package jalview.io;
import java.io.IOException;
-import java.text.ParseException;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.HashMap;
-import java.util.Hashtable;
-import java.util.List;
-import java.util.Map;
-import java.util.Map.Entry;
-import java.util.TreeMap;
import jalview.bin.Cache;
import jalview.datamodel.DBRefEntry;
-import jalview.datamodel.DBRefSource;
-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.MapList;
-import jalview.util.MappingUtils;
/**
* A class that provides selective parsing of the EMBL flatfile format.
* @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 FlatFile
{
- private static final String QUOTE = "\"";
-
- private static final String DOUBLED_QUOTE = QUOTE + QUOTE;
-
- /**
- * when true, interpret the mol_type 'source' feature attribute and generate
- * an RNA sequence from the DNA record
- */
- private boolean produceRna = true;
-
/**
- * 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
-
- List<DBRefEntry> xrefs = new ArrayList<>(); // from CDS /db_xref qualifiers
-
- Map<String, String> 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<DBRefEntry> dbrefs; // from DR
-
- private boolean sequenceStringIsRNA = false;
-
- private String sequenceString; // from SQ lines
-
- /*
- * parsed CDS data fields, keyed by protein_id
- */
- private Map<String, CdsData> cds;
-
- /**
- * Constructor
+ * Constructor given a data source and the id of the source database
*
* @param fp
* @param sourceId
*/
public EmblFlatFile(FileParse fp, String sourceId) throws IOException
{
- super(false, fp); // don't parse immediately
- this.sourceDb = sourceId;
- dbrefs = new ArrayList<>();
-
- /*
- * using TreeMap gives CDS sequences in alphabetical, so readable, order
- */
- cds = new TreeMap<>(String.CASE_INSENSITIVE_ORDER);
+ super(fp, sourceId);
}
/**
*
* @throws IOException
*/
+ @Override
public void parse() throws IOException
{
String line = nextLine();
}
else if (line.startsWith("SQ"))
{
- line = parseSQ();
+ line = parseSequence();
}
else if (line.startsWith("FT"))
{
- line = parseFT(line);
+ line = parseFeature(line.substring(2));
}
else
{
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]) && !"source".equals(tokens[1])))
- {
- return nextLine();
- }
-
- if (tokens[1].equals("source"))
- {
- return parseSourceQualifiers(tokens);
- }
-
- /*
- * parse location - which may be over more than one line e.g. EAW51554
- */
- CdsData data = new CdsData();
- data.cdsLocation = tokens[2];
- // TODO location can be over >1 line e.g. EAW51554
-
- 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"
- * - the value may extend over more than one line
- * - if the value has enclosing quotes, these are removed
- * - escaped double quotes ("") are reduced to a single character
- */
- int slashPos = line.indexOf('/');
- if (slashPos == -1)
- {
- Cache.log.error("Unexpected EMBL line ignored: " + line);
- line = nextLine();
- continue;
- }
- int eqPos = line.indexOf('=', slashPos + 1);
- if (eqPos == -1)
- {
- // can happen, e.g. /ribosomal_slippage
- // Cache.log.error("Unexpected EMBL line ignored: " + line);
- line = nextLine();
- continue;
- }
- String qualifier = line.substring(slashPos + 1, eqPos);
- String value = line.substring(eqPos + 1);
- value = removeQuotes(value);
- StringBuilder sb = new StringBuilder().append(value);
- line = parseFeatureQualifier(sb, qualifier);
- String featureValue = sb.toString();
-
- if ("protein_id".equals(qualifier))
- {
- data.proteinId = featureValue;
- }
- else if ("codon_start".equals(qualifier))
- {
- try
- {
- data.codonStart = Integer.parseInt(featureValue.trim());
- } catch (NumberFormatException e)
- {
- Cache.log.error("Invalid codon_start in XML for " + this.accession
- + ": " + e.getMessage());
- }
- }
- else if ("db_xref".equals(qualifier))
- {
- String[] parts = featureValue.split(":");
- if (parts.length == 2)
- {
- String db = parts[0].trim();
- db = DBRefUtils.getCanonicalName(db);
- DBRefEntry dbref = new DBRefEntry(db, "0", parts[1].trim());
- data.xrefs.add(dbref);
- }
- }
- else if ("product".equals(qualifier))
- {
- data.proteinName = featureValue;
- }
- else if ("translation".equals(qualifier))
- {
- data.translation = featureValue;
- }
- else if (!"".equals(featureValue))
- {
- // throw anything else into the additional properties hash
- data.cdsProps.put(qualifier, featureValue);
- }
- }
-
- if (data.proteinId != null)
- {
- this.cds.put(data.proteinId, data);
- }
- else
- {
- Cache.log.error("Ignoring CDS feature with no protein_id for "
- + sourceDb + ":" + accession);
- }
-
- return line;
- }
-
- /**
- * process attributes for 'source' until the next FT feature entry only
- * interested in 'mol_type'
- *
- * @param tokens
- * @return
- * @throws IOException
- */
- private String parseSourceQualifiers(String[] tokens) throws IOException
- {
- if (!"source".equals(tokens[1]))
- {
- throw (new RuntimeException("Not given a source qualifier"));
- }
- // search for mol_type attribute
-
- StringBuilder sb = new StringBuilder().append(tokens[2]); // extent of
- // sequence
-
- String line = parseFeatureQualifier(sb, "source");
- while (line != null)
- {
- if (!line.startsWith("FT ")) // four spaces, end of this feature table
- // entry
- {
- return line;
- }
-
- int p = line.indexOf("\\mol_type");
- int qs = line.indexOf("\"", p);
- int qe = line.indexOf("\"", qs + 1);
- String qualifier = line.substring(qs, qe).toLowerCase();
- if (qualifier.indexOf("rna") > -1)
- {
- sequenceStringIsRNA = true;
- }
- if (qualifier.indexOf("dna") > -1)
- {
- sequenceStringIsRNA = false;
- }
- line = parseFeatureQualifier(sb, "source");
- }
- return line;
- }
-
- /**
- * Removes leading or trailing double quotes (") unless doubled, and changes
- * any 'escaped' (doubled) double quotes to single characters. As per the
- * Feature Table specification for Qualifiers, Free Text.
- *
- * @param value
- * @return
- */
- static String removeQuotes(String value)
- {
- if (value == null)
- {
- return null;
- }
- if (value.startsWith(QUOTE) && !value.startsWith(DOUBLED_QUOTE))
- {
- value = value.substring(1);
- }
- if (value.endsWith(QUOTE) && !value.endsWith(DOUBLED_QUOTE))
- {
- value = value.substring(0, value.length() - 1);
- }
- value = value.replace(DOUBLED_QUOTE, QUOTE);
- return value;
- }
-
- /**
- * Reads the value of a feature (FT) qualifier from one or more lines of the
- * file, and returns the next line after that. Values are appended to the
- * string buffer, which should be already primed with the value read from the
- * first line for the qualifier (with any leading double quote removed).
- * Enclosing double quotes are removed, and escaped (repeated) double quotes
- * reduced to one only. For example for
- *
- * <pre>
- * FT /note="gene_id=hCG28070.3
- * FT ""foobar"" isoform=CRA_b"
- * the returned value is
- * gene_id=hCG28070.3 "foobar" isoform=CRA_b
- * </pre>
- *
- * Note the side-effect of this method, to advance data reading to the next
- * line after the feature qualifier.
- *
- * @param sb
- * a string buffer primed with the first line of the value
- * @param qualifierName
- * @return
- * @throws IOException
- */
- String parseFeatureQualifier(StringBuilder sb, String qualifierName)
- throws IOException
- {
- 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 for " + this.accession
- + ": " + line);
- break;
- }
- if (tokens[1].startsWith("/"))
- {
- break; // next feature qualifier
- }
-
- /*
- * heuristic rule: most multi-line value (e.g. /product) are text,
- * so add a space for word boundary at a new line; not for translation
- */
- if (!"translation".equals(qualifierName))
- {
- sb.append(" ");
- }
-
- /*
- * remove trailing " and unescape doubled ""
- */
- String data = removeQuotes(tokens[1]);
- sb.append(data);
- }
-
- return line;
- }
-
- /**
- * Constructs and saves the sequence from parsed components
- */
- void buildSequence()
- {
- if (this.accession == null || this.sequenceString == null)
- {
- Cache.log.error("Failed to parse data from EMBL");
- return;
- }
-
- String name = this.accession;
- if (this.sourceDb != null)
- {
- name = this.sourceDb + "|" + name;
- }
-
- if (produceRna && sequenceStringIsRNA)
- {
- sequenceString = sequenceString.replace('T', 'U').replace('t', 'u');
- }
-
- 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);
- }
-
- processCDSFeatures(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 processCDSFeatures(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<String, SequenceI> proteins = new HashMap<>();
- for (CdsData data : cds.values())
- {
- processCDSFeature(seq, data, proteins);
- }
- }
-
- /**
- * Processes data for one parsed CDS feature to
- * <ul>
- * <li>create a protein product sequence for the translation</li>
- * <li>create a cross-reference to protein with mapping from dna</li>
- * <li>add a CDS feature to the sequence for each CDS start-end range</li>
- * <li>add any CDS dbrefs to the sequence and to the protein product</li>
- * </ul>
- *
- * @param SequenceI
- * dna
- * @param proteins
- * map of protein products so far derived from CDS data
- */
- void processCDSFeature(SequenceI dna, CdsData data,
- Map<String, SequenceI> proteins)
- {
- /*
- * parse location into a list of [start, end, start, end] positions
- */
- int[] exons = getCdsRanges(this.accession, data.cdsLocation);
-
- MapList maplist = buildMappingToProtein(dna, exons, data);
-
- 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<String, String> 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);
- }
-
- boolean hasUniprotDbref = false;
- for (DBRefEntry xref : data.xrefs)
- {
- dna.addDBRef(xref);
- if (xref.getSource().equals(DBRefSource.UNIPROT))
- {
- /*
- * construct (or find) the sequence for (data.protein_id, data.translation)
- */
- SequenceI protein = buildProteinProduct(dna, xref, data, proteins);
- Mapping map = new Mapping(protein, maplist);
- map.setMappedFromId(data.proteinId);
- xref.setMap(map);
-
- /*
- * add DBRefs with mappings from dna to protein and the inverse
- */
- DBRefEntry db1 = new DBRefEntry(sourceDb, version, accession);
- db1.setMap(new Mapping(dna, maplist.getInverse()));
- protein.addDBRef(db1);
-
- hasUniprotDbref = true;
- }
- }
-
- /*
- * if we have a product (translation) but no explicit Uniprot dbref
- * (example: EMBL M19487 protein_id AAB02592.1)
- * then construct mappings to an assumed EMBLCDSPROTEIN accession
- */
- if (!hasUniprotDbref)
- {
- SequenceI protein = proteins.get(data.proteinId);
- if (protein == null)
- {
- protein = new Sequence(data.proteinId, data.translation);
- protein.setDescription(data.proteinName);
- proteins.put(data.proteinId, protein);
- }
- // assuming CDSPROTEIN sequence version = dna version (?!)
- DBRefEntry db1 = new DBRefEntry(DBRefSource.EMBLCDSProduct,
- this.version, data.proteinId);
- protein.addDBRef(db1);
-
- DBRefEntry dnaToEmblProteinRef = new DBRefEntry(
- DBRefSource.EMBLCDSProduct, this.version, data.proteinId);
- Mapping map = new Mapping(protein, maplist);
- map.setMappedFromId(data.proteinId);
- dnaToEmblProteinRef.setMap(map);
- dna.addDBRef(dnaToEmblProteinRef);
- }
-
- /*
- * comment brought forward from EmblXmlSource, lines 447-451:
- * TODO: if retrieved from EMBLCDS, add a DBRef back to the parent EMBL
- * sequence with the exon map; if given a dataset reference, search
- * dataset for parent EMBL sequence if it exists and set its map;
- * make a new feature annotating the coding contig
- */
- }
-
- /**
- * Computes a mapping from CDS positions in DNA sequence to protein product
- * positions, with allowance for stop codon or incomplete start codon
- *
- * @param dna
- * @param exons
- * @param data
- * @return
- */
- MapList buildMappingToProtein(final SequenceI dna, final int[] exons,
- final CdsData data)
- {
- MapList dnaToProteinMapping = null;
- int peptideLength = data.translation.length();
-
- int[] proteinRange = new int[] { 1, peptideLength };
- if (exons != null && exons.length > 0)
- {
- /*
- * We were able to parse 'location'; do a final
- * product length truncation check
- */
- int[] cdsRanges = adjustForProteinLength(peptideLength, exons);
- dnaToProteinMapping = new MapList(cdsRanges, proteinRange, 3, 1);
- }
- else
- {
- /*
- * workaround until we handle all 'location' formats fully
- * e.g. X53828.1:60..1058 or <123..>289
- */
- Cache.log.error(String.format(
- "Implementation Notice: EMBLCDS location '%s'not properly supported yet"
- + " - Making up the CDNA region of (%s:%s)... may be incorrect",
- data.cdsLocation, sourceDb, this.accession));
-
- int completeCodonsLength = 1 - data.codonStart + dna.getLength();
- int mappedDnaEnd = dna.getEnd();
- if (peptideLength * 3 == completeCodonsLength)
- {
- // this might occur for CDS sequences where no features are marked
- Cache.log.warn("Assuming no stop codon at end of cDNA fragment");
- mappedDnaEnd = dna.getEnd();
- }
- else if ((peptideLength + 1) * 3 == completeCodonsLength)
- {
- Cache.log.warn("Assuming stop codon at end of cDNA fragment");
- mappedDnaEnd = dna.getEnd() - 3;
- }
-
- if (mappedDnaEnd != -1)
- {
- int[] cdsRanges = new int[] {
- dna.getStart() + (data.codonStart - 1), mappedDnaEnd };
- dnaToProteinMapping = new MapList(cdsRanges, proteinRange, 3, 1);
- }
- }
-
- return dnaToProteinMapping;
- }
-
- /**
- * 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 xref
- * @param data
- * @param proteins
- * @return
- */
- SequenceI buildProteinProduct(SequenceI dna, DBRefEntry xref,
- CdsData data, Map<String, SequenceI> proteins)
- {
- /*
- * check we have some data to work with
- */
- if (data.proteinId == null || data.translation == null)
- {
- return null;
- }
-
- /*
- * Construct the protein sequence (if not already seen)
- */
- String proteinSeqName = xref.getSource() + "|" + xref.getAccessionId();
- SequenceI protein = proteins.get(proteinSeqName);
- if (protein == null)
- {
- protein = new Sequence(proteinSeqName, data.translation, 1,
- data.translation.length());
- protein.setDescription(data.proteinName != null ? data.proteinName
- : "Protein Product from " + sourceDb);
- proteins.put(proteinSeqName, protein);
- }
-
- return 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<int[]> ranges = DnaUtils.parseLocation(location);
- return MappingUtils.rangeListToArray(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)
- {
- return null;
- }
-
- /**
- * Truncates (if necessary) the exon intervals to match 3 times the length of
- * the protein; also accepts 3 bases longer (for stop codon not included in
- * protein)
- *
- * @param proteinLength
- * @param exon
- * an array of [start, end, start, end...] intervals
- * @return the same array (if unchanged) or a truncated copy
- */
- static int[] adjustForProteinLength(int proteinLength, int[] exon)
+ protected boolean isFeatureContinuationLine(String line)
{
- if (proteinLength <= 0 || exon == null)
- {
- return exon;
- }
- int expectedCdsLength = proteinLength * 3;
- int exonLength = MappingUtils.getLength(Arrays.asList(exon));
-
- /*
- * if exon length matches protein, or is shorter, or longer by the
- * length of a stop codon (3 bases), then leave it unchanged
- */
- if (expectedCdsLength >= exonLength
- || expectedCdsLength == exonLength - 3)
- {
- return exon;
- }
-
- int origxon[];
- int sxpos = -1;
- int endxon = 0;
- origxon = new int[exon.length];
- System.arraycopy(exon, 0, origxon, 0, exon.length);
- int cdspos = 0;
- for (int x = 0; x < exon.length; x += 2)
- {
- cdspos += Math.abs(exon[x + 1] - exon[x]) + 1;
- if (expectedCdsLength <= cdspos)
- {
- // advanced beyond last codon.
- sxpos = x;
- if (expectedCdsLength != cdspos)
- {
- // System.err
- // .println("Truncating final exon interval on region by "
- // + (cdspos - cdslength));
- }
-
- /*
- * shrink the final exon - reduce end position if forward
- * strand, increase it if reverse
- */
- if (exon[x + 1] >= exon[x])
- {
- endxon = exon[x + 1] - cdspos + expectedCdsLength;
- }
- else
- {
- endxon = exon[x + 1] + cdspos - expectedCdsLength;
- }
- break;
- }
- }
-
- if (sxpos != -1)
- {
- // and trim the exon interval set if necessary
- int[] nxon = new int[sxpos + 2];
- System.arraycopy(exon, 0, nxon, 0, sxpos + 2);
- nxon[sxpos + 1] = endxon; // update the end boundary for the new exon
- // set
- exon = nxon;
- }
- return exon;
+ return line.startsWith("FT "); // 4 spaces
}
}
--- /dev/null
+package jalview.io;
+
+import java.io.IOException;
+import java.text.ParseException;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.HashMap;
+import java.util.Hashtable;
+import java.util.List;
+import java.util.Map;
+import java.util.Map.Entry;
+import java.util.TreeMap;
+
+import jalview.bin.Cache;
+import jalview.datamodel.DBRefEntry;
+import jalview.datamodel.DBRefSource;
+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.MapList;
+import jalview.util.MappingUtils;
+
+/**
+ * A base class to support parsing of GenBank, EMBL or DDBJ flat file format
+ * data. Example files (rather than formal specifications) are provided at
+ *
+ * <pre>
+ * https://ena-docs.readthedocs.io/en/latest/submit/fileprep/flat-file-example.html
+ * https://www.ncbi.nlm.nih.gov/Sitemap/samplerecord.html
+ * </pre>
+ *
+ * or to compare the same entry, see
+ *
+ * <pre>
+ * https://www.ebi.ac.uk/ena/browser/api/embl/X81322.1
+ * https://www.ncbi.nlm.nih.gov/nuccore/X81322.1
+ * </pre>
+ *
+ * The feature table part of the file has a common definition, only the start of
+ * each line is formatted differently in GenBank and EMBL. See
+ * http://www.insdc.org/files/feature_table.html#7.1.
+ */
+public abstract class FlatFile extends AlignFile
+{
+ protected static final String LOCATION = "location";
+
+ protected static final String QUOTE = "\"";
+
+ protected static final String DOUBLED_QUOTE = QUOTE + QUOTE;
+
+ protected static final String WHITESPACE = "\\s+";
+
+ /**
+ * Removes leading or trailing double quotes (") unless doubled, and changes
+ * any 'escaped' (doubled) double quotes to single characters. As per the
+ * Feature Table specification for Qualifiers, Free Text.
+ *
+ * @param value
+ * @return
+ */
+ protected static String removeQuotes(String value)
+ {
+ if (value == null)
+ {
+ return null;
+ }
+ if (value.startsWith(QUOTE) && !value.startsWith(DOUBLED_QUOTE))
+ {
+ value = value.substring(1);
+ }
+ if (value.endsWith(QUOTE) && !value.endsWith(DOUBLED_QUOTE))
+ {
+ value = value.substring(0, value.length() - 1);
+ }
+ value = value.replace(DOUBLED_QUOTE, QUOTE);
+ return value;
+ }
+
+ /**
+ * Truncates (if necessary) the exon intervals to match 3 times the length of
+ * the protein; also accepts 3 bases longer (for stop codon not included in
+ * protein)
+ *
+ * @param proteinLength
+ * @param exon
+ * an array of [start, end, start, end...] intervals
+ * @return the same array (if unchanged) or a truncated copy
+ */
+ protected static int[] adjustForProteinLength(int proteinLength,
+ int[] exon)
+ {
+ if (proteinLength <= 0 || exon == null)
+ {
+ return exon;
+ }
+ int expectedCdsLength = proteinLength * 3;
+ int exonLength = MappingUtils.getLength(Arrays.asList(exon));
+
+ /*
+ * if exon length matches protein, or is shorter, or longer by the
+ * length of a stop codon (3 bases), then leave it unchanged
+ */
+ if (expectedCdsLength >= exonLength
+ || expectedCdsLength == exonLength - 3)
+ {
+ return exon;
+ }
+
+ int origxon[];
+ int sxpos = -1;
+ int endxon = 0;
+ origxon = new int[exon.length];
+ System.arraycopy(exon, 0, origxon, 0, exon.length);
+ int cdspos = 0;
+ for (int x = 0; x < exon.length; x += 2)
+ {
+ cdspos += Math.abs(exon[x + 1] - exon[x]) + 1;
+ if (expectedCdsLength <= cdspos)
+ {
+ // advanced beyond last codon.
+ sxpos = x;
+ if (expectedCdsLength != cdspos)
+ {
+ // System.err
+ // .println("Truncating final exon interval on region by "
+ // + (cdspos - cdslength));
+ }
+
+ /*
+ * shrink the final exon - reduce end position if forward
+ * strand, increase it if reverse
+ */
+ if (exon[x + 1] >= exon[x])
+ {
+ endxon = exon[x + 1] - cdspos + expectedCdsLength;
+ }
+ else
+ {
+ endxon = exon[x + 1] + cdspos - expectedCdsLength;
+ }
+ break;
+ }
+ }
+
+ if (sxpos != -1)
+ {
+ // and trim the exon interval set if necessary
+ int[] nxon = new int[sxpos + 2];
+ System.arraycopy(exon, 0, nxon, 0, sxpos + 2);
+ nxon[sxpos + 1] = endxon; // update the end boundary for the new exon
+ // set
+ exon = nxon;
+ }
+ return exon;
+ }
+
+ /*
+ * values parsed from the data file
+ */
+ protected String sourceDb;
+
+ protected String accession;
+
+ protected String version;
+
+ protected String description;
+
+ protected int length = 128;
+
+ protected List<DBRefEntry> dbrefs;
+
+ protected String sequenceString;
+
+ protected Map<String, CdsData> cds;
+
+ /**
+ * Constructor
+ *
+ * @param fp
+ * @param sourceId
+ * @throws IOException
+ */
+ public FlatFile(FileParse fp, String sourceId) throws IOException
+ {
+ super(false, fp); // don't parse immediately
+ this.sourceDb = sourceId;
+ dbrefs = new ArrayList<>();
+
+ /*
+ * using TreeMap gives CDS sequences in alphabetical, so readable, order
+ */
+ cds = new TreeMap<>(String.CASE_INSENSITIVE_ORDER);
+ }
+
+ /**
+ * Parses one (GenBank or EMBL format) CDS feature, saves the parsed data, and
+ * returns the next line
+ *
+ * @param location
+ * @return
+ * @throws IOException
+ */
+ protected String parseCDSFeature(String location) throws IOException
+ {
+ String line;
+
+ /*
+ * parse location, which can be over >1 line e.g. EAW51554
+ */
+ CdsData data = new CdsData();
+ StringBuilder sb = new StringBuilder().append(location);
+ line = parseFeatureQualifier(sb, LOCATION);
+ data.cdsLocation = sb.toString();
+
+ while (line != null)
+ {
+ if (!isFeatureContinuationLine(line))
+ {
+ // e.g. start of next feature "FT source..."
+ break;
+ }
+
+ /*
+ * extract qualifier, e.g. FT /protein_id="CAA37824.1"
+ * - the value may extend over more than one line
+ * - if the value has enclosing quotes, these are removed
+ * - escaped double quotes ("") are reduced to a single character
+ */
+ int slashPos = line.indexOf('/');
+ if (slashPos == -1)
+ {
+ Cache.log.error("Unexpected EMBL line ignored: " + line);
+ line = nextLine();
+ continue;
+ }
+ int eqPos = line.indexOf('=', slashPos + 1);
+ if (eqPos == -1)
+ {
+ // can happen, e.g. /ribosomal_slippage
+ line = nextLine();
+ continue;
+ }
+ String qualifier = line.substring(slashPos + 1, eqPos);
+ String value = line.substring(eqPos + 1);
+ value = removeQuotes(value);
+ sb = new StringBuilder().append(value);
+ line = parseFeatureQualifier(sb, qualifier);
+ String featureValue = sb.toString();
+
+ if ("protein_id".equals(qualifier))
+ {
+ data.proteinId = featureValue;
+ }
+ else if ("codon_start".equals(qualifier))
+ {
+ try
+ {
+ data.codonStart = Integer.parseInt(featureValue.trim());
+ } catch (NumberFormatException e)
+ {
+ Cache.log.error("Invalid codon_start in XML for " + this.accession
+ + ": " + e.getMessage());
+ }
+ }
+ else if ("db_xref".equals(qualifier))
+ {
+ String[] parts = featureValue.split(":");
+ if (parts.length == 2)
+ {
+ String db = parts[0].trim();
+ db = DBRefUtils.getCanonicalName(db);
+ DBRefEntry dbref = new DBRefEntry(db, "0", parts[1].trim());
+ data.xrefs.add(dbref);
+ }
+ }
+ else if ("product".equals(qualifier))
+ {
+ data.proteinName = featureValue;
+ }
+ else if ("translation".equals(qualifier))
+ {
+ data.translation = featureValue;
+ }
+ else if (!"".equals(featureValue))
+ {
+ // throw anything else into the additional properties hash
+ data.cdsProps.put(qualifier, featureValue);
+ }
+ }
+
+ if (data.proteinId != null)
+ {
+ this.cds.put(data.proteinId, data);
+ }
+ else
+ {
+ Cache.log.error("Ignoring CDS feature with no protein_id for "
+ + sourceDb + ":" + accession);
+ }
+
+ return line;
+ }
+
+ protected abstract boolean isFeatureContinuationLine(String line);
+
+ /**
+ * Output (print) is not (yet) implemented for flat file format
+ */
+ @Override
+ public String print(SequenceI[] seqs, boolean jvsuffix)
+ {
+ return null;
+ }
+
+ /**
+ * Constructs and saves the sequence from parsed components
+ */
+ protected void buildSequence()
+ {
+ if (this.accession == null || this.sequenceString == null)
+ {
+ Cache.log.error("Failed to parse data from EMBL");
+ return;
+ }
+
+ 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);
+ }
+
+ processCDSFeatures(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 processCDSFeatures(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<String, SequenceI> proteins = new HashMap<>();
+ for (CdsData data : cds.values())
+ {
+ processCDSFeature(seq, data, proteins);
+ }
+ }
+
+ /**
+ * Processes data for one parsed CDS feature to
+ * <ul>
+ * <li>create a protein product sequence for the translation</li>
+ * <li>create a cross-reference to protein with mapping from dna</li>
+ * <li>add a CDS feature to the sequence for each CDS start-end range</li>
+ * <li>add any CDS dbrefs to the sequence and to the protein product</li>
+ * </ul>
+ *
+ * @param SequenceI
+ * dna
+ * @param proteins
+ * map of protein products so far derived from CDS data
+ */
+ void processCDSFeature(SequenceI dna, CdsData data,
+ Map<String, SequenceI> proteins)
+ {
+ /*
+ * parse location into a list of [start, end, start, end] positions
+ */
+ int[] exons = getCdsRanges(this.accession, data.cdsLocation);
+
+ MapList maplist = buildMappingToProtein(dna, exons, data);
+
+ 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<String, String> 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);
+ }
+
+ boolean hasUniprotDbref = false;
+ for (DBRefEntry xref : data.xrefs)
+ {
+ dna.addDBRef(xref);
+ if (xref.getSource().equals(DBRefSource.UNIPROT))
+ {
+ /*
+ * construct (or find) the sequence for (data.protein_id, data.translation)
+ */
+ SequenceI protein = buildProteinProduct(dna, xref, data, proteins);
+ Mapping map = new Mapping(protein, maplist);
+ map.setMappedFromId(data.proteinId);
+ xref.setMap(map);
+
+ /*
+ * add DBRefs with mappings from dna to protein and the inverse
+ */
+ DBRefEntry db1 = new DBRefEntry(sourceDb, version, accession);
+ db1.setMap(new Mapping(dna, maplist.getInverse()));
+ protein.addDBRef(db1);
+
+ hasUniprotDbref = true;
+ }
+ }
+
+ /*
+ * if we have a product (translation) but no explicit Uniprot dbref
+ * (example: EMBL M19487 protein_id AAB02592.1)
+ * then construct mappings to an assumed EMBLCDSPROTEIN accession
+ */
+ if (!hasUniprotDbref)
+ {
+ SequenceI protein = proteins.get(data.proteinId);
+ if (protein == null)
+ {
+ protein = new Sequence(data.proteinId, data.translation);
+ protein.setDescription(data.proteinName);
+ proteins.put(data.proteinId, protein);
+ }
+ // assuming CDSPROTEIN sequence version = dna version (?!)
+ DBRefEntry db1 = new DBRefEntry(DBRefSource.EMBLCDSProduct,
+ this.version, data.proteinId);
+ protein.addDBRef(db1);
+
+ DBRefEntry dnaToEmblProteinRef = new DBRefEntry(
+ DBRefSource.EMBLCDSProduct, this.version, data.proteinId);
+ Mapping map = new Mapping(protein, maplist);
+ map.setMappedFromId(data.proteinId);
+ dnaToEmblProteinRef.setMap(map);
+ dna.addDBRef(dnaToEmblProteinRef);
+ }
+
+ /*
+ * comment brought forward from EmblXmlSource, lines 447-451:
+ * TODO: if retrieved from EMBLCDS, add a DBRef back to the parent EMBL
+ * sequence with the exon map; if given a dataset reference, search
+ * dataset for parent EMBL sequence if it exists and set its map;
+ * make a new feature annotating the coding contig
+ */
+ }
+
+ /**
+ * Computes a mapping from CDS positions in DNA sequence to protein product
+ * positions, with allowance for stop codon or incomplete start codon
+ *
+ * @param dna
+ * @param exons
+ * @param data
+ * @return
+ */
+ MapList buildMappingToProtein(final SequenceI dna, final int[] exons,
+ final CdsData data)
+ {
+ MapList dnaToProteinMapping = null;
+ int peptideLength = data.translation.length();
+
+ int[] proteinRange = new int[] { 1, peptideLength };
+ if (exons != null && exons.length > 0)
+ {
+ /*
+ * We were able to parse 'location'; do a final
+ * product length truncation check
+ */
+ int[] cdsRanges = adjustForProteinLength(peptideLength, exons);
+ dnaToProteinMapping = new MapList(cdsRanges, proteinRange, 3, 1);
+ }
+ else
+ {
+ /*
+ * workaround until we handle all 'location' formats fully
+ * e.g. X53828.1:60..1058 or <123..>289
+ */
+ Cache.log.error(String.format(
+ "Implementation Notice: EMBLCDS location '%s'not properly supported yet"
+ + " - Making up the CDNA region of (%s:%s)... may be incorrect",
+ data.cdsLocation, sourceDb, this.accession));
+
+ int completeCodonsLength = 1 - data.codonStart + dna.getLength();
+ int mappedDnaEnd = dna.getEnd();
+ if (peptideLength * 3 == completeCodonsLength)
+ {
+ // this might occur for CDS sequences where no features are marked
+ Cache.log.warn("Assuming no stop codon at end of cDNA fragment");
+ mappedDnaEnd = dna.getEnd();
+ }
+ else if ((peptideLength + 1) * 3 == completeCodonsLength)
+ {
+ Cache.log.warn("Assuming stop codon at end of cDNA fragment");
+ mappedDnaEnd = dna.getEnd() - 3;
+ }
+
+ if (mappedDnaEnd != -1)
+ {
+ int[] cdsRanges = new int[] {
+ dna.getStart() + (data.codonStart - 1), mappedDnaEnd };
+ dnaToProteinMapping = new MapList(cdsRanges, proteinRange, 3, 1);
+ }
+ }
+
+ return dnaToProteinMapping;
+ }
+
+ /**
+ * 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 xref
+ * @param data
+ * @param proteins
+ * @return
+ */
+ SequenceI buildProteinProduct(SequenceI dna, DBRefEntry xref,
+ CdsData data, Map<String, SequenceI> proteins)
+ {
+ /*
+ * check we have some data to work with
+ */
+ if (data.proteinId == null || data.translation == null)
+ {
+ return null;
+ }
+
+ /*
+ * Construct the protein sequence (if not already seen)
+ */
+ String proteinSeqName = xref.getSource() + "|" + xref.getAccessionId();
+ SequenceI protein = proteins.get(proteinSeqName);
+ if (protein == null)
+ {
+ protein = new Sequence(proteinSeqName, data.translation, 1,
+ data.translation.length());
+ protein.setDescription(data.proteinName != null ? data.proteinName
+ : "Protein Product from " + sourceDb);
+ proteins.put(proteinSeqName, protein);
+ }
+
+ return 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<int[]> ranges = DnaUtils.parseLocation(location);
+ return MappingUtils.rangeListToArray(ranges);
+ } catch (ParseException e)
+ {
+ Cache.log.warn(
+ String.format("Not parsing inexact CDS location %s in ENA %s",
+ location, accession));
+ return new int[] {};
+ }
+ }
+
+ /**
+ * Reads the value of a feature (FT) qualifier from one or more lines of the
+ * file, and returns the next line after that. Values are appended to the
+ * string buffer, which should be already primed with the value read from the
+ * first line for the qualifier (with any leading double quote removed).
+ * Enclosing double quotes are removed, and escaped (repeated) double quotes
+ * reduced to one only. For example for
+ *
+ * <pre>
+ * FT /note="gene_id=hCG28070.3
+ * FT ""foobar"" isoform=CRA_b"
+ * the returned value is
+ * gene_id=hCG28070.3 "foobar" isoform=CRA_b
+ * </pre>
+ *
+ * Note the side-effect of this method, to advance data reading to the next
+ * line after the feature qualifier (which could be another qualifier, a
+ * different feature, a non-feature line, or null at end of file).
+ *
+ * @param sb
+ * a string buffer primed with the first line of the value
+ * @param qualifierName
+ * @return
+ * @throws IOException
+ */
+ String parseFeatureQualifier(StringBuilder sb, String qualifierName)
+ throws IOException
+ {
+ String line;
+ while ((line = nextLine()) != null)
+ {
+ if (!isFeatureContinuationLine(line))
+ {
+ break; // reached next feature or other input line
+ }
+ String[] tokens = line.split(WHITESPACE);
+ if (tokens.length < 2)
+ {
+ Cache.log.error("Ignoring bad EMBL line for " + this.accession
+ + ": " + line);
+ break;
+ }
+ if (tokens[1].startsWith("/"))
+ {
+ break; // next feature qualifier
+ }
+
+ /*
+ * heuristic rule: most multi-line value (e.g. /product) are text,
+ * so add a space for word boundary at a new line; not for translation
+ */
+ if (!"translation".equals(qualifierName)
+ && !LOCATION.equals(qualifierName))
+ {
+ sb.append(" ");
+ }
+
+ /*
+ * remove trailing " and unescape doubled ""
+ */
+ String data = removeQuotes(tokens[1]);
+ sb.append(data);
+ }
+
+ return line;
+ }
+
+ /**
+ * Reads and saves the sequence, read from the lines following the ORIGIN
+ * (GenBank) or SQ (EMBL) 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
+ */
+ protected String parseSequence() throws IOException
+ {
+ StringBuilder sb = new StringBuilder(this.length);
+ String line = nextLine();
+ while (line != null && line.startsWith(" "))
+ {
+ line = line.trim();
+ String[] blocks = line.split(WHITESPACE);
+
+ /*
+ * the first or last block on each line might be a position count - omit
+ */
+ for (int i = 0; i < blocks.length; i++)
+ {
+ try
+ {
+ Long.parseLong(blocks[i]);
+ // position counter - ignore it
+ } catch (NumberFormatException e)
+ {
+ // sequence data - append it
+ sb.append(blocks[i]);
+ }
+ }
+ line = nextLine();
+ }
+ this.sequenceString = sb.toString();
+
+ return line;
+ }
+
+ /**
+ * Processes a feature 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
+ * the first line for the feature (with initial FT omitted for EMBL
+ * format)
+ * @return
+ * @throws IOException
+ */
+ protected String parseFeature(String line) throws IOException
+ {
+ String[] tokens = line.trim().split(WHITESPACE);
+ if (tokens.length < 2 || !"CDS".equals(tokens[0]))
+ {
+ return nextLine();
+ }
+
+ return parseCDSFeature(tokens[1]);
+ }
+}
+
+/**
+ * A data bean class to hold values parsed from one CDS Feature
+ */
+class CdsData
+{
+ String translation; // from /translation qualifier
+
+ String cdsLocation; // the raw value e.g. join(1..1234,2012..2837)
+
+ int codonStart = 1; // from /codon_start qualifier
+
+ String proteinName; // from /product qualifier; used for protein description
+
+ String proteinId; // from /protein_id qualifier
+
+ List<DBRefEntry> xrefs = new ArrayList<>(); // from /db_xref qualifiers
+
+ Map<String, String> cdsProps = new Hashtable<>(); // other qualifiers
+}
--- /dev/null
+package jalview.io;
+
+import java.io.IOException;
+
+import jalview.bin.Cache;
+
+/**
+ * A class that provides selective parsing of the GenBank flatfile format.
+ * <p>
+ * The initial implementation is limited to extracting fields used by Jalview
+ * after fetching an EMBL or EMBLCDS entry:
+ *
+ * <pre>
+ * accession, version, sequence, xref
+ * and (for CDS feature) location, protein_id, product, codon_start, translation
+ * </pre>
+ *
+ * @author gmcarstairs
+ * @see https://www.ncbi.nlm.nih.gov/Sitemap/samplerecord.html
+ */
+public class GenBankFile extends FlatFile
+{
+ private static final String DEFINITION = "DEFINITION";
+
+ /**
+ * Constructor given a data source and the id of the source database
+ *
+ * @param fp
+ * @param sourceId
+ * @throws IOException
+ */
+ public GenBankFile(FileParse fp, String sourceId) throws IOException
+ {
+ super(fp, sourceId);
+ }
+
+ /**
+ * Parses the flatfile, and if successful, saves as an annotated sequence
+ * which may be retrieved by calling {@code getSequence()}
+ *
+ * @throws IOException
+ * @see https://www.ncbi.nlm.nih.gov/Sitemap/samplerecord.html
+ */
+ @Override
+ public void parse() throws IOException
+ {
+ String line = nextLine();
+ while (line != null)
+ {
+ if (line.startsWith(DEFINITION))
+ {
+ line = parseDefinition(line);
+ }
+ else if (line.startsWith("ACCESSION"))
+ {
+ this.accession = line.split(WHITESPACE)[1];
+ line = nextLine();
+ }
+ else if (line.startsWith("VERSION"))
+ {
+ line = parseVersion(line);
+ }
+ else if (line.startsWith("ORIGIN"))
+ {
+ line = parseSequence();
+ }
+ else if (line.startsWith("FEATURES"))
+ {
+ line = nextLine();
+ while (line.startsWith(" "))
+ {
+ line = parseFeature(line);
+ }
+ }
+ else
+ {
+ line = nextLine();
+ }
+ }
+ buildSequence();
+ }
+
+ /**
+ * Extracts and saves the primary accession and version (SV value) from an ID
+ * line, or null if not found. Returns the next line after the one processed.
+ *
+ * @param line
+ * @throws IOException
+ */
+ String parseLocus(String line) throws IOException
+ {
+ String[] tokens = line.substring(2).split(";");
+
+ /*
+ * first is primary accession
+ */
+ String token = tokens[0].trim();
+ if (!token.isEmpty())
+ {
+ this.accession = token;
+ }
+
+ /*
+ * second token is 'SV versionNo'
+ */
+ if (tokens.length > 1)
+ {
+ token = tokens[1].trim();
+ if (token.startsWith("SV"))
+ {
+ String[] bits = token.trim().split(WHITESPACE);
+ this.version = bits[bits.length - 1];
+ }
+ }
+
+ /*
+ * seventh token is 'length BP'
+ */
+ if (tokens.length > 6)
+ {
+ token = tokens[6].trim();
+ String[] bits = token.trim().split(WHITESPACE);
+ try
+ {
+ this.length = Integer.valueOf(bits[0]);
+ } catch (NumberFormatException e)
+ {
+ Cache.log.error("bad length read in flatfile, line: " + line);
+ }
+ }
+
+ return nextLine();
+ }
+
+ /**
+ * Reads sequence description from DEFINITION lines. Any trailing period is
+ * discarded. Returns the next line after the definition line(s).
+ *
+ * @param line
+ * @return
+ * @throws IOException
+ */
+ String parseDefinition(String line) throws IOException
+ {
+ String desc = line.substring(DEFINITION.length()).trim();
+ if (desc.endsWith("."))
+ {
+ desc = desc.substring(0, desc.length() - 1);
+ }
+
+ /*
+ * pass over any additional DE lines
+ */
+ while ((line = nextLine()) != null)
+ {
+ if (line.startsWith(" "))
+ {
+ // definition continuation line
+ desc += line.trim();
+ }
+ else
+ {
+ break;
+ }
+ }
+ this.description = desc;
+
+ return line;
+ }
+
+ /**
+ * Parses the VERSION line e.g.
+ *
+ * <pre>
+ * VERSION X81322.1
+ * </pre>
+ *
+ * and returns the next line
+ *
+ * @param line
+ * @throws IOException
+ */
+ String parseVersion(String line) throws IOException
+ {
+ /*
+ * extract version part of <accession>.<version>
+ * https://www.ncbi.nlm.nih.gov/Sitemap/samplerecord.html#VersionB
+ */
+ String[] tokens = line.split(WHITESPACE);
+ if (tokens.length > 1)
+ {
+ tokens = tokens[1].split("\\.");
+ if (tokens.length > 1)
+ {
+ this.version = tokens[1];
+ }
+ }
+
+ return nextLine();
+ }
+
+ @Override
+ protected boolean isFeatureContinuationLine(String line)
+ {
+ return line.startsWith(" "); // 6 spaces
+ }
+}
public static List<int[]> parseLocation(String location)
throws ParseException
{
+ location = location.trim(); // failsafe for untidy input data
if (location.startsWith("join("))
{
return parseJoin(location);
import static org.testng.Assert.assertEquals;
import static org.testng.Assert.assertTrue;
import static org.testng.AssertJUnit.assertNotNull;
+import static org.testng.AssertJUnit.assertNull;
import static org.testng.AssertJUnit.assertSame;
import static org.testng.AssertJUnit.fail;
-import static org.testng.AssertJUnit.assertNull;
import java.io.File;
import java.io.IOException;
import java.util.List;
import java.util.Set;
+import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
+import jalview.bin.Cache;
import jalview.datamodel.DBRefEntry;
import jalview.datamodel.Mapping;
import jalview.datamodel.Sequence.DBModList;
public class EmblFlatFileTest
{
+ @BeforeClass(alwaysRun = true)
+ public void setUp()
+ {
+ Cache.initLogger();
+ }
+
/**
* A fairly tough test, using J03321 (circular DNA), which has 8 CDS features,
* one of them reverse strand
--- /dev/null
+package jalview.io;
+
+import static org.testng.Assert.assertEquals;
+import static org.testng.Assert.assertTrue;
+import static org.testng.AssertJUnit.assertNull;
+
+import java.io.File;
+import java.io.IOException;
+import java.net.MalformedURLException;
+import java.util.Arrays;
+import java.util.List;
+import java.util.Set;
+
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.Test;
+
+import jalview.bin.Cache;
+import jalview.datamodel.DBRefEntry;
+import jalview.datamodel.Mapping;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceI;
+import jalview.datamodel.features.SequenceFeatures;
+import jalview.util.MapList;
+
+public class GenBankFileTest
+{
+ @BeforeClass(alwaysRun = true)
+ public void setUp()
+ {
+ Cache.initLogger();
+ }
+
+ /**
+ * A fairly tough test, using J03321 (circular DNA), which has 8 CDS features,
+ * one of them reverse strand
+ *
+ * @throws MalformedURLException
+ * @throws IOException
+ */
+ @Test(groups = "Functional")
+ public void testParse() throws MalformedURLException, IOException
+ {
+ File dataFile = new File("test/jalview/io/J03321.gb");
+ FileParse fp = new FileParse(dataFile.getAbsolutePath(),
+ DataSourceType.FILE);
+ FlatFile parser = new GenBankFile(fp, "GenBankTest");
+ parser.parse();
+ List<SequenceI> seqs = parser.getSeqs();
+
+ assertEquals(seqs.size(), 1);
+ SequenceI seq = seqs.get(0);
+ assertEquals(seq.getName(), "GenBankTest|J03321");
+ assertEquals(seq.getLength(), 7502);
+ assertEquals(seq.getDescription(),
+ "Chlamydia trachomatis plasmid pCHL1, complete sequence");
+
+ /*
+ * should be 9 CDS features (one is a 'join' of two exons)
+ */
+ Set<String> featureTypes = seq.getFeatures().getFeatureTypes();
+ assertEquals(featureTypes.size(), 1);
+ assertTrue(featureTypes.contains("CDS"));
+
+ /*
+ * inspect some features (sorted just for convenience of test assertions)
+ */
+ List<SequenceFeature> features = seq.getFeatures()
+ .getAllFeatures("CDS");
+ SequenceFeatures.sortFeatures(features, true);
+ assertEquals(features.size(), 9);
+
+ SequenceFeature sf = features.get(0);
+ assertEquals(sf.getBegin(), 1);
+ assertEquals(sf.getEnd(), 437);
+ assertEquals(sf.getDescription(),
+ "Exon 2 for protein EMBLCDS:AAA91567.1");
+ assertEquals(sf.getFeatureGroup(), "GenBankTest");
+ assertEquals(sf.getEnaLocation(), "join(7022..7502,1..437)");
+ assertEquals(sf.getPhase(), "0");
+ assertEquals(sf.getStrand(), 1);
+ assertEquals(sf.getValue("note"), "pGP7-D");
+ // this is the second exon of circular CDS!
+ assertEquals(sf.getValue("exon number"), 2);
+ assertEquals(sf.getValue("product"), "hypothetical protein");
+ assertEquals(sf.getValue("transl_table"), "11");
+
+ sf = features.get(1);
+ assertEquals(sf.getBegin(), 488);
+ assertEquals(sf.getEnd(), 1480);
+ assertEquals(sf.getDescription(),
+ "Exon 1 for protein EMBLCDS:AAA91568.1");
+ assertEquals(sf.getFeatureGroup(), "GenBankTest");
+ assertEquals(sf.getEnaLocation(), "complement(488..1480)");
+ assertEquals(sf.getPhase(), "0");
+ assertEquals(sf.getStrand(), -1); // reverse strand!
+ assertEquals(sf.getValue("note"), "pGP8-D");
+ assertEquals(sf.getValue("exon number"), 1);
+ assertEquals(sf.getValue("product"), "hypothetical protein");
+
+ sf = features.get(7);
+ assertEquals(sf.getBegin(), 6045);
+ assertEquals(sf.getEnd(), 6788);
+ assertEquals(sf.getDescription(),
+ "Exon 1 for protein EMBLCDS:AAA91574.1");
+ assertEquals(sf.getFeatureGroup(), "GenBankTest");
+ assertEquals(sf.getEnaLocation(), "6045..6788");
+ assertEquals(sf.getPhase(), "0");
+ assertEquals(sf.getStrand(), 1);
+ assertEquals(sf.getValue("note"), "pGP6-D (gtg start codon)");
+ assertEquals(sf.getValue("exon number"), 1);
+ assertEquals(sf.getValue("product"), "hypothetical protein");
+
+ /*
+ * CDS at 7022-7502 is the first exon of the circular CDS
+ */
+ sf = features.get(8);
+ assertEquals(sf.getBegin(), 7022);
+ assertEquals(sf.getEnd(), 7502);
+ assertEquals(sf.getDescription(),
+ "Exon 1 for protein EMBLCDS:AAA91567.1");
+ assertEquals(sf.getFeatureGroup(), "GenBankTest");
+ assertEquals(sf.getEnaLocation(), "join(7022..7502,1..437)");
+ assertEquals(sf.getPhase(), "0");
+ assertEquals(sf.getStrand(), 1);
+ assertEquals(sf.getValue("note"), "pGP7-D");
+ assertEquals(sf.getValue("exon number"), 1);
+ assertEquals(sf.getValue("product"), "hypothetical protein");
+
+ /*
+ * GenBank doesn't declare accession or CDS xrefs;
+ * dbrefs are added by Jalview for
+ * xref to self : 1
+ * protein products: 8
+ */
+ List<DBRefEntry> dbrefs = Arrays.asList(seq.getDBRefs());
+
+ assertEquals(dbrefs.size(), 9);
+ // xref to 'self':
+ DBRefEntry selfRef = new DBRefEntry("GENBANKTEST", "1", "J03321");
+ int[] range = new int[] { 1, seq.getLength() };
+ selfRef.setMap(new Mapping(null, range, range, 1, 1));
+ assertTrue(dbrefs.contains(selfRef));
+
+ /*
+ * dna should have dbref to itself, and to EMBLCDSPROTEIN
+ * for each /protein_id (synthesized as no UNIPROT xref)
+ */
+ // TODO check if we should synthesize EMBLCDSPROTEIN dbrefs
+ DBRefEntry dbref = dbrefs.get(0);
+ assertEquals(dbref.getSource(), "GENBANKTEST");
+ assertEquals(dbref.getAccessionId(), "J03321");
+ Mapping mapping = dbref.getMap();
+ assertNull(mapping.getTo());
+ MapList map = mapping.getMap();
+ assertEquals(map.getFromLowest(), 1);
+ assertEquals(map.getFromHighest(), 7502);
+ assertEquals(map.getToLowest(), 1);
+ assertEquals(map.getToHighest(), 7502);
+ assertEquals(map.getFromRatio(), 1);
+ assertEquals(map.getToRatio(), 1);
+
+ // dbref to inferred EMBLCDSPROTEIN for first CDS
+ dbref = dbrefs.get(1);
+ assertEquals(dbref.getSource(), "EMBLCDSPROTEIN");
+ assertEquals(dbref.getAccessionId(), "AAA91567.1");
+ mapping = dbref.getMap();
+ SequenceI mapTo = mapping.getTo();
+ assertEquals(mapTo.getName(), "AAA91567.1");
+ // the /product qualifier transfers to protein product description
+ assertEquals(mapTo.getDescription(), "hypothetical protein");
+ String seqString = mapTo.getSequenceAsString();
+ assertEquals(seqString.length(), 305);
+ assertTrue(seqString.startsWith("MGSMAF"));
+ assertTrue(seqString.endsWith("QTPTIL"));
+ map = mapping.getMap();
+ assertEquals(map.getFromLowest(), 1);
+ assertEquals(map.getFromHighest(), 7502);
+ assertEquals(map.getToLowest(), 1);
+ assertEquals(map.getToHighest(), 305);
+ assertEquals(map.getFromRatio(), 3);
+ assertEquals(map.getToRatio(), 1);
+
+ // dbref to inferred EMBLCDSPROTEIN for last CDS
+ dbref = dbrefs.get(8);
+ assertEquals(dbref.getSource(), "EMBLCDSPROTEIN");
+ assertEquals(dbref.getAccessionId(), "AAA91574.1");
+ mapping = dbref.getMap();
+ mapTo = mapping.getTo();
+ assertEquals(mapTo.getName(), "AAA91574.1");
+ // the /product qualifier transfers to protein product description
+ assertEquals(mapTo.getDescription(), "hypothetical protein");
+ seqString = mapTo.getSequenceAsString();
+ assertEquals(seqString.length(), 247);
+ assertTrue(seqString.startsWith("MNKLK"));
+ assertTrue(seqString.endsWith("FKQKS"));
+ map = mapping.getMap();
+ assertEquals(map.getFromLowest(), 6045);
+ assertEquals(map.getFromHighest(), 6788);
+ assertEquals(map.getToLowest(), 1);
+ assertEquals(map.getToHighest(), 247);
+ assertEquals(map.getFromRatio(), 3);
+ assertEquals(map.getToRatio(), 1);
+ }
+}
FT /mol_type="genomic DNA"
FT /isolation_source="trachoma"
FT /db_xref="taxon:813"
-FT CDS join(7022..7502,1..437)
+XX next line artificially split for test purposes!
+FT CDS join(7022..7502,
+FT 1..437)
FT /codon_start=1
FT /transl_table=11
FT /product="hypothetical protein"
--- /dev/null
+LOCUS CH1L1CG 7502 bp DNA circular BCT 06-APR-2020
+DEFINITION Chlamydia trachomatis plasmid pCHL1, complete sequence.
+ACCESSION J03321
+VERSION J03321.1
+DBLINK BioSample: SAMN14225621
+KEYWORDS .
+SOURCE Chlamydia trachomatis
+ ORGANISM Chlamydia trachomatis
+ Bacteria; Chlamydiae; Chlamydiales; Chlamydiaceae;
+ Chlamydia/Chlamydophila group; Chlamydia.
+REFERENCE 1 (bases 1 to 7502)
+ AUTHORS Comanducci,M., Ricci,S., Cevenini,R. and Ratti,G.
+ TITLE Diversity of the Chlamydia trachomatis common plasmid in biovars
+ with different pathogenicity
+ JOURNAL Plasmid 23 (2), 149-154 (1990)
+ PUBMED 2194229
+REFERENCE 2 (bases 1 to 7502)
+ AUTHORS Comanducci,M., Ricci,S., Cevenini,R. and Ratti,G.
+ TITLE Direct Submission
+ JOURNAL Submitted (23-JUN-2010) Sclavo Research Centre, Siena, Italy
+COMMENT Draft entry and computer-readable sequence kindly submitted by
+ G.Ratti, 28-MAR-1990.
+ ! CDS location split below (and this line added), for Jalview test purposes !
+FEATURES Location/Qualifiers
+ source 1..7502
+ /organism="Chlamydia trachomatis"
+ /mol_type="genomic DNA"
+ /serotype="D"
+ /isolate="G0/86"
+ /isolation_source="trachoma"
+ /db_xref="taxon:813"
+ /plasmid="pCHL1"
+ CDS join(7022..7502,
+ 1..437)
+ /note="pGP7-D"
+ /codon_start=1
+ /transl_table=11
+ /product="hypothetical protein"
+ /protein_id="AAA91567.1"
+ /translation="MGSMAFHKSRLFLTFGDASEIWLSTLSYLTRKNYASGINFLVSL
+ EILDLSETLIKAISLDHSESLFKIKSLDVFNGKVVSEASKQARAACYISFTKFLYRLT
+ KGYIKPAIPLKDFGNTTFFKIRDKIKTESISKQEWTVFFEALRIVNYRDYLIGKLIVQ
+ GIRKLDEILSLRTDDLFFASNQISFRIKKRQNKETKILITFPISLMEELQKYTCGRNG
+ RVFVSKIGIPVTTSQVAHNFRLAEFHSAMKIKITPRVLRASALIHLKQIGLKDEEIMR
+ ISCLSSRQSVCSYCSGEEVIPLVQTPTIL"
+ CDS complement(488..1480)
+ /note="pGP8-D"
+ /codon_start=1
+ /transl_table=11
+ /product="hypothetical protein"
+ /protein_id="AAA91568.1"
+ /translation="MGKGILSLQQEMSLEYSEKSYQEVLKIRQESYWKRMKSFSLFEV
+ IMHWTASLNKHTCRSYRGSFLSLEKIGLLSLDMNLQEFSLLNHNLILDAIKKVSSAKT
+ SWTEGTKQVRAASYISLTRFLNRMTQGIVAIAQPSKQENSRTFFKTREIVKTDAMNSL
+ QTASFLKELKKINARDWLIAQTMLQGGKRSSEVLSLEISQICFQQATISFSQLKNRQT
+ EKRIIITYPQKFMHFLQEYIGQRRGFVFVTRSGKMVGLRQIARTFSQAGLQAAIPFKI
+ TPHVLRATAVTEYKRLGCSDSDIMKVTGHATAKMIFAYDKSSREDNASKKMALI"
+ CDS 1579..2934
+ /note="pGP1-D"
+ /codon_start=1
+ /transl_table=11
+ /product="hypothetical protein"
+ /protein_id="AAA91569.1"
+ /translation="MKTRSEIENRMQDIEYALLGKALIFEDSTEYILRQLANYEFKCS
+ HHKNIFIVFKHLKDNGLPITVDSAWEELLRRRIKDMDKSYLGLMLHDALSNDKLRSVS
+ HTVFLDDLSVCSAEENLSNFIFRSFNEYNENPLRRSPFLLLERIKGRLDSAIAKTFSI
+ RSARGRSIYDIFSQSEIGVLARIKKRRVAFSENQNSFFDGFPTGYKDIDDKGVILAKG
+ NFVIIAARPSIGKTALAIDMAINLAVTQQRRVGFLSLEMSAGQIVERIIANLTGISGE
+ KLQRGDLSKEELFRVEEAGETVRESHFYICSDSQYKLNLIANQIRLLRKEDRVDVIFI
+ DYLQLINSSVGENRQNEIADISRTLRGLASELNIPIVCLSQLSRKVEDRANKVPMLSD
+ LRDSGQIEQDADVILFINRKESSSNCEITVGKNRHGSVFSSVLHFDPKISKFSAIKKV
+ W"
+ CDS 2928..3992
+ /note="pGP2-D"
+ /codon_start=1
+ /transl_table=11
+ /product="hypothetical protein"
+ /protein_id="AAA91570.1"
+ /translation="MVNYSNCHFIKSPIHLENQKFGRRPGQSIKISPKLAQNGMVEVI
+ GLDFLSSHYHALAAIQRLLTATNYKGNTKGVVLSRESNSFQFEGWIPRIRFTKTEFLE
+ AYGVKRYKTSRNKYEFSGKEAETALEALYHLGHQPFLIVATRTRWTNGTQIVDRYQTL
+ SPIIRIYEGWEGLTDEENIDIDLTPFNSPPTRKHKGFVVEPCPILVDQIESYFVIKPA
+ NVYQEIKMRFPNASKYAYTFIDWVITAAAKKRRKLTKDNSWPENLLLNVNVKSLAYIL
+ RMNRYICTRNWKKIELAIDKCIEIAIQLGWLSRRKRIEFLDSSKLSKKEILYLNKERF
+ EEITKKSKEQMEQLEQESIN"
+ CDS 4054..4848
+ /note="pGP3-D"
+ /codon_start=1
+ /transl_table=11
+ /product="hypothetical protein"
+ /protein_id="AAA91571.1"
+ /translation="MGNSGFYLYNTENCVFADNIKVGQMTEPLKDQQIILGTTSTPVA
+ AKMTASDGISLTVSNNSSTNASITIGLDAEKAYQLILEKLGDQILDGIADTIVDSTVQ
+ DILDKIKTDPSLGLLKAFNNFPITNKIQCNGLFTPSNIETLLGGTEIGKFTVTPKSSG
+ SMFLVSADIIASRMEGGVVLALVREGDSKPCAISYGYSSGIPNLCSLRTSITNTGLTP
+ TTYSLRVGGLESGVVWVNALSNGNDILGITNTSNVSFLEVIPQTNA"
+ CDS 4918..5226
+ /note="pGP4-D"
+ /codon_start=1
+ /transl_table=11
+ /product="hypothetical protein"
+ /protein_id="AAA91572.1"
+ /translation="MQNKRKVRDDFIKIVKDVKKDFPELDLKIRVNKEKVTFLNSPLE
+ LYHKSVSLILGLLQQIENSLGLFPDSPVLEKLEDNSLKLKKALIMLILSRKDMFSKAE
+ "
+ CDS 5317..6048
+ /note="pGP5-D (gtg start codon)"
+ /codon_start=1
+ /transl_table=11
+ /product="hypothetical protein"
+ /protein_id="AAA91573.1"
+ /translation="MGCNLAQFLGKKVLLADLDPQSNLSSGLGASVRSDQKGLHDIVY
+ TSNDLKSIICETKKDSVDLIPASFSSEQFRELDIHRGPSNNLKLFLNEYCAPFYDICI
+ IDTPPSLGGLTKEAFVAGDKLIACLTPEPFSILGLQKIREFLSSVGKPEEEHILGIAL
+ SFWDDRNSTNQMYIDIIESIYKNKLFSTKIRRDISLSRSLLKEDSVANVYPNSRAAED
+ ILKLTHEIANILHIEYERDYSQRTT"
+ CDS 6045..6788
+ /note="pGP6-D (gtg start codon)"
+ /codon_start=1
+ /transl_table=11
+ /product="hypothetical protein"
+ /protein_id="AAA91574.1"
+ /translation="MNKLKKEADVFFKKNQTAASLDFKKTLPSIELFSATLNSEESQS
+ LDRLFLSESQNYSDEEFYQEDILAVKLLTGQIKSIQKQHVLLLGEKIYNARKILSKDH
+ FSSTTFSSWIELVFRTKSSAYNALAYYELFINLPNQTLQKEFQSIPYKSAYILAARKG
+ DLKTKVDVIGKVCGMSNSSAIRVLDQFLPSSRNKDVRETIDKSDSEKNRQLSDFLIEI
+ LRIMCSGVSLSSYNENLLQQLFELFKQKS"
+ repeat_region 6857..6945
+ /note="four tandem 22bp repeats"
+ORIGIN
+ 1 ggatccgtaa gttagacgaa attttgtctt tgcgcacaga cgatctattt tttgcatcca
+ 61 atcagatttc ctttcgcatt aaaaaaagac agaataaaga aaccaaaatt ctaatcacat
+ 121 ttcctatcag cttaatggaa gagttgcaaa aatacacttg tgggagaaat gggagagtat
+ 181 ttgtttctaa aatagggatt cctgtaacaa caagtcaggt tgcgcataat tttaggcttg
+ 241 cagagttcca tagtgctatg aaaataaaaa ttactcccag agtacttcgt gcaagcgctt
+ 301 tgattcattt aaagcaaata ggattaaaag atgaggaaat catgcgtatt tcctgtcttt
+ 361 catcgagaca aagtgtgtgt tcttattgtt ctggggaaga ggtaattcct ctagtacaaa
+ 421 cacccacaat attgtgatat aattaaaatt atattcatat tctgttgcca gaaaaaacac
+ 481 ctttaggcta tattagagcc atcttctttg aagcgttgtc ttctcgagaa gatttatcgt
+ 541 acgcaaatat catctttgcg gttgcgtgtc ctgtgacctt cattatgtcg gagtctgagc
+ 601 accctaggcg tttgtactcc gtcacagcgg ttgctcgaag cacgtgcggg gttattttaa
+ 661 aagggattgc agcttgtagt cctgcttgag agaacgtgcg ggcgatttgc cttaacccca
+ 721 ccatttttcc ggagcgagtt acgaagacaa aacctcttcg ttgaccgatg tactcttgta
+ 781 gaaagtgcat aaacttctga ggataagtta taataatcct cttttctgtc tgacggttct
+ 841 taagctggga gaaagaaatg gtagcttgtt ggaaacaaat ctgactaatc tccaagctta
+ 901 agacttcaga ggagcgttta cctccttgga gcattgtctg ggcgatcaac caatcccggg
+ 961 cattgatttt ttttagctct tttaggaagg atgctgtttg caaactgttc atcgcatccg
+ 1021 tttttactat ttccctggtt ttaaaaaatg ttcgactatt ttcttgttta gaaggttgcg
+ 1081 ctatagcgac tattccttga gtcatcctgt ttaggaatct tgttaaggaa atatagcttg
+ 1141 ctgctcgaac ttgtttagta ccttcggtcc aagaagtctt ggcagaggaa acttttttaa
+ 1201 tcgcatctag gattagatta tgatttaaaa gggaaaactc ttgcagattc atatccaagg
+ 1261 acaatagacc aatcttttct aaagacaaaa aagatcctcg atatgatcta caagtatgtt
+ 1321 tgttgagtga tgcggtccaa tgcataataa cttcgaataa ggagaagctt ttcatgcgtt
+ 1381 tccaatagga ttcttggcga atttttaaaa cttcctgata agacttttca ctatattcta
+ 1441 acgacatttc ttgctgcaaa gataaaatcc ctttacccat gaaatccctc gtgatataac
+ 1501 ctatccgtaa aatgtcctga ttagtgaaat aatcaggttg ttaacaggat agcacgctcg
+ 1561 gtattttttt atataaacat gaaaactcgt tccgaaatag aaaatcgcat gcaagatatc
+ 1621 gagtatgcgt tgttaggtaa agctctgata tttgaagact ctactgagta tattctgagg
+ 1681 cagcttgcta attatgagtt taagtgttct catcataaaa acatattcat agtatttaaa
+ 1741 cacttaaaag acaatggatt acctataact gtagactcgg cttgggaaga gcttttgcgg
+ 1801 cgtcgtatca aagatatgga caaatcgtat ctcgggttaa tgttgcatga tgctttatca
+ 1861 aatgacaagc ttagatccgt ttctcatacg gttttcctcg atgatttgag cgtgtgtagc
+ 1921 gctgaagaaa atttgagtaa tttcattttc cgctcgttta atgagtacaa tgaaaatcca
+ 1981 ttgcgtagat ctccgtttct attgcttgag cgtataaagg gaaggcttga tagtgctata
+ 2041 gcaaagactt tttctattcg cagcgctaga ggccggtcta tttatgatat attctcacag
+ 2101 tcagaaattg gagtgctggc tcgtataaaa aaaagacgag tagcgttctc tgagaatcaa
+ 2161 aattctttct ttgatggctt cccaacagga tacaaggata ttgatgataa aggagttatc
+ 2221 ttagctaaag gtaatttcgt gattatagca gctagaccat ctatagggaa aacagcttta
+ 2281 gctatagaca tggcgataaa tcttgcggtt actcaacagc gtagagttgg tttcctatct
+ 2341 ctagaaatga gcgcaggtca aattgttgag cggattattg ctaatttaac aggaatatct
+ 2401 ggtgaaaaat tacaaagagg ggatctctct aaagaagaat tattccgagt agaagaagct
+ 2461 ggagaaacgg ttagagaatc acatttttat atctgcagtg atagtcagta taagcttaac
+ 2521 ttaatcgcga atcagatccg gttgctgaga aaagaagatc gagtagacgt aatatttatc
+ 2581 gattacttgc agttgatcaa ctcatcggtt ggagaaaatc gtcaaaatga aatagcagat
+ 2641 atatctagaa ccttaagagg tttagcctca gagctaaaca ttcctatagt ttgtttatcc
+ 2701 caactatcta gaaaagttga ggatagagca aataaagttc ccatgctttc agatttgcga
+ 2761 gacagcggtc aaatagagca agacgcagat gtgattttgt ttatcaatag gaaggaatcg
+ 2821 tcttctaatt gtgagataac tgttgggaaa aatagacatg gatcggtttt ctcttcggta
+ 2881 ttacatttcg atccaaaaat tagtaaattc tccgctatta aaaaagtatg gtaaattata
+ 2941 gtaactgcca cttcatcaaa agtcctatcc accttgaaaa tcagaagttt ggaagaagac
+ 3001 ctggtcaatc tattaagata tctcccaaat tggctcaaaa tgggatggta gaagttatag
+ 3061 gtcttgattt tctttcatct cattaccatg cattagcagc tatccaaaga ttactgaccg
+ 3121 caacgaatta caaggggaac acaaaagggg ttgttttatc cagagaatca aatagttttc
+ 3181 aatttgaagg atggatacca agaatccgtt ttacaaaaac tgaattctta gaggcttatg
+ 3241 gagttaagcg gtataaaaca tccagaaata agtatgagtt tagtggaaaa gaagctgaaa
+ 3301 ctgctttaga agccttatac catttaggac atcaaccgtt tttaatagtg gcaactagaa
+ 3361 ctcgatggac taatggaaca caaatagtag accgttacca aactctttct ccgatcatta
+ 3421 ggatttacga aggatgggaa ggtttaactg acgaagaaaa tatagatata gacttaacac
+ 3481 cttttaattc accacctaca cggaaacata aagggttcgt tgtagagcca tgtcctatct
+ 3541 tggtagatca aatagaatcc tactttgtaa tcaagcctgc aaatgtatac caagaaataa
+ 3601 aaatgcgttt cccaaatgca tcaaagtatg cttacacatt tatcgactgg gtgattacag
+ 3661 cagctgcgaa aaagagacga aaattaacta aggataattc ttggccagaa aacttgttat
+ 3721 taaacgttaa cgttaaaagt cttgcatata ttttaaggat gaatcggtac atctgtacaa
+ 3781 ggaactggaa aaaaatcgag ttagctatcg ataaatgtat agaaatcgcc attcagcttg
+ 3841 gctggttatc tagaagaaaa cgcattgaat ttctggattc ttctaaactc tctaaaaaag
+ 3901 aaattctata tctaaataaa gagcgctttg aagaaataac taagaaatct aaagaacaaa
+ 3961 tggaacaatt agaacaagaa tctattaatt aatagcaagc ttgaaactaa aaacctaatt
+ 4021 tatttaaagc tcaaaataaa aaagagtttt aaaatgggaa attctggttt ttatttgtat
+ 4081 aacactgaaa actgcgtctt tgctgataat atcaaagttg ggcaaatgac agagccgctc
+ 4141 aaggaccagc aaataatcct tgggacaaca tcaacacctg tcgcagccaa aatgacagct
+ 4201 tctgatggaa tatctttaac agtctccaat aattcatcaa ccaatgcttc tattacaatt
+ 4261 ggtttggatg cggaaaaagc ttaccagctt attctagaaa agttgggaga tcaaattctt
+ 4321 gatggaattg ctgatactat tgttgatagt acagtccaag atattttaga caaaatcaaa
+ 4381 acagaccctt ctctaggttt gttgaaagct tttaacaact ttccaatcac taataaaatt
+ 4441 caatgcaacg ggttattcac tcccagtaac attgaaactt tattaggagg aactgaaata
+ 4501 ggaaaattca cagtcacacc caaaagctct gggagcatgt tcttagtctc agcagatatt
+ 4561 attgcatcaa gaatggaagg cggcgttgtt ctagctttgg tacgagaagg tgattctaag
+ 4621 ccctgcgcga ttagttatgg atactcatca ggcattccta atttatgtag tctaagaacc
+ 4681 agtattacta atacaggatt gactccgaca acgtattcat tacgtgtagg cggtttagaa
+ 4741 agcggtgtgg tatgggttaa tgccctttct aatggcaatg atattttagg aataacaaat
+ 4801 acttctaatg tatctttttt agaggtaata cctcaaacaa acgcttaaac aatttttatt
+ 4861 ggatttttct tataggtttt atatttagag aaaacagttc gaattacggg gtttgttatg
+ 4921 caaaataaaa gaaaagtgag ggacgatttt attaaaattg ttaaagatgt gaaaaaagat
+ 4981 ttccccgaat tagacctaaa aatacgagta aacaaggaaa aagtaacttt cttaaattct
+ 5041 cccttagaac tctaccataa aagtgtctca ctaattctag gactgcttca acaaatagaa
+ 5101 aactctttag gattattccc agactctcct gttcttgaaa aattagagga taacagttta
+ 5161 aagctaaaaa aggctttgat tatgcttatc ttgtctagaa aagacatgtt ttccaaggct
+ 5221 gaatagacaa cttactctaa cgttggagtt gatttgcaca ccttagtttt ttgctctttt
+ 5281 aagggaggaa ctggaaaaac aacactttct ctaaacgtgg gatgcaactt ggcccaattt
+ 5341 ttagggaaaa aagtgttact tgctgaccta gacccgcaat ccaatttatc ttctggattg
+ 5401 ggggctagtg tcagaagtga ccaaaaaggc ttgcacgaca tagtatacac atcaaacgat
+ 5461 ttaaaatcaa tcatttgcga aacaaaaaaa gatagtgtgg acctaattcc tgcatcattt
+ 5521 tcatccgaac agtttagaga attggatatt catagaggac ctagtaacaa cttaaagtta
+ 5581 tttctgaatg agtactgcgc tcctttttat gacatctgca taatagacac tccacctagc
+ 5641 ctaggagggt taacgaaaga agcttttgtt gcaggagaca aattaattgc ttgtttaact
+ 5701 ccagaacctt tttctattct agggttacaa aagatacgtg aattcttaag ttcggtcgga
+ 5761 aaacctgaag aagaacacat tcttggaata gctttgtctt tttgggatga tcgtaactcg
+ 5821 actaaccaaa tgtatataga cattatcgag tctatttaca aaaacaagct tttttcaaca
+ 5881 aaaattcgtc gagatatttc tctcagccgt tctcttctta aagaagattc tgtagctaat
+ 5941 gtctatccaa attctagggc cgcagaagat attctgaagt taacgcatga aatagcaaat
+ 6001 attttgcata tcgaatatga acgagattac tctcagagga caacgtgaac aaactaaaaa
+ 6061 aagaagcgga tgtctttttt aaaaaaaatc aaactgccgc ttctctagat tttaagaaga
+ 6121 cgcttccctc cattgaacta ttctcagcaa ctttgaattc tgaggaaagt cagagtttgg
+ 6181 atcgattatt tttatcagag tcccaaaact attcggatga agaattttat caagaagaca
+ 6241 tcctagcggt aaaactgctt actggtcaga taaaatccat acagaagcaa cacgtacttc
+ 6301 ttttaggaga aaaaatctat aatgctagaa aaatcctgag taaggatcac ttctcctcaa
+ 6361 caactttttc atcttggata gagttagttt ttagaactaa gtcttctgct tacaatgctc
+ 6421 ttgcatatta cgagcttttt ataaacctcc ccaaccaaac tctacaaaaa gagtttcaat
+ 6481 cgatccccta taaatccgca tatattttgg ccgctagaaa aggcgattta aaaaccaagg
+ 6541 tcgatgtgat agggaaagta tgtggaatgt cgaactcatc ggcgataagg gtgttggatc
+ 6601 aatttcttcc ttcatctaga aacaaagacg ttagagaaac gatagataag tctgattcag
+ 6661 agaagaatcg ccaattatct gatttcttaa tagagatact tcgcatcatg tgttccggag
+ 6721 tttctttgtc ctcctataac gaaaatcttc tacaacagct ttttgaactt tttaagcaaa
+ 6781 agagctgatc ctccgtcagc tcatatatat atatctatta tatatatata tttagggatt
+ 6841 tgatttcacg agagagattt gcaactcttg gtggtagact ttgcaactct tggtggtaga
+ 6901 ctttgcaact cttggtggta gactttgcaa ctcttggtgg tagacttggt cataatggac
+ 6961 ttttgttaaa aaatttatta aaatcttaga gctccgattt tgaatagctt tggttaagaa
+ 7021 aatgggctcg atggctttcc ataaaagtag attgttttta acttttgggg acgcgtcgga
+ 7081 aatttggtta tctactttat cttatctaac tagaaaaaat tatgcgtctg ggattaactt
+ 7141 tcttgtttct ttagagattc tggatttatc ggaaaccttg ataaaggcta tttctcttga
+ 7201 ccacagcgaa tctttgttta aaatcaagtc tctagatgtt tttaatggaa aagttgtttc
+ 7261 agaggcatct aaacaggcta gagcggcatg ctacatatct ttcacaaagt ttttgtatag
+ 7321 attgaccaag ggatatatta aacccgctat tccattgaaa gattttggaa acactacatt
+ 7381 ttttaaaatc cgagacaaaa tcaaaacaga atcgatttct aagcaggaat ggacagtttt
+ 7441 ttttgaagcg ctccggatag tgaattatag agactattta atcggtaaat tgattgtaca
+ 7501 ag
+//
+
git://source.jalview.org / jalview.git / commitdiff