org.nmdp.ngs.sra.jaxb.analysis.Analysis Maven / Gradle / Ivy
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//
// 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: 2015.06.22 at 10:48:06 AM CDT
//
package org.nmdp.ngs.sra.jaxb.analysis;
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;
import javax.xml.datatype.XMLGregorianCalendar;
/**
* A SRA analysis object captures sequence analysis results including sequence alignments, sequence variations and sequence annotations.
*
*
* Java class for AnalysisType complex type.
*
*
The following schema fragment specifies the expected content contained within this class.
*
*
* <complexType name="AnalysisType">
* <complexContent>
* <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
* <sequence>
* <element name="IDENTIFIERS" type="{SRA.common}IdentifierType" minOccurs="0"/>
* <element name="TITLE" type="{http://www.w3.org/2001/XMLSchema}string"/>
* <element name="DESCRIPTION" type="{http://www.w3.org/2001/XMLSchema}string"/>
* <element name="STUDY_REF" minOccurs="0">
* <complexType>
* <complexContent>
* <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
* <sequence>
* <element name="IDENTIFIERS" type="{SRA.common}IdentifierType" minOccurs="0"/>
* </sequence>
* <attGroup ref="{SRA.common}RefNameGroup"/>
* </restriction>
* </complexContent>
* </complexType>
* </element>
* <element name="SAMPLE_REF" maxOccurs="unbounded" minOccurs="0">
* <complexType>
* <complexContent>
* <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
* <sequence>
* <element name="IDENTIFIERS" type="{SRA.common}IdentifierType" minOccurs="0"/>
* </sequence>
* <attGroup ref="{SRA.common}RefNameGroup"/>
* <attribute name="label" type="{http://www.w3.org/2001/XMLSchema}string" />
* </restriction>
* </complexContent>
* </complexType>
* </element>
* <element name="RUN_REF" maxOccurs="unbounded" minOccurs="0">
* <complexType>
* <complexContent>
* <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
* <sequence>
* <element name="IDENTIFIERS" type="{SRA.common}IdentifierType" minOccurs="0"/>
* </sequence>
* <attGroup ref="{SRA.common}RefNameGroup"/>
* <attribute name="label" type="{http://www.w3.org/2001/XMLSchema}string" />
* </restriction>
* </complexContent>
* </complexType>
* </element>
* <element name="ANALYSIS_REF" maxOccurs="unbounded" minOccurs="0">
* <complexType>
* <complexContent>
* <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
* <sequence>
* <element name="IDENTIFIERS" type="{SRA.common}IdentifierType" minOccurs="0"/>
* </sequence>
* <attGroup ref="{SRA.common}RefNameGroup"/>
* <attribute name="label" type="{http://www.w3.org/2001/XMLSchema}string" />
* </restriction>
* </complexContent>
* </complexType>
* </element>
* <element name="ANALYSIS_TYPE">
* <complexType>
* <complexContent>
* <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
* <choice>
* <element name="REFERENCE_ALIGNMENT" type="{SRA.common}ReferenceSequenceType"/>
* <element name="SEQUENCE_VARIATION">
* <complexType>
* <complexContent>
* <extension base="{SRA.common}ReferenceSequenceType">
* <sequence>
* <element name="EXPERIMENT_TYPE" maxOccurs="unbounded" minOccurs="0">
* <simpleType>
* <restriction base="{http://www.w3.org/2001/XMLSchema}string">
* <enumeration value="Whole genome sequencing"/>
* <enumeration value="Exome sequencing"/>
* <enumeration value="Genotyping by array"/>
* <enumeration value="Curation"/>
* </restriction>
* </simpleType>
* </element>
* <element name="PROGRAM" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
* <element name="PLATFORM" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
* <element name="IMPUTATION" type="{http://www.w3.org/2001/XMLSchema}boolean" minOccurs="0"/>
* </sequence>
* </extension>
* </complexContent>
* </complexType>
* </element>
* <element name="SEQUENCE_ASSEMBLY">
* <complexType>
* <complexContent>
* <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
* <sequence>
* <element name="NAME" type="{http://www.w3.org/2001/XMLSchema}string"/>
* <element name="PARTIAL" type="{http://www.w3.org/2001/XMLSchema}boolean"/>
* <element name="COVERAGE" type="{http://www.w3.org/2001/XMLSchema}string"/>
* <element name="PROGRAM" type="{http://www.w3.org/2001/XMLSchema}string"/>
* <element name="PLATFORM" type="{http://www.w3.org/2001/XMLSchema}string"/>
* <element name="MIN_GAP_LENGTH" type="{http://www.w3.org/2001/XMLSchema}integer" minOccurs="0"/>
* </sequence>
* </restriction>
* </complexContent>
* </complexType>
* </element>
* <element name="SEQUENCE_ANNOTATION">
* <complexType>
* <complexContent>
* <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
* </restriction>
* </complexContent>
* </complexType>
* </element>
* <element name="REFERENCE_SEQUENCE" type="{http://www.w3.org/2001/XMLSchema}anyType"/>
* <element name="SAMPLE_PHENOTYPE">
* <complexType>
* <complexContent>
* <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
* </restriction>
* </complexContent>
* </complexType>
* </element>
* </choice>
* </restriction>
* </complexContent>
* </complexType>
* </element>
* <sequence>
* <element name="FILES">
* <complexType>
* <complexContent>
* <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
* <sequence>
* <element name="FILE" type="{}AnalysisFileType" maxOccurs="unbounded"/>
* </sequence>
* </restriction>
* </complexContent>
* </complexType>
* </element>
* </sequence>
* <element name="ANALYSIS_LINKS" minOccurs="0">
* <complexType>
* <complexContent>
* <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
* <sequence maxOccurs="unbounded">
* <element name="ANALYSIS_LINK" type="{SRA.common}LinkType"/>
* </sequence>
* </restriction>
* </complexContent>
* </complexType>
* </element>
* <element name="ANALYSIS_ATTRIBUTES" minOccurs="0">
* <complexType>
* <complexContent>
* <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
* <sequence maxOccurs="unbounded">
* <element name="ANALYSIS_ATTRIBUTE" type="{SRA.common}AttributeType"/>
* </sequence>
* </restriction>
* </complexContent>
* </complexType>
* </element>
* </sequence>
* <attGroup ref="{SRA.common}NameGroup"/>
* <attribute name="analysis_center" type="{http://www.w3.org/2001/XMLSchema}string" />
* <attribute name="analysis_date" type="{http://www.w3.org/2001/XMLSchema}dateTime" />
* </restriction>
* </complexContent>
* </complexType>
*
*
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
@XmlType(name = "AnalysisType", namespace = "", propOrder = {
"identifiers",
"title",
"description",
"studyRef",
"sampleReves",
"runReves",
"analysisReves",
"analysisType",
"files",
"analysisLinks",
"analysisAttributes"
})
@XmlRootElement(name = "ANALYSIS", namespace = "")
public class Analysis {
@XmlElement(name = "IDENTIFIERS")
protected IdentifierType identifiers;
@XmlElement(name = "TITLE", required = true)
protected String title;
@XmlElement(name = "DESCRIPTION", required = true)
protected String description;
@XmlElement(name = "STUDY_REF")
protected Analysis.StudyRef studyRef;
@XmlElement(name = "SAMPLE_REF")
protected List sampleReves;
@XmlElement(name = "RUN_REF")
protected List runReves;
@XmlElement(name = "ANALYSIS_REF")
protected List analysisReves;
@XmlElement(name = "ANALYSIS_TYPE", required = true)
protected Analysis.AnalysisType analysisType;
@XmlElement(name = "FILES", required = true)
protected Analysis.Files files;
@XmlElement(name = "ANALYSIS_LINKS")
protected Analysis.AnalysisLinks analysisLinks;
@XmlElement(name = "ANALYSIS_ATTRIBUTES")
protected Analysis.AnalysisAttributes analysisAttributes;
@XmlAttribute(name = "analysis_center")
protected String analysisCenter;
@XmlAttribute(name = "analysis_date")
@XmlSchemaType(name = "dateTime")
protected XMLGregorianCalendar analysisDate;
@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 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 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 studyRef property.
*
* @return
* possible object is
* {@link Analysis.StudyRef }
*
*/
public Analysis.StudyRef getStudyRef() {
return studyRef;
}
/**
* Sets the value of the studyRef property.
*
* @param value
* allowed object is
* {@link Analysis.StudyRef }
*
*/
public void setStudyRef(Analysis.StudyRef value) {
this.studyRef = value;
}
/**
* Gets the value of the sampleReves 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 sampleReves property.
*
*
* For example, to add a new item, do as follows:
*
* getSampleReves().add(newItem);
*
*
*
*
* Objects of the following type(s) are allowed in the list
* {@link Analysis.SampleRef }
*
*
*/
public List getSampleReves() {
if (sampleReves == null) {
sampleReves = new ArrayList();
}
return this.sampleReves;
}
/**
* Gets the value of the runReves 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 runReves property.
*
*
* For example, to add a new item, do as follows:
*
* getRunReves().add(newItem);
*
*
*
*
* Objects of the following type(s) are allowed in the list
* {@link Analysis.RunRef }
*
*
*/
public List getRunReves() {
if (runReves == null) {
runReves = new ArrayList();
}
return this.runReves;
}
/**
* Gets the value of the analysisReves 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 analysisReves property.
*
*
* For example, to add a new item, do as follows:
*
* getAnalysisReves().add(newItem);
*
*
*
*
* Objects of the following type(s) are allowed in the list
* {@link Analysis.AnalysisRef }
*
*
*/
public List getAnalysisReves() {
if (analysisReves == null) {
analysisReves = new ArrayList();
}
return this.analysisReves;
}
/**
* Gets the value of the analysisType property.
*
* @return
* possible object is
* {@link Analysis.AnalysisType }
*
*/
public Analysis.AnalysisType getAnalysisType() {
return analysisType;
}
/**
* Sets the value of the analysisType property.
*
* @param value
* allowed object is
* {@link Analysis.AnalysisType }
*
*/
public void setAnalysisType(Analysis.AnalysisType value) {
this.analysisType = value;
}
/**
* Gets the value of the files property.
*
* @return
* possible object is
* {@link Analysis.Files }
*
*/
public Analysis.Files getFiles() {
return files;
}
/**
* Sets the value of the files property.
*
* @param value
* allowed object is
* {@link Analysis.Files }
*
*/
public void setFiles(Analysis.Files value) {
this.files = value;
}
/**
* Gets the value of the analysisLinks property.
*
* @return
* possible object is
* {@link Analysis.AnalysisLinks }
*
*/
public Analysis.AnalysisLinks getAnalysisLinks() {
return analysisLinks;
}
/**
* Sets the value of the analysisLinks property.
*
* @param value
* allowed object is
* {@link Analysis.AnalysisLinks }
*
*/
public void setAnalysisLinks(Analysis.AnalysisLinks value) {
this.analysisLinks = value;
}
/**
* Gets the value of the analysisAttributes property.
*
* @return
* possible object is
* {@link Analysis.AnalysisAttributes }
*
*/
public Analysis.AnalysisAttributes getAnalysisAttributes() {
return analysisAttributes;
}
/**
* Sets the value of the analysisAttributes property.
*
* @param value
* allowed object is
* {@link Analysis.AnalysisAttributes }
*
*/
public void setAnalysisAttributes(Analysis.AnalysisAttributes value) {
this.analysisAttributes = value;
}
/**
* Gets the value of the analysisCenter property.
*
* @return
* possible object is
* {@link String }
*
*/
public String getAnalysisCenter() {
return analysisCenter;
}
/**
* Sets the value of the analysisCenter property.
*
* @param value
* allowed object is
* {@link String }
*
*/
public void setAnalysisCenter(String value) {
this.analysisCenter = value;
}
/**
* Gets the value of the analysisDate property.
*
* @return
* possible object is
* {@link XMLGregorianCalendar }
*
*/
public XMLGregorianCalendar getAnalysisDate() {
return analysisDate;
}
/**
* Sets the value of the analysisDate property.
*
* @param value
* allowed object is
* {@link XMLGregorianCalendar }
*
*/
public void setAnalysisDate(XMLGregorianCalendar value) {
this.analysisDate = 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">
* <sequence maxOccurs="unbounded">
* <element name="ANALYSIS_ATTRIBUTE" type="{SRA.common}AttributeType"/>
* </sequence>
* </restriction>
* </complexContent>
* </complexType>
*
*
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
@XmlType(name = "", propOrder = {
"analysisAttributes"
})
public static class AnalysisAttributes {
@XmlElement(name = "ANALYSIS_ATTRIBUTE", required = true)
protected List analysisAttributes;
/**
* Gets the value of the analysisAttributes 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 analysisAttributes property.
*
*
* For example, to add a new item, do as follows:
*
* getAnalysisAttributes().add(newItem);
*
*
*
*
* Objects of the following type(s) are allowed in the list
* {@link AttributeType }
*
*
*/
public List getAnalysisAttributes() {
if (analysisAttributes == null) {
analysisAttributes = new ArrayList();
}
return this.analysisAttributes;
}
}
/**
* 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="ANALYSIS_LINK" type="{SRA.common}LinkType"/>
* </sequence>
* </restriction>
* </complexContent>
* </complexType>
*
*
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
@XmlType(name = "", propOrder = {
"analysisLinks"
})
public static class AnalysisLinks {
@XmlElement(name = "ANALYSIS_LINK", required = true)
protected List analysisLinks;
/**
* Gets the value of the analysisLinks 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 analysisLinks property.
*
*
* For example, to add a new item, do as follows:
*
* getAnalysisLinks().add(newItem);
*
*
*
*
* Objects of the following type(s) are allowed in the list
* {@link LinkType }
*
*
*/
public List getAnalysisLinks() {
if (analysisLinks == null) {
analysisLinks = new ArrayList();
}
return this.analysisLinks;
}
}
/**
* 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="IDENTIFIERS" type="{SRA.common}IdentifierType" minOccurs="0"/>
* </sequence>
* <attGroup ref="{SRA.common}RefNameGroup"/>
* <attribute name="label" type="{http://www.w3.org/2001/XMLSchema}string" />
* </restriction>
* </complexContent>
* </complexType>
*
*
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
@XmlType(name = "", propOrder = {
"identifiers"
})
public static class AnalysisRef {
@XmlElement(name = "IDENTIFIERS")
protected IdentifierType identifiers;
@XmlAttribute(name = "label")
protected String label;
@XmlAttribute(name = "refname")
protected String refname;
@XmlAttribute(name = "refcenter")
protected String refcenter;
@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 label property.
*
* @return
* possible object is
* {@link String }
*
*/
public String getLabel() {
return label;
}
/**
* Sets the value of the label property.
*
* @param value
* allowed object is
* {@link String }
*
*/
public void setLabel(String value) {
this.label = value;
}
/**
* Gets the value of the refname property.
*
* @return
* possible object is
* {@link String }
*
*/
public String getRefname() {
return refname;
}
/**
* Sets the value of the refname property.
*
* @param value
* allowed object is
* {@link String }
*
*/
public void setRefname(String value) {
this.refname = value;
}
/**
* Gets the value of the refcenter property.
*
* @return
* possible object is
* {@link String }
*
*/
public String getRefcenter() {
return refcenter;
}
/**
* Sets the value of the refcenter property.
*
* @param value
* allowed object is
* {@link String }
*
*/
public void setRefcenter(String value) {
this.refcenter = 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">
* <choice>
* <element name="REFERENCE_ALIGNMENT" type="{SRA.common}ReferenceSequenceType"/>
* <element name="SEQUENCE_VARIATION">
* <complexType>
* <complexContent>
* <extension base="{SRA.common}ReferenceSequenceType">
* <sequence>
* <element name="EXPERIMENT_TYPE" maxOccurs="unbounded" minOccurs="0">
* <simpleType>
* <restriction base="{http://www.w3.org/2001/XMLSchema}string">
* <enumeration value="Whole genome sequencing"/>
* <enumeration value="Exome sequencing"/>
* <enumeration value="Genotyping by array"/>
* <enumeration value="Curation"/>
* </restriction>
* </simpleType>
* </element>
* <element name="PROGRAM" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
* <element name="PLATFORM" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
* <element name="IMPUTATION" type="{http://www.w3.org/2001/XMLSchema}boolean" minOccurs="0"/>
* </sequence>
* </extension>
* </complexContent>
* </complexType>
* </element>
* <element name="SEQUENCE_ASSEMBLY">
* <complexType>
* <complexContent>
* <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
* <sequence>
* <element name="NAME" type="{http://www.w3.org/2001/XMLSchema}string"/>
* <element name="PARTIAL" type="{http://www.w3.org/2001/XMLSchema}boolean"/>
* <element name="COVERAGE" type="{http://www.w3.org/2001/XMLSchema}string"/>
* <element name="PROGRAM" type="{http://www.w3.org/2001/XMLSchema}string"/>
* <element name="PLATFORM" type="{http://www.w3.org/2001/XMLSchema}string"/>
* <element name="MIN_GAP_LENGTH" type="{http://www.w3.org/2001/XMLSchema}integer" minOccurs="0"/>
* </sequence>
* </restriction>
* </complexContent>
* </complexType>
* </element>
* <element name="SEQUENCE_ANNOTATION">
* <complexType>
* <complexContent>
* <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
* </restriction>
* </complexContent>
* </complexType>
* </element>
* <element name="REFERENCE_SEQUENCE" type="{http://www.w3.org/2001/XMLSchema}anyType"/>
* <element name="SAMPLE_PHENOTYPE">
* <complexType>
* <complexContent>
* <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
* </restriction>
* </complexContent>
* </complexType>
* </element>
* </choice>
* </restriction>
* </complexContent>
* </complexType>
*
*
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
@XmlType(name = "", propOrder = {
"samplePhenotype",
"referenceSequence",
"sequenceAnnotation",
"sequenceAssembly",
"sequenceVariation",
"referenceAlignment"
})
public static class AnalysisType {
@XmlElement(name = "SAMPLE_PHENOTYPE")
protected Analysis.AnalysisType.SamplePhenotype samplePhenotype;
@XmlElement(name = "REFERENCE_SEQUENCE")
protected Object referenceSequence;
@XmlElement(name = "SEQUENCE_ANNOTATION")
protected Analysis.AnalysisType.SequenceAnnotation sequenceAnnotation;
@XmlElement(name = "SEQUENCE_ASSEMBLY")
protected Analysis.AnalysisType.SequenceAssembly sequenceAssembly;
@XmlElement(name = "SEQUENCE_VARIATION")
protected Analysis.AnalysisType.SequenceVariation sequenceVariation;
@XmlElement(name = "REFERENCE_ALIGNMENT")
protected ReferenceSequenceType referenceAlignment;
/**
* Gets the value of the samplePhenotype property.
*
* @return
* possible object is
* {@link Analysis.AnalysisType.SamplePhenotype }
*
*/
public Analysis.AnalysisType.SamplePhenotype getSamplePhenotype() {
return samplePhenotype;
}
/**
* Sets the value of the samplePhenotype property.
*
* @param value
* allowed object is
* {@link Analysis.AnalysisType.SamplePhenotype }
*
*/
public void setSamplePhenotype(Analysis.AnalysisType.SamplePhenotype value) {
this.samplePhenotype = value;
}
/**
* Gets the value of the referenceSequence property.
*
* @return
* possible object is
* {@link Object }
*
*/
public Object getReferenceSequence() {
return referenceSequence;
}
/**
* Sets the value of the referenceSequence property.
*
* @param value
* allowed object is
* {@link Object }
*
*/
public void setReferenceSequence(Object value) {
this.referenceSequence = value;
}
/**
* Gets the value of the sequenceAnnotation property.
*
* @return
* possible object is
* {@link Analysis.AnalysisType.SequenceAnnotation }
*
*/
public Analysis.AnalysisType.SequenceAnnotation getSequenceAnnotation() {
return sequenceAnnotation;
}
/**
* Sets the value of the sequenceAnnotation property.
*
* @param value
* allowed object is
* {@link Analysis.AnalysisType.SequenceAnnotation }
*
*/
public void setSequenceAnnotation(Analysis.AnalysisType.SequenceAnnotation value) {
this.sequenceAnnotation = value;
}
/**
* Gets the value of the sequenceAssembly property.
*
* @return
* possible object is
* {@link Analysis.AnalysisType.SequenceAssembly }
*
*/
public Analysis.AnalysisType.SequenceAssembly getSequenceAssembly() {
return sequenceAssembly;
}
/**
* Sets the value of the sequenceAssembly property.
*
* @param value
* allowed object is
* {@link Analysis.AnalysisType.SequenceAssembly }
*
*/
public void setSequenceAssembly(Analysis.AnalysisType.SequenceAssembly value) {
this.sequenceAssembly = value;
}
/**
* Gets the value of the sequenceVariation property.
*
* @return
* possible object is
* {@link Analysis.AnalysisType.SequenceVariation }
*
*/
public Analysis.AnalysisType.SequenceVariation getSequenceVariation() {
return sequenceVariation;
}
/**
* Sets the value of the sequenceVariation property.
*
* @param value
* allowed object is
* {@link Analysis.AnalysisType.SequenceVariation }
*
*/
public void setSequenceVariation(Analysis.AnalysisType.SequenceVariation value) {
this.sequenceVariation = value;
}
/**
* Gets the value of the referenceAlignment property.
*
* @return
* possible object is
* {@link ReferenceSequenceType }
*
*/
public ReferenceSequenceType getReferenceAlignment() {
return referenceAlignment;
}
/**
* Sets the value of the referenceAlignment property.
*
* @param value
* allowed object is
* {@link ReferenceSequenceType }
*
*/
public void setReferenceAlignment(ReferenceSequenceType value) {
this.referenceAlignment = 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">
* </restriction>
* </complexContent>
* </complexType>
*
*
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
@XmlType(name = "")
public static class SamplePhenotype {
}
/**
* 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">
* </restriction>
* </complexContent>
* </complexType>
*
*
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
@XmlType(name = "")
public static class SequenceAnnotation {
}
/**
* 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="NAME" type="{http://www.w3.org/2001/XMLSchema}string"/>
* <element name="PARTIAL" type="{http://www.w3.org/2001/XMLSchema}boolean"/>
* <element name="COVERAGE" type="{http://www.w3.org/2001/XMLSchema}string"/>
* <element name="PROGRAM" type="{http://www.w3.org/2001/XMLSchema}string"/>
* <element name="PLATFORM" type="{http://www.w3.org/2001/XMLSchema}string"/>
* <element name="MIN_GAP_LENGTH" type="{http://www.w3.org/2001/XMLSchema}integer" minOccurs="0"/>
* </sequence>
* </restriction>
* </complexContent>
* </complexType>
*
*
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
@XmlType(name = "", propOrder = {
"name",
"partial",
"coverage",
"program",
"platform",
"minGapLength"
})
public static class SequenceAssembly {
@XmlElement(name = "NAME", required = true)
protected String name;
@XmlElement(name = "PARTIAL")
protected boolean partial;
@XmlElement(name = "COVERAGE", required = true)
protected String coverage;
@XmlElement(name = "PROGRAM", required = true)
protected String program;
@XmlElement(name = "PLATFORM", required = true)
protected String platform;
@XmlElement(name = "MIN_GAP_LENGTH")
protected BigInteger minGapLength;
/**
* 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 partial property.
*
*/
public boolean isPartial() {
return partial;
}
/**
* Sets the value of the partial property.
*
*/
public void setPartial(boolean value) {
this.partial = value;
}
/**
* Gets the value of the coverage property.
*
* @return
* possible object is
* {@link String }
*
*/
public String getCoverage() {
return coverage;
}
/**
* Sets the value of the coverage property.
*
* @param value
* allowed object is
* {@link String }
*
*/
public void setCoverage(String value) {
this.coverage = value;
}
/**
* Gets the value of the program property.
*
* @return
* possible object is
* {@link String }
*
*/
public String getProgram() {
return program;
}
/**
* Sets the value of the program property.
*
* @param value
* allowed object is
* {@link String }
*
*/
public void setProgram(String value) {
this.program = value;
}
/**
* Gets the value of the platform property.
*
* @return
* possible object is
* {@link String }
*
*/
public String getPlatform() {
return platform;
}
/**
* Sets the value of the platform property.
*
* @param value
* allowed object is
* {@link String }
*
*/
public void setPlatform(String value) {
this.platform = value;
}
/**
* Gets the value of the minGapLength property.
*
* @return
* possible object is
* {@link BigInteger }
*
*/
public BigInteger getMinGapLength() {
return minGapLength;
}
/**
* Sets the value of the minGapLength property.
*
* @param value
* allowed object is
* {@link BigInteger }
*
*/
public void setMinGapLength(BigInteger value) {
this.minGapLength = value;
}
}
/**
* Java class for anonymous complex type.
*
*
The following schema fragment specifies the expected content contained within this class.
*
*
* <complexType>
* <complexContent>
* <extension base="{SRA.common}ReferenceSequenceType">
* <sequence>
* <element name="EXPERIMENT_TYPE" maxOccurs="unbounded" minOccurs="0">
* <simpleType>
* <restriction base="{http://www.w3.org/2001/XMLSchema}string">
* <enumeration value="Whole genome sequencing"/>
* <enumeration value="Exome sequencing"/>
* <enumeration value="Genotyping by array"/>
* <enumeration value="Curation"/>
* </restriction>
* </simpleType>
* </element>
* <element name="PROGRAM" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
* <element name="PLATFORM" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
* <element name="IMPUTATION" type="{http://www.w3.org/2001/XMLSchema}boolean" minOccurs="0"/>
* </sequence>
* </extension>
* </complexContent>
* </complexType>
*
*
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
@XmlType(name = "", propOrder = {
"experimentTypes",
"program",
"platform",
"imputation"
})
public static class SequenceVariation
extends ReferenceSequenceType
{
@XmlElement(name = "EXPERIMENT_TYPE")
protected List experimentTypes;
@XmlElement(name = "PROGRAM")
protected String program;
@XmlElement(name = "PLATFORM")
protected String platform;
@XmlElement(name = "IMPUTATION")
protected Boolean imputation;
/**
* Gets the value of the experimentTypes 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 experimentTypes property.
*
*
* For example, to add a new item, do as follows:
*
* getExperimentTypes().add(newItem);
*
*
*
*
* Objects of the following type(s) are allowed in the list
* {@link String }
*
*
*/
public List getExperimentTypes() {
if (experimentTypes == null) {
experimentTypes = new ArrayList();
}
return this.experimentTypes;
}
/**
* Gets the value of the program property.
*
* @return
* possible object is
* {@link String }
*
*/
public String getProgram() {
return program;
}
/**
* Sets the value of the program property.
*
* @param value
* allowed object is
* {@link String }
*
*/
public void setProgram(String value) {
this.program = value;
}
/**
* Gets the value of the platform property.
*
* @return
* possible object is
* {@link String }
*
*/
public String getPlatform() {
return platform;
}
/**
* Sets the value of the platform property.
*
* @param value
* allowed object is
* {@link String }
*
*/
public void setPlatform(String value) {
this.platform = value;
}
/**
* Gets the value of the imputation property.
*
* @return
* possible object is
* {@link Boolean }
*
*/
public Boolean isImputation() {
return imputation;
}
/**
* Sets the value of the imputation property.
*
* @param value
* allowed object is
* {@link Boolean }
*
*/
public void setImputation(Boolean value) {
this.imputation = 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="FILE" type="{}AnalysisFileType" maxOccurs="unbounded"/>
* </sequence>
* </restriction>
* </complexContent>
* </complexType>
*
*
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
@XmlType(name = "", propOrder = {
"files"
})
public static class Files {
@XmlElement(name = "FILE", required = true)
protected List files;
/**
* Gets the value of the files 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 files property.
*
*
* For example, to add a new item, do as follows:
*
* getFiles().add(newItem);
*
*
*
*
* Objects of the following type(s) are allowed in the list
* {@link AnalysisFileType }
*
*
*/
public List getFiles() {
if (files == null) {
files = new ArrayList();
}
return this.files;
}
}
/**
* 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="IDENTIFIERS" type="{SRA.common}IdentifierType" minOccurs="0"/>
* </sequence>
* <attGroup ref="{SRA.common}RefNameGroup"/>
* <attribute name="label" type="{http://www.w3.org/2001/XMLSchema}string" />
* </restriction>
* </complexContent>
* </complexType>
*
*
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
@XmlType(name = "", propOrder = {
"identifiers"
})
public static class RunRef {
@XmlElement(name = "IDENTIFIERS")
protected IdentifierType identifiers;
@XmlAttribute(name = "label")
protected String label;
@XmlAttribute(name = "refname")
protected String refname;
@XmlAttribute(name = "refcenter")
protected String refcenter;
@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 label property.
*
* @return
* possible object is
* {@link String }
*
*/
public String getLabel() {
return label;
}
/**
* Sets the value of the label property.
*
* @param value
* allowed object is
* {@link String }
*
*/
public void setLabel(String value) {
this.label = value;
}
/**
* Gets the value of the refname property.
*
* @return
* possible object is
* {@link String }
*
*/
public String getRefname() {
return refname;
}
/**
* Sets the value of the refname property.
*
* @param value
* allowed object is
* {@link String }
*
*/
public void setRefname(String value) {
this.refname = value;
}
/**
* Gets the value of the refcenter property.
*
* @return
* possible object is
* {@link String }
*
*/
public String getRefcenter() {
return refcenter;
}
/**
* Sets the value of the refcenter property.
*
* @param value
* allowed object is
* {@link String }
*
*/
public void setRefcenter(String value) {
this.refcenter = 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">
* <sequence>
* <element name="IDENTIFIERS" type="{SRA.common}IdentifierType" minOccurs="0"/>
* </sequence>
* <attGroup ref="{SRA.common}RefNameGroup"/>
* <attribute name="label" type="{http://www.w3.org/2001/XMLSchema}string" />
* </restriction>
* </complexContent>
* </complexType>
*
*
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
@XmlType(name = "", propOrder = {
"identifiers"
})
public static class SampleRef {
@XmlElement(name = "IDENTIFIERS")
protected IdentifierType identifiers;
@XmlAttribute(name = "label")
protected String label;
@XmlAttribute(name = "refname")
protected String refname;
@XmlAttribute(name = "refcenter")
protected String refcenter;
@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 label property.
*
* @return
* possible object is
* {@link String }
*
*/
public String getLabel() {
return label;
}
/**
* Sets the value of the label property.
*
* @param value
* allowed object is
* {@link String }
*
*/
public void setLabel(String value) {
this.label = value;
}
/**
* Gets the value of the refname property.
*
* @return
* possible object is
* {@link String }
*
*/
public String getRefname() {
return refname;
}
/**
* Sets the value of the refname property.
*
* @param value
* allowed object is
* {@link String }
*
*/
public void setRefname(String value) {
this.refname = value;
}
/**
* Gets the value of the refcenter property.
*
* @return
* possible object is
* {@link String }
*
*/
public String getRefcenter() {
return refcenter;
}
/**
* Sets the value of the refcenter property.
*
* @param value
* allowed object is
* {@link String }
*
*/
public void setRefcenter(String value) {
this.refcenter = 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">
* <sequence>
* <element name="IDENTIFIERS" type="{SRA.common}IdentifierType" minOccurs="0"/>
* </sequence>
* <attGroup ref="{SRA.common}RefNameGroup"/>
* </restriction>
* </complexContent>
* </complexType>
*
*
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
@XmlType(name = "", propOrder = {
"identifiers"
})
public static class StudyRef {
@XmlElement(name = "IDENTIFIERS")
protected IdentifierType identifiers;
@XmlAttribute(name = "refname")
protected String refname;
@XmlAttribute(name = "refcenter")
protected String refcenter;
@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 refname property.
*
* @return
* possible object is
* {@link String }
*
*/
public String getRefname() {
return refname;
}
/**
* Sets the value of the refname property.
*
* @param value
* allowed object is
* {@link String }
*
*/
public void setRefname(String value) {
this.refname = value;
}
/**
* Gets the value of the refcenter property.
*
* @return
* possible object is
* {@link String }
*
*/
public String getRefcenter() {
return refcenter;
}
/**
* Sets the value of the refcenter property.
*
* @param value
* allowed object is
* {@link String }
*
*/
public void setRefcenter(String value) {
this.refcenter = 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;
}
}
}