X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FEmblFlatFile.java;h=75b89811a56376585016c7df972788e3d9c10ab3;hb=caa5930cf71ef14a4af891f2c17aa4a6e0f72bcf;hp=5be4364d60ea1574841ca559d35af2beb2df988e;hpb=168bc534d8dd1d1bb0cd0f9afffba522848ea5c2;p=jalview.git diff --git a/src/jalview/io/EmblFlatFile.java b/src/jalview/io/EmblFlatFile.java index 5be4364..75b8981 100644 --- a/src/jalview/io/EmblFlatFile.java +++ b/src/jalview/io/EmblFlatFile.java @@ -1,24 +1,10 @@ package jalview.io; import java.io.IOException; -import java.text.ParseException; -import java.util.ArrayList; -import java.util.HashMap; -import java.util.Hashtable; -import java.util.List; -import java.util.Map; -import java.util.Map.Entry; -import jalview.bin.Cache; +import jalview.bin.Console; import jalview.datamodel.DBRefEntry; -import jalview.datamodel.FeatureProperties; -import jalview.datamodel.Mapping; -import jalview.datamodel.Sequence; -import jalview.datamodel.SequenceFeature; -import jalview.datamodel.SequenceI; import jalview.util.DBRefUtils; -import jalview.util.DnaUtils; -import jalview.util.MappingUtils; /** * A class that provides selective parsing of the EMBL flatfile format. @@ -39,49 +25,10 @@ import jalview.util.MappingUtils; * @see ftp://ftp.ebi.ac.uk/pub/databases/ena/sequence/release/doc/usrman.txt * @see ftp://ftp.ebi.ac.uk/pub/databases/embl/doc/FT_current.html */ -public class EmblFlatFile extends AlignFile // FileParse +public class EmblFlatFile extends EMBLLikeFlatFile { /** - * A data bean class to hold values parsed from one CDS Feature (FT) - */ - class CdsData - { - String translation; // from CDS feature /translation - - String cdsLocation; // CDS /location raw value - - int codonStart = 1; // from CDS /codon_start - - String proteinName; // from CDS /product; used for protein description - - String proteinId; // from CDS /protein_id - - Map cdsProps = new Hashtable<>(); // CDS other qualifiers - } - - private static final String WHITESPACE = "\\s+"; - - private String sourceDb; - - /* - * values parsed from the EMBL flatfile record - */ - private String accession; // from ID (first token) - - private String version; // from ID (second token) - - private String description; // from (first) DE line - - private int length = 128; // from ID (7th token), with usable default - - private List dbrefs; // from DR and also CDS /db_xref qualifiers - - private String sequenceString; // from SQ lines - - private List cds; - - /** - * Constructor + * Constructor given a data source and the id of the source database * * @param fp * @param sourceId @@ -89,10 +36,7 @@ public class EmblFlatFile extends AlignFile // FileParse */ public EmblFlatFile(FileParse fp, String sourceId) throws IOException { - super(false, fp); // don't parse immediately - this.sourceDb = sourceId; - dbrefs = new ArrayList<>(); - cds = new ArrayList<>(); + super(fp, sourceId); } /** @@ -101,6 +45,7 @@ public class EmblFlatFile extends AlignFile // FileParse * * @throws IOException */ + @Override public void parse() throws IOException { String line = nextLine(); @@ -120,18 +65,18 @@ public class EmblFlatFile extends AlignFile // FileParse } else if (line.startsWith("SQ")) { - line = parseSQ(); + line = parseSequence(); } else if (line.startsWith("FT")) { - line = parseFT(line); + line = parseFeature(line.substring(2)); } else { line = nextLine(); } } - assembleSequence(); + buildSequence(); } /** @@ -179,7 +124,7 @@ public class EmblFlatFile extends AlignFile // FileParse this.length = Integer.valueOf(bits[0]); } catch (NumberFormatException e) { - Cache.log.error("bad length read in flatfile, line: " + line); + Console.error("bad length read in flatfile, line: " + line); } } @@ -256,352 +201,9 @@ public class EmblFlatFile extends AlignFile // FileParse return nextLine(); } - /** - * Reads and saves the sequence, read from the lines following the SQ line. - * Whitespace and position counters are discarded. Returns the next line - * following the sequence data (the next line that doesn't start with - * whitespace). - * - * @throws IOException - */ - String parseSQ() throws IOException - { - StringBuilder sb = new StringBuilder(this.length); - String line = nextLine(); - while (line != null && line.startsWith(" ")) - { - line = line.trim(); - String[] blocks = line.split(WHITESPACE); - - /* - * omit the last block (position counter) on each line - */ - for (int i = 0; i < blocks.length - 1; i++) - { - sb.append(blocks[i]); - } - line = nextLine(); - } - this.sequenceString = sb.toString(); - - return line; - } - - /** - * Processes an FT line. If it declares a feature type of interest (currently, - * only CDS is processed), processes all of the associated lines (feature - * qualifiers), and returns the next line after that, otherwise simply returns - * the next line. - * - * @param line - * @return - * @throws IOException - */ - String parseFT(String line) throws IOException - { - String[] tokens = line.split(WHITESPACE); - if (tokens.length < 3 || !"CDS".equals(tokens[1])) - { - return nextLine(); - } - - CdsData data = new CdsData(); - data.cdsLocation = tokens[2]; - - line = nextLine(); - while (line != null) - { - if (!line.startsWith("FT ")) // 4 spaces - { - // e.g. start of next feature "FT source..." - break; - } - - /* - * extract qualifier, e.g. FT /protein_id="CAA37824.1" - */ - int slashPos = line.indexOf('/'); - if (slashPos == -1) - { - Cache.log.error("Unexpected EMBL line ignored: " + line); - continue; - } - int eqPos = line.indexOf('=', slashPos + 1); - if (eqPos == -1) - { - Cache.log.error("Unexpected EMBL line ignored: " + line); - continue; - } - String qualifier = line.substring(slashPos + 1, eqPos); - String value = line.substring(eqPos + 1); - if (value.startsWith("\"") && value.endsWith("\"")) - { - value = value.substring(1, value.length() - 1); - } - - if ("protein_id".equals(qualifier)) - { - data.proteinId = value; - line = nextLine(); - } - else if ("codon_start".equals(qualifier)) - { - try - { - data.codonStart = Integer.parseInt(value.trim()); - } catch (NumberFormatException e) - { - Cache.log.error("Invalid codon_start in XML for " + this.accession - + ": " + e.getMessage()); - } - line = nextLine(); - } - else if ("db_xref".equals(qualifier)) - { - String[] parts = value.split(":"); - if (parts.length == 2) - { - String db = parts[0].trim(); - db = DBRefUtils.getCanonicalName(db); - DBRefEntry dbref = new DBRefEntry(db, "0", parts[1].trim()); - this.dbrefs.add(dbref); - } - line = nextLine(); - } - else if ("product".equals(qualifier)) - { - // sometimes name is returned e.g. for V00488 - data.proteinName = value; - line = nextLine(); - } - else if ("translation".equals(qualifier)) - { - line = readTranslation(value, data); - } - else if (!"".equals(value)) - { - // throw anything else into the additional properties hash - data.cdsProps.put(qualifier, value); - line = nextLine(); - } - } - - this.cds.add(data); - - return line; - } - - /** - * Reads and returns the CDS translation from one or more lines of the file, - * and returns the next line after that - * - * @param value - * the first line of the translation (likely quoted) - * @param data - * @return - * @throws IOException - */ - String readTranslation(String value, CdsData data) throws IOException - { - StringBuilder sb = new StringBuilder(this.length / 3 + 1); - sb.append(value.replace("\"", "")); - - String line; - while ((line = nextLine()) != null) - { - if (!line.startsWith("FT ")) - { - break; // reached next feature or other input line - } - String[] tokens = line.split(WHITESPACE); - if (tokens.length < 2) - { - Cache.log.error("Ignoring bad EMBL line: " + line); - break; - } - if (tokens[1].startsWith("/")) - { - break; // next feature qualifier - } - sb.append(tokens[1].replace("\"", "")); - } - - data.translation = sb.toString(); - - return line; - } - - /** - * Constructs and saves the sequence from parsed components - */ - void assembleSequence() - { - String name = this.accession; - if (this.sourceDb != null) - { - name = this.sourceDb + "|" + name; - } - SequenceI seq = new Sequence(name, this.sequenceString); - seq.setDescription(this.description); - - /* - * add a DBRef to itself - */ - DBRefEntry selfRef = new DBRefEntry(sourceDb, version, accession); - int[] startEnd = new int[] { 1, seq.getLength() }; - selfRef.setMap(new Mapping(null, startEnd, startEnd, 1, 1)); - seq.addDBRef(selfRef); - - for (DBRefEntry dbref : this.dbrefs) - { - seq.addDBRef(dbref); - } - - processAllCDS(seq); - - seq.deriveSequence(); - - addSequence(seq); - } - - /** - * Process the CDS features, including generation of cross-references and - * mappings to the protein products (translation) - * - * @param seq - */ - protected void processAllCDS(SequenceI seq) - { - /* - * record protein products found to avoid duplication i.e. >1 CDS with - * the same /protein_id [though not sure I can find an example of this] - */ - Map proteins = new HashMap<>(); - for (CdsData data : cds) - { - processOneCDS(seq, data, proteins); - } - } - - /** - * Processes the parsed CDS feature data to - *
    - *
  • add a CDS feature to the sequence for each CDS start-end range
    • - *
  • create a protein product sequence for the translation
    • - *
  • create a cross-reference to protein with mapping from dna
    • - *
  • add any CDS dbrefs to the sequence and to the protein product
    • - *
- * - * @param SequenceI - * dna - * @param proteins - * map of protein products so far derived from CDS data - */ - void processOneCDS(SequenceI dna, CdsData data, - Map proteins) - { - /* - * parse location into a list of [start, end, start, end] positions - */ - int[] exons = getCdsRanges(this.accession, data.cdsLocation); - int exonNumber = 0; - - for (int xint = 0; exons != null && xint < exons.length - 1; xint += 2) - { - int exonStart = exons[xint]; - int exonEnd = exons[xint + 1]; - int begin = Math.min(exonStart, exonEnd); - int end = Math.max(exonStart, exonEnd); - exonNumber++; - String desc = String.format("Exon %d for protein EMBLCDS:%s", - exonNumber, data.proteinId); - - SequenceFeature sf = new SequenceFeature("CDS", desc, begin, end, - this.sourceDb); - for (Entry val : data.cdsProps.entrySet()) - { - sf.setValue(val.getKey(), val.getValue()); - } - - sf.setEnaLocation(data.cdsLocation); - boolean forwardStrand = exonStart <= exonEnd; - sf.setStrand(forwardStrand ? "+" : "-"); - sf.setPhase(String.valueOf(data.codonStart - 1)); - sf.setValue(FeatureProperties.EXONPOS, exonNumber); - sf.setValue(FeatureProperties.EXONPRODUCT, data.proteinName); - - dna.addSequenceFeature(sf); - - linkProteinProduct(dna, data, proteins); - } - } - - /** - * Constructs a sequence for the protein product for the CDS data (if there is - * one), and dbrefs with mappings from CDS to protein and the reverse - * - * @param dna - * @param data - * @param proteins - */ - void linkProteinProduct(SequenceI dna, CdsData data, Map proteins) - { - /* - * check we have some data to work with - */ - if (data.proteinId == null || data.translation == null) - { - return; - } - - /* - * Construct the protein sequence (if not already seen) - */ - SequenceI protein = proteins.get(data.proteinId); - if (protein == null) - { - protein = new Sequence(data.proteinId, data.translation, 1, - data.translation.length()); - protein.setDescription(data.proteinName != null ? data.proteinName - : "Protein Product from " + sourceDb); - proteins.put(data.proteinId, protein); - } - } - - /** - * Returns the CDS location as a single array of [start, end, start, end...] - * positions. If on the reverse strand, these will be in descending order. - * - * @param accession - * @param location - * @return - */ - protected int[] getCdsRanges(String accession, String location) - { - if (location == null) - { - return new int[] {}; - } - - try - { - List ranges = DnaUtils.parseLocation(location); - return MappingUtils.listToArray(ranges); - } catch (ParseException e) - { - Cache.log.warn( - String.format("Not parsing inexact CDS location %s in ENA %s", - location, accession)); - return new int[] {}; - } - } - - /** - * Output (print) is not implemented for EMBL flat file format - */ @Override - public String print(SequenceI[] seqs, boolean jvsuffix) + protected boolean isFeatureContinuationLine(String line) { - return null; + return line.startsWith("FT "); // 4 spaces } }