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

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.PeptideEvidence
All Implemented Interfaces:
Serializable, CvParamListCapable, ParamGroupCapable

public class PeptideEvidence
extends Identifiable
implements Serializable, ParamGroupCapable

PeptideEvidence links a specific Peptide element to a specific position in a DBSequence. There must only be one PeptideEvidence item per Peptide-to-DBSequence-position.

Java class for PeptideEvidenceType complex type.

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

 <complexType name="PeptideEvidenceType">
   <complexContent>
     <extension base="{http://psidev.info/psi/pi/mzIdentML/1.1}IdentifiableType">
       <sequence>
         <group ref="{http://psidev.info/psi/pi/mzIdentML/1.1}ParamGroup" maxOccurs="unbounded" minOccurs="0"/>
       </sequence>
       <attribute name="dBSequence_ref" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
       <attribute name="peptide_ref" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
       <attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" />
       <attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" />
       <attribute name="pre">
         <simpleType>
           <restriction base="{http://www.w3.org/2001/XMLSchema}string">
             <pattern value="[ABCDEFGHIJKLMNOPQRSTUVWXYZ?\-]{1}"/>
           </restriction>
         </simpleType>
       </attribute>
       <attribute name="post">
         <simpleType>
           <restriction base="{http://www.w3.org/2001/XMLSchema}string">
             <pattern value="[ABCDEFGHIJKLMNOPQRSTUVWXYZ?\-]{1}"/>
           </restriction>
         </simpleType>
       </attribute>
       <attribute name="translationTable_ref" type="{http://www.w3.org/2001/XMLSchema}string" />
       <attribute name="frame" type="{http://psidev.info/psi/pi/mzIdentML/1.1}allowed_frames" />
       <attribute name="isDecoy" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
     </extension>
   </complexContent>
 </complexType>
 

See Also:
Serialized Form

Field Summary
protected  DBSequence dbSequence
           
protected  String dbSequenceRef
           
protected  Integer end
           
protected  Integer frame
           
protected  Boolean isDecoy
           
protected  List<AbstractParam> paramGroup
           
protected  Peptide peptide
           
protected  String peptideRef
           
protected  String post
           
protected  String pre
           
protected  Integer start
           
protected  TranslationTable translationTable
           
protected  String translationTableRef
           
 
Fields inherited from class uk.ac.ebi.jmzidml.model.mzidml.Identifiable
id, name
 
Constructor Summary
PeptideEvidence()
           
 
Method Summary
 List<CvParam> getCvParam()
           
 DBSequence getDBSequence()
           
 String getDBSequenceRef()
          Gets the value of the dbSequenceRef property.
 Integer getEnd()
          Gets the value of the end property.
 Integer getFrame()
          Gets the value of the frame property.
 List<AbstractParam> getParamGroup()
          Additional parameters or descriptors for the PeptideEvidence.Gets the value of the paramGroup property.
 Peptide getPeptide()
           
 String getPeptideRef()
          Gets the value of the peptideRef property.
 String getPost()
          Gets the value of the post property.
 String getPre()
          Gets the value of the pre property.
 Integer getStart()
          Gets the value of the start property.
 TranslationTable getTranslationTable()
           
 String getTranslationTableRef()
          Gets the value of the translationTableRef property.
 List<UserParam> getUserParam()
           
 boolean isIsDecoy()
          Gets the value of the isDecoy property.
 void setDBSequence(DBSequence dbSequence)
           
 void setEnd(Integer value)
          Sets the value of the end property.
 void setFrame(Integer value)
          Sets the value of the frame property.
 void setIsDecoy(Boolean value)
          Sets the value of the isDecoy property.
 void setPeptide(Peptide peptide)
           
 void setPost(String value)
          Sets the value of the post property.
 void setPre(String value)
          Sets the value of the pre property.
 void setStart(Integer value)
          Sets the value of the start property.
 void setTranslationTable(TranslationTable translationTable)
           
 
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

paramGroup

protected List<AbstractParam> paramGroup

dbSequenceRef

protected String dbSequenceRef

peptideRef

protected String peptideRef

start

protected Integer start

end

protected Integer end

pre

protected String pre

post

protected String post

translationTableRef

protected String translationTableRef

frame

protected Integer frame

isDecoy

protected Boolean isDecoy

dbSequence

protected DBSequence dbSequence

peptide

protected Peptide peptide

translationTable

protected TranslationTable translationTable
Constructor Detail

PeptideEvidence

public PeptideEvidence()
Method Detail

getPeptide

public Peptide getPeptide()

setPeptide

public void setPeptide(Peptide peptide)

getDBSequence

public DBSequence getDBSequence()

setDBSequence

public void setDBSequence(DBSequence dbSequence)

getTranslationTable

public TranslationTable getTranslationTable()

setTranslationTable

public void setTranslationTable(TranslationTable translationTable)

getParamGroup

public List<AbstractParam> getParamGroup()
Additional parameters or descriptors for the PeptideEvidence.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


getDBSequenceRef

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

Returns:
possible object is String

getPeptideRef

public String getPeptideRef()
Gets the value of the peptideRef property.

Returns:
possible object is String

getStart

public Integer getStart()
Gets the value of the start property.

Returns:
possible object is Integer

setStart

public void setStart(Integer value)
Sets the value of the start property.

Parameters:
value - allowed object is Integer

getEnd

public Integer getEnd()
Gets the value of the end property.

Returns:
possible object is Integer

setEnd

public void setEnd(Integer value)
Sets the value of the end property.

Parameters:
value - allowed object is Integer

getPre

public String getPre()
Gets the value of the pre property.

Returns:
possible object is String

setPre

public void setPre(String value)
Sets the value of the pre property.

Parameters:
value - allowed object is String

getPost

public String getPost()
Gets the value of the post property.

Returns:
possible object is String

setPost

public void setPost(String value)
Sets the value of the post property.

Parameters:
value - allowed object is String

getTranslationTableRef

public String getTranslationTableRef()
Gets the value of the translationTableRef property.

Returns:
possible object is String

getFrame

public Integer getFrame()
Gets the value of the frame property.

Returns:
possible object is Integer

setFrame

public void setFrame(Integer value)
Sets the value of the frame property.

Parameters:
value - allowed object is Integer

isIsDecoy

public boolean isIsDecoy()
Gets the value of the isDecoy property.

Returns:
possible object is Boolean

setIsDecoy

public void setIsDecoy(Boolean value)
Sets the value of the isDecoy property.

Parameters:
value - allowed object is Boolean

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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