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

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.ProteinDetectionHypothesis
All Implemented Interfaces:
Serializable, CvParamListCapable, ParamGroupCapable

public class ProteinDetectionHypothesis
extends Identifiable
implements Serializable, ParamGroupCapable

A single result of the ProteinDetection analysis (i.e. a protein).

Java class for ProteinDetectionHypothesisType complex type.

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

 <complexType name="ProteinDetectionHypothesisType">
   <complexContent>
     <extension base="{http://psidev.info/psi/pi/mzIdentML/1.1}IdentifiableType">
       <sequence>
         <element name="PeptideHypothesis" type="{http://psidev.info/psi/pi/mzIdentML/1.1}PeptideHypothesisType" maxOccurs="unbounded"/>
         <group ref="{http://psidev.info/psi/pi/mzIdentML/1.1}ParamGroup" maxOccurs="unbounded" minOccurs="0"/>
       </sequence>
       <attribute name="dBSequence_ref" type="{http://www.w3.org/2001/XMLSchema}string" />
       <attribute name="passThreshold" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
     </extension>
   </complexContent>
 </complexType>
 

See Also:
Serialized Form

Field Summary
protected  DBSequence dbSequence
           
protected  String dbSequenceRef
           
protected  List<AbstractParam> paramGroup
           
protected  boolean passThreshold
           
protected  List<PeptideHypothesis> peptideHypothesis
           
 
Fields inherited from class uk.ac.ebi.jmzidml.model.mzidml.Identifiable
id, name
 
Constructor Summary
ProteinDetectionHypothesis()
           
 
Method Summary
 List<CvParam> getCvParam()
           
 DBSequence getDBSequence()
           
 String getDBSequenceRef()
          Gets the value of the dbSequenceRef property.
 List<AbstractParam> getParamGroup()
          Scores or parameters associated with this ProteinDetectionHypothesis e.g.
 List<PeptideHypothesis> getPeptideHypothesis()
          Gets the value of the peptideHypothesis property.
 List<UserParam> getUserParam()
           
 boolean isPassThreshold()
          Gets the value of the passThreshold property.
 void setDBSequence(DBSequence dbSequence)
           
 void setPassThreshold(boolean value)
          Sets the value of the passThreshold 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

peptideHypothesis

protected List<PeptideHypothesis> peptideHypothesis

paramGroup

protected List<AbstractParam> paramGroup

dbSequenceRef

protected String dbSequenceRef

passThreshold

protected boolean passThreshold

dbSequence

protected DBSequence dbSequence
Constructor Detail

ProteinDetectionHypothesis

public ProteinDetectionHypothesis()
Method Detail

getPeptideHypothesis

public List<PeptideHypothesis> getPeptideHypothesis()
Gets the value of the peptideHypothesis 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 peptideHypothesis property.

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

    getPeptideHypothesis().add(newItem);
 

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


getParamGroup

public List<AbstractParam> getParamGroup()
Scores or parameters associated with this ProteinDetectionHypothesis e.g. p-value 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 CvParam UserParam


getDBSequenceRef

public String getDBSequenceRef()
Gets the value of the dbSequenceRef property.

Returns:
possible object is String

isPassThreshold

public boolean isPassThreshold()
Gets the value of the passThreshold property.


setPassThreshold

public void setPassThreshold(boolean value)
Sets the value of the passThreshold property.


getDBSequence

public DBSequence getDBSequence()

setDBSequence

public void setDBSequence(DBSequence dbSequence)

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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