uk.ac.ebi.jmzidml.model.mzidml
Class DBSequence

java.lang.Object
  extended by uk.ac.ebi.jmzidml.model.MzIdentMLObject
      extended by uk.ac.ebi.jmzidml.model.mzidml.Identifiable
          extended by uk.ac.ebi.jmzidml.model.mzidml.DBSequence
All Implemented Interfaces:
Serializable, CvParamListCapable, ParamGroupCapable

public class DBSequence
extends Identifiable
implements Serializable, ParamGroupCapable

A database sequence from the specified SearchDatabase (nucleic acid or amino acid). If the sequence is nucleic acid, the source nucleic acid sequence should be given in the seq attribute rather than a translated sequence.

Java class for DBSequenceType complex type.

The following schema fragment specifies the expected content contained within this class.

 <complexType name="DBSequenceType">
   <complexContent>
     <extension base="{http://psidev.info/psi/pi/mzIdentML/1.1}IdentifiableType">
       <sequence>
         <element name="Seq" type="{http://psidev.info/psi/pi/mzIdentML/1.1}sequence" minOccurs="0"/>
         <group ref="{http://psidev.info/psi/pi/mzIdentML/1.1}ParamGroup" maxOccurs="unbounded" minOccurs="0"/>
       </sequence>
       <attribute name="length" type="{http://www.w3.org/2001/XMLSchema}int" />
       <attribute name="searchDatabase_ref" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
       <attribute name="accession" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
     </extension>
   </complexContent>
 </complexType>
 

See Also:
Serialized Form

Field Summary
protected  String accession
           
protected  Integer length
           
protected  List<AbstractParam> paramGroup
           
protected  SearchDatabase searchDatabase
           
protected  String searchDatabaseRef
           
protected  String seq
           
 
Fields inherited from class uk.ac.ebi.jmzidml.model.mzidml.Identifiable
id, name
 
Constructor Summary
DBSequence()
           
 
Method Summary
 String getAccession()
          Gets the value of the accession property.
 List<CvParam> getCvParam()
           
 Integer getLength()
          Gets the value of the length property.
 List<AbstractParam> getParamGroup()
          Additional descriptors for the sequence, such as taxon, description line etc.Gets the value of the paramGroup property.
 SearchDatabase getSearchDatabase()
           
 String getSearchDatabaseRef()
          Gets the value of the searchDatabaseRef property.
 String getSeq()
          Gets the value of the seq property.
 List<UserParam> getUserParam()
           
 void setAccession(String value)
          Sets the value of the accession property.
 void setLength(Integer value)
          Sets the value of the length property.
 void setSearchDatabase(SearchDatabase searchDatabase)
           
 void setSeq(String value)
          Sets the value of the seq property.
 
Methods inherited from class uk.ac.ebi.jmzidml.model.mzidml.Identifiable
getId, getName, setId, setName
 
Methods inherited from class uk.ac.ebi.jmzidml.model.MzIdentMLObject
getHid
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

seq

protected String seq

paramGroup

protected List<AbstractParam> paramGroup

length

protected Integer length

searchDatabaseRef

protected String searchDatabaseRef

accession

protected String accession

searchDatabase

protected SearchDatabase searchDatabase
Constructor Detail

DBSequence

public DBSequence()
Method Detail

getSeq

public String getSeq()
Gets the value of the seq property.

Returns:
possible object is String

setSeq

public void setSeq(String value)
Sets the value of the seq property.

Parameters:
value - allowed object is String

getParamGroup

public List<AbstractParam> getParamGroup()
Additional descriptors for the sequence, such as taxon, description line etc.Gets the value of the paramGroup 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 paramGroup property.

For example, to add a new item, do as follows:

    getParamGroup().add(newItem);
 

Objects of the following type(s) are allowed in the list UserParam CvParam


getLength

public Integer getLength()
Gets the value of the length property.

Returns:
possible object is Integer

setLength

public void setLength(Integer value)
Sets the value of the length property.

Parameters:
value - allowed object is Integer

getSearchDatabaseRef

public String getSearchDatabaseRef()
Gets the value of the searchDatabaseRef property.

Returns:
possible object is String

getAccession

public String getAccession()
Gets the value of the accession property.

Returns:
possible object is String

setAccession

public void setAccession(String value)
Sets the value of the accession property.

Parameters:
value - allowed object is String

getSearchDatabase

public SearchDatabase getSearchDatabase()

setSearchDatabase

public void setSearchDatabase(SearchDatabase searchDatabase)

getCvParam

public List<CvParam> getCvParam()
Specified by:
getCvParam in interface CvParamListCapable
Specified by:
getCvParam in interface ParamGroupCapable
Returns:
A List of CvParam objects.

getUserParam

public List<UserParam> getUserParam()
Specified by:
getUserParam in interface ParamGroupCapable


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