--- /dev/null
+<?xml version="1.0" encoding="UTF-8" standalone="no"?>
+<!--
+ Retrieved for Jalview 14-Sep-2018 from ftp://ftp.sra.ebi.ac.uk/meta/xsd/sra_1_5/ENA.embl.xsd
+ Modified to match ftp://ftp.sra.ebi.ac.uk/meta/xsd/sra_1_5/ENA.root.xsd with only ENA.embl.xsd included
+ root element "ROOT" contains a <choice> of "entry" (single accession) or "entrySet" (one or more accessions)
+ Java binding classes are generated by
+ xjc schemas/embl.xsd -b schemas/embl_bindings.xml -d src -p jalview.xml.binding.embl
+-->
+<xs:schema xmlns:ebi="http://www.ebi.ac.uk/embl/schema"
+ xmlns:xs="http://www.w3.org/2001/XMLSchema"
+ attributeFormDefault="unqualified" elementFormDefault="qualified"
+ version="1.1">
+ <xs:complexType name="XrefType">
+ <xs:annotation>
+ <xs:documentation>Database cross-reference.</xs:documentation>
+ </xs:annotation>
+ <xs:attribute name="db" type="xs:string" use="required" />
+ <xs:attribute name="id" type="xs:string" use="required" />
+ <xs:attribute name="secondaryId" type="xs:string"
+ use="optional" />
+ </xs:complexType>
+ <xs:complexType name="EntrySetType">
+ <xs:sequence minOccurs="1" maxOccurs="unbounded">
+ <xs:element name="entry" type="EntryType" />
+ </xs:sequence>
+ </xs:complexType>
+ <xs:complexType name="EntryType">
+ <xs:sequence>
+ <xs:element maxOccurs="unbounded" minOccurs="0"
+ name="secondaryAccession" type="xs:string" />
+ <xs:element maxOccurs="unbounded" minOccurs="0"
+ name="projectAccession" type="xs:string" />
+ <xs:element maxOccurs="1" minOccurs="1" name="description"
+ type="xs:string" />
+ <xs:element maxOccurs="1" minOccurs="0" name="comment"
+ type="xs:string" />
+ <xs:element maxOccurs="unbounded" minOccurs="0"
+ name="keyword" type="xs:string" />
+ <xs:element maxOccurs="unbounded" minOccurs="0"
+ name="reference">
+ <xs:annotation>
+ <xs:documentation>Not supported for EMBL-CDS.</xs:documentation>
+ </xs:annotation>
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element maxOccurs="1" minOccurs="0" name="title"
+ type="xs:string" />
+ <xs:element maxOccurs="unbounded" minOccurs="0"
+ name="author" type="xs:string" />
+ <xs:element maxOccurs="unbounded" minOccurs="0"
+ name="applicant" type="xs:string">
+ <xs:annotation>
+ <xs:documentation>Patent applicant.</xs:documentation>
+ </xs:annotation>
+ </xs:element>
+ <xs:element maxOccurs="1" minOccurs="0"
+ name="consortium" type="xs:string" />
+ <xs:element maxOccurs="1" minOccurs="0"
+ name="submissionDate" type="xs:date">
+ <xs:annotation>
+ <xs:documentation>The submission date (used only for submission
+ references).</xs:documentation>
+ </xs:annotation>
+ </xs:element>
+ <xs:element maxOccurs="1" minOccurs="0" name="journal"
+ type="xs:string">
+ <xs:annotation>
+ <xs:documentation>The journal name (used only for article
+ references).</xs:documentation>
+ </xs:annotation>
+ </xs:element>
+ <xs:element maxOccurs="1" minOccurs="0" name="year"
+ type="xs:string">
+ <xs:annotation>
+ <xs:documentation>The publication year (used only for article
+ references).</xs:documentation>
+ </xs:annotation>
+ </xs:element>
+ <xs:element maxOccurs="1" minOccurs="0" name="volume"
+ type="xs:string">
+ <xs:annotation>
+ <xs:documentation>The volume number (used only for article
+ references).</xs:documentation>
+ </xs:annotation>
+ </xs:element>
+ <xs:element maxOccurs="1" minOccurs="0" name="issue"
+ type="xs:string">
+ <xs:annotation>
+ <xs:documentation>The issue number (used only for article
+ references).</xs:documentation>
+ </xs:annotation>
+ </xs:element>
+ <xs:element maxOccurs="1" minOccurs="0"
+ name="firstPage" type="xs:string">
+ <xs:annotation>
+ <xs:documentation>The first page (used only for article
+ references).</xs:documentation>
+ </xs:annotation>
+ </xs:element>
+ <xs:element maxOccurs="1" minOccurs="0" name="lastPage"
+ type="xs:string">
+ <xs:annotation>
+ <xs:documentation>The last page (used only for article
+ references).</xs:documentation>
+ </xs:annotation>
+ </xs:element>
+ <xs:element maxOccurs="1" minOccurs="0" name="comment"
+ type="xs:string" />
+ <xs:element maxOccurs="1" minOccurs="0"
+ name="referenceLocation" type="xs:string" />
+ <xs:element maxOccurs="unbounded" minOccurs="0"
+ name="xref" type="XrefType" />
+ </xs:sequence>
+ <xs:attribute name="type" use="required">
+ <xs:simpleType>
+ <xs:restriction base="xs:string">
+ <xs:enumeration value="submission" />
+ <xs:enumeration value="book" />
+ <xs:enumeration value="article" />
+ <xs:enumeration value="patent" />
+ <xs:enumeration value="thesis" />
+ <xs:enumeration value="unpublished" />
+ </xs:restriction>
+ </xs:simpleType>
+ </xs:attribute>
+ <xs:attribute name="number" type="xs:integer"
+ use="required" />
+ <xs:attribute name="location" type="xs:string" />
+ </xs:complexType>
+ </xs:element>
+ <xs:element maxOccurs="unbounded" minOccurs="0"
+ name="xref" type="XrefType" />
+ <xs:element maxOccurs="unbounded" minOccurs="0"
+ name="feature">
+ <xs:annotation>
+ <xs:documentation>Sequence feature.</xs:documentation>
+ </xs:annotation>
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element maxOccurs="1" minOccurs="0" name="taxon">
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element maxOccurs="1" minOccurs="0"
+ name="lineage">
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element maxOccurs="unbounded" minOccurs="1"
+ name="taxon">
+ <xs:complexType>
+ <xs:attribute name="scientificName"
+ type="xs:string" use="required" />
+ </xs:complexType>
+ </xs:element>
+ </xs:sequence>
+ </xs:complexType>
+ </xs:element>
+ </xs:sequence>
+ <xs:attribute name="scientificName"
+ type="xs:string" use="required" />
+ <xs:attribute name="commonName" type="xs:string"
+ use="optional" />
+ <xs:attribute name="taxId" type="xs:integer"
+ use="optional" />
+ </xs:complexType>
+ </xs:element>
+ <xs:element maxOccurs="unbounded" minOccurs="0"
+ name="xref" type="XrefType" />
+ <xs:element maxOccurs="unbounded" minOccurs="0"
+ name="qualifier">
+ <xs:annotation>
+ <xs:documentation>Sequence feature qualifier.</xs:documentation>
+ </xs:annotation>
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element maxOccurs="1" minOccurs="0" name="value"
+ type="xs:string" />
+ </xs:sequence>
+ <xs:attribute name="name" type="xs:string"
+ use="required" />
+ </xs:complexType>
+ </xs:element>
+ </xs:sequence>
+ <xs:attribute name="name" type="xs:string"
+ use="required" />
+ <xs:attribute name="location" type="xs:string"
+ use="required" />
+ </xs:complexType>
+ </xs:element>
+ <xs:element maxOccurs="1" minOccurs="0" name="assembly">
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element maxOccurs="unbounded" minOccurs="1"
+ name="range">
+ <xs:complexType>
+ <xs:attribute name="begin" type="xs:integer"
+ use="required" />
+ <xs:attribute name="end" type="xs:integer"
+ use="required" />
+ <xs:attribute name="primaryBegin" type="xs:integer"
+ use="optional" />
+ <xs:attribute name="primaryEnd" type="xs:integer"
+ use="optional" />
+ <xs:attribute name="accession" type="xs:string"
+ use="required" />
+ <xs:attribute name="version" type="xs:integer"
+ use="required" />
+ <xs:attribute default="false" name="complement"
+ type="xs:boolean" use="optional" />
+ </xs:complexType>
+ </xs:element>
+ </xs:sequence>
+ </xs:complexType>
+ </xs:element>
+ <xs:element maxOccurs="1" minOccurs="0" name="contig">
+ <xs:complexType>
+ <xs:sequence>
+ <xs:choice maxOccurs="unbounded" minOccurs="0">
+ <xs:element maxOccurs="1" minOccurs="1" name="range">
+ <xs:complexType>
+ <xs:attribute name="begin" type="xs:integer"
+ use="required" />
+ <xs:attribute name="end" type="xs:integer"
+ use="required" />
+ <xs:attribute name="primaryBegin"
+ type="xs:integer" use="optional" />
+ <xs:attribute name="primaryEnd" type="xs:integer"
+ use="optional" />
+ <xs:attribute name="accession" type="xs:string"
+ use="required" />
+ <xs:attribute name="version" type="xs:integer"
+ use="required" />
+ <xs:attribute default="false" name="complement"
+ type="xs:boolean" use="optional" />
+ </xs:complexType>
+ </xs:element>
+ <xs:element maxOccurs="1" minOccurs="1" name="gap">
+ <xs:complexType>
+ <xs:attribute name="begin" type="xs:integer"
+ use="required" />
+ <xs:attribute name="end" type="xs:integer"
+ use="required" />
+ <xs:attribute name="length" type="xs:integer"
+ use="required" />
+ <xs:attribute default="false" name="unknownLength"
+ type="xs:boolean" use="optional" />
+ </xs:complexType>
+ </xs:element>
+ </xs:choice>
+ </xs:sequence>
+ </xs:complexType>
+ </xs:element>
+ <xs:element maxOccurs="1" minOccurs="0" name="sequence"
+ type="xs:string" />
+ </xs:sequence>
+ <xs:attribute name="accession" type="xs:string"
+ use="required" />
+ <xs:attribute name="version" type="xs:integer"
+ use="required" />
+ <xs:attribute name="entryVersion" type="xs:integer">
+ <xs:annotation>
+ <xs:documentation>Not supported for EMBL-CDS.</xs:documentation>
+ </xs:annotation>
+ </xs:attribute>
+ <xs:attribute name="dataClass" type="xs:string"
+ use="required" />
+ <xs:attribute name="taxonomicDivision" type="xs:string"
+ use="required" />
+ <xs:attribute name="moleculeType" type="xs:string"
+ use="required" />
+ <xs:attribute name="sequenceLength" type="xs:integer"
+ use="required" />
+ <xs:attribute name="topology" use="required">
+ <xs:simpleType>
+ <xs:restriction base="xs:string">
+ <xs:enumeration value="circular" />
+ <xs:enumeration value="linear" />
+ </xs:restriction>
+ </xs:simpleType>
+ </xs:attribute>
+ <xs:attribute name="firstPublic" type="xs:date">
+ <xs:annotation>
+ <xs:documentation>Not supported for EMBL-CDS.</xs:documentation>
+ </xs:annotation>
+ </xs:attribute>
+ <xs:attribute name="firstPublicRelease" type="xs:integer">
+ <xs:annotation>
+ <xs:documentation>Not supported for EMBL-CDS.</xs:documentation>
+ </xs:annotation>
+ </xs:attribute>
+ <xs:attribute name="lastUpdated" type="xs:date">
+ <xs:annotation>
+ <xs:documentation>Not supported for EMBL-CDS.</xs:documentation>
+ </xs:annotation>
+ </xs:attribute>
+ <xs:attribute name="lastUpdatedRelease" type="xs:integer">
+ <xs:annotation>
+ <xs:documentation>Not supported for EMBL-CDS.</xs:documentation>
+ </xs:annotation>
+ </xs:attribute>
+ </xs:complexType>
+ <xs:element name="ROOT">
+ <xs:complexType>
+ <xs:choice>
+ <xs:element name="entrySet" type="EntrySetType" />
+ <xs:element name="entry" type="EntryType" />
+ </xs:choice>
+ </xs:complexType>
+ </xs:element>
+</xs:schema>
--- /dev/null
+<!--
+ Binding file stops the nested 'taxon' elements generating invalid Java (nested type hiding enclosing type).
+ The binding converts EntryType/feature/taxon to EntryType$Feature$FeatureTaxon.
+ EntryType/feature/taxon/lineage/taxon generates EntryType$Feature$FeatureTaxon$Lineage$Taxon.
+-->
+<jaxb:bindings
+ xmlns:xsd="http://www.w3.org/2001/XMLSchema"
+ xmlns:jaxb="http://java.sun.com/xml/ns/jaxb" version="2.1">
+ <jaxb:bindings schemaLocation="embl.xsd">
+ <jaxb:bindings
+ node="/xsd:schema/xsd:complexType[@name='EntryType']/xsd:sequence/xsd:element[@name='feature']/xsd:complexType/xsd:sequence/xsd:element[@name='taxon']/xsd:complexType">
+ <jaxb:class name="FeatureTaxon" />
+ </jaxb:bindings>
+ </jaxb:bindings>
+</jaxb:bindings>
\ No newline at end of file
*******************************************************************************-->
<xs:schema targetNamespace="http://uniprot.org/uniprot" xmlns:xs="http://www.w3.org/2001/XMLSchema"
xmlns="http://uniprot.org/uniprot" elementFormDefault="qualified">
+<!--
+ Retrieved for Jalview 13-Sep-2018 from https://www.uniprot.org/docs/uniprot.xsd
+ Java binding classes are generated by
+ xjc schemas/uniprot.xsd -d src -p jalview.xml.binding.uniprot
+-->
<!-- XML Schema definition for the UniProtKB XML format
Tested with:
-XSV (XML Schema Validator), http://www.w3.org/2001/03/webdata/xsv
+++ /dev/null
-/*
- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ The Jalview Authors
- *
- * This file is part of Jalview.
- *
- * Jalview is free software: you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3
- * of the License, or (at your option) any later version.
- *
- * Jalview is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
- * PURPOSE. See the GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
- * The Jalview Authors are detailed in the 'AUTHORS' file.
- */
-package jalview.datamodel.xdb.embl;
-
-import jalview.analysis.SequenceIdMatcher;
-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;
-import jalview.util.StringUtils;
-
-import java.text.ParseException;
-import java.util.Arrays;
-import java.util.Hashtable;
-import java.util.List;
-import java.util.Map;
-import java.util.Map.Entry;
-import java.util.Vector;
-import java.util.regex.Pattern;
-
-/**
- * Data model for one entry returned from an EMBL query, as marshalled by a
- * Castor binding file
- *
- * For example: http://www.ebi.ac.uk/ena/data/view/J03321&display=xml
- *
- * @see embl_mapping.xml
- */
-public class EmblEntry
-{
- private static final Pattern SPACE_PATTERN = Pattern.compile(" ");
-
- String accession;
-
- String entryVersion;
-
- String sequenceVersion;
-
- String dataClass;
-
- String moleculeType;
-
- String topology;
-
- String sequenceLength;
-
- String taxonomicDivision;
-
- String description;
-
- String firstPublicDate;
-
- String firstPublicRelease;
-
- String lastUpdatedDate;
-
- String lastUpdatedRelease;
-
- Vector<String> keywords;
-
- Vector<DBRefEntry> dbRefs;
-
- Vector<EmblFeature> features;
-
- EmblSequence sequence;
-
- /**
- * @return the accession
- */
- public String getAccession()
- {
- return accession;
- }
-
- /**
- * @param accession
- * the accession to set
- */
- public void setAccession(String accession)
- {
- this.accession = accession;
- }
-
- /**
- * @return the dbRefs
- */
- public Vector<DBRefEntry> getDbRefs()
- {
- return dbRefs;
- }
-
- /**
- * @param dbRefs
- * the dbRefs to set
- */
- public void setDbRefs(Vector<DBRefEntry> dbRefs)
- {
- this.dbRefs = dbRefs;
- }
-
- /**
- * @return the features
- */
- public Vector<EmblFeature> getFeatures()
- {
- return features;
- }
-
- /**
- * @param features
- * the features to set
- */
- public void setFeatures(Vector<EmblFeature> features)
- {
- this.features = features;
- }
-
- /**
- * @return the keywords
- */
- public Vector<String> getKeywords()
- {
- return keywords;
- }
-
- /**
- * @param keywords
- * the keywords to set
- */
- public void setKeywords(Vector<String> keywords)
- {
- this.keywords = keywords;
- }
-
- /**
- * @return the sequence
- */
- public EmblSequence getSequence()
- {
- return sequence;
- }
-
- /**
- * @param sequence
- * the sequence to set
- */
- public void setSequence(EmblSequence sequence)
- {
- this.sequence = sequence;
- }
-
- /**
- * Recover annotated sequences from EMBL file
- *
- * @param sourceDb
- * @param peptides
- * a list of protein products found so far (to add to)
- * @return dna dataset sequence with DBRefs and features
- */
- public SequenceI getSequence(String sourceDb, List<SequenceI> peptides)
- {
- SequenceI dna = makeSequence(sourceDb);
- if (dna == null)
- {
- return null;
- }
- dna.setDescription(description);
- DBRefEntry retrievedref = new DBRefEntry(sourceDb, getSequenceVersion(),
- accession);
- dna.addDBRef(retrievedref);
- // add map to indicate the sequence is a valid coordinate frame for the
- // dbref
- retrievedref
- .setMap(new Mapping(null, new int[]
- { 1, dna.getLength() }, new int[] { 1, dna.getLength() }, 1,
- 1));
-
- /*
- * transform EMBL Database refs to canonical form
- */
- if (dbRefs != null)
- {
- for (DBRefEntry dbref : dbRefs)
- {
- dbref.setSource(DBRefUtils.getCanonicalName(dbref.getSource()));
- dna.addDBRef(dbref);
- }
- }
-
- SequenceIdMatcher matcher = new SequenceIdMatcher(peptides);
- try
- {
- for (EmblFeature feature : features)
- {
- if (FeatureProperties.isCodingFeature(sourceDb, feature.getName()))
- {
- parseCodingFeature(feature, sourceDb, dna, peptides, matcher);
- }
- }
- } catch (Exception e)
- {
- System.err.println("EMBL Record Features parsing error!");
- System.err
- .println("Please report the following to help@jalview.org :");
- System.err.println("EMBL Record " + accession);
- System.err.println("Resulted in exception: " + e.getMessage());
- e.printStackTrace(System.err);
- }
-
- return dna;
- }
-
- /**
- * @param sourceDb
- * @return
- */
- SequenceI makeSequence(String sourceDb)
- {
- if (sequence == null)
- {
- System.err.println(
- "No sequence was returned for ENA accession " + accession);
- return null;
- }
- SequenceI dna = new Sequence(sourceDb + "|" + accession,
- sequence.getSequence());
- return dna;
- }
-
- /**
- * Extracts coding region and product from a CDS feature and properly decorate
- * it with annotations.
- *
- * @param feature
- * coding feature
- * @param sourceDb
- * source database for the EMBLXML
- * @param dna
- * parent dna sequence for this record
- * @param peptides
- * list of protein product sequences for Embl entry
- * @param matcher
- * helper to match xrefs in already retrieved sequences
- */
- void parseCodingFeature(EmblFeature feature, String sourceDb,
- SequenceI dna, List<SequenceI> peptides,
- SequenceIdMatcher matcher)
- {
- boolean isEmblCdna = sourceDb.equals(DBRefSource.EMBLCDS);
-
- int[] exons = getCdsRanges(feature);
-
- String translation = null;
- String proteinName = "";
- String proteinId = null;
- Map<String, String> vals = new Hashtable<>();
-
- /*
- * codon_start 1/2/3 in EMBL corresponds to phase 0/1/2 in CDS
- * (phase is required for CDS features in GFF3 format)
- */
- int codonStart = 1;
-
- /*
- * parse qualifiers, saving protein translation, protein id,
- * codon start position, product (name), and 'other values'
- */
- if (feature.getQualifiers() != null)
- {
- for (Qualifier q : feature.getQualifiers())
- {
- String qname = q.getName();
- if (qname.equals("translation"))
- {
- // remove all spaces (precompiled String.replaceAll(" ", ""))
- translation = SPACE_PATTERN.matcher(q.getValues()[0])
- .replaceAll("");
- }
- else if (qname.equals("protein_id"))
- {
- proteinId = q.getValues()[0].trim();
- }
- else if (qname.equals("codon_start"))
- {
- try
- {
- codonStart = Integer.parseInt(q.getValues()[0].trim());
- } catch (NumberFormatException e)
- {
- System.err.println("Invalid codon_start in XML for " + accession
- + ": " + e.getMessage());
- }
- }
- else if (qname.equals("product"))
- {
- // sometimes name is returned e.g. for V00488
- proteinName = q.getValues()[0].trim();
- }
- else
- {
- // throw anything else into the additional properties hash
- String[] qvals = q.getValues();
- if (qvals != null)
- {
- String commaSeparated = StringUtils.arrayToSeparatorList(qvals,
- ",");
- vals.put(qname, commaSeparated);
- }
- }
- }
- }
-
- DBRefEntry proteinToEmblProteinRef = null;
- exons = MappingUtils.removeStartPositions(codonStart - 1, exons);
-
- SequenceI product = null;
- Mapping dnaToProteinMapping = null;
- if (translation != null && proteinName != null && proteinId != null)
- {
- int translationLength = translation.length();
-
- /*
- * look for product in peptides list, if not found, add it
- */
- product = matcher.findIdMatch(proteinId);
- if (product == null)
- {
- product = new Sequence(proteinId, translation, 1,
- translationLength);
- product.setDescription(((proteinName.length() == 0)
- ? "Protein Product from " + sourceDb
- : proteinName));
- peptides.add(product);
- matcher.add(product);
- }
-
- // we have everything - create the mapping and perhaps the protein
- // sequence
- if (exons == null || exons.length == 0)
- {
- /*
- * workaround until we handle dna location for CDS sequence
- * e.g. location="X53828.1:60..1058" correctly
- */
- System.err.println(
- "Implementation Notice: EMBLCDS records not properly supported yet - Making up the CDNA region of this sequence... may be incorrect ("
- + sourceDb + ":" + getAccession() + ")");
- int dnaLength = dna.getLength();
- if (translationLength * 3 == (1 - codonStart + dnaLength))
- {
- System.err.println(
- "Not allowing for additional stop codon at end of cDNA fragment... !");
- // this might occur for CDS sequences where no features are marked
- exons = new int[] { dna.getStart() + (codonStart - 1),
- dna.getEnd() };
- dnaToProteinMapping = new Mapping(product, exons,
- new int[]
- { 1, translationLength }, 3, 1);
- }
- if ((translationLength + 1) * 3 == (1 - codonStart + dnaLength))
- {
- System.err.println(
- "Allowing for additional stop codon at end of cDNA fragment... will probably cause an error in VAMSAs!");
- exons = new int[] { dna.getStart() + (codonStart - 1),
- dna.getEnd() - 3 };
- dnaToProteinMapping = new Mapping(product, exons,
- new int[]
- { 1, translationLength }, 3, 1);
- }
- }
- else
- {
- // Trim the exon mapping if necessary - the given product may only be a
- // fragment of a larger protein. (EMBL:AY043181 is an example)
-
- if (isEmblCdna)
- {
- // TODO: 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
- }
- else
- {
- // final product length truncation check
- int[] cdsRanges = adjustForProteinLength(translationLength,
- exons);
- dnaToProteinMapping = new Mapping(product, cdsRanges,
- new int[]
- { 1, translationLength }, 3, 1);
- if (product != null)
- {
- /*
- * make xref with mapping from protein to EMBL dna
- */
- DBRefEntry proteinToEmblRef = new DBRefEntry(DBRefSource.EMBL,
- getSequenceVersion(), proteinId,
- new Mapping(dnaToProteinMapping.getMap().getInverse()));
- product.addDBRef(proteinToEmblRef);
-
- /*
- * make xref from protein to EMBLCDS; we assume here that the
- * CDS sequence version is same as dna sequence (?!)
- */
- MapList proteinToCdsMapList = new MapList(
- new int[]
- { 1, translationLength },
- new int[]
- { 1 + (codonStart - 1),
- (codonStart - 1) + 3 * translationLength },
- 1, 3);
- DBRefEntry proteinToEmblCdsRef = new DBRefEntry(
- DBRefSource.EMBLCDS, getSequenceVersion(), proteinId,
- new Mapping(proteinToCdsMapList));
- product.addDBRef(proteinToEmblCdsRef);
-
- /*
- * make 'direct' xref from protein to EMBLCDSPROTEIN
- */
- proteinToEmblProteinRef = new DBRefEntry(proteinToEmblCdsRef);
- proteinToEmblProteinRef.setSource(DBRefSource.EMBLCDSProduct);
- proteinToEmblProteinRef.setMap(null);
- product.addDBRef(proteinToEmblProteinRef);
- }
- }
- }
-
- /*
- * add cds features to dna sequence
- */
- String cds = feature.getName(); // "CDS"
- 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);
- int exonNumber = xint / 2 + 1;
- String desc = String.format("Exon %d for protein '%s' EMBLCDS:%s",
- exonNumber, proteinName, proteinId);
-
- SequenceFeature sf = makeCdsFeature(cds, desc, begin, end,
- sourceDb, vals);
-
- sf.setEnaLocation(feature.getLocation());
- boolean forwardStrand = exonStart <= exonEnd;
- sf.setStrand(forwardStrand ? "+" : "-");
- sf.setPhase(String.valueOf(codonStart - 1));
- sf.setValue(FeatureProperties.EXONPOS, exonNumber);
- sf.setValue(FeatureProperties.EXONPRODUCT, proteinName);
-
- dna.addSequenceFeature(sf);
- }
- }
-
- /*
- * add feature dbRefs to sequence, and mappings for Uniprot xrefs
- */
- boolean hasUniprotDbref = false;
- if (feature.dbRefs != null)
- {
- boolean mappingUsed = false;
- for (DBRefEntry ref : feature.dbRefs)
- {
- /*
- * ensure UniProtKB/Swiss-Prot converted to UNIPROT
- */
- String source = DBRefUtils.getCanonicalName(ref.getSource());
- ref.setSource(source);
- DBRefEntry proteinDbRef = new DBRefEntry(ref.getSource(),
- ref.getVersion(), ref.getAccessionId());
- if (source.equals(DBRefSource.UNIPROT))
- {
- String proteinSeqName = DBRefSource.UNIPROT + "|"
- + ref.getAccessionId();
- if (dnaToProteinMapping != null
- && dnaToProteinMapping.getTo() != null)
- {
- if (mappingUsed)
- {
- /*
- * two or more Uniprot xrefs for the same CDS -
- * each needs a distinct Mapping (as to a different sequence)
- */
- dnaToProteinMapping = new Mapping(dnaToProteinMapping);
- }
- mappingUsed = true;
-
- /*
- * try to locate the protein mapped to (possibly by a
- * previous CDS feature); if not found, construct it from
- * the EMBL translation
- */
- SequenceI proteinSeq = matcher.findIdMatch(proteinSeqName);
- if (proteinSeq == null)
- {
- proteinSeq = new Sequence(proteinSeqName,
- product.getSequenceAsString());
- matcher.add(proteinSeq);
- peptides.add(proteinSeq);
- }
- dnaToProteinMapping.setTo(proteinSeq);
- dnaToProteinMapping.setMappedFromId(proteinId);
- proteinSeq.addDBRef(proteinDbRef);
- ref.setMap(dnaToProteinMapping);
- }
- hasUniprotDbref = true;
- }
- if (product != null)
- {
- /*
- * copy feature dbref to our protein product
- */
- DBRefEntry pref = proteinDbRef;
- pref.setMap(null); // reference is direct
- product.addDBRef(pref);
- // Add converse mapping reference
- if (dnaToProteinMapping != null)
- {
- Mapping pmap = new Mapping(dna,
- dnaToProteinMapping.getMap().getInverse());
- pref = new DBRefEntry(sourceDb, getSequenceVersion(),
- this.getAccession());
- pref.setMap(pmap);
- if (dnaToProteinMapping.getTo() != null)
- {
- dnaToProteinMapping.getTo().addDBRef(pref);
- }
- }
- }
- dna.addDBRef(ref);
- }
- }
-
- /*
- * if we have a product (translation) but no explicit Uniprot dbref
- * (example: EMBL AAFI02000057 protein_id EAL65544.1)
- * then construct mappings to an assumed EMBLCDSPROTEIN accession
- */
- if (!hasUniprotDbref && product != null)
- {
- if (proteinToEmblProteinRef == null)
- {
- // assuming CDSPROTEIN sequence version = dna version (?!)
- proteinToEmblProteinRef = new DBRefEntry(DBRefSource.EMBLCDSProduct,
- getSequenceVersion(), proteinId);
- }
- product.addDBRef(proteinToEmblProteinRef);
-
- if (dnaToProteinMapping != null
- && dnaToProteinMapping.getTo() != null)
- {
- DBRefEntry dnaToEmblProteinRef = new DBRefEntry(
- DBRefSource.EMBLCDSProduct, getSequenceVersion(),
- proteinId);
- dnaToEmblProteinRef.setMap(dnaToProteinMapping);
- dnaToProteinMapping.setMappedFromId(proteinId);
- dna.addDBRef(dnaToEmblProteinRef);
- }
- }
- }
-
- /**
- * Helper method to construct a SequenceFeature for one cds range
- *
- * @param type
- * feature type ("CDS")
- * @param desc
- * description
- * @param begin
- * start position
- * @param end
- * end position
- * @param group
- * feature group
- * @param vals
- * map of 'miscellaneous values' for feature
- * @return
- */
- protected SequenceFeature makeCdsFeature(String type, String desc,
- int begin, int end, String group, Map<String, String> vals)
- {
- SequenceFeature sf = new SequenceFeature(type, desc, begin, end, group);
- if (!vals.isEmpty())
- {
- StringBuilder sb = new StringBuilder();
- boolean first = true;
- for (Entry<String, String> val : vals.entrySet())
- {
- if (!first)
- {
- sb.append(";");
- }
- sb.append(val.getKey()).append("=").append(val.getValue());
- first = false;
- sf.setValue(val.getKey(), val.getValue());
- }
- sf.setAttributes(sb.toString());
- }
- return sf;
- }
-
- /**
- * Returns the CDS positions as a single array of [start, end, start, end...]
- * positions. If on the reverse strand, these will be in descending order.
- *
- * @param feature
- * @return
- */
- protected int[] getCdsRanges(EmblFeature feature)
- {
- if (feature.location == null)
- {
- return new int[] {};
- }
-
- try
- {
- List<int[]> ranges = DnaUtils.parseLocation(feature.location);
- return listToArray(ranges);
- } catch (ParseException e)
- {
- Cache.log.warn(
- String.format("Not parsing inexact CDS location %s in ENA %s",
- feature.location, this.accession));
- return new int[] {};
- }
- }
-
- /**
- * Converts a list of [start, end] ranges to a single array of [start, end,
- * start, end ...]
- *
- * @param ranges
- * @return
- */
- int[] listToArray(List<int[]> ranges)
- {
- int[] result = new int[ranges.size() * 2];
- int i = 0;
- for (int[] range : ranges)
- {
- result[i++] = range[0];
- result[i++] = range[1];
- }
- return result;
- }
-
- /**
- * 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)
- {
- 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;
- }
-
- public String getSequenceVersion()
- {
- return sequenceVersion;
- }
-
- public void setSequenceVersion(String sequenceVersion)
- {
- this.sequenceVersion = sequenceVersion;
- }
-
- public String getSequenceLength()
- {
- return sequenceLength;
- }
-
- public void setSequenceLength(String sequenceLength)
- {
- this.sequenceLength = sequenceLength;
- }
-
- public String getEntryVersion()
- {
- return entryVersion;
- }
-
- public void setEntryVersion(String entryVersion)
- {
- this.entryVersion = entryVersion;
- }
-
- public String getMoleculeType()
- {
- return moleculeType;
- }
-
- public void setMoleculeType(String moleculeType)
- {
- this.moleculeType = moleculeType;
- }
-
- public String getTopology()
- {
- return topology;
- }
-
- public void setTopology(String topology)
- {
- this.topology = topology;
- }
-
- public String getTaxonomicDivision()
- {
- return taxonomicDivision;
- }
-
- public void setTaxonomicDivision(String taxonomicDivision)
- {
- this.taxonomicDivision = taxonomicDivision;
- }
-
- public String getDescription()
- {
- return description;
- }
-
- public void setDescription(String description)
- {
- this.description = description;
- }
-
- public String getFirstPublicDate()
- {
- return firstPublicDate;
- }
-
- public void setFirstPublicDate(String firstPublicDate)
- {
- this.firstPublicDate = firstPublicDate;
- }
-
- public String getFirstPublicRelease()
- {
- return firstPublicRelease;
- }
-
- public void setFirstPublicRelease(String firstPublicRelease)
- {
- this.firstPublicRelease = firstPublicRelease;
- }
-
- public String getLastUpdatedDate()
- {
- return lastUpdatedDate;
- }
-
- public void setLastUpdatedDate(String lastUpdatedDate)
- {
- this.lastUpdatedDate = lastUpdatedDate;
- }
-
- public String getLastUpdatedRelease()
- {
- return lastUpdatedRelease;
- }
-
- public void setLastUpdatedRelease(String lastUpdatedRelease)
- {
- this.lastUpdatedRelease = lastUpdatedRelease;
- }
-
- public String getDataClass()
- {
- return dataClass;
- }
-
- public void setDataClass(String dataClass)
- {
- this.dataClass = dataClass;
- }
-}
+++ /dev/null
-/*
- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ The Jalview Authors
- *
- * This file is part of Jalview.
- *
- * Jalview is free software: you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3
- * of the License, or (at your option) any later version.
- *
- * Jalview is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
- * PURPOSE. See the GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
- * The Jalview Authors are detailed in the 'AUTHORS' file.
- */
-package jalview.datamodel.xdb.embl;
-
-/**
- * Data model mapped from any <error> elements returned from an EMBL query
- *
- * @see embl_mapping.xml
- */
-public class EmblError
-{
- String accession;
-
- /**
- * @return the accession
- */
- public String getAccession()
- {
- return accession;
- }
-
- /**
- * @param accession
- * the accession to set
- */
- public void setAccession(String accession)
- {
- this.accession = accession;
- }
-}
+++ /dev/null
-/*
- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ The Jalview Authors
- *
- * This file is part of Jalview.
- *
- * Jalview is free software: you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3
- * of the License, or (at your option) any later version.
- *
- * Jalview is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
- * PURPOSE. See the GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
- * The Jalview Authors are detailed in the 'AUTHORS' file.
- */
-package jalview.datamodel.xdb.embl;
-
-import jalview.datamodel.DBRefEntry;
-
-import java.util.Vector;
-
-/**
- * Data model for a <feature> element returned from an EMBL query reply
- *
- * @see embl_mapping.xml
- */
-public class EmblFeature
-{
- String name;
-
- Vector<DBRefEntry> dbRefs;
-
- Vector<Qualifier> qualifiers;
-
- String location;
-
- /**
- * @return the dbRefs
- */
- public Vector<DBRefEntry> getDbRefs()
- {
- return dbRefs;
- }
-
- /**
- * @param dbRefs
- * the dbRefs to set
- */
- public void setDbRefs(Vector<DBRefEntry> dbRefs)
- {
- this.dbRefs = dbRefs;
- }
-
- /**
- * @return the location
- */
- public String getLocation()
- {
- return location;
- }
-
- /**
- * @param loc
- */
- public void setLocation(String loc)
- {
- this.location = loc;
- }
-
- /**
- * @return the name
- */
- public String getName()
- {
- return name;
- }
-
- /**
- * @param name
- * the name to set
- */
- public void setName(String name)
- {
- this.name = name;
- }
-
- /**
- * @return the qualifiers
- */
- public Vector<Qualifier> getQualifiers()
- {
- return qualifiers;
- }
-
- /**
- * @param qualifiers
- * the qualifiers to set
- */
- public void setQualifiers(Vector<Qualifier> qualifiers)
- {
- this.qualifiers = qualifiers;
- }
-}
+++ /dev/null
-/*
- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ The Jalview Authors
- *
- * This file is part of Jalview.
- *
- * Jalview is free software: you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3
- * of the License, or (at your option) any later version.
- *
- * Jalview is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
- * PURPOSE. See the GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
- * The Jalview Authors are detailed in the 'AUTHORS' file.
- */
-package jalview.datamodel.xdb.embl;
-
-import jalview.datamodel.DBRefEntry;
-import jalview.ws.dbsources.Uniprot;
-
-import java.io.File;
-import java.io.FileReader;
-import java.io.PrintWriter;
-import java.io.Reader;
-import java.util.Vector;
-
-import org.exolab.castor.mapping.Mapping;
-import org.exolab.castor.xml.Unmarshaller;
-
-/**
- * Data model for entries returned from an EMBL query, as marshalled by a Castor
- * binding file
- *
- * For example: http://www.ebi.ac.uk/Tools/dbfetch/dbfetch/embl/x53828/emblxml
- *
- * @see embl_mapping.xml
- */
-public class EmblFile
-{
- Vector<EmblEntry> entries;
-
- Vector<EmblError> errors;
-
- String text;
-
- /**
- * @return the entries
- */
- public Vector<EmblEntry> getEntries()
- {
- return entries;
- }
-
- /**
- * @param entries
- * the entries to set
- */
- public void setEntries(Vector<EmblEntry> entries)
- {
- this.entries = entries;
- }
-
- /**
- * @return the errors
- */
- public Vector<EmblError> getErrors()
- {
- return errors;
- }
-
- /**
- * @param errors
- * the errors to set
- */
- public void setErrors(Vector<EmblError> errors)
- {
- this.errors = errors;
- }
-
- /**
- * Parse an EmblXML file into an EmblFile object
- *
- * @param file
- * @return parsed EmblXML or null if exceptions were raised
- */
- public static EmblFile getEmblFile(File file)
- {
- if (file == null)
- {
- return null;
- }
- try
- {
- return EmblFile.getEmblFile(new FileReader(file));
- } catch (Exception e)
- {
- System.err.println("Exception whilst reading EMBLfile from " + file);
- e.printStackTrace(System.err);
- }
- return null;
- }
-
- public static EmblFile getEmblFile(Reader file)
- {
- EmblFile record = new EmblFile();
- try
- {
- // 1. Load the mapping information from the file
- Mapping map = new Mapping(record.getClass().getClassLoader());
-
- java.net.URL url = record.getClass().getResource("/embl_mapping.xml");
- map.loadMapping(url);
-
- // 2. Unmarshal the data
- Unmarshaller unmar = new Unmarshaller(record);
- try
- {
- // uncomment to DEBUG EMBLFile reading
- if (jalview.bin.Cache
- .getDefault(jalview.bin.Cache.CASTORLOGLEVEL, "debug")
- .equalsIgnoreCase("DEBUG"))
- {
- unmar.setDebug(jalview.bin.Cache.log.isDebugEnabled());
- }
- } catch (Exception e)
- {
- }
- unmar.setIgnoreExtraElements(true);
- unmar.setIgnoreExtraAttributes(true);
- unmar.setMapping(map);
- unmar.setLogWriter(new PrintWriter(System.out));
- record = (EmblFile) unmar.unmarshal(file);
-
- canonicaliseDbRefs(record);
- } catch (Exception e)
- {
- e.printStackTrace(System.err);
- record = null;
- }
-
- return record;
- }
-
- /**
- * Change blank version to "0" in any DBRefEntry, to ensure consistent
- * comparison with other DBRefEntry in Jalview
- *
- * @param record
- * @see Uniprot#getDbVersion
- */
- static void canonicaliseDbRefs(EmblFile record)
- {
- if (record.getEntries() == null)
- {
- return;
- }
- for (EmblEntry entry : record.getEntries())
- {
- if (entry.getDbRefs() != null)
- {
- for (DBRefEntry dbref : entry.getDbRefs())
- {
- if ("".equals(dbref.getVersion()))
- {
- dbref.setVersion("0");
- }
- }
- }
-
- if (entry.getFeatures() != null)
- {
- for (EmblFeature feature : entry.getFeatures())
- {
- if (feature.getDbRefs() != null)
- {
- for (DBRefEntry dbref : feature.getDbRefs())
- {
- if ("".equals(dbref.getVersion()))
- {
- dbref.setVersion("0");
- }
- }
- }
- }
- }
- }
- }
-
- public String getText()
- {
- return text;
- }
-
- public void setText(String text)
- {
- this.text = text;
- }
-}
+++ /dev/null
-/*
- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ The Jalview Authors
- *
- * This file is part of Jalview.
- *
- * Jalview is free software: you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3
- * of the License, or (at your option) any later version.
- *
- * Jalview is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
- * PURPOSE. See the GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
- * The Jalview Authors are detailed in the 'AUTHORS' file.
- */
-package jalview.datamodel.xdb.embl;
-
-/**
- * Data model for the sequence extracted from an EMBL query reply
- *
- * @see embl_mapping.xml
- */
-public class EmblSequence
-{
- String sequence;
-
- /**
- * @return the sequence
- */
- public String getSequence()
- {
- return sequence;
- }
-
- /**
- * @param sequence
- * the sequence to set
- */
- public void setSequence(String sequence)
- {
- // remove spaces introduced by unmarshalling of newline characters
- this.sequence = sequence.replace(" ", "");
- }
-}
+++ /dev/null
-/*
- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ The Jalview Authors
- *
- * This file is part of Jalview.
- *
- * Jalview is free software: you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3
- * of the License, or (at your option) any later version.
- *
- * Jalview is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
- * PURPOSE. See the GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
- * The Jalview Authors are detailed in the 'AUTHORS' file.
- */
-package jalview.datamodel.xdb.embl;
-
-/**
- * Data model for a <qualifier> child element of a <feature> read
- * from an EMBL query reply
- *
- * @see embl_mapping.xml
- */
-public class Qualifier
-{
- String name;
-
- String[] values;
-
- String[] evidence;
-
- /**
- * @return the name
- */
- public String getName()
- {
- return name;
- }
-
- /**
- * @param name
- * the name to set
- */
- public void setName(String name)
- {
- this.name = name;
- }
-
- /**
- * @return the values
- */
- public String[] getValues()
- {
- return values;
- }
-
- /**
- * @param values
- * the values to set
- */
- public void setValues(String[] values)
- {
- this.values = values;
- }
-
- public void addEvidence(String qevidence)
- {
- // TODO - not used? can remove?
- if (evidence == null)
- {
- evidence = new String[1];
- }
- else
- {
- String[] temp = new String[evidence.length + 1];
- System.arraycopy(evidence, 0, temp, 0, evidence.length);
- evidence = temp;
- }
- evidence[evidence.length - 1] = qevidence;
- }
-
- public void addValues(String value)
- {
- // TODO - not used? can remove?
- if (values == null)
- {
- values = new String[1];
- }
- else
- {
- String[] temp = new String[values.length + 1];
- System.arraycopy(values, 0, temp, 0, values.length);
- values = temp;
- }
- values[values.length - 1] = value;
- }
-
- /**
- * @return the evidence
- */
- public String[] getEvidence()
- {
- return evidence;
- }
-
- /**
- * @param evidence
- * the evidence to set
- */
- public void setEvidence(String[] evidence)
- {
- this.evidence = evidence;
- }
-}
int aSize = alignPanels.size();
- tabbedPane.setVisible(aSize > 1 || ap.av.viewName != null);
+ tabbedPane.setVisible(aSize > 1 || ap.av.getViewName() != null);
- if (aSize == 1 && ap.av.viewName == null)
+ if (aSize == 1 && ap.av.getViewName() == null)
{
this.getContentPane().add(ap, BorderLayout.CENTER);
}
expandViews.setEnabled(true);
gatherViews.setEnabled(true);
- tabbedPane.addTab(ap.av.viewName, ap);
+ tabbedPane.addTab(ap.av.getViewName(), ap);
ap.setVisible(false);
}
gatherViews.setEnabled(true);
tabbedPane.setVisible(true);
AlignmentPanel first = alignPanels.get(0);
- tabbedPane.addTab(first.av.viewName, first);
+ tabbedPane.addTab(first.av.getViewName(), first);
this.getContentPane().add(tabbedPane, BorderLayout.CENTER);
}
* @param av
* AlignViewport
*/
- void setMenusFromViewport(AlignViewport av)
+ public void setMenusFromViewport(AlignViewport av)
{
padGapsMenuitem.setSelected(av.isPadGaps());
colourTextMenuItem.setSelected(av.isShowColourText());
newap.av.setGatherViewsHere(false);
- if (viewport.viewName == null)
+ if (viewport.getViewName() == null)
{
- viewport.viewName = MessageManager
- .getString("label.view_name_original");
+ viewport.setViewName(MessageManager
+ .getString("label.view_name_original"));
}
/*
newap.refresh(true); // adjust layout of annotations
}
- newap.av.viewName = getNewViewName(viewTitle);
+ newap.av.setViewName(getNewViewName(viewTitle));
addAlignmentPanel(newap, true);
newap.alignmentChanged();
if (comp instanceof AlignmentPanel)
{
AlignmentPanel ap = (AlignmentPanel) comp;
- if (!existingNames.contains(ap.av.viewName))
+ if (!existingNames.contains(ap.av.getViewName()))
{
- existingNames.add(ap.av.viewName);
+ existingNames.add(ap.av.getViewName());
}
}
}
frameTitle += " from ";
- if (viewport.viewName != null)
+ if (viewport.getViewName() != null)
{
- frameTitle += viewport.viewName + " of ";
+ frameTitle += viewport.getViewName() + " of ";
}
frameTitle += this.title;
if (reply != null)
{
- viewport.viewName = reply;
+ viewport.setViewName(reply);
// TODO warn if reply is in getExistingViewNames()?
tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
}
private Rectangle explodedGeometry;
- String viewName;
+ private String viewName;
/*
* Flag set true on the view that should 'gather' multiple views of the same
}
fr.setTransparency(featureSettings.getTransparency());
}
+
+ public String getViewName()
+ {
+ return viewName;
+ }
+
+ public void setViewName(String viewName)
+ {
+ this.viewName = viewName;
+ }
}
@Override
public String getViewName()
{
- return av.viewName;
+ return av.getViewName();
}
/**
setMinimumSize(new Dimension(325, height - 10));
String title = MessageManager.getString("label.choose_calculation");
- if (af.getViewport().viewName != null)
+ if (af.getViewport().getViewName() != null)
{
- title = title + " (" + af.getViewport().viewName + ")";
+ title = title + " (" + af.getViewport().getViewName() + ")";
}
Desktop.addInternalFrame(frame, title, width, height, false);
public FontChooser(TreePanel treePanel)
{
this.tp = treePanel;
- ap = treePanel.treeCanvas.ap;
+ ap = treePanel.getTreeCanvas().getAssociatedPanel();
oldFont = treePanel.getTreeFont();
defaultButton.setVisible(false);
smoothFont.setEnabled(false);
{
TreePanel tp = (TreePanel) frames[t];
- if (tp.treeCanvas.av.getAlignment() == jal)
+ if (tp.getTreeCanvas().getViewport().getAlignment() == jal)
{
Tree tree = new Tree();
tree.setTitle(tp.getTitle());
tree.setCurrentTree((av.getCurrentTree() == tp.getTree()));
tree.setNewick(tp.getTree().print());
- tree.setThreshold(tp.treeCanvas.threshold);
+ tree.setThreshold(tp.getTreeCanvas().getThreshold());
tree.setFitToWindow(tp.fitToWindow.getState());
tree.setFontName(tp.getTreeFont().getName());
{
view.setComplementId(av.getCodingComplement().getViewId());
}
- view.setViewName(av.viewName);
+ view.setViewName(av.getViewName());
view.setGatheredViews(av.isGatherViewsHere());
Rectangle size = ap.av.getExplodedGeometry();
tp.setTitle(tree.getTitle());
tp.setBounds(new Rectangle(tree.getXpos(), tree.getYpos(),
tree.getWidth(), tree.getHeight()));
- tp.av = av; // af.viewport; // TODO: verify 'associate with all
+ tp.setViewport(av); // af.viewport; // TODO: verify 'associate with all
// views'
// works still
- tp.treeCanvas.av = av; // af.viewport;
- tp.treeCanvas.ap = ap; // af.alignPanel;
+ tp.getTreeCanvas().setViewport(av); // af.viewport;
+ tp.getTreeCanvas().setAssociatedPanel(ap); // af.alignPanel;
}
if (tp == null)
tp.showBootstrap(tree.getShowBootstrap());
tp.showDistances(tree.getShowDistances());
- tp.treeCanvas.threshold = tree.getThreshold();
+ tp.getTreeCanvas().setThreshold(tree.getThreshold());
if (tree.getCurrentTree())
{
if (view.getViewName() != null)
{
- af.viewport.viewName = view.getViewName();
+ af.viewport.setViewName(view.getViewName());
af.setInitialTabVisible();
}
af.setBounds(view.getXpos(), view.getYpos(), view.getWidth(),
tp.showBootstrap(tree.getShowBootstrap());
tp.showDistances(tree.getShowDistances());
- tp.treeCanvas.threshold = tree.getThreshold();
+ tp.getTreeCanvas().setThreshold(tree.getThreshold());
if (tree.getCurrentTree())
{
for (i = 0; i < iSize; i++)
{
final AlignmentPanel ap = aps[i];
- item = new JRadioButtonMenuItem(ap.av.viewName, ap.av == rc.av);
+ item = new JRadioButtonMenuItem(ap.av.getViewName(), ap.av == rc.av);
buttonGroup.add(item);
item.addActionListener(new ActionListener()
{
topFrame.setDisplayedView(newTopPanel);
}
- newBottomPanel.av.viewName = newTopPanel.av.viewName;
+ newBottomPanel.av.setViewName(newTopPanel.av.getViewName());
newTopPanel.av.setCodingComplement(newBottomPanel.av);
/*
TreePanel tp;
- AlignViewport av;
+ private AlignViewport av;
- AlignmentPanel ap;
+ private AlignmentPanel ap;
Font font;
int offy;
- float threshold;
+ private float threshold;
String longestName;
{
this.tp = tp;
this.av = ap.av;
- this.ap = ap;
+ this.setAssociatedPanel(ap);
font = av.getFont();
scrollPane = scroller;
addMouseListener(this);
if (col != null)
{
setColor(highlightNode, col);
- PaintRefresher.Refresh(tp, ap.av.getSequenceSetId());
+ PaintRefresher.Refresh(tp, getAssociatedPanel().av.getSequenceSetId());
repaint();
}
}
if (ob instanceof SequenceI)
{
treeSelectionChanged((Sequence) ob);
- PaintRefresher.Refresh(tp, ap.av.getSequenceSetId());
+ PaintRefresher.Refresh(tp, getAssociatedPanel().av.getSequenceSetId());
repaint();
av.sendSelection();
return;
}
}
- PaintRefresher.Refresh(tp, ap.av.getSequenceSetId());
+ PaintRefresher.Refresh(tp, getAssociatedPanel().av.getSequenceSetId());
repaint();
}
}
else
{
- return new AlignmentPanel[] { ap };
+ return new AlignmentPanel[] { getAssociatedPanel() };
}
}
+
+ public AlignmentPanel getAssociatedPanel()
+ {
+ return ap;
+ }
+
+ public void setAssociatedPanel(AlignmentPanel ap)
+ {
+ this.ap = ap;
+ }
+
+ public AlignViewport getViewport()
+ {
+ return av;
+ }
+
+ public void setViewport(AlignViewport av)
+ {
+ this.av = av;
+ }
+
+ public float getThreshold()
+ {
+ return threshold;
+ }
+
+ public void setThreshold(float threshold)
+ {
+ this.threshold = threshold;
+ }
}
SimilarityParamsI similarityParams;
- TreeCanvas treeCanvas;
+ private TreeCanvas treeCanvas;
TreeModel tree;
- AlignViewport av;
+ private AlignViewport av;
/**
* Creates a new TreePanel object.
public AlignmentI getAlignment()
{
- return treeCanvas.av.getAlignment();
+ return getTreeCanvas().getViewport().getAlignment();
}
public AlignmentViewport getViewPort()
{
- return treeCanvas.av;
+ return getTreeCanvas().getViewport();
}
void initTreePanel(AlignmentPanel ap, String type, String modelName,
NewickFile newTree, AlignmentView inputData)
{
- av = ap.av;
+ setViewport(ap.av);
this.treeType = type;
this.scoreModelName = modelName;
treeCanvas = new TreeCanvas(this, ap, scrollPane);
- scrollPane.setViewportView(treeCanvas);
+ scrollPane.setViewportView(getTreeCanvas());
PaintRefresher.Register(this, ap.av.getSequenceSetId());
@Override
public void internalFrameClosed(InternalFrameEvent evt)
{
- if (av != null)
+ if (getViewport() != null)
{
- av.removePropertyChangeListener(listener);
+ getViewport().removePropertyChangeListener(listener);
}
}
});
}
tree.updatePlaceHolders((List<SequenceI>) evt.getNewValue());
- treeCanvas.nameHash.clear(); // reset the mapping between canvas
+ getTreeCanvas().nameHash.clear(); // reset the mapping between canvas
// rectangles and leafnodes
repaint();
}
}
};
- av.addPropertyChangeListener(listener);
+ getViewport().addPropertyChangeListener(listener);
return listener;
}
void buildAssociatedViewMenu()
{
AlignmentPanel[] aps = PaintRefresher
- .getAssociatedPanels(av.getSequenceSetId());
- if (aps.length == 1 && treeCanvas.ap == aps[0])
+ .getAssociatedPanels(getViewport().getSequenceSetId());
+ if (aps.length == 1 && getTreeCanvas().getAssociatedPanel() == aps[0])
{
associateLeavesMenu.setVisible(false);
return;
for (i = 0; i < iSize; i++)
{
final AlignmentPanel ap = aps[i];
- item = new JRadioButtonMenuItem(ap.av.viewName, ap == treeCanvas.ap);
+ item = new JRadioButtonMenuItem(ap.av.getViewName(), ap == getTreeCanvas().getAssociatedPanel());
buttonGroup.add(item);
item.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent evt)
{
- treeCanvas.applyToAllViews = false;
- treeCanvas.ap = ap;
- treeCanvas.av = ap.av;
+ getTreeCanvas().applyToAllViews = false;
+ getTreeCanvas().setAssociatedPanel(ap);
+ getTreeCanvas().setViewport(ap.av);
PaintRefresher.Register(thisTreePanel, ap.av.getSequenceSetId());
}
});
final JRadioButtonMenuItem itemf = new JRadioButtonMenuItem(
MessageManager.getString("label.all_views"));
buttonGroup.add(itemf);
- itemf.setSelected(treeCanvas.applyToAllViews);
+ itemf.setSelected(getTreeCanvas().applyToAllViews);
itemf.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent evt)
{
- treeCanvas.applyToAllViews = itemf.isSelected();
+ getTreeCanvas().applyToAllViews = itemf.isSelected();
}
});
associateLeavesMenu.add(itemf);
if (newtree != null)
{
- tree = new TreeModel(av.getAlignment().getSequencesArray(), odata,
+ tree = new TreeModel(getViewport().getAlignment().getSequencesArray(), odata,
newtree);
if (tree.getOriginalData() == null)
{
else
{
ScoreModelI sm = ScoreModels.getInstance()
- .getScoreModel(scoreModelName, treeCanvas.ap);
+ .getScoreModel(scoreModelName, getTreeCanvas().getAssociatedPanel());
TreeBuilder njtree = treeType.equals(TreeBuilder.NEIGHBOUR_JOINING)
- ? new NJTree(av, sm, similarityParams)
- : new AverageDistanceTree(av, sm, similarityParams);
+ ? new NJTree(getViewport(), sm, similarityParams)
+ : new AverageDistanceTree(getViewport(), sm, similarityParams);
tree = new TreeModel(njtree);
showDistances(true);
}
tree.reCount(tree.getTopNode());
tree.findHeight(tree.getTopNode());
- treeCanvas.setTree(tree);
- treeCanvas.repaint();
- av.setCurrentTree(tree);
- if (av.getSortByTree())
+ getTreeCanvas().setTree(tree);
+ getTreeCanvas().repaint();
+ getViewport().setCurrentTree(tree);
+ if (getViewport().getSortByTree())
{
sortByTree_actionPerformed();
}
public void showDistances(boolean b)
{
- treeCanvas.setShowDistances(b);
+ getTreeCanvas().setShowDistances(b);
distanceMenu.setSelected(b);
}
public void showBootstrap(boolean b)
{
- treeCanvas.setShowBootstrap(b);
+ getTreeCanvas().setShowBootstrap(b);
bootstrapMenu.setSelected(b);
}
public void showPlaceholders(boolean b)
{
placeholdersMenu.setState(b);
- treeCanvas.setMarkPlaceholders(b);
+ getTreeCanvas().setMarkPlaceholders(b);
}
/**
public void printMenu_actionPerformed(ActionEvent e)
{
// Putting in a thread avoids Swing painting problems
- treeCanvas.startPrinting();
+ getTreeCanvas().startPrinting();
}
@Override
{
// we try to get the associated view's gap character
// but this may fail if the view was closed...
- gc = av.getGapCharacter();
+ gc = getViewport().getGapCharacter();
} catch (Exception ex)
{
// AlignmentOrder origorder = new AlignmentOrder(alAndColsel[0]);
AlignmentI al = new Alignment((SequenceI[]) alAndColsel[0]);
- AlignmentI dataset = (av != null && av.getAlignment() != null)
- ? av.getAlignment().getDataset()
+ AlignmentI dataset = (getViewport() != null && getViewport().getAlignment() != null)
+ ? getViewport().getAlignment().getDataset()
: null;
if (dataset != null)
{
@Override
public void fitToWindow_actionPerformed(ActionEvent e)
{
- treeCanvas.fitToWindow = fitToWindow.isSelected();
+ getTreeCanvas().fitToWindow = fitToWindow.isSelected();
repaint();
}
public void sortByTree_actionPerformed()
{
- if (treeCanvas.applyToAllViews)
+ if (getTreeCanvas().applyToAllViews)
{
final ArrayList<CommandI> commands = new ArrayList<>();
for (AlignmentPanel ap : PaintRefresher
- .getAssociatedPanels(av.getSequenceSetId()))
+ .getAssociatedPanels(getViewport().getSequenceSetId()))
{
commands.add(sortAlignmentIn(ap.av.getAlignPanel()));
}
- av.getAlignPanel().alignFrame.addHistoryItem(new CommandI()
+ getViewport().getAlignPanel().alignFrame.addHistoryItem(new CommandI()
{
@Override
}
});
for (AlignmentPanel ap : PaintRefresher
- .getAssociatedPanels(av.getSequenceSetId()))
+ .getAssociatedPanels(getViewport().getSequenceSetId()))
{
// ensure all the alignFrames refresh their GI after adding an undo item
ap.alignFrame.updateEditMenuBar();
}
else
{
- treeCanvas.ap.alignFrame
- .addHistoryItem(sortAlignmentIn(treeCanvas.ap));
+ getTreeCanvas().getAssociatedPanel().alignFrame
+ .addHistoryItem(sortAlignmentIn(getTreeCanvas().getAssociatedPanel()));
}
}
@Override
public void font_actionPerformed(ActionEvent e)
{
- if (treeCanvas == null)
+ if (getTreeCanvas() == null)
{
return;
}
public Font getTreeFont()
{
- return treeCanvas.font;
+ return getTreeCanvas().font;
}
public void setTreeFont(Font f)
{
- if (treeCanvas != null)
+ if (getTreeCanvas() != null)
{
- treeCanvas.setFont(f);
+ getTreeCanvas().setFont(f);
}
}
@Override
public void distanceMenu_actionPerformed(ActionEvent e)
{
- treeCanvas.setShowDistances(distanceMenu.isSelected());
+ getTreeCanvas().setShowDistances(distanceMenu.isSelected());
}
/**
@Override
public void bootstrapMenu_actionPerformed(ActionEvent e)
{
- treeCanvas.setShowBootstrap(bootstrapMenu.isSelected());
+ getTreeCanvas().setShowBootstrap(bootstrapMenu.isSelected());
}
/**
@Override
public void placeholdersMenu_actionPerformed(ActionEvent e)
{
- treeCanvas.setMarkPlaceholders(placeholdersMenu.isSelected());
+ getTreeCanvas().setMarkPlaceholders(placeholdersMenu.isSelected());
}
/**
accurateText = false;
}
- int width = treeCanvas.getWidth();
- int height = treeCanvas.getHeight();
+ int width = getTreeCanvas().getWidth();
+ int height = getTreeCanvas().getHeight();
try
{
pg.setAccurateTextMode(accurateText);
- treeCanvas.draw(pg, width, height);
+ getTreeCanvas().draw(pg, width, height);
pg.flush();
pg.close();
@Override
public void pngTree_actionPerformed(ActionEvent e)
{
- int width = treeCanvas.getWidth();
- int height = treeCanvas.getHeight();
+ int width = getTreeCanvas().getWidth();
+ int height = getTreeCanvas().getHeight();
try
{
BufferedImage.TYPE_INT_RGB);
Graphics png = bi.getGraphics();
- treeCanvas.draw(png, width, height);
+ getTreeCanvas().draw(png, width, height);
ImageIO.write(bi, "png", out);
out.close();
treecalcnm, smn);
return ttl;
}
+
+ public AlignViewport getViewport()
+ {
+ return av;
+ }
+
+ public void setViewport(AlignViewport av)
+ {
+ this.av = av;
+ }
+
+ public TreeCanvas getTreeCanvas()
+ {
+ return treeCanvas;
+ }
}
errorsDuringUpdate = true;
Cache.log.error("Exception synchronizing " + af.getTitle()
+ " "
- + (af.getViewport().viewName == null ? ""
- : " view " + af.getViewport().viewName)
+ + (af.getViewport().getViewName() == null ? ""
+ : " view " + af.getViewport().getViewName())
+ " to document.", e);
stored = false;
}
*/
package jalview.ws.dbsources;
+import jalview.analysis.SequenceIdMatcher;
+import jalview.bin.Cache;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentI;
+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.datamodel.xdb.embl.EmblEntry;
-import jalview.datamodel.xdb.embl.EmblFile;
+import jalview.util.DBRefUtils;
+import jalview.util.DnaUtils;
+import jalview.util.MapList;
+import jalview.util.MappingUtils;
import jalview.util.MessageManager;
import jalview.ws.ebi.EBIFetchClient;
+import jalview.xml.binding.embl.EntryType;
+import jalview.xml.binding.embl.EntryType.Feature;
+import jalview.xml.binding.embl.EntryType.Feature.Qualifier;
+import jalview.xml.binding.embl.XrefType;
import java.io.File;
+import java.io.FileInputStream;
+import java.io.InputStream;
+import java.text.ParseException;
import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Hashtable;
import java.util.List;
+import java.util.Map;
+import java.util.Map.Entry;
+import java.util.regex.Pattern;
+
+import javax.xml.bind.JAXBContext;
+import javax.xml.bind.JAXBException;
+import javax.xml.stream.FactoryConfigurationError;
+import javax.xml.stream.XMLInputFactory;
+import javax.xml.stream.XMLStreamException;
+import javax.xml.stream.XMLStreamReader;
public abstract class EmblXmlSource extends EbiFileRetrievedProxy
{
*/
private static final String EMBL_NOT_FOUND_REPLY = "ERROR 12 No entries found.";
+ private static final Pattern SPACE_PATTERN = Pattern.compile(" ");
+
public EmblXmlSource()
{
super();
}
/**
- * retrieve and parse an emblxml file
+ * Retrieves and parses an emblxml file, and returns an alignment containing
+ * the parsed sequences, or null if none were found
*
* @param emprefx
- * either EMBL or EMBLCDS strings are allowed - anything else will
- * not retrieve emblxml
+ * "EMBL" or "EMBLCDS" - anything else will not retrieve emblxml
* @param query
* @return
* @throws Exception
public AlignmentI getEmblSequenceRecords(String emprefx, String query,
File reply) throws Exception
{
- EmblFile efile = null;
- List<SequenceI> seqs = new ArrayList<>();
-
+ List<EntryType> entries = null;
if (reply != null && reply.exists())
{
file = reply.getAbsolutePath();
if (reply.length() > EMBL_NOT_FOUND_REPLY.length())
{
- efile = EmblFile.getEmblFile(reply);
+ InputStream is = new FileInputStream(reply);
+ entries = getEmblEntries(is);
}
}
* EmbFile reads something like (e.g.) this ungrammatical phrase
* Entry: <acc> display type is either not supported or entry is not found.
*/
+ AlignmentI al = null;
+ List<SequenceI> seqs = new ArrayList<>();
List<SequenceI> peptides = new ArrayList<>();
- if (efile != null && efile.getEntries() != null)
+ if (entries != null)
{
- for (EmblEntry entry : efile.getEntries())
+ for (EntryType entry : entries)
{
- SequenceI seq = entry.getSequence(emprefx, peptides);
+ SequenceI seq = getSequence(emprefx, entry, peptides);
if (seq != null)
{
seqs.add(seq.deriveSequence());
// place DBReferences on dataset and refer
}
}
+ if (!seqs.isEmpty())
+ {
+ al = new Alignment(seqs.toArray(new SequenceI[seqs.size()]));
+ }
+ else
+ {
+ System.out.println(
+ "No record found for '" + emprefx + ":" + query + "'");
+ }
}
- AlignmentI al = null;
- if (!seqs.isEmpty())
- {
- al = new Alignment(seqs.toArray(new SequenceI[seqs.size()]));
- }
stopQuery();
return al;
}
+ /**
+ * Reads the XML reply from file and unmarshals it to Java objects. Answers a
+ * (possibly empty) list of <code>EntryType</code> objects.
+ *
+ * is
+ *
+ * @return
+ */
+ List<EntryType> getEmblEntries(InputStream is)
+ {
+ List<EntryType> entries = new ArrayList<>();
+ try
+ {
+ JAXBContext jc = JAXBContext.newInstance("jalview.xml.binding.embl");
+ XMLStreamReader streamReader = XMLInputFactory.newInstance()
+ .createXMLStreamReader(is);
+ javax.xml.bind.Unmarshaller um = jc.createUnmarshaller();
+ jalview.xml.binding.embl.ROOT root = (jalview.xml.binding.embl.ROOT) um
+ .unmarshal(streamReader);
+
+ /*
+ * document root contains either "entry" or "entrySet"
+ */
+ if (root == null)
+ {
+ return entries;
+ }
+ if (root.getEntrySet() != null)
+ {
+ entries = root.getEntrySet().getEntry();
+ }
+ else if (root.getEntry() != null)
+ {
+ entries.add(root.getEntry());
+ }
+ } catch (JAXBException | XMLStreamException
+ | FactoryConfigurationError e)
+ {
+ e.printStackTrace();
+ }
+ return entries;
+ }
+
+ /**
+ * A helper method to parse XML data and construct a sequence, with any
+ * available database references and features
+ *
+ * @param emprefx
+ * @param entry
+ * @param peptides
+ * @return
+ */
+ SequenceI getSequence(String sourceDb, EntryType entry,
+ List<SequenceI> peptides)
+ {
+ String seqString = entry.getSequence();
+ if (seqString == null)
+ {
+ return null;
+ }
+ seqString = seqString.replace(" ", "").replace("\n", "").replace("\t",
+ "");
+ String accession = entry.getAccession();
+ SequenceI dna = new Sequence(sourceDb + "|" + accession, seqString);
+
+ dna.setDescription(entry.getDescription());
+ String sequenceVersion = String.valueOf(entry.getVersion().intValue());
+ DBRefEntry selfRref = new DBRefEntry(sourceDb, sequenceVersion,
+ accession);
+ dna.addDBRef(selfRref);
+ selfRref.setMap(
+ new Mapping(null, new int[]
+ { 1, dna.getLength() }, new int[] { 1, dna.getLength() }, 1,
+ 1));
+
+ /*
+ * add db references
+ */
+ List<XrefType> dbRefs = entry.getXref();
+ if (dbRefs != null)
+ {
+ for (XrefType dbref : dbRefs)
+ {
+ String acc = dbref.getId();
+ String source = DBRefUtils.getCanonicalName(dbref.getDb());
+ String version = dbref.getSecondaryId();
+ dna.addDBRef(new DBRefEntry(source, version, acc));
+ }
+ }
+
+ SequenceIdMatcher matcher = new SequenceIdMatcher(peptides);
+ try
+ {
+ List<Feature> features = entry.getFeature();
+ if (features != null)
+ {
+ for (Feature feature : features)
+ {
+ if (FeatureProperties.isCodingFeature(sourceDb,
+ feature.getName()))
+ {
+ parseCodingFeature(entry, feature, sourceDb, dna, peptides,
+ matcher);
+ }
+ }
+ }
+ } catch (Exception e)
+ {
+ System.err.println("EMBL Record Features parsing error!");
+ System.err
+ .println("Please report the following to help@jalview.org :");
+ System.err.println("EMBL Record " + accession);
+ System.err.println("Resulted in exception: " + e.getMessage());
+ e.printStackTrace(System.err);
+ }
+
+ return dna;
+ }
+
+ /**
+ * Extracts coding region and product from a CDS feature and decorates it with
+ * annotations
+ *
+ * @param entry
+ * @param feature
+ * @param sourceDb
+ * @param dna
+ * @param peptides
+ * @param matcher
+ */
+ void parseCodingFeature(EntryType entry, Feature feature, String sourceDb,
+ SequenceI dna, List<SequenceI> peptides,
+ SequenceIdMatcher matcher)
+ {
+ final boolean isEmblCdna = sourceDb.equals(DBRefSource.EMBLCDS);
+ final String accession = entry.getAccession();
+ final String sequenceVersion = entry.getVersion().toString();
+
+ int[] exons = getCdsRanges(entry.getAccession(), feature);
+
+ String translation = null;
+ String proteinName = "";
+ String proteinId = null;
+ Map<String, String> vals = new Hashtable<>();
+
+ /*
+ * codon_start 1/2/3 in EMBL corresponds to phase 0/1/2 in CDS
+ * (phase is required for CDS features in GFF3 format)
+ */
+ int codonStart = 1;
+
+ /*
+ * parse qualifiers, saving protein translation, protein id,
+ * codon start position, product (name), and 'other values'
+ */
+ if (feature.getQualifier() != null)
+ {
+ for (Qualifier q : feature.getQualifier())
+ {
+ String qname = q.getName();
+ String value = q.getValue();
+ value = value == null ? ""
+ : value.trim().replace(" ", "").replace("\n", "")
+ .replace("\t", "");
+ if (qname.equals("translation"))
+ {
+ translation = value;
+ }
+ else if (qname.equals("protein_id"))
+ {
+ proteinId = value;
+ }
+ else if (qname.equals("codon_start"))
+ {
+ try
+ {
+ codonStart = Integer.parseInt(value.trim());
+ } catch (NumberFormatException e)
+ {
+ System.err.println("Invalid codon_start in XML for "
+ + entry.getAccession() + ": " + e.getMessage());
+ }
+ }
+ else if (qname.equals("product"))
+ {
+ // sometimes name is returned e.g. for V00488
+ proteinName = value;
+ }
+ else
+ {
+ // throw anything else into the additional properties hash
+ if (!"".equals(value))
+ {
+ vals.put(qname, value);
+ }
+ }
+ }
+ }
+
+ DBRefEntry proteinToEmblProteinRef = null;
+ exons = MappingUtils.removeStartPositions(codonStart - 1, exons);
+
+ SequenceI product = null;
+ Mapping dnaToProteinMapping = null;
+ if (translation != null && proteinName != null && proteinId != null)
+ {
+ int translationLength = translation.length();
+
+ /*
+ * look for product in peptides list, if not found, add it
+ */
+ product = matcher.findIdMatch(proteinId);
+ if (product == null)
+ {
+ product = new Sequence(proteinId, translation, 1,
+ translationLength);
+ product.setDescription(((proteinName.length() == 0)
+ ? "Protein Product from " + sourceDb
+ : proteinName));
+ peptides.add(product);
+ matcher.add(product);
+ }
+
+ // we have everything - create the mapping and perhaps the protein
+ // sequence
+ if (exons == null || exons.length == 0)
+ {
+ /*
+ * workaround until we handle dna location for CDS sequence
+ * e.g. location="X53828.1:60..1058" correctly
+ */
+ System.err.println(
+ "Implementation Notice: EMBLCDS records not properly supported yet - Making up the CDNA region of this sequence... may be incorrect ("
+ + sourceDb + ":" + entry.getAccession() + ")");
+ int dnaLength = dna.getLength();
+ if (translationLength * 3 == (1 - codonStart + dnaLength))
+ {
+ System.err.println(
+ "Not allowing for additional stop codon at end of cDNA fragment... !");
+ // this might occur for CDS sequences where no features are marked
+ exons = new int[] { dna.getStart() + (codonStart - 1),
+ dna.getEnd() };
+ dnaToProteinMapping = new Mapping(product, exons,
+ new int[]
+ { 1, translationLength }, 3, 1);
+ }
+ if ((translationLength + 1) * 3 == (1 - codonStart + dnaLength))
+ {
+ System.err.println(
+ "Allowing for additional stop codon at end of cDNA fragment... will probably cause an error in VAMSAs!");
+ exons = new int[] { dna.getStart() + (codonStart - 1),
+ dna.getEnd() - 3 };
+ dnaToProteinMapping = new Mapping(product, exons,
+ new int[]
+ { 1, translationLength }, 3, 1);
+ }
+ }
+ else
+ {
+ // Trim the exon mapping if necessary - the given product may only be a
+ // fragment of a larger protein. (EMBL:AY043181 is an example)
+
+ if (isEmblCdna)
+ {
+ // TODO: 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
+ }
+ else
+ {
+ // final product length truncation check
+ int[] cdsRanges = adjustForProteinLength(translationLength,
+ exons);
+ dnaToProteinMapping = new Mapping(product, cdsRanges,
+ new int[]
+ { 1, translationLength }, 3, 1);
+ if (product != null)
+ {
+ /*
+ * make xref with mapping from protein to EMBL dna
+ */
+ DBRefEntry proteinToEmblRef = new DBRefEntry(DBRefSource.EMBL,
+ sequenceVersion, proteinId,
+ new Mapping(dnaToProteinMapping.getMap().getInverse()));
+ product.addDBRef(proteinToEmblRef);
+
+ /*
+ * make xref from protein to EMBLCDS; we assume here that the
+ * CDS sequence version is same as dna sequence (?!)
+ */
+ MapList proteinToCdsMapList = new MapList(
+ new int[]
+ { 1, translationLength },
+ new int[]
+ { 1 + (codonStart - 1),
+ (codonStart - 1) + 3 * translationLength },
+ 1, 3);
+ DBRefEntry proteinToEmblCdsRef = new DBRefEntry(
+ DBRefSource.EMBLCDS, sequenceVersion, proteinId,
+ new Mapping(proteinToCdsMapList));
+ product.addDBRef(proteinToEmblCdsRef);
+
+ /*
+ * make 'direct' xref from protein to EMBLCDSPROTEIN
+ */
+ proteinToEmblProteinRef = new DBRefEntry(proteinToEmblCdsRef);
+ proteinToEmblProteinRef.setSource(DBRefSource.EMBLCDSProduct);
+ proteinToEmblProteinRef.setMap(null);
+ product.addDBRef(proteinToEmblProteinRef);
+ }
+ }
+ }
+
+ /*
+ * add cds features to dna sequence
+ */
+ String cds = feature.getName(); // "CDS"
+ 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);
+ int exonNumber = xint / 2 + 1;
+ String desc = String.format("Exon %d for protein '%s' EMBLCDS:%s",
+ exonNumber, proteinName, proteinId);
+
+ SequenceFeature sf = makeCdsFeature(cds, desc, begin, end, sourceDb,
+ vals);
+
+ sf.setEnaLocation(feature.getLocation());
+ boolean forwardStrand = exonStart <= exonEnd;
+ sf.setStrand(forwardStrand ? "+" : "-");
+ sf.setPhase(String.valueOf(codonStart - 1));
+ sf.setValue(FeatureProperties.EXONPOS, exonNumber);
+ sf.setValue(FeatureProperties.EXONPRODUCT, proteinName);
+
+ dna.addSequenceFeature(sf);
+ }
+ }
+
+ /*
+ * add feature dbRefs to sequence, and mappings for Uniprot xrefs
+ */
+ boolean hasUniprotDbref = false;
+ List<XrefType> xrefs = feature.getXref();
+ if (xrefs != null)
+ {
+ boolean mappingUsed = false;
+ for (XrefType xref : xrefs)
+ {
+ /*
+ * ensure UniProtKB/Swiss-Prot converted to UNIPROT
+ */
+ String source = DBRefUtils.getCanonicalName(xref.getDb());
+ DBRefEntry dbref = new DBRefEntry(source, xref.getSecondaryId(),
+ xref.getId());
+ DBRefEntry proteinDbRef = new DBRefEntry(dbref.getSource(),
+ dbref.getVersion(), dbref.getAccessionId());
+ if (source.equals(DBRefSource.UNIPROT))
+ {
+ String proteinSeqName = DBRefSource.UNIPROT + "|"
+ + dbref.getAccessionId();
+ if (dnaToProteinMapping != null
+ && dnaToProteinMapping.getTo() != null)
+ {
+ if (mappingUsed)
+ {
+ /*
+ * two or more Uniprot xrefs for the same CDS -
+ * each needs a distinct Mapping (as to a different sequence)
+ */
+ dnaToProteinMapping = new Mapping(dnaToProteinMapping);
+ }
+ mappingUsed = true;
+
+ /*
+ * try to locate the protein mapped to (possibly by a
+ * previous CDS feature); if not found, construct it from
+ * the EMBL translation
+ */
+ SequenceI proteinSeq = matcher.findIdMatch(proteinSeqName);
+ if (proteinSeq == null)
+ {
+ proteinSeq = new Sequence(proteinSeqName,
+ product.getSequenceAsString());
+ matcher.add(proteinSeq);
+ peptides.add(proteinSeq);
+ }
+ dnaToProteinMapping.setTo(proteinSeq);
+ dnaToProteinMapping.setMappedFromId(proteinId);
+ proteinSeq.addDBRef(proteinDbRef);
+ dbref.setMap(dnaToProteinMapping);
+ }
+ hasUniprotDbref = true;
+ }
+ if (product != null)
+ {
+ /*
+ * copy feature dbref to our protein product
+ */
+ DBRefEntry pref = proteinDbRef;
+ pref.setMap(null); // reference is direct
+ product.addDBRef(pref);
+ // Add converse mapping reference
+ if (dnaToProteinMapping != null)
+ {
+ Mapping pmap = new Mapping(dna,
+ dnaToProteinMapping.getMap().getInverse());
+ pref = new DBRefEntry(sourceDb, sequenceVersion, accession);
+ pref.setMap(pmap);
+ if (dnaToProteinMapping.getTo() != null)
+ {
+ dnaToProteinMapping.getTo().addDBRef(pref);
+ }
+ }
+ }
+ dna.addDBRef(dbref);
+ }
+ }
+
+ /*
+ * if we have a product (translation) but no explicit Uniprot dbref
+ * (example: EMBL AAFI02000057 protein_id EAL65544.1)
+ * then construct mappings to an assumed EMBLCDSPROTEIN accession
+ */
+ if (!hasUniprotDbref && product != null)
+ {
+ if (proteinToEmblProteinRef == null)
+ {
+ // assuming CDSPROTEIN sequence version = dna version (?!)
+ proteinToEmblProteinRef = new DBRefEntry(DBRefSource.EMBLCDSProduct,
+ sequenceVersion, proteinId);
+ }
+ product.addDBRef(proteinToEmblProteinRef);
+
+ if (dnaToProteinMapping != null
+ && dnaToProteinMapping.getTo() != null)
+ {
+ DBRefEntry dnaToEmblProteinRef = new DBRefEntry(
+ DBRefSource.EMBLCDSProduct, sequenceVersion,
+ proteinId);
+ dnaToEmblProteinRef.setMap(dnaToProteinMapping);
+ dnaToProteinMapping.setMappedFromId(proteinId);
+ dna.addDBRef(dnaToEmblProteinRef);
+ }
+ }
+ }
+
@Override
public boolean isDnaCoding()
{
return true;
}
+ /**
+ * Returns the CDS positions as a single array of [start, end, start, end...]
+ * positions. If on the reverse strand, these will be in descending order.
+ *
+ * @param accession
+ * @param feature
+ * @return
+ */
+ protected int[] getCdsRanges(String accession, Feature feature)
+ {
+ String location = feature.getLocation();
+ if (location == null)
+ {
+ return new int[] {};
+ }
+
+ try
+ {
+ List<int[]> ranges = DnaUtils.parseLocation(location);
+ return listToArray(ranges);
+ } catch (ParseException e)
+ {
+ Cache.log.warn(
+ String.format("Not parsing inexact CDS location %s in ENA %s",
+ location, accession));
+ return new int[] {};
+ }
+ }
+
+ /**
+ * Converts a list of [start, end] ranges to a single array of [start, end,
+ * start, end ...]
+ *
+ * @param ranges
+ * @return
+ */
+ int[] listToArray(List<int[]> ranges)
+ {
+ int[] result = new int[ranges.size() * 2];
+ int i = 0;
+ for (int[] range : ranges)
+ {
+ result[i++] = range[0];
+ result[i++] = range[1];
+ }
+ return result;
+ }
+
+ /**
+ * Helper method to construct a SequenceFeature for one cds range
+ *
+ * @param type
+ * feature type ("CDS")
+ * @param desc
+ * description
+ * @param begin
+ * start position
+ * @param end
+ * end position
+ * @param group
+ * feature group
+ * @param vals
+ * map of 'miscellaneous values' for feature
+ * @return
+ */
+ protected SequenceFeature makeCdsFeature(String type, String desc,
+ int begin, int end, String group, Map<String, String> vals)
+ {
+ SequenceFeature sf = new SequenceFeature(type, desc, begin, end, group);
+ if (!vals.isEmpty())
+ {
+ StringBuilder sb = new StringBuilder();
+ boolean first = true;
+ for (Entry<String, String> val : vals.entrySet())
+ {
+ if (!first)
+ {
+ sb.append(";");
+ }
+ sb.append(val.getKey()).append("=").append(val.getValue());
+ first = false;
+ sf.setValue(val.getKey(), val.getValue());
+ }
+ sf.setAttributes(sb.toString());
+ }
+ return sf;
+ }
+
+ /**
+ * 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)
+ {
+ 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;
+ }
+
}
*/
if (seqString.indexOf(' ') > -1)
{
- seqString = seqString.replaceAll(" ", "");
+ seqString = seqString.replace(" ", "");
}
SequenceI sequence = new Sequence(id,
seqString);
--- /dev/null
+//
+// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
+// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
+// Any modifications to this file will be lost upon recompilation of the source schema.
+// Generated on: 2018.09.14 at 02:46:00 PM BST
+//
+
+
+package jalview.xml.binding.embl;
+
+import java.util.ArrayList;
+import java.util.List;
+import javax.xml.bind.annotation.XmlAccessType;
+import javax.xml.bind.annotation.XmlAccessorType;
+import javax.xml.bind.annotation.XmlElement;
+import javax.xml.bind.annotation.XmlType;
+
+
+/**
+ * <p>Java class for EntrySetType complex type.
+ *
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ *
+ * <pre>
+ * <complexType name="EntrySetType">
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence maxOccurs="unbounded">
+ * <element name="entry" type="{}EntryType"/>
+ * </sequence>
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+@XmlAccessorType(XmlAccessType.FIELD)
+@XmlType(name = "EntrySetType", propOrder = {
+ "entry"
+})
+public class EntrySetType {
+
+ @XmlElement(required = true)
+ protected List<EntryType> entry;
+
+ /**
+ * Gets the value of the entry property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the entry property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getEntry().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link EntryType }
+ *
+ *
+ */
+ public List<EntryType> getEntry() {
+ if (entry == null) {
+ entry = new ArrayList<EntryType>();
+ }
+ return this.entry;
+ }
+
+}
--- /dev/null
+//
+// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
+// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
+// Any modifications to this file will be lost upon recompilation of the source schema.
+// Generated on: 2018.09.14 at 02:46:00 PM BST
+//
+
+
+package jalview.xml.binding.embl;
+
+import java.math.BigInteger;
+import java.util.ArrayList;
+import java.util.List;
+import javax.xml.bind.annotation.XmlAccessType;
+import javax.xml.bind.annotation.XmlAccessorType;
+import javax.xml.bind.annotation.XmlAttribute;
+import javax.xml.bind.annotation.XmlElement;
+import javax.xml.bind.annotation.XmlElements;
+import javax.xml.bind.annotation.XmlSchemaType;
+import javax.xml.bind.annotation.XmlType;
+import javax.xml.datatype.XMLGregorianCalendar;
+
+
+/**
+ * <p>Java class for EntryType complex type.
+ *
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ *
+ * <pre>
+ * <complexType name="EntryType">
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="secondaryAccession" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded" minOccurs="0"/>
+ * <element name="projectAccession" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded" minOccurs="0"/>
+ * <element name="description" type="{http://www.w3.org/2001/XMLSchema}string"/>
+ * <element name="comment" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
+ * <element name="keyword" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded" minOccurs="0"/>
+ * <element name="reference" maxOccurs="unbounded" minOccurs="0">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="title" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
+ * <element name="author" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded" minOccurs="0"/>
+ * <element name="applicant" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded" minOccurs="0"/>
+ * <element name="consortium" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
+ * <element name="submissionDate" type="{http://www.w3.org/2001/XMLSchema}date" minOccurs="0"/>
+ * <element name="journal" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
+ * <element name="year" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
+ * <element name="volume" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
+ * <element name="issue" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
+ * <element name="firstPage" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
+ * <element name="lastPage" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
+ * <element name="comment" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
+ * <element name="referenceLocation" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
+ * <element name="xref" type="{}XrefType" maxOccurs="unbounded" minOccurs="0"/>
+ * </sequence>
+ * <attribute name="type" use="required">
+ * <simpleType>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}string">
+ * <enumeration value="submission"/>
+ * <enumeration value="book"/>
+ * <enumeration value="article"/>
+ * <enumeration value="patent"/>
+ * <enumeration value="thesis"/>
+ * <enumeration value="unpublished"/>
+ * </restriction>
+ * </simpleType>
+ * </attribute>
+ * <attribute name="number" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
+ * <attribute name="location" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * <element name="xref" type="{}XrefType" maxOccurs="unbounded" minOccurs="0"/>
+ * <element name="feature" maxOccurs="unbounded" minOccurs="0">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="taxon" minOccurs="0">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="lineage" minOccurs="0">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="taxon" maxOccurs="unbounded">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attribute name="scientificName" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * </sequence>
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * </sequence>
+ * <attribute name="scientificName" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="commonName" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="taxId" type="{http://www.w3.org/2001/XMLSchema}integer" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * <element name="xref" type="{}XrefType" maxOccurs="unbounded" minOccurs="0"/>
+ * <element name="qualifier" maxOccurs="unbounded" minOccurs="0">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="value" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
+ * </sequence>
+ * <attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * </sequence>
+ * <attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="location" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * <element name="assembly" minOccurs="0">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="range" maxOccurs="unbounded">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attribute name="begin" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
+ * <attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
+ * <attribute name="primaryBegin" type="{http://www.w3.org/2001/XMLSchema}integer" />
+ * <attribute name="primaryEnd" type="{http://www.w3.org/2001/XMLSchema}integer" />
+ * <attribute name="accession" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="version" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
+ * <attribute name="complement" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * </sequence>
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * <element name="contig" minOccurs="0">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <choice maxOccurs="unbounded" minOccurs="0">
+ * <element name="range">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attribute name="begin" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
+ * <attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
+ * <attribute name="primaryBegin" type="{http://www.w3.org/2001/XMLSchema}integer" />
+ * <attribute name="primaryEnd" type="{http://www.w3.org/2001/XMLSchema}integer" />
+ * <attribute name="accession" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="version" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
+ * <attribute name="complement" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * <element name="gap">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attribute name="begin" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
+ * <attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
+ * <attribute name="length" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
+ * <attribute name="unknownLength" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * </choice>
+ * </sequence>
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * <element name="sequence" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
+ * </sequence>
+ * <attribute name="accession" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="version" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
+ * <attribute name="entryVersion" type="{http://www.w3.org/2001/XMLSchema}integer" />
+ * <attribute name="dataClass" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="taxonomicDivision" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="moleculeType" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="sequenceLength" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
+ * <attribute name="topology" use="required">
+ * <simpleType>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}string">
+ * <enumeration value="circular"/>
+ * <enumeration value="linear"/>
+ * </restriction>
+ * </simpleType>
+ * </attribute>
+ * <attribute name="firstPublic" type="{http://www.w3.org/2001/XMLSchema}date" />
+ * <attribute name="firstPublicRelease" type="{http://www.w3.org/2001/XMLSchema}integer" />
+ * <attribute name="lastUpdated" type="{http://www.w3.org/2001/XMLSchema}date" />
+ * <attribute name="lastUpdatedRelease" type="{http://www.w3.org/2001/XMLSchema}integer" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+@XmlAccessorType(XmlAccessType.FIELD)
+@XmlType(name = "EntryType", propOrder = {
+ "secondaryAccession",
+ "projectAccession",
+ "description",
+ "comment",
+ "keyword",
+ "reference",
+ "xref",
+ "feature",
+ "assembly",
+ "contig",
+ "sequence"
+})
+public class EntryType {
+
+ protected List<String> secondaryAccession;
+ protected List<String> projectAccession;
+ @XmlElement(required = true)
+ protected String description;
+ protected String comment;
+ protected List<String> keyword;
+ protected List<EntryType.Reference> reference;
+ protected List<XrefType> xref;
+ protected List<EntryType.Feature> feature;
+ protected EntryType.Assembly assembly;
+ protected EntryType.Contig contig;
+ protected String sequence;
+ @XmlAttribute(name = "accession", required = true)
+ protected String accession;
+ @XmlAttribute(name = "version", required = true)
+ protected BigInteger version;
+ @XmlAttribute(name = "entryVersion")
+ protected BigInteger entryVersion;
+ @XmlAttribute(name = "dataClass", required = true)
+ protected String dataClass;
+ @XmlAttribute(name = "taxonomicDivision", required = true)
+ protected String taxonomicDivision;
+ @XmlAttribute(name = "moleculeType", required = true)
+ protected String moleculeType;
+ @XmlAttribute(name = "sequenceLength", required = true)
+ protected BigInteger sequenceLength;
+ @XmlAttribute(name = "topology", required = true)
+ protected String topology;
+ @XmlAttribute(name = "firstPublic")
+ @XmlSchemaType(name = "date")
+ protected XMLGregorianCalendar firstPublic;
+ @XmlAttribute(name = "firstPublicRelease")
+ protected BigInteger firstPublicRelease;
+ @XmlAttribute(name = "lastUpdated")
+ @XmlSchemaType(name = "date")
+ protected XMLGregorianCalendar lastUpdated;
+ @XmlAttribute(name = "lastUpdatedRelease")
+ protected BigInteger lastUpdatedRelease;
+
+ /**
+ * Gets the value of the secondaryAccession property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the secondaryAccession property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getSecondaryAccession().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link String }
+ *
+ *
+ */
+ public List<String> getSecondaryAccession() {
+ if (secondaryAccession == null) {
+ secondaryAccession = new ArrayList<String>();
+ }
+ return this.secondaryAccession;
+ }
+
+ /**
+ * Gets the value of the projectAccession property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the projectAccession property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getProjectAccession().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link String }
+ *
+ *
+ */
+ public List<String> getProjectAccession() {
+ if (projectAccession == null) {
+ projectAccession = new ArrayList<String>();
+ }
+ return this.projectAccession;
+ }
+
+ /**
+ * Gets the value of the description property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getDescription() {
+ return description;
+ }
+
+ /**
+ * Sets the value of the description property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setDescription(String value) {
+ this.description = value;
+ }
+
+ /**
+ * Gets the value of the comment property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getComment() {
+ return comment;
+ }
+
+ /**
+ * Sets the value of the comment property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setComment(String value) {
+ this.comment = value;
+ }
+
+ /**
+ * Gets the value of the keyword property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the keyword property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getKeyword().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link String }
+ *
+ *
+ */
+ public List<String> getKeyword() {
+ if (keyword == null) {
+ keyword = new ArrayList<String>();
+ }
+ return this.keyword;
+ }
+
+ /**
+ * Gets the value of the reference property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the reference property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getReference().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link EntryType.Reference }
+ *
+ *
+ */
+ public List<EntryType.Reference> getReference() {
+ if (reference == null) {
+ reference = new ArrayList<EntryType.Reference>();
+ }
+ return this.reference;
+ }
+
+ /**
+ * Gets the value of the xref property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the xref property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getXref().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link XrefType }
+ *
+ *
+ */
+ public List<XrefType> getXref() {
+ if (xref == null) {
+ xref = new ArrayList<XrefType>();
+ }
+ return this.xref;
+ }
+
+ /**
+ * Gets the value of the feature property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the feature property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getFeature().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link EntryType.Feature }
+ *
+ *
+ */
+ public List<EntryType.Feature> getFeature() {
+ if (feature == null) {
+ feature = new ArrayList<EntryType.Feature>();
+ }
+ return this.feature;
+ }
+
+ /**
+ * Gets the value of the assembly property.
+ *
+ * @return
+ * possible object is
+ * {@link EntryType.Assembly }
+ *
+ */
+ public EntryType.Assembly getAssembly() {
+ return assembly;
+ }
+
+ /**
+ * Sets the value of the assembly property.
+ *
+ * @param value
+ * allowed object is
+ * {@link EntryType.Assembly }
+ *
+ */
+ public void setAssembly(EntryType.Assembly value) {
+ this.assembly = value;
+ }
+
+ /**
+ * Gets the value of the contig property.
+ *
+ * @return
+ * possible object is
+ * {@link EntryType.Contig }
+ *
+ */
+ public EntryType.Contig getContig() {
+ return contig;
+ }
+
+ /**
+ * Sets the value of the contig property.
+ *
+ * @param value
+ * allowed object is
+ * {@link EntryType.Contig }
+ *
+ */
+ public void setContig(EntryType.Contig value) {
+ this.contig = value;
+ }
+
+ /**
+ * Gets the value of the sequence property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getSequence() {
+ return sequence;
+ }
+
+ /**
+ * Sets the value of the sequence property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setSequence(String value) {
+ this.sequence = value;
+ }
+
+ /**
+ * Gets the value of the accession property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getAccession() {
+ return accession;
+ }
+
+ /**
+ * Sets the value of the accession property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setAccession(String value) {
+ this.accession = value;
+ }
+
+ /**
+ * Gets the value of the version property.
+ *
+ * @return
+ * possible object is
+ * {@link BigInteger }
+ *
+ */
+ public BigInteger getVersion() {
+ return version;
+ }
+
+ /**
+ * Sets the value of the version property.
+ *
+ * @param value
+ * allowed object is
+ * {@link BigInteger }
+ *
+ */
+ public void setVersion(BigInteger value) {
+ this.version = value;
+ }
+
+ /**
+ * Gets the value of the entryVersion property.
+ *
+ * @return
+ * possible object is
+ * {@link BigInteger }
+ *
+ */
+ public BigInteger getEntryVersion() {
+ return entryVersion;
+ }
+
+ /**
+ * Sets the value of the entryVersion property.
+ *
+ * @param value
+ * allowed object is
+ * {@link BigInteger }
+ *
+ */
+ public void setEntryVersion(BigInteger value) {
+ this.entryVersion = value;
+ }
+
+ /**
+ * Gets the value of the dataClass property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getDataClass() {
+ return dataClass;
+ }
+
+ /**
+ * Sets the value of the dataClass property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setDataClass(String value) {
+ this.dataClass = value;
+ }
+
+ /**
+ * Gets the value of the taxonomicDivision property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getTaxonomicDivision() {
+ return taxonomicDivision;
+ }
+
+ /**
+ * Sets the value of the taxonomicDivision property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setTaxonomicDivision(String value) {
+ this.taxonomicDivision = value;
+ }
+
+ /**
+ * Gets the value of the moleculeType property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getMoleculeType() {
+ return moleculeType;
+ }
+
+ /**
+ * Sets the value of the moleculeType property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setMoleculeType(String value) {
+ this.moleculeType = value;
+ }
+
+ /**
+ * Gets the value of the sequenceLength property.
+ *
+ * @return
+ * possible object is
+ * {@link BigInteger }
+ *
+ */
+ public BigInteger getSequenceLength() {
+ return sequenceLength;
+ }
+
+ /**
+ * Sets the value of the sequenceLength property.
+ *
+ * @param value
+ * allowed object is
+ * {@link BigInteger }
+ *
+ */
+ public void setSequenceLength(BigInteger value) {
+ this.sequenceLength = value;
+ }
+
+ /**
+ * Gets the value of the topology property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getTopology() {
+ return topology;
+ }
+
+ /**
+ * Sets the value of the topology property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setTopology(String value) {
+ this.topology = value;
+ }
+
+ /**
+ * Gets the value of the firstPublic property.
+ *
+ * @return
+ * possible object is
+ * {@link XMLGregorianCalendar }
+ *
+ */
+ public XMLGregorianCalendar getFirstPublic() {
+ return firstPublic;
+ }
+
+ /**
+ * Sets the value of the firstPublic property.
+ *
+ * @param value
+ * allowed object is
+ * {@link XMLGregorianCalendar }
+ *
+ */
+ public void setFirstPublic(XMLGregorianCalendar value) {
+ this.firstPublic = value;
+ }
+
+ /**
+ * Gets the value of the firstPublicRelease property.
+ *
+ * @return
+ * possible object is
+ * {@link BigInteger }
+ *
+ */
+ public BigInteger getFirstPublicRelease() {
+ return firstPublicRelease;
+ }
+
+ /**
+ * Sets the value of the firstPublicRelease property.
+ *
+ * @param value
+ * allowed object is
+ * {@link BigInteger }
+ *
+ */
+ public void setFirstPublicRelease(BigInteger value) {
+ this.firstPublicRelease = value;
+ }
+
+ /**
+ * Gets the value of the lastUpdated property.
+ *
+ * @return
+ * possible object is
+ * {@link XMLGregorianCalendar }
+ *
+ */
+ public XMLGregorianCalendar getLastUpdated() {
+ return lastUpdated;
+ }
+
+ /**
+ * Sets the value of the lastUpdated property.
+ *
+ * @param value
+ * allowed object is
+ * {@link XMLGregorianCalendar }
+ *
+ */
+ public void setLastUpdated(XMLGregorianCalendar value) {
+ this.lastUpdated = value;
+ }
+
+ /**
+ * Gets the value of the lastUpdatedRelease property.
+ *
+ * @return
+ * possible object is
+ * {@link BigInteger }
+ *
+ */
+ public BigInteger getLastUpdatedRelease() {
+ return lastUpdatedRelease;
+ }
+
+ /**
+ * Sets the value of the lastUpdatedRelease property.
+ *
+ * @param value
+ * allowed object is
+ * {@link BigInteger }
+ *
+ */
+ public void setLastUpdatedRelease(BigInteger value) {
+ this.lastUpdatedRelease = value;
+ }
+
+
+ /**
+ * <p>Java class for anonymous complex type.
+ *
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ *
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="range" maxOccurs="unbounded">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attribute name="begin" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
+ * <attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
+ * <attribute name="primaryBegin" type="{http://www.w3.org/2001/XMLSchema}integer" />
+ * <attribute name="primaryEnd" type="{http://www.w3.org/2001/XMLSchema}integer" />
+ * <attribute name="accession" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="version" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
+ * <attribute name="complement" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * </sequence>
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "", propOrder = {
+ "range"
+ })
+ public static class Assembly {
+
+ @XmlElement(required = true)
+ protected List<EntryType.Assembly.Range> range;
+
+ /**
+ * Gets the value of the range property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the range property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getRange().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link EntryType.Assembly.Range }
+ *
+ *
+ */
+ public List<EntryType.Assembly.Range> getRange() {
+ if (range == null) {
+ range = new ArrayList<EntryType.Assembly.Range>();
+ }
+ return this.range;
+ }
+
+
+ /**
+ * <p>Java class for anonymous complex type.
+ *
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ *
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attribute name="begin" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
+ * <attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
+ * <attribute name="primaryBegin" type="{http://www.w3.org/2001/XMLSchema}integer" />
+ * <attribute name="primaryEnd" type="{http://www.w3.org/2001/XMLSchema}integer" />
+ * <attribute name="accession" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="version" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
+ * <attribute name="complement" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "")
+ public static class Range {
+
+ @XmlAttribute(name = "begin", required = true)
+ protected BigInteger begin;
+ @XmlAttribute(name = "end", required = true)
+ protected BigInteger end;
+ @XmlAttribute(name = "primaryBegin")
+ protected BigInteger primaryBegin;
+ @XmlAttribute(name = "primaryEnd")
+ protected BigInteger primaryEnd;
+ @XmlAttribute(name = "accession", required = true)
+ protected String accession;
+ @XmlAttribute(name = "version", required = true)
+ protected BigInteger version;
+ @XmlAttribute(name = "complement")
+ protected Boolean complement;
+
+ /**
+ * Gets the value of the begin property.
+ *
+ * @return
+ * possible object is
+ * {@link BigInteger }
+ *
+ */
+ public BigInteger getBegin() {
+ return begin;
+ }
+
+ /**
+ * Sets the value of the begin property.
+ *
+ * @param value
+ * allowed object is
+ * {@link BigInteger }
+ *
+ */
+ public void setBegin(BigInteger value) {
+ this.begin = value;
+ }
+
+ /**
+ * Gets the value of the end property.
+ *
+ * @return
+ * possible object is
+ * {@link BigInteger }
+ *
+ */
+ public BigInteger getEnd() {
+ return end;
+ }
+
+ /**
+ * Sets the value of the end property.
+ *
+ * @param value
+ * allowed object is
+ * {@link BigInteger }
+ *
+ */
+ public void setEnd(BigInteger value) {
+ this.end = value;
+ }
+
+ /**
+ * Gets the value of the primaryBegin property.
+ *
+ * @return
+ * possible object is
+ * {@link BigInteger }
+ *
+ */
+ public BigInteger getPrimaryBegin() {
+ return primaryBegin;
+ }
+
+ /**
+ * Sets the value of the primaryBegin property.
+ *
+ * @param value
+ * allowed object is
+ * {@link BigInteger }
+ *
+ */
+ public void setPrimaryBegin(BigInteger value) {
+ this.primaryBegin = value;
+ }
+
+ /**
+ * Gets the value of the primaryEnd property.
+ *
+ * @return
+ * possible object is
+ * {@link BigInteger }
+ *
+ */
+ public BigInteger getPrimaryEnd() {
+ return primaryEnd;
+ }
+
+ /**
+ * Sets the value of the primaryEnd property.
+ *
+ * @param value
+ * allowed object is
+ * {@link BigInteger }
+ *
+ */
+ public void setPrimaryEnd(BigInteger value) {
+ this.primaryEnd = value;
+ }
+
+ /**
+ * Gets the value of the accession property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getAccession() {
+ return accession;
+ }
+
+ /**
+ * Sets the value of the accession property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setAccession(String value) {
+ this.accession = value;
+ }
+
+ /**
+ * Gets the value of the version property.
+ *
+ * @return
+ * possible object is
+ * {@link BigInteger }
+ *
+ */
+ public BigInteger getVersion() {
+ return version;
+ }
+
+ /**
+ * Sets the value of the version property.
+ *
+ * @param value
+ * allowed object is
+ * {@link BigInteger }
+ *
+ */
+ public void setVersion(BigInteger value) {
+ this.version = value;
+ }
+
+ /**
+ * Gets the value of the complement property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public boolean isComplement() {
+ if (complement == null) {
+ return false;
+ } else {
+ return complement;
+ }
+ }
+
+ /**
+ * Sets the value of the complement property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setComplement(Boolean value) {
+ this.complement = value;
+ }
+
+ }
+
+ }
+
+
+ /**
+ * <p>Java class for anonymous complex type.
+ *
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ *
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <choice maxOccurs="unbounded" minOccurs="0">
+ * <element name="range">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attribute name="begin" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
+ * <attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
+ * <attribute name="primaryBegin" type="{http://www.w3.org/2001/XMLSchema}integer" />
+ * <attribute name="primaryEnd" type="{http://www.w3.org/2001/XMLSchema}integer" />
+ * <attribute name="accession" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="version" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
+ * <attribute name="complement" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * <element name="gap">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attribute name="begin" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
+ * <attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
+ * <attribute name="length" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
+ * <attribute name="unknownLength" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * </choice>
+ * </sequence>
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "", propOrder = {
+ "rangeOrGap"
+ })
+ public static class Contig {
+
+ @XmlElements({
+ @XmlElement(name = "range", type = EntryType.Contig.Range.class),
+ @XmlElement(name = "gap", type = EntryType.Contig.Gap.class)
+ })
+ protected List<Object> rangeOrGap;
+
+ /**
+ * Gets the value of the rangeOrGap property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the rangeOrGap property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getRangeOrGap().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link EntryType.Contig.Range }
+ * {@link EntryType.Contig.Gap }
+ *
+ *
+ */
+ public List<Object> getRangeOrGap() {
+ if (rangeOrGap == null) {
+ rangeOrGap = new ArrayList<Object>();
+ }
+ return this.rangeOrGap;
+ }
+
+
+ /**
+ * <p>Java class for anonymous complex type.
+ *
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ *
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attribute name="begin" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
+ * <attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
+ * <attribute name="length" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
+ * <attribute name="unknownLength" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "")
+ public static class Gap {
+
+ @XmlAttribute(name = "begin", required = true)
+ protected BigInteger begin;
+ @XmlAttribute(name = "end", required = true)
+ protected BigInteger end;
+ @XmlAttribute(name = "length", required = true)
+ protected BigInteger length;
+ @XmlAttribute(name = "unknownLength")
+ protected Boolean unknownLength;
+
+ /**
+ * Gets the value of the begin property.
+ *
+ * @return
+ * possible object is
+ * {@link BigInteger }
+ *
+ */
+ public BigInteger getBegin() {
+ return begin;
+ }
+
+ /**
+ * Sets the value of the begin property.
+ *
+ * @param value
+ * allowed object is
+ * {@link BigInteger }
+ *
+ */
+ public void setBegin(BigInteger value) {
+ this.begin = value;
+ }
+
+ /**
+ * Gets the value of the end property.
+ *
+ * @return
+ * possible object is
+ * {@link BigInteger }
+ *
+ */
+ public BigInteger getEnd() {
+ return end;
+ }
+
+ /**
+ * Sets the value of the end property.
+ *
+ * @param value
+ * allowed object is
+ * {@link BigInteger }
+ *
+ */
+ public void setEnd(BigInteger value) {
+ this.end = value;
+ }
+
+ /**
+ * Gets the value of the length property.
+ *
+ * @return
+ * possible object is
+ * {@link BigInteger }
+ *
+ */
+ public BigInteger getLength() {
+ return length;
+ }
+
+ /**
+ * Sets the value of the length property.
+ *
+ * @param value
+ * allowed object is
+ * {@link BigInteger }
+ *
+ */
+ public void setLength(BigInteger value) {
+ this.length = value;
+ }
+
+ /**
+ * Gets the value of the unknownLength property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public boolean isUnknownLength() {
+ if (unknownLength == null) {
+ return false;
+ } else {
+ return unknownLength;
+ }
+ }
+
+ /**
+ * Sets the value of the unknownLength property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setUnknownLength(Boolean value) {
+ this.unknownLength = value;
+ }
+
+ }
+
+
+ /**
+ * <p>Java class for anonymous complex type.
+ *
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ *
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attribute name="begin" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
+ * <attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
+ * <attribute name="primaryBegin" type="{http://www.w3.org/2001/XMLSchema}integer" />
+ * <attribute name="primaryEnd" type="{http://www.w3.org/2001/XMLSchema}integer" />
+ * <attribute name="accession" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="version" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
+ * <attribute name="complement" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "")
+ public static class Range {
+
+ @XmlAttribute(name = "begin", required = true)
+ protected BigInteger begin;
+ @XmlAttribute(name = "end", required = true)
+ protected BigInteger end;
+ @XmlAttribute(name = "primaryBegin")
+ protected BigInteger primaryBegin;
+ @XmlAttribute(name = "primaryEnd")
+ protected BigInteger primaryEnd;
+ @XmlAttribute(name = "accession", required = true)
+ protected String accession;
+ @XmlAttribute(name = "version", required = true)
+ protected BigInteger version;
+ @XmlAttribute(name = "complement")
+ protected Boolean complement;
+
+ /**
+ * Gets the value of the begin property.
+ *
+ * @return
+ * possible object is
+ * {@link BigInteger }
+ *
+ */
+ public BigInteger getBegin() {
+ return begin;
+ }
+
+ /**
+ * Sets the value of the begin property.
+ *
+ * @param value
+ * allowed object is
+ * {@link BigInteger }
+ *
+ */
+ public void setBegin(BigInteger value) {
+ this.begin = value;
+ }
+
+ /**
+ * Gets the value of the end property.
+ *
+ * @return
+ * possible object is
+ * {@link BigInteger }
+ *
+ */
+ public BigInteger getEnd() {
+ return end;
+ }
+
+ /**
+ * Sets the value of the end property.
+ *
+ * @param value
+ * allowed object is
+ * {@link BigInteger }
+ *
+ */
+ public void setEnd(BigInteger value) {
+ this.end = value;
+ }
+
+ /**
+ * Gets the value of the primaryBegin property.
+ *
+ * @return
+ * possible object is
+ * {@link BigInteger }
+ *
+ */
+ public BigInteger getPrimaryBegin() {
+ return primaryBegin;
+ }
+
+ /**
+ * Sets the value of the primaryBegin property.
+ *
+ * @param value
+ * allowed object is
+ * {@link BigInteger }
+ *
+ */
+ public void setPrimaryBegin(BigInteger value) {
+ this.primaryBegin = value;
+ }
+
+ /**
+ * Gets the value of the primaryEnd property.
+ *
+ * @return
+ * possible object is
+ * {@link BigInteger }
+ *
+ */
+ public BigInteger getPrimaryEnd() {
+ return primaryEnd;
+ }
+
+ /**
+ * Sets the value of the primaryEnd property.
+ *
+ * @param value
+ * allowed object is
+ * {@link BigInteger }
+ *
+ */
+ public void setPrimaryEnd(BigInteger value) {
+ this.primaryEnd = value;
+ }
+
+ /**
+ * Gets the value of the accession property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getAccession() {
+ return accession;
+ }
+
+ /**
+ * Sets the value of the accession property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setAccession(String value) {
+ this.accession = value;
+ }
+
+ /**
+ * Gets the value of the version property.
+ *
+ * @return
+ * possible object is
+ * {@link BigInteger }
+ *
+ */
+ public BigInteger getVersion() {
+ return version;
+ }
+
+ /**
+ * Sets the value of the version property.
+ *
+ * @param value
+ * allowed object is
+ * {@link BigInteger }
+ *
+ */
+ public void setVersion(BigInteger value) {
+ this.version = value;
+ }
+
+ /**
+ * Gets the value of the complement property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public boolean isComplement() {
+ if (complement == null) {
+ return false;
+ } else {
+ return complement;
+ }
+ }
+
+ /**
+ * Sets the value of the complement property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setComplement(Boolean value) {
+ this.complement = value;
+ }
+
+ }
+
+ }
+
+
+ /**
+ * <p>Java class for anonymous complex type.
+ *
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ *
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="taxon" minOccurs="0">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="lineage" minOccurs="0">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="taxon" maxOccurs="unbounded">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attribute name="scientificName" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * </sequence>
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * </sequence>
+ * <attribute name="scientificName" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="commonName" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="taxId" type="{http://www.w3.org/2001/XMLSchema}integer" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * <element name="xref" type="{}XrefType" maxOccurs="unbounded" minOccurs="0"/>
+ * <element name="qualifier" maxOccurs="unbounded" minOccurs="0">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="value" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
+ * </sequence>
+ * <attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * </sequence>
+ * <attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="location" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "", propOrder = {
+ "taxon",
+ "xref",
+ "qualifier"
+ })
+ public static class Feature {
+
+ protected EntryType.Feature.FeatureTaxon taxon;
+ protected List<XrefType> xref;
+ protected List<EntryType.Feature.Qualifier> qualifier;
+ @XmlAttribute(name = "name", required = true)
+ protected String name;
+ @XmlAttribute(name = "location", required = true)
+ protected String location;
+
+ /**
+ * Gets the value of the taxon property.
+ *
+ * @return
+ * possible object is
+ * {@link EntryType.Feature.FeatureTaxon }
+ *
+ */
+ public EntryType.Feature.FeatureTaxon getTaxon() {
+ return taxon;
+ }
+
+ /**
+ * Sets the value of the taxon property.
+ *
+ * @param value
+ * allowed object is
+ * {@link EntryType.Feature.FeatureTaxon }
+ *
+ */
+ public void setTaxon(EntryType.Feature.FeatureTaxon value) {
+ this.taxon = value;
+ }
+
+ /**
+ * Gets the value of the xref property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the xref property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getXref().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link XrefType }
+ *
+ *
+ */
+ public List<XrefType> getXref() {
+ if (xref == null) {
+ xref = new ArrayList<XrefType>();
+ }
+ return this.xref;
+ }
+
+ /**
+ * Gets the value of the qualifier property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the qualifier property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getQualifier().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link EntryType.Feature.Qualifier }
+ *
+ *
+ */
+ public List<EntryType.Feature.Qualifier> getQualifier() {
+ if (qualifier == null) {
+ qualifier = new ArrayList<EntryType.Feature.Qualifier>();
+ }
+ return this.qualifier;
+ }
+
+ /**
+ * Gets the value of the name property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getName() {
+ return name;
+ }
+
+ /**
+ * Sets the value of the name property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setName(String value) {
+ this.name = value;
+ }
+
+ /**
+ * Gets the value of the location property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getLocation() {
+ return location;
+ }
+
+ /**
+ * Sets the value of the location property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setLocation(String value) {
+ this.location = value;
+ }
+
+
+ /**
+ * <p>Java class for anonymous complex type.
+ *
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ *
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="lineage" minOccurs="0">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="taxon" maxOccurs="unbounded">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attribute name="scientificName" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * </sequence>
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * </sequence>
+ * <attribute name="scientificName" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="commonName" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="taxId" type="{http://www.w3.org/2001/XMLSchema}integer" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "", propOrder = {
+ "lineage"
+ })
+ public static class FeatureTaxon {
+
+ protected EntryType.Feature.FeatureTaxon.Lineage lineage;
+ @XmlAttribute(name = "scientificName", required = true)
+ protected String scientificName;
+ @XmlAttribute(name = "commonName")
+ protected String commonName;
+ @XmlAttribute(name = "taxId")
+ protected BigInteger taxId;
+
+ /**
+ * Gets the value of the lineage property.
+ *
+ * @return
+ * possible object is
+ * {@link EntryType.Feature.FeatureTaxon.Lineage }
+ *
+ */
+ public EntryType.Feature.FeatureTaxon.Lineage getLineage() {
+ return lineage;
+ }
+
+ /**
+ * Sets the value of the lineage property.
+ *
+ * @param value
+ * allowed object is
+ * {@link EntryType.Feature.FeatureTaxon.Lineage }
+ *
+ */
+ public void setLineage(EntryType.Feature.FeatureTaxon.Lineage value) {
+ this.lineage = value;
+ }
+
+ /**
+ * Gets the value of the scientificName property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getScientificName() {
+ return scientificName;
+ }
+
+ /**
+ * Sets the value of the scientificName property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setScientificName(String value) {
+ this.scientificName = value;
+ }
+
+ /**
+ * Gets the value of the commonName property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getCommonName() {
+ return commonName;
+ }
+
+ /**
+ * Sets the value of the commonName property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setCommonName(String value) {
+ this.commonName = value;
+ }
+
+ /**
+ * Gets the value of the taxId property.
+ *
+ * @return
+ * possible object is
+ * {@link BigInteger }
+ *
+ */
+ public BigInteger getTaxId() {
+ return taxId;
+ }
+
+ /**
+ * Sets the value of the taxId property.
+ *
+ * @param value
+ * allowed object is
+ * {@link BigInteger }
+ *
+ */
+ public void setTaxId(BigInteger value) {
+ this.taxId = value;
+ }
+
+
+ /**
+ * <p>Java class for anonymous complex type.
+ *
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ *
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="taxon" maxOccurs="unbounded">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attribute name="scientificName" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * </sequence>
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "", propOrder = {
+ "taxon"
+ })
+ public static class Lineage {
+
+ @XmlElement(required = true)
+ protected List<EntryType.Feature.FeatureTaxon.Lineage.Taxon> taxon;
+
+ /**
+ * Gets the value of the taxon property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the taxon property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getTaxon().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link EntryType.Feature.FeatureTaxon.Lineage.Taxon }
+ *
+ *
+ */
+ public List<EntryType.Feature.FeatureTaxon.Lineage.Taxon> getTaxon() {
+ if (taxon == null) {
+ taxon = new ArrayList<EntryType.Feature.FeatureTaxon.Lineage.Taxon>();
+ }
+ return this.taxon;
+ }
+
+
+ /**
+ * <p>Java class for anonymous complex type.
+ *
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ *
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attribute name="scientificName" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "")
+ public static class Taxon {
+
+ @XmlAttribute(name = "scientificName", required = true)
+ protected String scientificName;
+
+ /**
+ * Gets the value of the scientificName property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getScientificName() {
+ return scientificName;
+ }
+
+ /**
+ * Sets the value of the scientificName property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setScientificName(String value) {
+ this.scientificName = value;
+ }
+
+ }
+
+ }
+
+ }
+
+
+ /**
+ * <p>Java class for anonymous complex type.
+ *
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ *
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="value" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
+ * </sequence>
+ * <attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "", propOrder = {
+ "value"
+ })
+ public static class Qualifier {
+
+ protected String value;
+ @XmlAttribute(name = "name", required = true)
+ protected String name;
+
+ /**
+ * Gets the value of the value property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getValue() {
+ return value;
+ }
+
+ /**
+ * Sets the value of the value property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setValue(String value) {
+ this.value = value;
+ }
+
+ /**
+ * Gets the value of the name property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getName() {
+ return name;
+ }
+
+ /**
+ * Sets the value of the name property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setName(String value) {
+ this.name = value;
+ }
+
+ }
+
+ }
+
+
+ /**
+ * <p>Java class for anonymous complex type.
+ *
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ *
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="title" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
+ * <element name="author" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded" minOccurs="0"/>
+ * <element name="applicant" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded" minOccurs="0"/>
+ * <element name="consortium" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
+ * <element name="submissionDate" type="{http://www.w3.org/2001/XMLSchema}date" minOccurs="0"/>
+ * <element name="journal" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
+ * <element name="year" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
+ * <element name="volume" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
+ * <element name="issue" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
+ * <element name="firstPage" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
+ * <element name="lastPage" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
+ * <element name="comment" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
+ * <element name="referenceLocation" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
+ * <element name="xref" type="{}XrefType" maxOccurs="unbounded" minOccurs="0"/>
+ * </sequence>
+ * <attribute name="type" use="required">
+ * <simpleType>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}string">
+ * <enumeration value="submission"/>
+ * <enumeration value="book"/>
+ * <enumeration value="article"/>
+ * <enumeration value="patent"/>
+ * <enumeration value="thesis"/>
+ * <enumeration value="unpublished"/>
+ * </restriction>
+ * </simpleType>
+ * </attribute>
+ * <attribute name="number" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
+ * <attribute name="location" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "", propOrder = {
+ "title",
+ "author",
+ "applicant",
+ "consortium",
+ "submissionDate",
+ "journal",
+ "year",
+ "volume",
+ "issue",
+ "firstPage",
+ "lastPage",
+ "comment",
+ "referenceLocation",
+ "xref"
+ })
+ public static class Reference {
+
+ protected String title;
+ protected List<String> author;
+ protected List<String> applicant;
+ protected String consortium;
+ @XmlSchemaType(name = "date")
+ protected XMLGregorianCalendar submissionDate;
+ protected String journal;
+ protected String year;
+ protected String volume;
+ protected String issue;
+ protected String firstPage;
+ protected String lastPage;
+ protected String comment;
+ protected String referenceLocation;
+ protected List<XrefType> xref;
+ @XmlAttribute(name = "type", required = true)
+ protected String type;
+ @XmlAttribute(name = "number", required = true)
+ protected BigInteger number;
+ @XmlAttribute(name = "location")
+ protected String location;
+
+ /**
+ * Gets the value of the title property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getTitle() {
+ return title;
+ }
+
+ /**
+ * Sets the value of the title property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setTitle(String value) {
+ this.title = value;
+ }
+
+ /**
+ * Gets the value of the author property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the author property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getAuthor().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link String }
+ *
+ *
+ */
+ public List<String> getAuthor() {
+ if (author == null) {
+ author = new ArrayList<String>();
+ }
+ return this.author;
+ }
+
+ /**
+ * Gets the value of the applicant property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the applicant property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getApplicant().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link String }
+ *
+ *
+ */
+ public List<String> getApplicant() {
+ if (applicant == null) {
+ applicant = new ArrayList<String>();
+ }
+ return this.applicant;
+ }
+
+ /**
+ * Gets the value of the consortium property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getConsortium() {
+ return consortium;
+ }
+
+ /**
+ * Sets the value of the consortium property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setConsortium(String value) {
+ this.consortium = value;
+ }
+
+ /**
+ * Gets the value of the submissionDate property.
+ *
+ * @return
+ * possible object is
+ * {@link XMLGregorianCalendar }
+ *
+ */
+ public XMLGregorianCalendar getSubmissionDate() {
+ return submissionDate;
+ }
+
+ /**
+ * Sets the value of the submissionDate property.
+ *
+ * @param value
+ * allowed object is
+ * {@link XMLGregorianCalendar }
+ *
+ */
+ public void setSubmissionDate(XMLGregorianCalendar value) {
+ this.submissionDate = value;
+ }
+
+ /**
+ * Gets the value of the journal property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getJournal() {
+ return journal;
+ }
+
+ /**
+ * Sets the value of the journal property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setJournal(String value) {
+ this.journal = value;
+ }
+
+ /**
+ * Gets the value of the year property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getYear() {
+ return year;
+ }
+
+ /**
+ * Sets the value of the year property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setYear(String value) {
+ this.year = value;
+ }
+
+ /**
+ * Gets the value of the volume property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getVolume() {
+ return volume;
+ }
+
+ /**
+ * Sets the value of the volume property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setVolume(String value) {
+ this.volume = value;
+ }
+
+ /**
+ * Gets the value of the issue property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getIssue() {
+ return issue;
+ }
+
+ /**
+ * Sets the value of the issue property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setIssue(String value) {
+ this.issue = value;
+ }
+
+ /**
+ * Gets the value of the firstPage property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getFirstPage() {
+ return firstPage;
+ }
+
+ /**
+ * Sets the value of the firstPage property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setFirstPage(String value) {
+ this.firstPage = value;
+ }
+
+ /**
+ * Gets the value of the lastPage property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getLastPage() {
+ return lastPage;
+ }
+
+ /**
+ * Sets the value of the lastPage property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setLastPage(String value) {
+ this.lastPage = value;
+ }
+
+ /**
+ * Gets the value of the comment property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getComment() {
+ return comment;
+ }
+
+ /**
+ * Sets the value of the comment property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setComment(String value) {
+ this.comment = value;
+ }
+
+ /**
+ * Gets the value of the referenceLocation property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getReferenceLocation() {
+ return referenceLocation;
+ }
+
+ /**
+ * Sets the value of the referenceLocation property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setReferenceLocation(String value) {
+ this.referenceLocation = value;
+ }
+
+ /**
+ * Gets the value of the xref property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the xref property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getXref().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link XrefType }
+ *
+ *
+ */
+ public List<XrefType> getXref() {
+ if (xref == null) {
+ xref = new ArrayList<XrefType>();
+ }
+ return this.xref;
+ }
+
+ /**
+ * Gets the value of the type property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getType() {
+ return type;
+ }
+
+ /**
+ * Sets the value of the type property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setType(String value) {
+ this.type = value;
+ }
+
+ /**
+ * Gets the value of the number property.
+ *
+ * @return
+ * possible object is
+ * {@link BigInteger }
+ *
+ */
+ public BigInteger getNumber() {
+ return number;
+ }
+
+ /**
+ * Sets the value of the number property.
+ *
+ * @param value
+ * allowed object is
+ * {@link BigInteger }
+ *
+ */
+ public void setNumber(BigInteger value) {
+ this.number = value;
+ }
+
+ /**
+ * Gets the value of the location property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getLocation() {
+ return location;
+ }
+
+ /**
+ * Sets the value of the location property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setLocation(String value) {
+ this.location = value;
+ }
+
+ }
+
+}
--- /dev/null
+//
+// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
+// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
+// Any modifications to this file will be lost upon recompilation of the source schema.
+// Generated on: 2018.09.14 at 02:46:00 PM BST
+//
+
+
+package jalview.xml.binding.embl;
+
+import javax.xml.bind.annotation.XmlRegistry;
+
+
+/**
+ * This object contains factory methods for each
+ * Java content interface and Java element interface
+ * generated in the jalview.xml.binding.embl package.
+ * <p>An ObjectFactory allows you to programatically
+ * construct new instances of the Java representation
+ * for XML content. The Java representation of XML
+ * content can consist of schema derived interfaces
+ * and classes representing the binding of schema
+ * type definitions, element declarations and model
+ * groups. Factory methods for each of these are
+ * provided in this class.
+ *
+ */
+@XmlRegistry
+public class ObjectFactory {
+
+
+ /**
+ * Create a new ObjectFactory that can be used to create new instances of schema derived classes for package: jalview.xml.binding.embl
+ *
+ */
+ public ObjectFactory() {
+ }
+
+ /**
+ * Create an instance of {@link EntryType }
+ *
+ */
+ public EntryType createEntryType() {
+ return new EntryType();
+ }
+
+ /**
+ * Create an instance of {@link EntryType.Contig }
+ *
+ */
+ public EntryType.Contig createEntryTypeContig() {
+ return new EntryType.Contig();
+ }
+
+ /**
+ * Create an instance of {@link EntryType.Assembly }
+ *
+ */
+ public EntryType.Assembly createEntryTypeAssembly() {
+ return new EntryType.Assembly();
+ }
+
+ /**
+ * Create an instance of {@link EntryType.Feature }
+ *
+ */
+ public EntryType.Feature createEntryTypeFeature() {
+ return new EntryType.Feature();
+ }
+
+ /**
+ * Create an instance of {@link EntryType.Feature.FeatureTaxon }
+ *
+ */
+ public EntryType.Feature.FeatureTaxon createEntryTypeFeatureFeatureTaxon() {
+ return new EntryType.Feature.FeatureTaxon();
+ }
+
+ /**
+ * Create an instance of {@link EntryType.Feature.FeatureTaxon.Lineage }
+ *
+ */
+ public EntryType.Feature.FeatureTaxon.Lineage createEntryTypeFeatureFeatureTaxonLineage() {
+ return new EntryType.Feature.FeatureTaxon.Lineage();
+ }
+
+ /**
+ * Create an instance of {@link ROOT }
+ *
+ */
+ public ROOT createROOT() {
+ return new ROOT();
+ }
+
+ /**
+ * Create an instance of {@link EntrySetType }
+ *
+ */
+ public EntrySetType createEntrySetType() {
+ return new EntrySetType();
+ }
+
+ /**
+ * Create an instance of {@link XrefType }
+ *
+ */
+ public XrefType createXrefType() {
+ return new XrefType();
+ }
+
+ /**
+ * Create an instance of {@link EntryType.Reference }
+ *
+ */
+ public EntryType.Reference createEntryTypeReference() {
+ return new EntryType.Reference();
+ }
+
+ /**
+ * Create an instance of {@link EntryType.Contig.Range }
+ *
+ */
+ public EntryType.Contig.Range createEntryTypeContigRange() {
+ return new EntryType.Contig.Range();
+ }
+
+ /**
+ * Create an instance of {@link EntryType.Contig.Gap }
+ *
+ */
+ public EntryType.Contig.Gap createEntryTypeContigGap() {
+ return new EntryType.Contig.Gap();
+ }
+
+ /**
+ * Create an instance of {@link EntryType.Assembly.Range }
+ *
+ */
+ public EntryType.Assembly.Range createEntryTypeAssemblyRange() {
+ return new EntryType.Assembly.Range();
+ }
+
+ /**
+ * Create an instance of {@link EntryType.Feature.Qualifier }
+ *
+ */
+ public EntryType.Feature.Qualifier createEntryTypeFeatureQualifier() {
+ return new EntryType.Feature.Qualifier();
+ }
+
+ /**
+ * Create an instance of {@link EntryType.Feature.FeatureTaxon.Lineage.Taxon }
+ *
+ */
+ public EntryType.Feature.FeatureTaxon.Lineage.Taxon createEntryTypeFeatureFeatureTaxonLineageTaxon() {
+ return new EntryType.Feature.FeatureTaxon.Lineage.Taxon();
+ }
+
+}
--- /dev/null
+//
+// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
+// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
+// Any modifications to this file will be lost upon recompilation of the source schema.
+// Generated on: 2018.09.14 at 02:46:00 PM BST
+//
+
+
+package jalview.xml.binding.embl;
+
+import javax.xml.bind.annotation.XmlAccessType;
+import javax.xml.bind.annotation.XmlAccessorType;
+import javax.xml.bind.annotation.XmlRootElement;
+import javax.xml.bind.annotation.XmlType;
+
+
+/**
+ * <p>Java class for anonymous complex type.
+ *
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ *
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <choice>
+ * <element name="entrySet" type="{}EntrySetType"/>
+ * <element name="entry" type="{}EntryType"/>
+ * </choice>
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+@XmlAccessorType(XmlAccessType.FIELD)
+@XmlType(name = "", propOrder = {
+ "entrySet",
+ "entry"
+})
+@XmlRootElement(name = "ROOT")
+public class ROOT {
+
+ protected EntrySetType entrySet;
+ protected EntryType entry;
+
+ /**
+ * Gets the value of the entrySet property.
+ *
+ * @return
+ * possible object is
+ * {@link EntrySetType }
+ *
+ */
+ public EntrySetType getEntrySet() {
+ return entrySet;
+ }
+
+ /**
+ * Sets the value of the entrySet property.
+ *
+ * @param value
+ * allowed object is
+ * {@link EntrySetType }
+ *
+ */
+ public void setEntrySet(EntrySetType value) {
+ this.entrySet = value;
+ }
+
+ /**
+ * Gets the value of the entry property.
+ *
+ * @return
+ * possible object is
+ * {@link EntryType }
+ *
+ */
+ public EntryType getEntry() {
+ return entry;
+ }
+
+ /**
+ * Sets the value of the entry property.
+ *
+ * @param value
+ * allowed object is
+ * {@link EntryType }
+ *
+ */
+ public void setEntry(EntryType value) {
+ this.entry = value;
+ }
+
+}
--- /dev/null
+//
+// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
+// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
+// Any modifications to this file will be lost upon recompilation of the source schema.
+// Generated on: 2018.09.14 at 02:46:00 PM BST
+//
+
+
+package jalview.xml.binding.embl;
+
+import javax.xml.bind.annotation.XmlAccessType;
+import javax.xml.bind.annotation.XmlAccessorType;
+import javax.xml.bind.annotation.XmlAttribute;
+import javax.xml.bind.annotation.XmlType;
+
+
+/**
+ * Database cross-reference.
+ *
+ * <p>Java class for XrefType complex type.
+ *
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ *
+ * <pre>
+ * <complexType name="XrefType">
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attribute name="db" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="secondaryId" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+@XmlAccessorType(XmlAccessType.FIELD)
+@XmlType(name = "XrefType")
+public class XrefType {
+
+ @XmlAttribute(name = "db", required = true)
+ protected String db;
+ @XmlAttribute(name = "id", required = true)
+ protected String id;
+ @XmlAttribute(name = "secondaryId")
+ protected String secondaryId;
+
+ /**
+ * Gets the value of the db property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getDb() {
+ return db;
+ }
+
+ /**
+ * Sets the value of the db property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setDb(String value) {
+ this.db = value;
+ }
+
+ /**
+ * Gets the value of the id property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getId() {
+ return id;
+ }
+
+ /**
+ * Sets the value of the id property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setId(String value) {
+ this.id = value;
+ }
+
+ /**
+ * Gets the value of the secondaryId property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getSecondaryId() {
+ return secondaryId;
+ }
+
+ /**
+ * Sets the value of the secondaryId property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setSecondaryId(String value) {
+ this.secondaryId = value;
+ }
+
+}
git://source.jalview.org / jalview.git / commitdiff