X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FFeaturesFile.java;h=7e62f6bc1a6e7ba4fd6bcadc0b1b5b183b824172;hb=2305d687bac5ed8a76ecb93c54c7b090a928e362;hp=39ec10de7b9e8c0ee03972a1d624baf17420240e;hpb=84ed42e8d0aa07b03441b045d240ebb51f94c53c;p=jalview.git diff --git a/src/jalview/io/FeaturesFile.java b/src/jalview/io/FeaturesFile.java index 39ec10d..7e62f6b 100755 --- a/src/jalview/io/FeaturesFile.java +++ b/src/jalview/io/FeaturesFile.java @@ -20,6 +20,19 @@ */ 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.Locale; +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; @@ -29,12 +42,13 @@ import jalview.api.FeaturesSourceI; import jalview.datamodel.AlignedCodonFrame; import jalview.datamodel.Alignment; import jalview.datamodel.AlignmentI; +import jalview.datamodel.MappedFeatures; import jalview.datamodel.SequenceDummy; import jalview.datamodel.SequenceFeature; import jalview.datamodel.SequenceI; import jalview.datamodel.features.FeatureMatcherSet; import jalview.datamodel.features.FeatureMatcherSetI; -import jalview.io.gff.GffHelperBase; +import jalview.gui.Desktop; import jalview.io.gff.GffHelperFactory; import jalview.io.gff.GffHelperI; import jalview.schemes.FeatureColour; @@ -43,16 +57,6 @@ 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.List; -import java.util.Map; -import java.util.Map.Entry; - /** * 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 @@ -71,6 +75,8 @@ import java.util.Map.Entry; */ 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"; @@ -83,8 +89,6 @@ 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; @@ -343,7 +347,8 @@ public class FeaturesFile extends AlignFile implements FeaturesSourceI String line; while ((line = nextLine()) != null) { - if (line.toUpperCase().startsWith(ENDFILTERS)) + // TODO: use .trim().equalsIgnoreCase here instead ? + if (line.toUpperCase(Locale.ROOT).startsWith(ENDFILTERS)) { return; } @@ -441,7 +446,7 @@ public class FeaturesFile extends AlignFile implements FeaturesSourceI float score = Float.NaN; try { - score = new Float(gffColumns[6]).floatValue(); + score = Float.valueOf(gffColumns[6]).floatValue(); } catch (NumberFormatException ex) { sf = new SequenceFeature(ft, desc, startPos, endPos, featureGroup); @@ -563,32 +568,30 @@ public class FeaturesFile extends AlignFile implements FeaturesSourceI } /** - * Returns contents of a Jalview format features file, for visible features, - * as filtered by type and group. Features with a null group are displayed if - * their feature type is visible. Non-positional features may optionally be - * included (with no check on type or group). + * Returns contents of a Jalview format features file, for visible features, as + * filtered by type and group. Features with a null group are displayed if their + * feature type is visible. Non-positional features may optionally be included + * (with no check on type or group). * * @param sequences * @param fr * @param includeNonPositional - * if true, include non-positional features (regardless of group or - * type) + * if true, include non-positional features + * (regardless of group or type) + * @param includeComplement + * if true, include visible complementary + * (CDS/protein) positional features, with + * locations converted to local sequence + * coordinates * @return */ public String printJalviewFormat(SequenceI[] sequences, - FeatureRenderer fr, boolean includeNonPositional) + FeatureRenderer fr, boolean includeNonPositional, + boolean includeComplement) { Map visibleColours = fr .getDisplayedFeatureCols(); Map featureFilters = fr.getFeatureFilters(); - List visibleFeatureGroups = fr.getDisplayedFeatureGroups(); - - if (!includeNonPositional - && (visibleColours == null || visibleColours.isEmpty())) - { - // no point continuing. - return "No Features Visible"; - } /* * write out feature colours (if we know them) @@ -616,42 +619,150 @@ public class FeaturesFile extends AlignFile implements FeaturesSourceI outputFeatureFilters(out, visibleColours, featureFilters); /* - * sort groups alphabetically, and ensure that features with a - * null or empty group are output after those in named groups + * output features within groups */ - List sortedGroups = new ArrayList<>(visibleFeatureGroups); - sortedGroups.remove(null); - sortedGroups.remove(""); - Collections.sort(sortedGroups); - sortedGroups.add(null); - sortedGroups.add(""); + int count = outputFeaturesByGroup(out, fr, types, sequences, + includeNonPositional); + + if (includeComplement) + { + count += outputComplementFeatures(out, fr, sequences); + } - boolean foundSome = false; + return count > 0 ? out.toString() : "No Features Visible"; + } + + /** + * 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 + * @param sequences + * @return + */ + private int outputComplementFeatures(StringBuilder out, + FeatureRenderer fr, SequenceI[] sequences) + { + AlignViewportI comp = fr.getViewport().getCodingComplement(); + FeatureRenderer fr2 = Desktop.getAlignFrameFor(comp) + .getFeatureRenderer(); /* - * first output any non-positional features + * bin features by feature group and sequence */ - if (includeNonPositional) + Map>> map = new TreeMap<>( + String.CASE_INSENSITIVE_ORDER); + int count = 0; + + for (SequenceI seq : sequences) { - for (int i = 0; i < sequences.length; i++) + /* + * find complementary features + */ + List complementary = findComplementaryFeatures(seq, + fr2); + String seqName = seq.getName(); + + for (SequenceFeature sf : complementary) { - String sequenceName = sequences[i].getName(); - for (SequenceFeature feature : sequences[i].getFeatures() - .getNonPositionalFeatures()) + String group = sf.getFeatureGroup(); + if (!map.containsKey(group)) + { + map.put(group, new LinkedHashMap<>()); // preserves sequence order + } + Map> groupFeatures = map.get(group); + if (!groupFeatures.containsKey(seqName)) { - foundSome = true; - out.append(formatJalviewFeature(sequenceName, feature)); + groupFeatures.put(seqName, new ArrayList<>()); } + List foundFeatures = groupFeatures.get(seqName); + foundFeatures.add(sf); + count++; } } /* - * positional features within groups + * output features by group */ - foundSome |= outputFeaturesByGroup(out, fr, sortedGroups, types, - sequences); + for (Entry>> groupFeatures : map.entrySet()) + { + out.append(newline); + String group = groupFeatures.getKey(); + if (!"".equals(group)) + { + out.append(STARTGROUP).append(TAB).append(group).append(newline); + } + Map> seqFeaturesMap = groupFeatures + .getValue(); + for (Entry> seqFeatures : seqFeaturesMap + .entrySet()) + { + String sequenceName = seqFeatures.getKey(); + for (SequenceFeature sf : seqFeatures.getValue()) + { + formatJalviewFeature(out, sequenceName, sf); + } + } + if (!"".equals(group)) + { + out.append(ENDGROUP).append(TAB).append(group).append(newline); + } + } + + return count; + } + + /** + * 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 foundSome ? out.toString() : "No Features Visible"; + return complementary; } /** @@ -697,72 +808,109 @@ public class FeaturesFile extends AlignFile implements FeaturesSourceI /** * Appends output of visible sequence features within feature groups to the * output buffer. Groups other than the null or empty group are sandwiched by - * STARTGROUP and ENDGROUP lines. Answers true if at least one feature was - * written, else false. + * STARTGROUP and ENDGROUP lines. Answers the number of features written. * * @param out * @param fr - * @param groups * @param featureTypes * @param sequences + * @param includeNonPositional * @return */ - private boolean outputFeaturesByGroup(StringBuilder out, - FeatureRenderer fr, List groups, String[] featureTypes, - SequenceI[] sequences) + private int outputFeaturesByGroup(StringBuilder out, + FeatureRenderer fr, String[] featureTypes, + SequenceI[] sequences, boolean includeNonPositional) { - boolean foundSome = false; - for (String group : groups) + List featureGroups = fr.getFeatureGroups(); + + /* + * sort groups alphabetically, and ensure that features with a + * null or empty group are output after those in named groups + */ + List sortedGroups = new ArrayList<>(featureGroups); + sortedGroups.remove(null); + sortedGroups.remove(""); + Collections.sort(sortedGroups); + sortedGroups.add(null); + sortedGroups.add(""); + + int count = 0; + List visibleGroups = fr.getDisplayedFeatureGroups(); + + /* + * loop over all groups (may be visible or not); + * non-positional features are output even if group is not visible + */ + for (String group : sortedGroups) { boolean firstInGroup = true; - boolean isNamedGroup = (group != null && !"".equals(group)); + boolean isNullGroup = group == null || "".equals(group); - /* - * output positional features within groups - */ for (int i = 0; i < sequences.length; i++) { String sequenceName = sequences[i].getName(); List features = new ArrayList<>(); - if (featureTypes.length > 0) + + /* + * get any non-positional features in this group, if wanted + * (for any feature type, whether visible or not) + */ + if (includeNonPositional) + { + features.addAll(sequences[i].getFeatures() + .getFeaturesForGroup(false, group)); + } + + /* + * add positional features for visible feature types, but + * (for named groups) only if feature group is visible + */ + if (featureTypes.length > 0 + && (isNullGroup || visibleGroups.contains(group))) { features.addAll(sequences[i].getFeatures().getFeaturesForGroup( true, group, featureTypes)); } - for (SequenceFeature sequenceFeature : features) + for (SequenceFeature sf : features) { - if (fr.isVisible(sequenceFeature)) + if (sf.isNonPositional() || fr.isVisible(sf)) { - foundSome = true; - if (firstInGroup && isNamedGroup) + count++; + if (firstInGroup) { - out.append(newline).append(STARTGROUP).append(TAB) - .append(group).append(newline); + out.append(newline); + if (!isNullGroup) + { + out.append(STARTGROUP).append(TAB).append(group) + .append(newline); + } } firstInGroup = false; - out.append(formatJalviewFeature(sequenceName, sequenceFeature)); + formatJalviewFeature(out, sequenceName, sf); } } } - if (isNamedGroup && !firstInGroup) + if (!isNullGroup && !firstInGroup) { out.append(ENDGROUP).append(TAB).append(group).append(newline); } } - return foundSome; + return count; } /** + * 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("")) { @@ -787,7 +935,8 @@ public class FeaturesFile extends AlignFile implements FeaturesSourceI if (sequenceFeature.description.indexOf(href) == -1) { - out.append(" " + label + ""); + out.append(" ") + .append(label).append(""); } } @@ -812,8 +961,6 @@ public class FeaturesFile extends AlignFile implements FeaturesSourceI out.append(sequenceFeature.score); } out.append(newline); - - return out.toString(); } /** @@ -872,34 +1019,40 @@ public class FeaturesFile extends AlignFile implements FeaturesSourceI * Returns features output in GFF2 format * * @param sequences - * the sequences whose features are to be output + * the sequences whose features are to be + * output * @param visible - * a map whose keys are the type names of visible features + * a map whose keys are the type names of + * visible features * @param visibleFeatureGroups * @param includeNonPositionalFeatures + * @param includeComplement * @return */ public String printGffFormat(SequenceI[] sequences, - FeatureRenderer fr, boolean includeNonPositionalFeatures) + 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) { @@ -909,51 +1062,29 @@ 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); } } @@ -962,15 +1093,154 @@ 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 */ @@ -1106,38 +1376,6 @@ 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.