append(source); + out.append(TAB); + out.append(sf.type); + out.append(TAB); + out.append(sf.begin); + out.append(TAB); + out.append(sf.end); + out.append(TAB); + out.append(sf.score); + out.append(TAB); + + int strand = sf.getStrand(); + out.append(strand == 1 ? "+" : (strand == -1 ? "-" : ".")); + out.append(TAB); + + String phase = sf.getPhase(); + out.append(phase == null ? "." : phase); + + if (sf.otherDetails != null && !sf.otherDetails.isEmpty()) + { + Map map = sf.otherDetails; + formatAttributes(out, map); + } + } + + /** + * A helper method that outputs attributes stored in the map as + * semicolon-delimited values e.g. + * + * 
+   * AC_Male=0;AF_NFE=0.00000e 00;Hom_FIN=0;GQ_MEDIAN=9
+   *
+ * + * A map-valued attribute is formatted as a comma-delimited list within braces, + * for example + * + * 
+   * jvmap_CSQ={ALLELE_NUM=1,UNIPARC=UPI0002841053,Feature=ENST00000585561}
+   *
+ * + * The {@code jvmap_} prefix designates a values map and is removed if the value + * is parsed when read in. (The GFF3 specification allows 'semi-structured data' + * to be represented provided the attribute name begins with a lower case + * letter.) + * + * @param sb + * @param map + * @see http://gmod.org/wiki/GFF3#GFF3_Format + */ + void formatAttributes(StringBuilder sb, Map map) + { + sb.append(TAB); + boolean first = true; + for (String key : map.keySet()) + { + if (SequenceFeature.STRAND.equals(key) + || SequenceFeature.PHASE.equals(key)) + { + /* + * values stashed in map but output to their own columns + */ + continue; + } + { + if (!first) + { + sb.append(";"); + } + } + first = false; + Object value = map.get(key); + if (value instanceof Map) + { + formatMapAttribute(sb, key, (Map) value); + } + else + { + String formatted = StringUtils.urlEncode(value.toString(), + GffHelperI.GFF_ENCODABLE); + sb.append(key).append(EQUALS).append(formatted); + } + } + } + + /** + * Formats the map entries as + * + * 
+   * key=key1=value1,key2=value2,...
+   *
+ * + * and appends this to the string buffer + * + * @param sb + * @param key + * @param map + */ + private void formatMapAttribute(StringBuilder sb, String key, + Map map) + { + if (map == null || map.isEmpty()) + { + return; + } + + /* + * AbstractMap.toString would be a shortcut here, but more reliable + * to code the required format in case toString changes in future + */ + sb.append(key).append(EQUALS); + boolean first = true; + for (Entry entry : map.entrySet()) + { + if (!first) + { + sb.append(","); + } + first = false; + sb.append(entry.getKey().toString()).append(EQUALS); + String formatted = StringUtils.urlEncode(entry.getValue().toString(), + GffHelperI.GFF_ENCODABLE); + sb.append(formatted); + } + } + + /** * Returns a mapping given list of one or more Align descriptors (exonerate * format) * * @param alignedRegions - * a list of "Align fromStart toStart fromCount" + * a list of "Align fromStart toStart fromCount" * @param mapIsFromCdna - * if true, 'from' is dna, else 'from' is protein + * if true, 'from' is dna, else 'from' is protein * @param strand - * either 1 (forward) or -1 (reverse) + * either 1 (forward) or -1 (reverse) * @return * @throws IOException */ @@ -1232,38 +1374,6 @@ public class FeaturesFile extends AlignFile implements FeaturesSourceI } /** - * Process the 'column 9' data of the GFF file. This is less formally defined, - * and its interpretation will vary depending on the tool that has generated - * it. - * - * @param attributes - * @param sf - */ - protected void processGffColumnNine(String attributes, SequenceFeature sf) - { - sf.setAttributes(attributes); - - /* - * Parse attributes in column 9 and add them to the sequence feature's - * 'otherData' table; use Note as a best proxy for description - */ - char nameValueSeparator = gffVersion == 3 ? '=' : ' '; - // TODO check we don't break GFF2 values which include commas here - Map> nameValues = GffHelperBase - .parseNameValuePairs(attributes, ";", nameValueSeparator, ","); - for (Entry> attr : nameValues.entrySet()) - { - String values = StringUtils.listToDelimitedString(attr.getValue(), - "; "); - sf.setValue(attr.getKey(), values); - if (NOTE.equals(attr.getKey())) - { - sf.setDescription(values); - } - } - } - - /** * After encountering ##fasta in a GFF3 file, process the remainder of the * file as FAST sequence data. Any placeholder sequences created during * feature parsing are updated with the actual sequences.