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java.lang.Objectuk.ac.ebi.jmzidml.model.MzIdentMLObject
uk.ac.ebi.jmzidml.model.mzidml.Identifiable
uk.ac.ebi.jmzidml.model.mzidml.PeptideEvidence
public class PeptideEvidence
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>
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 |
---|
protected List<AbstractParam> paramGroup
protected String dbSequenceRef
protected String peptideRef
protected Integer start
protected Integer end
protected String pre
protected String post
protected String translationTableRef
protected Integer frame
protected Boolean isDecoy
protected DBSequence dbSequence
protected Peptide peptide
protected TranslationTable translationTable
Constructor Detail |
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public PeptideEvidence()
Method Detail |
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public Peptide getPeptide()
public void setPeptide(Peptide peptide)
public DBSequence getDBSequence()
public void setDBSequence(DBSequence dbSequence)
public TranslationTable getTranslationTable()
public void setTranslationTable(TranslationTable translationTable)
public List<AbstractParam> getParamGroup()
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
public String getDBSequenceRef()
String
public String getPeptideRef()
String
public Integer getStart()
Integer
public void setStart(Integer value)
value
- allowed object is
Integer
public Integer getEnd()
Integer
public void setEnd(Integer value)
value
- allowed object is
Integer
public String getPre()
String
public void setPre(String value)
value
- allowed object is
String
public String getPost()
String
public void setPost(String value)
value
- allowed object is
String
public String getTranslationTableRef()
String
public Integer getFrame()
Integer
public void setFrame(Integer value)
value
- allowed object is
Integer
public boolean isIsDecoy()
Boolean
public void setIsDecoy(Boolean value)
value
- allowed object is
Boolean
public List<CvParam> getCvParam()
getCvParam
in interface CvParamListCapable
getCvParam
in interface ParamGroupCapable
public List<UserParam> getUserParam()
getUserParam
in interface ParamGroupCapable
|
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