public class Protein 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="analysis_result" maxOccurs="unbounded" minOccurs="0">
<complexType>
<complexContent>
<restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
<sequence>
<any processContents='lax'/>
</sequence>
<attribute name="analysis" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
<attribute name="id" type="{http://www.w3.org/2001/XMLSchema}nonNegativeInteger" default="1" />
</restriction>
</complexContent>
</complexType>
</element>
<element name="parameter" type="{http://regis-web.systemsbiology.net/protXML}nameValueType" maxOccurs="unbounded" minOccurs="0"/>
<element name="annotation" type="{http://regis-web.systemsbiology.net/protXML}protein_annotation" minOccurs="0"/>
<element name="indistinguishable_protein" maxOccurs="unbounded" minOccurs="0">
<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="annotation" type="{http://regis-web.systemsbiology.net/protXML}protein_annotation" minOccurs="0"/>
</sequence>
<attribute name="protein_name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
</restriction>
</complexContent>
</complexType>
</element>
<element name="peptide" maxOccurs="unbounded">
<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>
</element>
</sequence>
<attribute name="protein_name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
<attribute name="probability" use="required" type="{http://www.w3.org/2001/XMLSchema}double" />
<attribute name="percent_coverage" type="{http://www.w3.org/2001/XMLSchema}double" />
<attribute name="n_indistinguishable_proteins" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
<attribute name="unique_stripped_peptides" type="{http://www.w3.org/2001/XMLSchema}string" />
<attribute name="group_sibling_id" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
<attribute name="total_number_peptides" type="{http://www.w3.org/2001/XMLSchema}integer" />
<attribute name="total_number_distinct_peptides" type="{http://www.w3.org/2001/XMLSchema}integer" />
<attribute name="subsuming_protein_entry" type="{http://www.w3.org/2001/XMLSchema}string" />
<attribute name="pct_spectrum_ids" type="{http://www.w3.org/2001/XMLSchema}string" />
<attribute name="confidence" type="{http://www.w3.org/2001/XMLSchema}double" />
</restriction>
</complexContent>
</complexType>
| Modifier and Type | Field and Description |
|---|---|
protected List<AnalysisResult> |
analysisResult |
protected double |
confidence |
protected String |
groupSiblingId |
protected List<IndistinguishableProtein> |
indistinguishableProtein |
protected Integer |
nIndistinguishableProteins |
protected List<NameValueType> |
parameter |
protected String |
pctSpectrumIds |
protected List<Peptide> |
peptide |
protected double |
percentCoverage |
protected double |
probability |
protected ProteinAnnotation |
proteinAnnotation |
protected String |
proteinName |
protected String |
subsumingProteinEntry |
protected Integer |
totalNumberDistinctPeptides |
protected Integer |
totalNumberPeptides |
protected String |
uniqueStrippedPeptides |
| Constructor and Description |
|---|
Protein() |
| Modifier and Type | Method and Description |
|---|---|
List<AnalysisResult> |
getAnalysisResult()
Gets the value of the analysisResult property.
|
double |
getConfidence()
Gets the value of the confidence property.
|
String |
getGroupSiblingId()
Gets the value of the groupSiblingId property.
|
List<IndistinguishableProtein> |
getIndistinguishableProtein()
Gets the value of the indistinguishableProtein property.
|
Integer |
getNIndistinguishableProteins()
Gets the value of the nIndistinguishableProteins property.
|
List<NameValueType> |
getParameter()
Gets the value of the parameter property.
|
String |
getPctSpectrumIds()
Gets the value of the pctSpectrumIds property.
|
List<Peptide> |
getPeptide()
Gets the value of the peptide property.
|
double |
getPercentCoverage()
Gets the value of the percentCoverage property.
|
double |
getProbability()
Gets the value of the probability property.
|
ProteinAnnotation |
getProteinAnnotation()
Gets the value of the proteinAnnotation property.
|
String |
getProteinName()
Gets the value of the proteinName property.
|
String |
getSubsumingProteinEntry()
Gets the value of the subsumingProteinEntry property.
|
Integer |
getTotalNumberDistinctPeptides()
Gets the value of the totalNumberDistinctPeptides property.
|
Integer |
getTotalNumberPeptides()
Gets the value of the totalNumberPeptides property.
|
String |
getUniqueStrippedPeptides()
Gets the value of the uniqueStrippedPeptides property.
|
void |
setConfidence(double value)
Sets the value of the confidence property.
|
void |
setGroupSiblingId(String value)
Sets the value of the groupSiblingId property.
|
void |
setNIndistinguishableProteins(Integer value)
Sets the value of the nIndistinguishableProteins property.
|
void |
setPctSpectrumIds(String value)
Sets the value of the pctSpectrumIds property.
|
void |
setPercentCoverage(double value)
Sets the value of the percentCoverage property.
|
void |
setProbability(double value)
Sets the value of the probability property.
|
void |
setProteinAnnotation(ProteinAnnotation value)
Sets the value of the proteinAnnotation property.
|
void |
setProteinName(String value)
Sets the value of the proteinName property.
|
void |
setSubsumingProteinEntry(String value)
Sets the value of the subsumingProteinEntry property.
|
void |
setTotalNumberDistinctPeptides(Integer value)
Sets the value of the totalNumberDistinctPeptides property.
|
void |
setTotalNumberPeptides(Integer value)
Sets the value of the totalNumberPeptides property.
|
void |
setUniqueStrippedPeptides(String value)
Sets the value of the uniqueStrippedPeptides property.
|
protected List<AnalysisResult> analysisResult
protected List<NameValueType> parameter
protected ProteinAnnotation proteinAnnotation
protected List<IndistinguishableProtein> indistinguishableProtein
protected String proteinName
protected double probability
protected double percentCoverage
protected Integer nIndistinguishableProteins
protected String uniqueStrippedPeptides
protected String groupSiblingId
protected Integer totalNumberPeptides
protected Integer totalNumberDistinctPeptides
protected String subsumingProteinEntry
protected String pctSpectrumIds
protected double confidence
public List<AnalysisResult> getAnalysisResult()
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 analysisResult property.
For example, to add a new item, do as follows:
getAnalysisResult().add(newItem);
Objects of the following type(s) are allowed in the list
AnalysisResult
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 ProteinAnnotation getProteinAnnotation()
ProteinAnnotationpublic void setProteinAnnotation(ProteinAnnotation value)
value - allowed object is
ProteinAnnotationpublic List<IndistinguishableProtein> getIndistinguishableProtein()
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 indistinguishableProtein property.
For example, to add a new item, do as follows:
getIndistinguishableProtein().add(newItem);
Objects of the following type(s) are allowed in the list
IndistinguishableProtein
public List<Peptide> getPeptide()
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 peptide property.
For example, to add a new item, do as follows:
getPeptide().add(newItem);
Objects of the following type(s) are allowed in the list
Peptide
public String getProteinName()
Stringpublic void setProteinName(String value)
value - allowed object is
Stringpublic double getProbability()
public void setProbability(double value)
public double getPercentCoverage()
public void setPercentCoverage(double value)
public Integer getNIndistinguishableProteins()
Stringpublic void setNIndistinguishableProteins(Integer value)
value - allowed object is
Stringpublic String getUniqueStrippedPeptides()
Stringpublic void setUniqueStrippedPeptides(String value)
value - allowed object is
Stringpublic String getGroupSiblingId()
Stringpublic void setGroupSiblingId(String value)
value - allowed object is
Stringpublic Integer getTotalNumberPeptides()
Stringpublic void setTotalNumberPeptides(Integer value)
value - allowed object is
Stringpublic Integer getTotalNumberDistinctPeptides()
Stringpublic void setTotalNumberDistinctPeptides(Integer value)
value - allowed object is
Stringpublic String getSubsumingProteinEntry()
Stringpublic void setSubsumingProteinEntry(String value)
value - allowed object is
Stringpublic String getPctSpectrumIds()
Stringpublic void setPctSpectrumIds(String value)
value - allowed object is
Stringpublic double getConfidence()
public void setConfidence(double value)
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