org.nmdp.ngs.sra.jaxb.run.Run 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: 2014.09.27 at 10:29:51 AM CDT
//
package org.nmdp.ngs.sra.jaxb.run;
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 run contains a group of reads generated for a particular experiment.
*
*
* Java class for RunType complex type.
*
*
The following schema fragment specifies the expected content contained within this class.
*
*
* <complexType name="RunType">
* <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" minOccurs="0"/>
* <element name="EXPERIMENT_REF">
* <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="SPOT_DESCRIPTOR" type="{SRA.common}SpotDescriptorType" minOccurs="0"/>
* <element name="PLATFORM" type="{SRA.common}PlatformType" minOccurs="0"/>
* <element name="PROCESSING" type="{SRA.common}ProcessingType" minOccurs="0"/>
* <element name="RUN_TYPE" minOccurs="0">
* <complexType>
* <complexContent>
* <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
* <choice>
* <element name="REFERENCE_ALIGNMENT" type="{SRA.common}ReferenceSequenceType"/>
* </choice>
* </restriction>
* </complexContent>
* </complexType>
* </element>
* <sequence>
* <element name="DATA_BLOCK" minOccurs="0">
* <complexType>
* <complexContent>
* <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
* <sequence>
* <element name="FILES">
* <complexType>
* <complexContent>
* <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
* <sequence>
* <element name="FILE" maxOccurs="unbounded">
* <complexType>
* <complexContent>
* <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
* <sequence>
* <element name="READ_LABEL" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded" minOccurs="0"/>
* </sequence>
* <attribute name="filename" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
* <attribute name="filetype" use="required">
* <simpleType>
* <restriction base="{http://www.w3.org/2001/XMLSchema}string">
* <enumeration value="sra"/>
* <enumeration value="srf"/>
* <enumeration value="sff"/>
* <enumeration value="fastq"/>
* <enumeration value="fasta"/>
* <enumeration value="tab"/>
* <enumeration value="454_native"/>
* <enumeration value="454_native_seq"/>
* <enumeration value="454_native_qual"/>
* <enumeration value="Helicos_native"/>
* <enumeration value="Illumina_native"/>
* <enumeration value="Illumina_native_seq"/>
* <enumeration value="Illumina_native_prb"/>
* <enumeration value="Illumina_native_int"/>
* <enumeration value="Illumina_native_qseq"/>
* <enumeration value="Illumina_native_scarf"/>
* <enumeration value="SOLiD_native"/>
* <enumeration value="SOLiD_native_csfasta"/>
* <enumeration value="SOLiD_native_qual"/>
* <enumeration value="PacBio_HDF5"/>
* <enumeration value="bam"/>
* <enumeration value="cram"/>
* <enumeration value="CompleteGenomics_native"/>
* </restriction>
* </simpleType>
* </attribute>
* <attribute name="quality_scoring_system">
* <simpleType>
* <restriction base="{http://www.w3.org/2001/XMLSchema}string">
* <enumeration value="phred"/>
* <enumeration value="log-odds"/>
* </restriction>
* </simpleType>
* </attribute>
* <attribute name="quality_encoding">
* <simpleType>
* <restriction base="{http://www.w3.org/2001/XMLSchema}string">
* <enumeration value="ascii"/>
* <enumeration value="decimal"/>
* <enumeration value="hexadecimal"/>
* </restriction>
* </simpleType>
* </attribute>
* <attribute name="ascii_offset">
* <simpleType>
* <restriction base="{http://www.w3.org/2001/XMLSchema}string">
* <enumeration value="!"/>
* <enumeration value="@"/>
* </restriction>
* </simpleType>
* </attribute>
* <attribute name="checksum_method" use="required">
* <simpleType>
* <restriction base="{http://www.w3.org/2001/XMLSchema}string">
* <enumeration value="MD5"/>
* </restriction>
* </simpleType>
* </attribute>
* <attribute name="checksum" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
* <attribute name="unencrypted_checksum" type="{http://www.w3.org/2001/XMLSchema}string" />
* </restriction>
* </complexContent>
* </complexType>
* </element>
* </sequence>
* </restriction>
* </complexContent>
* </complexType>
* </element>
* </sequence>
* <attribute name="member_name" type="{http://www.w3.org/2001/XMLSchema}string" />
* </restriction>
* </complexContent>
* </complexType>
* </element>
* </sequence>
* <element name="RUN_LINKS" minOccurs="0">
* <complexType>
* <complexContent>
* <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
* <sequence>
* <element name="RUN_LINK" type="{SRA.common}LinkType" maxOccurs="unbounded"/>
* </sequence>
* </restriction>
* </complexContent>
* </complexType>
* </element>
* <element name="RUN_ATTRIBUTES" minOccurs="0">
* <complexType>
* <complexContent>
* <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
* <sequence>
* <element name="RUN_ATTRIBUTE" type="{SRA.common}AttributeType" maxOccurs="unbounded"/>
* </sequence>
* </restriction>
* </complexContent>
* </complexType>
* </element>
* </sequence>
* <attGroup ref="{SRA.common}NameGroup"/>
* <attribute name="run_date" type="{http://www.w3.org/2001/XMLSchema}dateTime" />
* <attribute name="run_center" type="{http://www.w3.org/2001/XMLSchema}string" />
* </restriction>
* </complexContent>
* </complexType>
*
*
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
@XmlType(name = "RunType", namespace = "", propOrder = {
"identifiers",
"title",
"experimentRef",
"spotDescriptor",
"platform",
"processing",
"runType",
"dataBlock",
"runLinks",
"runAttributes"
})
@XmlRootElement(name = "RUN", namespace = "")
public class Run {
@XmlElement(name = "IDENTIFIERS")
protected IdentifierType identifiers;
@XmlElement(name = "TITLE")
protected String title;
@XmlElement(name = "EXPERIMENT_REF", required = true)
protected Run.ExperimentRef experimentRef;
@XmlElement(name = "SPOT_DESCRIPTOR")
protected SpotDescriptorType spotDescriptor;
@XmlElement(name = "PLATFORM")
protected PlatformType platform;
@XmlElement(name = "PROCESSING")
protected ProcessingType processing;
@XmlElement(name = "RUN_TYPE")
protected Run.RunType runType;
@XmlElement(name = "DATA_BLOCK")
protected Run.DataBlock dataBlock;
@XmlElement(name = "RUN_LINKS")
protected Run.RunLinks runLinks;
@XmlElement(name = "RUN_ATTRIBUTES")
protected Run.RunAttributes runAttributes;
@XmlAttribute(name = "run_date")
@XmlSchemaType(name = "dateTime")
protected XMLGregorianCalendar runDate;
@XmlAttribute(name = "run_center")
protected String runCenter;
@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 experimentRef property.
*
* @return
* possible object is
* {@link Run.ExperimentRef }
*
*/
public Run.ExperimentRef getExperimentRef() {
return experimentRef;
}
/**
* Sets the value of the experimentRef property.
*
* @param value
* allowed object is
* {@link Run.ExperimentRef }
*
*/
public void setExperimentRef(Run.ExperimentRef value) {
this.experimentRef = value;
}
/**
* Gets the value of the spotDescriptor property.
*
* @return
* possible object is
* {@link SpotDescriptorType }
*
*/
public SpotDescriptorType getSpotDescriptor() {
return spotDescriptor;
}
/**
* Sets the value of the spotDescriptor property.
*
* @param value
* allowed object is
* {@link SpotDescriptorType }
*
*/
public void setSpotDescriptor(SpotDescriptorType value) {
this.spotDescriptor = value;
}
/**
* Gets the value of the platform property.
*
* @return
* possible object is
* {@link PlatformType }
*
*/
public PlatformType getPlatform() {
return platform;
}
/**
* Sets the value of the platform property.
*
* @param value
* allowed object is
* {@link PlatformType }
*
*/
public void setPlatform(PlatformType value) {
this.platform = value;
}
/**
* Gets the value of the processing property.
*
* @return
* possible object is
* {@link ProcessingType }
*
*/
public ProcessingType getProcessing() {
return processing;
}
/**
* Sets the value of the processing property.
*
* @param value
* allowed object is
* {@link ProcessingType }
*
*/
public void setProcessing(ProcessingType value) {
this.processing = value;
}
/**
* Gets the value of the runType property.
*
* @return
* possible object is
* {@link Run.RunType }
*
*/
public Run.RunType getRunType() {
return runType;
}
/**
* Sets the value of the runType property.
*
* @param value
* allowed object is
* {@link Run.RunType }
*
*/
public void setRunType(Run.RunType value) {
this.runType = value;
}
/**
* Gets the value of the dataBlock property.
*
* @return
* possible object is
* {@link Run.DataBlock }
*
*/
public Run.DataBlock getDataBlock() {
return dataBlock;
}
/**
* Sets the value of the dataBlock property.
*
* @param value
* allowed object is
* {@link Run.DataBlock }
*
*/
public void setDataBlock(Run.DataBlock value) {
this.dataBlock = value;
}
/**
* Gets the value of the runLinks property.
*
* @return
* possible object is
* {@link Run.RunLinks }
*
*/
public Run.RunLinks getRunLinks() {
return runLinks;
}
/**
* Sets the value of the runLinks property.
*
* @param value
* allowed object is
* {@link Run.RunLinks }
*
*/
public void setRunLinks(Run.RunLinks value) {
this.runLinks = value;
}
/**
* Gets the value of the runAttributes property.
*
* @return
* possible object is
* {@link Run.RunAttributes }
*
*/
public Run.RunAttributes getRunAttributes() {
return runAttributes;
}
/**
* Sets the value of the runAttributes property.
*
* @param value
* allowed object is
* {@link Run.RunAttributes }
*
*/
public void setRunAttributes(Run.RunAttributes value) {
this.runAttributes = value;
}
/**
* Gets the value of the runDate property.
*
* @return
* possible object is
* {@link XMLGregorianCalendar }
*
*/
public XMLGregorianCalendar getRunDate() {
return runDate;
}
/**
* Sets the value of the runDate property.
*
* @param value
* allowed object is
* {@link XMLGregorianCalendar }
*
*/
public void setRunDate(XMLGregorianCalendar value) {
this.runDate = value;
}
/**
* Gets the value of the runCenter property.
*
* @return
* possible object is
* {@link String }
*
*/
public String getRunCenter() {
return runCenter;
}
/**
* Sets the value of the runCenter property.
*
* @param value
* allowed object is
* {@link String }
*
*/
public void setRunCenter(String value) {
this.runCenter = 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>
* <element name="FILES">
* <complexType>
* <complexContent>
* <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
* <sequence>
* <element name="FILE" maxOccurs="unbounded">
* <complexType>
* <complexContent>
* <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
* <sequence>
* <element name="READ_LABEL" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded" minOccurs="0"/>
* </sequence>
* <attribute name="filename" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
* <attribute name="filetype" use="required">
* <simpleType>
* <restriction base="{http://www.w3.org/2001/XMLSchema}string">
* <enumeration value="sra"/>
* <enumeration value="srf"/>
* <enumeration value="sff"/>
* <enumeration value="fastq"/>
* <enumeration value="fasta"/>
* <enumeration value="tab"/>
* <enumeration value="454_native"/>
* <enumeration value="454_native_seq"/>
* <enumeration value="454_native_qual"/>
* <enumeration value="Helicos_native"/>
* <enumeration value="Illumina_native"/>
* <enumeration value="Illumina_native_seq"/>
* <enumeration value="Illumina_native_prb"/>
* <enumeration value="Illumina_native_int"/>
* <enumeration value="Illumina_native_qseq"/>
* <enumeration value="Illumina_native_scarf"/>
* <enumeration value="SOLiD_native"/>
* <enumeration value="SOLiD_native_csfasta"/>
* <enumeration value="SOLiD_native_qual"/>
* <enumeration value="PacBio_HDF5"/>
* <enumeration value="bam"/>
* <enumeration value="cram"/>
* <enumeration value="CompleteGenomics_native"/>
* </restriction>
* </simpleType>
* </attribute>
* <attribute name="quality_scoring_system">
* <simpleType>
* <restriction base="{http://www.w3.org/2001/XMLSchema}string">
* <enumeration value="phred"/>
* <enumeration value="log-odds"/>
* </restriction>
* </simpleType>
* </attribute>
* <attribute name="quality_encoding">
* <simpleType>
* <restriction base="{http://www.w3.org/2001/XMLSchema}string">
* <enumeration value="ascii"/>
* <enumeration value="decimal"/>
* <enumeration value="hexadecimal"/>
* </restriction>
* </simpleType>
* </attribute>
* <attribute name="ascii_offset">
* <simpleType>
* <restriction base="{http://www.w3.org/2001/XMLSchema}string">
* <enumeration value="!"/>
* <enumeration value="@"/>
* </restriction>
* </simpleType>
* </attribute>
* <attribute name="checksum_method" use="required">
* <simpleType>
* <restriction base="{http://www.w3.org/2001/XMLSchema}string">
* <enumeration value="MD5"/>
* </restriction>
* </simpleType>
* </attribute>
* <attribute name="checksum" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
* <attribute name="unencrypted_checksum" type="{http://www.w3.org/2001/XMLSchema}string" />
* </restriction>
* </complexContent>
* </complexType>
* </element>
* </sequence>
* </restriction>
* </complexContent>
* </complexType>
* </element>
* </sequence>
* <attribute name="member_name" type="{http://www.w3.org/2001/XMLSchema}string" />
* </restriction>
* </complexContent>
* </complexType>
*
*
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
@XmlType(name = "", propOrder = {
"files"
})
public static class DataBlock {
@XmlElement(name = "FILES", required = true)
protected Run.DataBlock.Files files;
@XmlAttribute(name = "member_name")
protected String memberName;
/**
* Gets the value of the files property.
*
* @return
* possible object is
* {@link Run.DataBlock.Files }
*
*/
public Run.DataBlock.Files getFiles() {
return files;
}
/**
* Sets the value of the files property.
*
* @param value
* allowed object is
* {@link Run.DataBlock.Files }
*
*/
public void setFiles(Run.DataBlock.Files value) {
this.files = value;
}
/**
* Gets the value of the memberName property.
*
* @return
* possible object is
* {@link String }
*
*/
public String getMemberName() {
return memberName;
}
/**
* Sets the value of the memberName property.
*
* @param value
* allowed object is
* {@link String }
*
*/
public void setMemberName(String value) {
this.memberName = 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" maxOccurs="unbounded">
* <complexType>
* <complexContent>
* <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
* <sequence>
* <element name="READ_LABEL" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded" minOccurs="0"/>
* </sequence>
* <attribute name="filename" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
* <attribute name="filetype" use="required">
* <simpleType>
* <restriction base="{http://www.w3.org/2001/XMLSchema}string">
* <enumeration value="sra"/>
* <enumeration value="srf"/>
* <enumeration value="sff"/>
* <enumeration value="fastq"/>
* <enumeration value="fasta"/>
* <enumeration value="tab"/>
* <enumeration value="454_native"/>
* <enumeration value="454_native_seq"/>
* <enumeration value="454_native_qual"/>
* <enumeration value="Helicos_native"/>
* <enumeration value="Illumina_native"/>
* <enumeration value="Illumina_native_seq"/>
* <enumeration value="Illumina_native_prb"/>
* <enumeration value="Illumina_native_int"/>
* <enumeration value="Illumina_native_qseq"/>
* <enumeration value="Illumina_native_scarf"/>
* <enumeration value="SOLiD_native"/>
* <enumeration value="SOLiD_native_csfasta"/>
* <enumeration value="SOLiD_native_qual"/>
* <enumeration value="PacBio_HDF5"/>
* <enumeration value="bam"/>
* <enumeration value="cram"/>
* <enumeration value="CompleteGenomics_native"/>
* </restriction>
* </simpleType>
* </attribute>
* <attribute name="quality_scoring_system">
* <simpleType>
* <restriction base="{http://www.w3.org/2001/XMLSchema}string">
* <enumeration value="phred"/>
* <enumeration value="log-odds"/>
* </restriction>
* </simpleType>
* </attribute>
* <attribute name="quality_encoding">
* <simpleType>
* <restriction base="{http://www.w3.org/2001/XMLSchema}string">
* <enumeration value="ascii"/>
* <enumeration value="decimal"/>
* <enumeration value="hexadecimal"/>
* </restriction>
* </simpleType>
* </attribute>
* <attribute name="ascii_offset">
* <simpleType>
* <restriction base="{http://www.w3.org/2001/XMLSchema}string">
* <enumeration value="!"/>
* <enumeration value="@"/>
* </restriction>
* </simpleType>
* </attribute>
* <attribute name="checksum_method" use="required">
* <simpleType>
* <restriction base="{http://www.w3.org/2001/XMLSchema}string">
* <enumeration value="MD5"/>
* </restriction>
* </simpleType>
* </attribute>
* <attribute name="checksum" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
* <attribute name="unencrypted_checksum" type="{http://www.w3.org/2001/XMLSchema}string" />
* </restriction>
* </complexContent>
* </complexType>
* </element>
* </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 Run.DataBlock.Files.File }
*
*
*/
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="READ_LABEL" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded" minOccurs="0"/>
* </sequence>
* <attribute name="filename" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
* <attribute name="filetype" use="required">
* <simpleType>
* <restriction base="{http://www.w3.org/2001/XMLSchema}string">
* <enumeration value="sra"/>
* <enumeration value="srf"/>
* <enumeration value="sff"/>
* <enumeration value="fastq"/>
* <enumeration value="fasta"/>
* <enumeration value="tab"/>
* <enumeration value="454_native"/>
* <enumeration value="454_native_seq"/>
* <enumeration value="454_native_qual"/>
* <enumeration value="Helicos_native"/>
* <enumeration value="Illumina_native"/>
* <enumeration value="Illumina_native_seq"/>
* <enumeration value="Illumina_native_prb"/>
* <enumeration value="Illumina_native_int"/>
* <enumeration value="Illumina_native_qseq"/>
* <enumeration value="Illumina_native_scarf"/>
* <enumeration value="SOLiD_native"/>
* <enumeration value="SOLiD_native_csfasta"/>
* <enumeration value="SOLiD_native_qual"/>
* <enumeration value="PacBio_HDF5"/>
* <enumeration value="bam"/>
* <enumeration value="cram"/>
* <enumeration value="CompleteGenomics_native"/>
* </restriction>
* </simpleType>
* </attribute>
* <attribute name="quality_scoring_system">
* <simpleType>
* <restriction base="{http://www.w3.org/2001/XMLSchema}string">
* <enumeration value="phred"/>
* <enumeration value="log-odds"/>
* </restriction>
* </simpleType>
* </attribute>
* <attribute name="quality_encoding">
* <simpleType>
* <restriction base="{http://www.w3.org/2001/XMLSchema}string">
* <enumeration value="ascii"/>
* <enumeration value="decimal"/>
* <enumeration value="hexadecimal"/>
* </restriction>
* </simpleType>
* </attribute>
* <attribute name="ascii_offset">
* <simpleType>
* <restriction base="{http://www.w3.org/2001/XMLSchema}string">
* <enumeration value="!"/>
* <enumeration value="@"/>
* </restriction>
* </simpleType>
* </attribute>
* <attribute name="checksum_method" use="required">
* <simpleType>
* <restriction base="{http://www.w3.org/2001/XMLSchema}string">
* <enumeration value="MD5"/>
* </restriction>
* </simpleType>
* </attribute>
* <attribute name="checksum" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
* <attribute name="unencrypted_checksum" type="{http://www.w3.org/2001/XMLSchema}string" />
* </restriction>
* </complexContent>
* </complexType>
*
*
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
@XmlType(name = "", propOrder = {
"readLabels"
})
public static class File {
@XmlElement(name = "READ_LABEL")
protected List readLabels;
@XmlAttribute(name = "filename", required = true)
protected String filename;
@XmlAttribute(name = "filetype", required = true)
protected String filetype;
@XmlAttribute(name = "quality_scoring_system")
protected String qualityScoringSystem;
@XmlAttribute(name = "quality_encoding")
protected String qualityEncoding;
@XmlAttribute(name = "ascii_offset")
protected String asciiOffset;
@XmlAttribute(name = "checksum_method", required = true)
protected String checksumMethod;
@XmlAttribute(name = "checksum", required = true)
protected String checksum;
@XmlAttribute(name = "unencrypted_checksum")
protected String unencryptedChecksum;
/**
* Gets the value of the readLabels 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 readLabels property.
*
*
* For example, to add a new item, do as follows:
*
* getReadLabels().add(newItem);
*
*
*
*
* Objects of the following type(s) are allowed in the list
* {@link String }
*
*
*/
public List getReadLabels() {
if (readLabels == null) {
readLabels = new ArrayList();
}
return this.readLabels;
}
/**
* Gets the value of the filename property.
*
* @return
* possible object is
* {@link String }
*
*/
public String getFilename() {
return filename;
}
/**
* Sets the value of the filename property.
*
* @param value
* allowed object is
* {@link String }
*
*/
public void setFilename(String value) {
this.filename = value;
}
/**
* Gets the value of the filetype property.
*
* @return
* possible object is
* {@link String }
*
*/
public String getFiletype() {
return filetype;
}
/**
* Sets the value of the filetype property.
*
* @param value
* allowed object is
* {@link String }
*
*/
public void setFiletype(String value) {
this.filetype = value;
}
/**
* Gets the value of the qualityScoringSystem property.
*
* @return
* possible object is
* {@link String }
*
*/
public String getQualityScoringSystem() {
return qualityScoringSystem;
}
/**
* Sets the value of the qualityScoringSystem property.
*
* @param value
* allowed object is
* {@link String }
*
*/
public void setQualityScoringSystem(String value) {
this.qualityScoringSystem = value;
}
/**
* Gets the value of the qualityEncoding property.
*
* @return
* possible object is
* {@link String }
*
*/
public String getQualityEncoding() {
return qualityEncoding;
}
/**
* Sets the value of the qualityEncoding property.
*
* @param value
* allowed object is
* {@link String }
*
*/
public void setQualityEncoding(String value) {
this.qualityEncoding = value;
}
/**
* Gets the value of the asciiOffset property.
*
* @return
* possible object is
* {@link String }
*
*/
public String getAsciiOffset() {
return asciiOffset;
}
/**
* Sets the value of the asciiOffset property.
*
* @param value
* allowed object is
* {@link String }
*
*/
public void setAsciiOffset(String value) {
this.asciiOffset = value;
}
/**
* Gets the value of the checksumMethod property.
*
* @return
* possible object is
* {@link String }
*
*/
public String getChecksumMethod() {
return checksumMethod;
}
/**
* Sets the value of the checksumMethod property.
*
* @param value
* allowed object is
* {@link String }
*
*/
public void setChecksumMethod(String value) {
this.checksumMethod = value;
}
/**
* Gets the value of the checksum property.
*
* @return
* possible object is
* {@link String }
*
*/
public String getChecksum() {
return checksum;
}
/**
* Sets the value of the checksum property.
*
* @param value
* allowed object is
* {@link String }
*
*/
public void setChecksum(String value) {
this.checksum = value;
}
/**
* Gets the value of the unencryptedChecksum property.
*
* @return
* possible object is
* {@link String }
*
*/
public String getUnencryptedChecksum() {
return unencryptedChecksum;
}
/**
* Sets the value of the unencryptedChecksum property.
*
* @param value
* allowed object is
* {@link String }
*
*/
public void setUnencryptedChecksum(String value) {
this.unencryptedChecksum = 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 ExperimentRef {
@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;
}
}
/**
* 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="RUN_ATTRIBUTE" type="{SRA.common}AttributeType" maxOccurs="unbounded"/>
* </sequence>
* </restriction>
* </complexContent>
* </complexType>
*
*
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
@XmlType(name = "", propOrder = {
"runAttributes"
})
public static class RunAttributes {
@XmlElement(name = "RUN_ATTRIBUTE", required = true)
protected List runAttributes;
/**
* Gets the value of the runAttributes 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 runAttributes property.
*
*
* For example, to add a new item, do as follows:
*
* getRunAttributes().add(newItem);
*
*
*
*
* Objects of the following type(s) are allowed in the list
* {@link AttributeType }
*
*
*/
public List getRunAttributes() {
if (runAttributes == null) {
runAttributes = new ArrayList();
}
return this.runAttributes;
}
}
/**
* 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="RUN_LINK" type="{SRA.common}LinkType" maxOccurs="unbounded"/>
* </sequence>
* </restriction>
* </complexContent>
* </complexType>
*
*
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
@XmlType(name = "", propOrder = {
"runLinks"
})
public static class RunLinks {
@XmlElement(name = "RUN_LINK", required = true)
protected List runLinks;
/**
* Gets the value of the runLinks 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 runLinks property.
*
*
* For example, to add a new item, do as follows:
*
* getRunLinks().add(newItem);
*
*
*
*
* Objects of the following type(s) are allowed in the list
* {@link LinkType }
*
*
*/
public List getRunLinks() {
if (runLinks == null) {
runLinks = new ArrayList();
}
return this.runLinks;
}
}
/**
* 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"/>
* </choice>
* </restriction>
* </complexContent>
* </complexType>
*
*
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
@XmlType(name = "", propOrder = {
"referenceAlignment"
})
public static class RunType {
@XmlElement(name = "REFERENCE_ALIGNMENT")
protected ReferenceSequenceType referenceAlignment;
/**
* 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;
}
}
}