// // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb // Any modifications to this file will be lost upon recompilation of the source schema. // Generated on: 2023.02.22 at 10:08:57 PM GMT // 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; /** *
Java class for EntryType complex type. * *
The following schema fragment specifies the expected content contained within this class. * *
* <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> ** * */ @XmlAccessorType(XmlAccessType.FIELD) @XmlType(name = "EntryType", propOrder = { "secondaryAccession", "projectAccession", "description", "comment", "keyword", "reference", "xref", "feature", "assembly", "contig", "sequence" }) public class EntryType { protected List
* 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 set
method for the secondaryAccession property.
*
*
* For example, to add a new item, do as follows: *
* getSecondaryAccession().add(newItem); ** * *
* Objects of the following type(s) are allowed in the list
* {@link String }
*
*
*/
public List
* 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
* For example, to add a new item, do as follows:
*
* Objects of the following type(s) are allowed in the list
* {@link String }
*
*
*/
public List
* 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
* For example, to add a new item, do as follows:
*
* Objects of the following type(s) are allowed in the list
* {@link String }
*
*
*/
public List
* 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
* For example, to add a new item, do as follows:
*
* Objects of the following type(s) are allowed in the list
* {@link EntryType.Reference }
*
*
*/
public List
* 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
* For example, to add a new item, do as follows:
*
* Objects of the following type(s) are allowed in the list
* {@link XrefType }
*
*
*/
public List
* 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
* For example, to add a new item, do as follows:
*
* Objects of the following type(s) are allowed in the list
* {@link EntryType.Feature }
*
*
*/
public List Java class for anonymous complex type.
*
* The following schema fragment specifies the expected content contained within this class.
*
*
* 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
* For example, to add a new item, do as follows:
*
* Objects of the following type(s) are allowed in the list
* {@link EntryType.Assembly.Range }
*
*
*/
public List Java class for anonymous complex type.
*
* The following schema fragment specifies the expected content contained within this class.
*
* Java class for anonymous complex type.
*
* The following schema fragment specifies the expected content contained within this class.
*
* set
method for the projectAccession property.
*
*
* getProjectAccession().add(newItem);
*
*
*
* set
method for the keyword property.
*
*
* getKeyword().add(newItem);
*
*
*
* set
method for the reference property.
*
*
* getReference().add(newItem);
*
*
*
* set
method for the xref property.
*
*
* getXref().add(newItem);
*
*
*
* set
method for the feature property.
*
*
* getFeature().add(newItem);
*
*
*
*
* <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>
*
*
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
@XmlType(name = "", propOrder = {
"range"
})
public static class Assembly {
@XmlElement(required = true)
protected Listset
method for the range property.
*
*
* getRange().add(newItem);
*
*
*
*
* <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>
*
*
*
*/
@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;
}
}
}
/**
*
* <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>
*
*
*
*/
@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