X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FFeaturesFile.java;h=7e62f6bc1a6e7ba4fd6bcadc0b1b5b183b824172;hb=2305d687bac5ed8a76ecb93c54c7b090a928e362;hp=fffa650bfa75e1b47381c5607962b6f6803e1f9b;hpb=51d3b1944c2c400e157dec7910c047c9521ba872;p=jalview.git diff --git a/src/jalview/io/FeaturesFile.java b/src/jalview/io/FeaturesFile.java index fffa650..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; @@ -36,7 +49,6 @@ 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 +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.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 +75,8 @@ 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 +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; @@ -347,7 +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; } @@ -713,6 +714,14 @@ public class FeaturesFile extends AlignFile implements FeaturesSourceI 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) { @@ -729,7 +738,6 @@ public class FeaturesFile extends AlignFile implements FeaturesSourceI if (mf != null) { - MapList mapping = mf.mapping.getMap(); for (SequenceFeature sf : mf.features) { /* @@ -745,9 +753,7 @@ public class FeaturesFile extends AlignFile implements FeaturesSourceI 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); + int[] range = mf.getMappedPositions(begin, end); SequenceFeature sf2 = new SequenceFeature(sf, range[0], range[1], group, sf.getScore()); complementary.add(sf2); @@ -1118,11 +1124,110 @@ public class FeaturesFile extends AlignFile implements FeaturesSourceI String phase = sf.getPhase(); out.append(phase == null ? "." : phase); - // miscellaneous key-values (GFF column 9) - String attributes = sf.getAttributes(); - if (attributes != null) + 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()) { - out.append(TAB).append(attributes); + 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); } } @@ -1131,11 +1236,11 @@ public class FeaturesFile extends AlignFile implements FeaturesSourceI * 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 */ @@ -1271,38 +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.