public class Peptide extends Object
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="parameter" type="{http://regis-web.systemsbiology.net/protXML}nameValueType" maxOccurs="unbounded" minOccurs="0"/>
<element name="modification_info" type="{http://regis-web.systemsbiology.net/protXML}modification_info" maxOccurs="unbounded" minOccurs="0"/>
<element name="peptide_parent_protein" maxOccurs="unbounded" minOccurs="0">
<complexType>
<complexContent>
<restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
<attribute name="protein_name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
</restriction>
</complexContent>
</complexType>
</element>
<element name="indistinguishable_peptide" maxOccurs="unbounded" minOccurs="0">
<complexType>
<complexContent>
<restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
<sequence>
<element name="modification_info" type="{http://regis-web.systemsbiology.net/protXML}modification_info" maxOccurs="unbounded" minOccurs="0"/>
</sequence>
<attribute name="peptide_sequence" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
<attribute name="charge" use="required" type="{http://www.w3.org/2001/XMLSchema}positiveInteger" />
<attribute name="calc_neutral_pep_mass" type="{http://www.w3.org/2001/XMLSchema}double" />
</restriction>
</complexContent>
</complexType>
</element>
</sequence>
<attribute name="peptide_sequence" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
<attribute name="charge" use="required" type="{http://www.w3.org/2001/XMLSchema}nonNegativeInteger" />
<attribute name="initial_probability" use="required" type="{http://www.w3.org/2001/XMLSchema}double" />
<attribute name="nsp_adjusted_probability" type="{http://www.w3.org/2001/XMLSchema}double" />
<attribute name="fpkm_adjusted_probability" type="{http://www.w3.org/2001/XMLSchema}double" />
<attribute name="ni_adjusted_probability" type="{http://www.w3.org/2001/XMLSchema}double" />
<attribute name="exp_sibling_ion_instances" type="{http://www.w3.org/2001/XMLSchema}double" />
<attribute name="exp_sibling_ion_bin" type="{http://www.w3.org/2001/XMLSchema}double" />
<attribute name="exp_tot_instances" type="{http://www.w3.org/2001/XMLSchema}double" />
<attribute name="peptide_group_designator" type="{http://www.w3.org/2001/XMLSchema}string" />
<attribute name="weight" type="{http://www.w3.org/2001/XMLSchema}double" default="1.0" />
<attribute name="is_nondegenerate_evidence" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
<attribute name="n_enzymatic_termini" use="required" type="{http://www.w3.org/2001/XMLSchema}nonNegativeInteger" />
<attribute name="n_sibling_peptides" type="{http://www.w3.org/2001/XMLSchema}double" />
<attribute name="n_sibling_peptides_bin" type="{http://www.w3.org/2001/XMLSchema}integer" default="0" />
<attribute name="max_fpkm" type="{http://www.w3.org/2001/XMLSchema}double" />
<attribute name="fpkm_bin" type="{http://www.w3.org/2001/XMLSchema}integer" default="0" />
<attribute name="n_instances" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
<attribute name="calc_neutral_pep_mass" type="{http://www.w3.org/2001/XMLSchema}double" />
<attribute name="is_contributing_evidence" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
</restriction>
</complexContent>
</complexType>
| Modifier and Type | Field and Description |
|---|---|
protected double |
calcNeutralPepMass |
protected Integer |
charge |
protected double |
expSiblingIonBin |
protected double |
expSiblingIonInstances |
protected double |
expTotInstances |
protected double |
fpkmAdjustedProbability |
protected Integer |
fpkmBin |
protected List<IndistinguishablePeptide> |
indistinguishablePeptide |
protected double |
initialProbability |
protected String |
isContributingEvidence |
protected String |
isNondegenerateEvidence |
protected double |
maxFpkm |
protected List<ModificationInfo> |
modificationInfo |
protected Integer |
nEnzymaticTermini |
protected double |
niAdjustedProbability |
protected Integer |
nInstances |
protected double |
nSiblingPeptides |
protected Integer |
nSiblingPeptidesBin |
protected double |
nspAdjustedProbability |
protected List<NameValueType> |
parameter |
protected String |
peptideGroupDesignator |
protected List<PeptideParentProtein> |
peptideParentProtein |
protected String |
peptideSequence |
protected double |
weight |
| Constructor and Description |
|---|
Peptide() |
| Modifier and Type | Method and Description |
|---|---|
double |
getCalcNeutralPepMass()
Gets the value of the calcNeutralPepMass property.
|
Integer |
getCharge()
Gets the value of the charge property.
|
double |
getExpSiblingIonBin()
Gets the value of the expSiblingIonBin property.
|
double |
getExpSiblingIonInstances()
Gets the value of the expSiblingIonInstances property.
|
double |
getExpTotInstances()
Gets the value of the expTotInstances property.
|
double |
getFpkmAdjustedProbability()
Gets the value of the fpkmAdjustedProbability property.
|
int |
getFpkmBin()
Gets the value of the fpkmBin property.
|
List<IndistinguishablePeptide> |
getIndistinguishablePeptide()
Gets the value of the indistinguishablePeptide property.
|
double |
getInitialProbability()
Gets the value of the initialProbability property.
|
String |
getIsContributingEvidence()
Gets the value of the isContributingEvidence property.
|
String |
getIsNondegenerateEvidence()
Gets the value of the isNondegenerateEvidence property.
|
double |
getMaxFpkm()
Gets the value of the maxFpkm property.
|
List<ModificationInfo> |
getModificationInfo()
Gets the value of the modificationInfo property.
|
Integer |
getNEnzymaticTermini()
Gets the value of the nEnzymaticTermini property.
|
double |
getNiAdjustedProbability()
Gets the value of the niAdjustedProbability property.
|
Integer |
getNInstances()
Gets the value of the nInstances property.
|
double |
getNSiblingPeptides()
Gets the value of the nSiblingPeptides property.
|
int |
getNSiblingPeptidesBin()
Gets the value of the nSiblingPeptidesBin property.
|
double |
getNspAdjustedProbability()
Gets the value of the nspAdjustedProbability property.
|
List<NameValueType> |
getParameter()
Gets the value of the parameter property.
|
String |
getPeptideGroupDesignator()
Gets the value of the peptideGroupDesignator property.
|
List<PeptideParentProtein> |
getPeptideParentProtein()
Gets the value of the peptideParentProtein property.
|
String |
getPeptideSequence()
Gets the value of the peptideSequence property.
|
double |
getWeight()
Gets the value of the weight property.
|
void |
setCalcNeutralPepMass(double value)
Sets the value of the calcNeutralPepMass property.
|
void |
setCharge(Integer value)
Sets the value of the charge property.
|
void |
setExpSiblingIonBin(double value)
Sets the value of the expSiblingIonBin property.
|
void |
setExpSiblingIonInstances(double value)
Sets the value of the expSiblingIonInstances property.
|
void |
setExpTotInstances(double value)
Sets the value of the expTotInstances property.
|
void |
setFpkmAdjustedProbability(double value)
Sets the value of the fpkmAdjustedProbability property.
|
void |
setFpkmBin(Integer value)
Sets the value of the fpkmBin property.
|
void |
setInitialProbability(double value)
Sets the value of the initialProbability property.
|
void |
setIsContributingEvidence(String value)
Sets the value of the isContributingEvidence property.
|
void |
setIsNondegenerateEvidence(String value)
Sets the value of the isNondegenerateEvidence property.
|
void |
setMaxFpkm(double value)
Sets the value of the maxFpkm property.
|
void |
setNEnzymaticTermini(Integer value)
Sets the value of the nEnzymaticTermini property.
|
void |
setNiAdjustedProbability(double value)
Sets the value of the niAdjustedProbability property.
|
void |
setNInstances(Integer value)
Sets the value of the nInstances property.
|
void |
setNSiblingPeptides(double value)
Sets the value of the nSiblingPeptides property.
|
void |
setNSiblingPeptidesBin(Integer value)
Sets the value of the nSiblingPeptidesBin property.
|
void |
setNspAdjustedProbability(double value)
Sets the value of the nspAdjustedProbability property.
|
void |
setPeptideGroupDesignator(String value)
Sets the value of the peptideGroupDesignator property.
|
void |
setPeptideSequence(String value)
Sets the value of the peptideSequence property.
|
void |
setWeight(double value)
Sets the value of the weight property.
|
protected List<NameValueType> parameter
protected List<ModificationInfo> modificationInfo
protected List<PeptideParentProtein> peptideParentProtein
protected List<IndistinguishablePeptide> indistinguishablePeptide
protected String peptideSequence
protected Integer charge
protected double initialProbability
protected double nspAdjustedProbability
protected double fpkmAdjustedProbability
protected double niAdjustedProbability
protected double expSiblingIonInstances
protected double expSiblingIonBin
protected double expTotInstances
protected String peptideGroupDesignator
protected double weight
protected String isNondegenerateEvidence
protected Integer nEnzymaticTermini
protected double nSiblingPeptides
protected Integer nSiblingPeptidesBin
protected double maxFpkm
protected Integer fpkmBin
protected Integer nInstances
protected double calcNeutralPepMass
protected String isContributingEvidence
public List<NameValueType> getParameter()
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 parameter property.
For example, to add a new item, do as follows:
getParameter().add(newItem);
Objects of the following type(s) are allowed in the list
NameValueType
public List<ModificationInfo> getModificationInfo()
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 modificationInfo property.
For example, to add a new item, do as follows:
getModificationInfo().add(newItem);
Objects of the following type(s) are allowed in the list
ModificationInfo
public List<PeptideParentProtein> getPeptideParentProtein()
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 peptideParentProtein property.
For example, to add a new item, do as follows:
getPeptideParentProtein().add(newItem);
Objects of the following type(s) are allowed in the list
PeptideParentProtein
public List<IndistinguishablePeptide> getIndistinguishablePeptide()
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 indistinguishablePeptide property.
For example, to add a new item, do as follows:
getIndistinguishablePeptide().add(newItem);
Objects of the following type(s) are allowed in the list
IndistinguishablePeptide
public String getPeptideSequence()
Stringpublic void setPeptideSequence(String value)
value - allowed object is
Stringpublic Integer getCharge()
Stringpublic void setCharge(Integer value)
value - allowed object is
Stringpublic double getInitialProbability()
public void setInitialProbability(double value)
public double getNspAdjustedProbability()
public void setNspAdjustedProbability(double value)
public double getFpkmAdjustedProbability()
public void setFpkmAdjustedProbability(double value)
public double getNiAdjustedProbability()
public void setNiAdjustedProbability(double value)
public double getExpSiblingIonInstances()
public void setExpSiblingIonInstances(double value)
public double getExpSiblingIonBin()
public void setExpSiblingIonBin(double value)
public double getExpTotInstances()
public void setExpTotInstances(double value)
public String getPeptideGroupDesignator()
Stringpublic void setPeptideGroupDesignator(String value)
value - allowed object is
Stringpublic double getWeight()
public void setWeight(double value)
public String getIsNondegenerateEvidence()
Stringpublic void setIsNondegenerateEvidence(String value)
value - allowed object is
Stringpublic Integer getNEnzymaticTermini()
Stringpublic void setNEnzymaticTermini(Integer value)
value - allowed object is
Stringpublic double getNSiblingPeptides()
public void setNSiblingPeptides(double value)
public int getNSiblingPeptidesBin()
Stringpublic void setNSiblingPeptidesBin(Integer value)
value - allowed object is
Stringpublic double getMaxFpkm()
public void setMaxFpkm(double value)
public int getFpkmBin()
Stringpublic void setFpkmBin(Integer value)
value - allowed object is
Stringpublic Integer getNInstances()
Stringpublic void setNInstances(Integer value)
value - allowed object is
Stringpublic double getCalcNeutralPepMass()
public void setCalcNeutralPepMass(double value)
public String getIsContributingEvidence()
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