org.nmdp.ngs.sra.jaxb.study.Study Maven / Gradle / Ivy
//
// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.10-b140310.1920
// See http://java.sun.com/xml/jaxb
// Any modifications to this file will be lost upon recompilation of the source schema.
// Generated on: 2015.01.21 at 09:06:41 PM CST
//
package org.nmdp.ngs.sra.jaxb.study;
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.XmlRootElement;
import javax.xml.bind.annotation.XmlSchemaType;
import javax.xml.bind.annotation.XmlType;
/**
*
* A Study is a container for a sequencing investigation that may comprise multiple experiments.
* The Study has an overall goal, but is otherwise minimally defined in the SRA.
* A Study is composed of a descriptor, zero or more experiments, and zero or more analyses.
* The submitter may decorate the Study with web links and properties.
*
*
* Java class for StudyType complex type.
*
*
The following schema fragment specifies the expected content contained within this class.
*
*
* <complexType name="StudyType">
* <complexContent>
* <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
* <sequence>
* <element name="IDENTIFIERS" type="{SRA.common}IdentifierType" minOccurs="0"/>
* <element name="DESCRIPTOR">
* <complexType>
* <complexContent>
* <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
* <all minOccurs="0">
* <element name="STUDY_TITLE" type="{http://www.w3.org/2001/XMLSchema}string"/>
* <element name="STUDY_TYPE">
* <complexType>
* <complexContent>
* <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
* <attribute name="existing_study_type" use="required">
* <simpleType>
* <restriction base="{http://www.w3.org/2001/XMLSchema}string">
* <enumeration value="Whole Genome Sequencing"/>
* <enumeration value="Metagenomics"/>
* <enumeration value="Transcriptome Analysis"/>
* <enumeration value="Resequencing"/>
* <enumeration value="Epigenetics"/>
* <enumeration value="Synthetic Genomics"/>
* <enumeration value="Forensic or Paleo-genomics"/>
* <enumeration value="Gene Regulation Study"/>
* <enumeration value="Cancer Genomics"/>
* <enumeration value="Population Genomics"/>
* <enumeration value="RNASeq"/>
* <enumeration value="Exome Sequencing"/>
* <enumeration value="Pooled Clone Sequencing"/>
* <enumeration value="Other"/>
* </restriction>
* </simpleType>
* </attribute>
* <attribute name="new_study_type" type="{http://www.w3.org/2001/XMLSchema}string" />
* </restriction>
* </complexContent>
* </complexType>
* </element>
* <element name="STUDY_ABSTRACT" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
* <element name="CENTER_NAME" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
* <element name="CENTER_PROJECT_NAME" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
* <element name="PROJECT_ID" type="{http://www.w3.org/2001/XMLSchema}nonNegativeInteger" minOccurs="0"/>
* <element name="RELATED_STUDIES" minOccurs="0">
* <complexType>
* <complexContent>
* <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
* <sequence>
* <element name="RELATED_STUDY" maxOccurs="unbounded">
* <complexType>
* <complexContent>
* <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
* <sequence>
* <element name="RELATED_LINK" type="{SRA.common}XRefType"/>
* <element name="IS_PRIMARY" type="{http://www.w3.org/2001/XMLSchema}boolean"/>
* </sequence>
* </restriction>
* </complexContent>
* </complexType>
* </element>
* </sequence>
* </restriction>
* </complexContent>
* </complexType>
* </element>
* <element name="STUDY_DESCRIPTION" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
* </all>
* </restriction>
* </complexContent>
* </complexType>
* </element>
* <element name="STUDY_LINKS" minOccurs="0">
* <complexType>
* <complexContent>
* <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
* <sequence maxOccurs="unbounded">
* <element name="STUDY_LINK" type="{SRA.common}LinkType"/>
* </sequence>
* </restriction>
* </complexContent>
* </complexType>
* </element>
* <element name="STUDY_ATTRIBUTES" minOccurs="0">
* <complexType>
* <complexContent>
* <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
* <sequence maxOccurs="unbounded">
* <element name="STUDY_ATTRIBUTE" type="{SRA.common}AttributeType"/>
* </sequence>
* </restriction>
* </complexContent>
* </complexType>
* </element>
* </sequence>
* <attGroup ref="{SRA.common}NameGroup"/>
* </restriction>
* </complexContent>
* </complexType>
*
*
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
@XmlType(name = "StudyType", namespace = "", propOrder = {
"identifiers",
"descriptor",
"studyLinks",
"studyAttributes"
})
@XmlRootElement(name = "STUDY", namespace = "")
public class Study {
@XmlElement(name = "IDENTIFIERS")
protected IdentifierType identifiers;
@XmlElement(name = "DESCRIPTOR", required = true)
protected Study.Descriptor descriptor;
@XmlElement(name = "STUDY_LINKS")
protected Study.StudyLinks studyLinks;
@XmlElement(name = "STUDY_ATTRIBUTES")
protected Study.StudyAttributes studyAttributes;
@XmlAttribute(name = "alias")
protected String alias;
@XmlAttribute(name = "center_name")
protected String centerName;
@XmlAttribute(name = "broker_name")
protected String brokerName;
@XmlAttribute(name = "accession")
protected String accession;
/**
* Gets the value of the identifiers property.
*
* @return
* possible object is
* {@link IdentifierType }
*
*/
public IdentifierType getIdentifiers() {
return identifiers;
}
/**
* Sets the value of the identifiers property.
*
* @param value
* allowed object is
* {@link IdentifierType }
*
*/
public void setIdentifiers(IdentifierType value) {
this.identifiers = value;
}
/**
* Gets the value of the descriptor property.
*
* @return
* possible object is
* {@link Study.Descriptor }
*
*/
public Study.Descriptor getDescriptor() {
return descriptor;
}
/**
* Sets the value of the descriptor property.
*
* @param value
* allowed object is
* {@link Study.Descriptor }
*
*/
public void setDescriptor(Study.Descriptor value) {
this.descriptor = value;
}
/**
* Gets the value of the studyLinks property.
*
* @return
* possible object is
* {@link Study.StudyLinks }
*
*/
public Study.StudyLinks getStudyLinks() {
return studyLinks;
}
/**
* Sets the value of the studyLinks property.
*
* @param value
* allowed object is
* {@link Study.StudyLinks }
*
*/
public void setStudyLinks(Study.StudyLinks value) {
this.studyLinks = value;
}
/**
* Gets the value of the studyAttributes property.
*
* @return
* possible object is
* {@link Study.StudyAttributes }
*
*/
public Study.StudyAttributes getStudyAttributes() {
return studyAttributes;
}
/**
* Sets the value of the studyAttributes property.
*
* @param value
* allowed object is
* {@link Study.StudyAttributes }
*
*/
public void setStudyAttributes(Study.StudyAttributes value) {
this.studyAttributes = value;
}
/**
* Gets the value of the alias property.
*
* @return
* possible object is
* {@link String }
*
*/
public String getAlias() {
return alias;
}
/**
* Sets the value of the alias property.
*
* @param value
* allowed object is
* {@link String }
*
*/
public void setAlias(String value) {
this.alias = value;
}
/**
* Gets the value of the centerName property.
*
* @return
* possible object is
* {@link String }
*
*/
public String getCenterName() {
return centerName;
}
/**
* Sets the value of the centerName property.
*
* @param value
* allowed object is
* {@link String }
*
*/
public void setCenterName(String value) {
this.centerName = value;
}
/**
* Gets the value of the brokerName property.
*
* @return
* possible object is
* {@link String }
*
*/
public String getBrokerName() {
return brokerName;
}
/**
* Sets the value of the brokerName property.
*
* @param value
* allowed object is
* {@link String }
*
*/
public void setBrokerName(String value) {
this.brokerName = 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;
}
/**
* Java class for anonymous complex type.
*
*
The following schema fragment specifies the expected content contained within this class.
*
*
* <complexType>
* <complexContent>
* <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
* <all minOccurs="0">
* <element name="STUDY_TITLE" type="{http://www.w3.org/2001/XMLSchema}string"/>
* <element name="STUDY_TYPE">
* <complexType>
* <complexContent>
* <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
* <attribute name="existing_study_type" use="required">
* <simpleType>
* <restriction base="{http://www.w3.org/2001/XMLSchema}string">
* <enumeration value="Whole Genome Sequencing"/>
* <enumeration value="Metagenomics"/>
* <enumeration value="Transcriptome Analysis"/>
* <enumeration value="Resequencing"/>
* <enumeration value="Epigenetics"/>
* <enumeration value="Synthetic Genomics"/>
* <enumeration value="Forensic or Paleo-genomics"/>
* <enumeration value="Gene Regulation Study"/>
* <enumeration value="Cancer Genomics"/>
* <enumeration value="Population Genomics"/>
* <enumeration value="RNASeq"/>
* <enumeration value="Exome Sequencing"/>
* <enumeration value="Pooled Clone Sequencing"/>
* <enumeration value="Other"/>
* </restriction>
* </simpleType>
* </attribute>
* <attribute name="new_study_type" type="{http://www.w3.org/2001/XMLSchema}string" />
* </restriction>
* </complexContent>
* </complexType>
* </element>
* <element name="STUDY_ABSTRACT" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
* <element name="CENTER_NAME" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
* <element name="CENTER_PROJECT_NAME" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
* <element name="PROJECT_ID" type="{http://www.w3.org/2001/XMLSchema}nonNegativeInteger" minOccurs="0"/>
* <element name="RELATED_STUDIES" minOccurs="0">
* <complexType>
* <complexContent>
* <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
* <sequence>
* <element name="RELATED_STUDY" maxOccurs="unbounded">
* <complexType>
* <complexContent>
* <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
* <sequence>
* <element name="RELATED_LINK" type="{SRA.common}XRefType"/>
* <element name="IS_PRIMARY" type="{http://www.w3.org/2001/XMLSchema}boolean"/>
* </sequence>
* </restriction>
* </complexContent>
* </complexType>
* </element>
* </sequence>
* </restriction>
* </complexContent>
* </complexType>
* </element>
* <element name="STUDY_DESCRIPTION" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
* </all>
* </restriction>
* </complexContent>
* </complexType>
*
*
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
@XmlType(name = "", propOrder = {
})
public static class Descriptor {
@XmlElement(name = "STUDY_TITLE")
protected String studyTitle;
@XmlElement(name = "STUDY_TYPE")
protected Study.Descriptor.StudyType studyType;
@XmlElement(name = "STUDY_ABSTRACT")
protected String studyAbstract;
@XmlElement(name = "CENTER_NAME")
protected String centerName;
@XmlElement(name = "CENTER_PROJECT_NAME")
protected String centerProjectName;
@XmlElement(name = "PROJECT_ID")
@XmlSchemaType(name = "nonNegativeInteger")
protected BigInteger projectId;
@XmlElement(name = "RELATED_STUDIES")
protected Study.Descriptor.RelatedStudies relatedStudies;
@XmlElement(name = "STUDY_DESCRIPTION")
protected String studyDescription;
/**
* Gets the value of the studyTitle property.
*
* @return
* possible object is
* {@link String }
*
*/
public String getStudyTitle() {
return studyTitle;
}
/**
* Sets the value of the studyTitle property.
*
* @param value
* allowed object is
* {@link String }
*
*/
public void setStudyTitle(String value) {
this.studyTitle = value;
}
/**
* Gets the value of the studyType property.
*
* @return
* possible object is
* {@link Study.Descriptor.StudyType }
*
*/
public Study.Descriptor.StudyType getStudyType() {
return studyType;
}
/**
* Sets the value of the studyType property.
*
* @param value
* allowed object is
* {@link Study.Descriptor.StudyType }
*
*/
public void setStudyType(Study.Descriptor.StudyType value) {
this.studyType = value;
}
/**
* Gets the value of the studyAbstract property.
*
* @return
* possible object is
* {@link String }
*
*/
public String getStudyAbstract() {
return studyAbstract;
}
/**
* Sets the value of the studyAbstract property.
*
* @param value
* allowed object is
* {@link String }
*
*/
public void setStudyAbstract(String value) {
this.studyAbstract = value;
}
/**
* Gets the value of the centerName property.
*
* @return
* possible object is
* {@link String }
*
*/
public String getCenterName() {
return centerName;
}
/**
* Sets the value of the centerName property.
*
* @param value
* allowed object is
* {@link String }
*
*/
public void setCenterName(String value) {
this.centerName = value;
}
/**
* Gets the value of the centerProjectName property.
*
* @return
* possible object is
* {@link String }
*
*/
public String getCenterProjectName() {
return centerProjectName;
}
/**
* Sets the value of the centerProjectName property.
*
* @param value
* allowed object is
* {@link String }
*
*/
public void setCenterProjectName(String value) {
this.centerProjectName = value;
}
/**
* Gets the value of the projectId property.
*
* @return
* possible object is
* {@link BigInteger }
*
*/
public BigInteger getProjectId() {
return projectId;
}
/**
* Sets the value of the projectId property.
*
* @param value
* allowed object is
* {@link BigInteger }
*
*/
public void setProjectId(BigInteger value) {
this.projectId = value;
}
/**
* Gets the value of the relatedStudies property.
*
* @return
* possible object is
* {@link Study.Descriptor.RelatedStudies }
*
*/
public Study.Descriptor.RelatedStudies getRelatedStudies() {
return relatedStudies;
}
/**
* Sets the value of the relatedStudies property.
*
* @param value
* allowed object is
* {@link Study.Descriptor.RelatedStudies }
*
*/
public void setRelatedStudies(Study.Descriptor.RelatedStudies value) {
this.relatedStudies = value;
}
/**
* Gets the value of the studyDescription property.
*
* @return
* possible object is
* {@link String }
*
*/
public String getStudyDescription() {
return studyDescription;
}
/**
* Sets the value of the studyDescription property.
*
* @param value
* allowed object is
* {@link String }
*
*/
public void setStudyDescription(String value) {
this.studyDescription = value;
}
/**
* Java class for anonymous complex type.
*
*
The following schema fragment specifies the expected content contained within this class.
*
*
* <complexType>
* <complexContent>
* <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
* <sequence>
* <element name="RELATED_STUDY" maxOccurs="unbounded">
* <complexType>
* <complexContent>
* <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
* <sequence>
* <element name="RELATED_LINK" type="{SRA.common}XRefType"/>
* <element name="IS_PRIMARY" type="{http://www.w3.org/2001/XMLSchema}boolean"/>
* </sequence>
* </restriction>
* </complexContent>
* </complexType>
* </element>
* </sequence>
* </restriction>
* </complexContent>
* </complexType>
*
*
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
@XmlType(name = "", propOrder = {
"relatedStudies"
})
public static class RelatedStudies {
@XmlElement(name = "RELATED_STUDY", required = true)
protected List relatedStudies;
/**
* Gets the value of the relatedStudies property.
*
*
* 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 relatedStudies property.
*
*
* For example, to add a new item, do as follows:
*
* getRelatedStudies().add(newItem);
*
*
*
*
* Objects of the following type(s) are allowed in the list
* {@link Study.Descriptor.RelatedStudies.RelatedStudy }
*
*
*/
public List getRelatedStudies() {
if (relatedStudies == null) {
relatedStudies = new ArrayList();
}
return this.relatedStudies;
}
/**
* Java class for anonymous complex type.
*
*
The following schema fragment specifies the expected content contained within this class.
*
*
* <complexType>
* <complexContent>
* <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
* <sequence>
* <element name="RELATED_LINK" type="{SRA.common}XRefType"/>
* <element name="IS_PRIMARY" type="{http://www.w3.org/2001/XMLSchema}boolean"/>
* </sequence>
* </restriction>
* </complexContent>
* </complexType>
*
*
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
@XmlType(name = "", propOrder = {
"relatedLink",
"isPrimary"
})
public static class RelatedStudy {
@XmlElement(name = "RELATED_LINK", required = true)
protected XRefType relatedLink;
@XmlElement(name = "IS_PRIMARY")
protected boolean isPrimary;
/**
* Gets the value of the relatedLink property.
*
* @return
* possible object is
* {@link XRefType }
*
*/
public XRefType getRelatedLink() {
return relatedLink;
}
/**
* Sets the value of the relatedLink property.
*
* @param value
* allowed object is
* {@link XRefType }
*
*/
public void setRelatedLink(XRefType value) {
this.relatedLink = value;
}
/**
* Gets the value of the isPrimary property.
*
*/
public boolean isIsPrimary() {
return isPrimary;
}
/**
* Sets the value of the isPrimary property.
*
*/
public void setIsPrimary(boolean value) {
this.isPrimary = value;
}
}
}
/**
* Java class for anonymous complex type.
*
*
The following schema fragment specifies the expected content contained within this class.
*
*
* <complexType>
* <complexContent>
* <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
* <attribute name="existing_study_type" use="required">
* <simpleType>
* <restriction base="{http://www.w3.org/2001/XMLSchema}string">
* <enumeration value="Whole Genome Sequencing"/>
* <enumeration value="Metagenomics"/>
* <enumeration value="Transcriptome Analysis"/>
* <enumeration value="Resequencing"/>
* <enumeration value="Epigenetics"/>
* <enumeration value="Synthetic Genomics"/>
* <enumeration value="Forensic or Paleo-genomics"/>
* <enumeration value="Gene Regulation Study"/>
* <enumeration value="Cancer Genomics"/>
* <enumeration value="Population Genomics"/>
* <enumeration value="RNASeq"/>
* <enumeration value="Exome Sequencing"/>
* <enumeration value="Pooled Clone Sequencing"/>
* <enumeration value="Other"/>
* </restriction>
* </simpleType>
* </attribute>
* <attribute name="new_study_type" type="{http://www.w3.org/2001/XMLSchema}string" />
* </restriction>
* </complexContent>
* </complexType>
*
*
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
@XmlType(name = "")
public static class StudyType {
@XmlAttribute(name = "existing_study_type", required = true)
protected String existingStudyType;
@XmlAttribute(name = "new_study_type")
protected String newStudyType;
/**
* Gets the value of the existingStudyType property.
*
* @return
* possible object is
* {@link String }
*
*/
public String getExistingStudyType() {
return existingStudyType;
}
/**
* Sets the value of the existingStudyType property.
*
* @param value
* allowed object is
* {@link String }
*
*/
public void setExistingStudyType(String value) {
this.existingStudyType = value;
}
/**
* Gets the value of the newStudyType property.
*
* @return
* possible object is
* {@link String }
*
*/
public String getNewStudyType() {
return newStudyType;
}
/**
* Sets the value of the newStudyType property.
*
* @param value
* allowed object is
* {@link String }
*
*/
public void setNewStudyType(String value) {
this.newStudyType = value;
}
}
}
/**
* Java class for anonymous complex type.
*
*
The following schema fragment specifies the expected content contained within this class.
*
*
* <complexType>
* <complexContent>
* <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
* <sequence maxOccurs="unbounded">
* <element name="STUDY_ATTRIBUTE" type="{SRA.common}AttributeType"/>
* </sequence>
* </restriction>
* </complexContent>
* </complexType>
*
*
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
@XmlType(name = "", propOrder = {
"studyAttributes"
})
public static class StudyAttributes {
@XmlElement(name = "STUDY_ATTRIBUTE", required = true)
protected List studyAttributes;
/**
* Gets the value of the studyAttributes property.
*
*
* 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 studyAttributes property.
*
*
* For example, to add a new item, do as follows:
*
* getStudyAttributes().add(newItem);
*
*
*
*
* Objects of the following type(s) are allowed in the list
* {@link AttributeType }
*
*
*/
public List getStudyAttributes() {
if (studyAttributes == null) {
studyAttributes = new ArrayList();
}
return this.studyAttributes;
}
}
/**
* Java class for anonymous complex type.
*
*
The following schema fragment specifies the expected content contained within this class.
*
*
* <complexType>
* <complexContent>
* <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
* <sequence maxOccurs="unbounded">
* <element name="STUDY_LINK" type="{SRA.common}LinkType"/>
* </sequence>
* </restriction>
* </complexContent>
* </complexType>
*
*
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
@XmlType(name = "", propOrder = {
"studyLinks"
})
public static class StudyLinks {
@XmlElement(name = "STUDY_LINK", required = true)
protected List studyLinks;
/**
* Gets the value of the studyLinks property.
*
*
* 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 studyLinks property.
*
*
* For example, to add a new item, do as follows:
*
* getStudyLinks().add(newItem);
*
*
*
*
* Objects of the following type(s) are allowed in the list
* {@link LinkType }
*
*
*/
public List getStudyLinks() {
if (studyLinks == null) {
studyLinks = new ArrayList();
}
return this.studyLinks;
}
}
}