MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit (MzJava 1.1.1-SNAPSHOT API)

java.lang.Object
- org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit

Enclosing class:: MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult

public static class MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit
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="alternative_protein" maxOccurs="unbounded" minOccurs="0">
           <complexType>
             <complexContent>
               <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
                 <attribute name="protein" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
                 <attribute name="protein_descr" type="{http://www.w3.org/2001/XMLSchema}string" />
                 <attribute name="num_tol_term" type="{http://www.w3.org/2001/XMLSchema}nonNegativeInteger" />
                 <attribute name="protein_mw" type="{http://www.w3.org/2001/XMLSchema}double" />
                 <attribute name="peptide_prev_aa" type="{http://www.w3.org/2001/XMLSchema}string" />
                 <attribute name="peptide_next_aa" type="{http://www.w3.org/2001/XMLSchema}string" />
               </restriction>
             </complexContent>
           </complexType>
         </element>
         <element name="modification_info" minOccurs="0">
           <complexType>
             <complexContent>
               <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
                 <sequence>
                   <element name="mod_aminoacid_mass" maxOccurs="unbounded" minOccurs="0">
                     <complexType>
                       <complexContent>
                         <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
                           <attribute name="position" use="required" type="{http://www.w3.org/2001/XMLSchema}nonNegativeInteger" />
                           <attribute name="mass" use="required" type="{http://www.w3.org/2001/XMLSchema}double" />
                         </restriction>
                       </complexContent>
                     </complexType>
                   </element>
                 </sequence>
                 <attribute name="mod_nterm_mass" type="{http://www.w3.org/2001/XMLSchema}double" />
                 <attribute name="mod_cterm_mass" type="{http://www.w3.org/2001/XMLSchema}double" />
                 <attribute name="modified_peptide" type="{http://www.w3.org/2001/XMLSchema}string" />
               </restriction>
             </complexContent>
           </complexType>
         </element>
         <element name="search_score" type="{http://regis-web.systemsbiology.net/pepXML}nameValueType" maxOccurs="unbounded" minOccurs="0"/>
         <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://regis-web.systemsbiology.net/pepXML}positiveInt" default="1" />
               </restriction>
             </complexContent>
           </complexType>
         </element>
         <element name="parameter" type="{http://regis-web.systemsbiology.net/pepXML}nameValueType" maxOccurs="unbounded" minOccurs="0"/>
       </sequence>
       <attribute name="hit_rank" use="required" type="{http://regis-web.systemsbiology.net/pepXML}positiveInt" />
       <attribute name="peptide" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
       <attribute name="peptide_prev_aa" type="{http://www.w3.org/2001/XMLSchema}string" />
       <attribute name="peptide_next_aa" type="{http://www.w3.org/2001/XMLSchema}string" />
       <attribute name="protein" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
       <attribute name="num_tot_proteins" use="required" type="{http://www.w3.org/2001/XMLSchema}unsignedInt" />
       <attribute name="num_matched_ions" type="{http://www.w3.org/2001/XMLSchema}nonNegativeInteger" />
       <attribute name="tot_num_ions" type="{http://www.w3.org/2001/XMLSchema}nonNegativeInteger" />
       <attribute name="calc_neutral_pep_mass" use="required" type="{http://www.w3.org/2001/XMLSchema}float" />
       <attribute name="massdiff" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
       <attribute name="num_tol_term" type="{http://www.w3.org/2001/XMLSchema}nonNegativeInteger" />
       <attribute name="num_missed_cleavages" type="{http://www.w3.org/2001/XMLSchema}integer" />
       <attribute name="is_rejected" default="0">
         <simpleType>
           <restriction base="{http://www.w3.org/2001/XMLSchema}nonNegativeInteger">
             <enumeration value="0"/>
             <enumeration value="1"/>
           </restriction>
         </simpleType>
       </attribute>
       <attribute name="protein_descr" type="{http://www.w3.org/2001/XMLSchema}string" />
       <attribute name="calc_pI" type="{http://www.w3.org/2001/XMLSchema}string" />
       <attribute name="protein_mw" type="{http://www.w3.org/2001/XMLSchema}double" />
     </restriction>
   </complexContent>
 </complexType>

Nested Class Summary

Nested Classes
Modifier and Type	Class and Description
`static class`	`MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit.AlternativeProtein` Java class for anonymous complex type.
`static class`	`MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit.AnalysisResult` Java class for anonymous complex type.
`static class`	`MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit.ModificationInfo` Java class for anonymous complex type.

Field Summary

Fields
Modifier and Type	Field and Description
`protected List<MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit.AlternativeProtein>`	`alternativeProtein`
`protected List<MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit.AnalysisResult>`	`analysisResult`
`protected float`	`calcNeutralPepMass`
`protected String`	`calcPI`
`protected long`	`hitRank`
`protected BigInteger`	`isRejected`
`protected String`	`massdiff`
`protected MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit.ModificationInfo`	`modificationInfo`
`protected BigInteger`	`numMatchedIons`
`protected BigInteger`	`numMissedCleavages`
`protected BigInteger`	`numTolTerm`
`protected long`	`numTotProteins`
`protected List<NameValueType>`	`parameter`
`protected String`	`peptide`
`protected String`	`peptideNextAa`
`protected String`	`peptidePrevAa`
`protected String`	`protein`
`protected String`	`proteinDescr`
`protected Double`	`proteinMw`
`protected List<NameValueType>`	`searchScore`
`protected BigInteger`	`totNumIons`

Constructor Summary

Constructors
Constructor and Description

MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit()

Constructors
Constructor and Description
`MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit()`

Method Summary

Methods
Modifier and Type	Method and Description
`List<MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit.AlternativeProtein>`	`getAlternativeProtein()` Gets the value of the alternativeProtein property.
`List<MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit.AnalysisResult>`	`getAnalysisResult()` Gets the value of the analysisResult property.
`float`	`getCalcNeutralPepMass()` Gets the value of the calcNeutralPepMass property.
`String`	`getCalcPI()` Gets the value of the calcPI property.
`long`	`getHitRank()` Gets the value of the hitRank property.
`BigInteger`	`getIsRejected()` Gets the value of the isRejected property.
`String`	`getMassdiff()` Gets the value of the massdiff property.
`MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit.ModificationInfo`	`getModificationInfo()` Gets the value of the modificationInfo property.
`BigInteger`	`getNumMatchedIons()` Gets the value of the numMatchedIons property.
`BigInteger`	`getNumMissedCleavages()` Gets the value of the numMissedCleavages property.
`BigInteger`	`getNumTolTerm()` Gets the value of the numTolTerm property.
`long`	`getNumTotProteins()` Gets the value of the numTotProteins property.
`List<NameValueType>`	`getParameter()` Gets the value of the parameter property.
`String`	`getPeptide()` Gets the value of the peptide property.
`String`	`getPeptideNextAa()` Gets the value of the peptideNextAa property.
`String`	`getPeptidePrevAa()` Gets the value of the peptidePrevAa property.
`String`	`getProtein()` Gets the value of the protein property.
`String`	`getProteinDescr()` Gets the value of the proteinDescr property.
`Double`	`getProteinMw()` Gets the value of the proteinMw property.
`List<NameValueType>`	`getSearchScore()` Gets the value of the searchScore property.
`BigInteger`	`getTotNumIons()` Gets the value of the totNumIons property.
`void`	`setCalcNeutralPepMass(float value)` Sets the value of the calcNeutralPepMass property.
`void`	`setCalcPI(String value)` Sets the value of the calcPI property.
`void`	`setHitRank(long value)` Sets the value of the hitRank property.
`void`	`setIsRejected(BigInteger value)` Sets the value of the isRejected property.
`void`	`setMassdiff(String value)` Sets the value of the massdiff property.
`void`	`setModificationInfo(MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit.ModificationInfo value)` Sets the value of the modificationInfo property.
`void`	`setNumMatchedIons(BigInteger value)` Sets the value of the numMatchedIons property.
`void`	`setNumMissedCleavages(BigInteger value)` Sets the value of the numMissedCleavages property.
`void`	`setNumTolTerm(BigInteger value)` Sets the value of the numTolTerm property.
`void`	`setNumTotProteins(long value)` Sets the value of the numTotProteins property.
`void`	`setPeptide(String value)` Sets the value of the peptide property.
`void`	`setPeptideNextAa(String value)` Sets the value of the peptideNextAa property.
`void`	`setPeptidePrevAa(String value)` Sets the value of the peptidePrevAa property.
`void`	`setProtein(String value)` Sets the value of the protein property.
`void`	`setProteinDescr(String value)` Sets the value of the proteinDescr property.
`void`	`setProteinMw(Double value)` Sets the value of the proteinMw property.
`void`	`setTotNumIons(BigInteger value)` Sets the value of the totNumIons property.

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

- Field Detail
  - alternativeProtein
```
protected List<MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit.AlternativeProtein> alternativeProtein
```
  - modificationInfo
```
protected MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit.ModificationInfo modificationInfo
```
  - searchScore
```
protected List<NameValueType> searchScore
```
  - analysisResult
```
protected List<MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit.AnalysisResult> analysisResult
```
  - parameter
```
protected List<NameValueType> parameter
```
  - hitRank
```
protected long hitRank
```
  - peptide
```
protected String peptide
```
  - peptidePrevAa
```
protected String peptidePrevAa
```
  - peptideNextAa
```
protected String peptideNextAa
```
  - protein
```
protected String protein
```
  - numTotProteins
```
protected long numTotProteins
```
  - numMatchedIons
```
protected BigInteger numMatchedIons
```
  - totNumIons
```
protected BigInteger totNumIons
```
  - calcNeutralPepMass
```
protected float calcNeutralPepMass
```
  - massdiff
```
protected String massdiff
```
  - numTolTerm
```
protected BigInteger numTolTerm
```
  - numMissedCleavages
```
protected BigInteger numMissedCleavages
```
  - isRejected
```
protected BigInteger isRejected
```
  - proteinDescr
```
protected String proteinDescr
```
  - calcPI
```
protected String calcPI
```
  - proteinMw
```
protected Double proteinMw
```
- Constructor Detail
  - MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit
```
public MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit()
```
- Method Detail
  - getAlternativeProtein
```
public List<MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit.AlternativeProtein> getAlternativeProtein()
```
    Gets the value of the alternativeProtein 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 alternativeProtein property.
    For example, to add a new item, do as follows:
```
    getAlternativeProtein().add(newItem);
 
```
    Objects of the following type(s) are allowed in the list MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit.AlternativeProtein
  - getModificationInfo
```
public MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit.ModificationInfo getModificationInfo()
```
    Gets the value of the modificationInfo property.
    
    Returns:
    possible object is MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit.ModificationInfo
  - setModificationInfo
```
public void setModificationInfo(MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit.ModificationInfo value)
```
    Sets the value of the modificationInfo property.
    
    Parameters:
    value - allowed object is MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit.ModificationInfo
  - getSearchScore
```
public List<NameValueType> getSearchScore()
```
    Gets the value of the searchScore 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 searchScore property.
    For example, to add a new item, do as follows:
```
    getSearchScore().add(newItem);
 
```
    Objects of the following type(s) are allowed in the list NameValueType
  - getAnalysisResult
```
public List<MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit.AnalysisResult> getAnalysisResult()
```
    Gets the value of the analysisResult 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 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 MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit.AnalysisResult
  - getParameter
```
public List<NameValueType> getParameter()
```
    Gets the value of the parameter 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 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
  - getHitRank
```
public long getHitRank()
```
    Gets the value of the hitRank property.
  - setHitRank
```
public void setHitRank(long value)
```
    Sets the value of the hitRank property.
  - getPeptide
```
public String getPeptide()
```
    Gets the value of the peptide property.
    
    Returns:
    possible object is String
  - setPeptide
```
public void setPeptide(String value)
```
    Sets the value of the peptide property.
    
    Parameters:
    value - allowed object is String
  - getPeptidePrevAa
```
public String getPeptidePrevAa()
```
    Gets the value of the peptidePrevAa property.
    
    Returns:
    possible object is String
  - setPeptidePrevAa
```
public void setPeptidePrevAa(String value)
```
    Sets the value of the peptidePrevAa property.
    
    Parameters:
    value - allowed object is String
  - getPeptideNextAa
```
public String getPeptideNextAa()
```
    Gets the value of the peptideNextAa property.
    
    Returns:
    possible object is String
  - setPeptideNextAa
```
public void setPeptideNextAa(String value)
```
    Sets the value of the peptideNextAa property.
    
    Parameters:
    value - allowed object is String
  - getProtein
```
public String getProtein()
```
    Gets the value of the protein property.
    
    Returns:
    possible object is String
  - setProtein
```
public void setProtein(String value)
```
    Sets the value of the protein property.
    
    Parameters:
    value - allowed object is String
  - getNumTotProteins
```
public long getNumTotProteins()
```
    Gets the value of the numTotProteins property.
  - setNumTotProteins
```
public void setNumTotProteins(long value)
```
    Sets the value of the numTotProteins property.
  - getNumMatchedIons
```
public BigInteger getNumMatchedIons()
```
    Gets the value of the numMatchedIons property.
    
    Returns:
    possible object is BigInteger
  - setNumMatchedIons
```
public void setNumMatchedIons(BigInteger value)
```
    Sets the value of the numMatchedIons property.
    
    Parameters:
    value - allowed object is BigInteger
  - getTotNumIons
```
public BigInteger getTotNumIons()
```
    Gets the value of the totNumIons property.
    
    Returns:
    possible object is BigInteger
  - setTotNumIons
```
public void setTotNumIons(BigInteger value)
```
    Sets the value of the totNumIons property.
    
    Parameters:
    value - allowed object is BigInteger
  - getCalcNeutralPepMass
```
public float getCalcNeutralPepMass()
```
    Gets the value of the calcNeutralPepMass property.
  - setCalcNeutralPepMass
```
public void setCalcNeutralPepMass(float value)
```
    Sets the value of the calcNeutralPepMass property.
  - getMassdiff
```
public String getMassdiff()
```
    Gets the value of the massdiff property.
    
    Returns:
    possible object is String
  - setMassdiff
```
public void setMassdiff(String value)
```
    Sets the value of the massdiff property.
    
    Parameters:
    value - allowed object is String
  - getNumTolTerm
```
public BigInteger getNumTolTerm()
```
    Gets the value of the numTolTerm property.
    
    Returns:
    possible object is BigInteger
  - setNumTolTerm
```
public void setNumTolTerm(BigInteger value)
```
    Sets the value of the numTolTerm property.
    
    Parameters:
    value - allowed object is BigInteger
  - getNumMissedCleavages
```
public BigInteger getNumMissedCleavages()
```
    Gets the value of the numMissedCleavages property.
    
    Returns:
    possible object is BigInteger
  - setNumMissedCleavages
```
public void setNumMissedCleavages(BigInteger value)
```
    Sets the value of the numMissedCleavages property.
    
    Parameters:
    value - allowed object is BigInteger
  - getIsRejected
```
public BigInteger getIsRejected()
```
    Gets the value of the isRejected property.
    
    Returns:
    possible object is BigInteger
  - setIsRejected
```
public void setIsRejected(BigInteger value)
```
    Sets the value of the isRejected property.
    
    Parameters:
    value - allowed object is BigInteger
  - getProteinDescr
```
public String getProteinDescr()
```
    Gets the value of the proteinDescr property.
    
    Returns:
    possible object is String
  - setProteinDescr
```
public void setProteinDescr(String value)
```
    Sets the value of the proteinDescr property.
    
    Parameters:
    value - allowed object is String
  - getCalcPI
```
public String getCalcPI()
```
    Gets the value of the calcPI property.
    
    Returns:
    possible object is String
  - setCalcPI
```
public void setCalcPI(String value)
```
    Sets the value of the calcPI property.
    
    Parameters:
    value - allowed object is String
  - getProteinMw
```
public Double getProteinMw()
```
    Gets the value of the proteinMw property.
    
    Returns:
    possible object is Double
  - setProteinMw
```
public void setProteinMw(Double value)
```
    Sets the value of the proteinMw property.
    
    Parameters:
    value - allowed object is Double

Class MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit

Nested Class Summary

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

alternativeProtein

modificationInfo

searchScore

analysisResult

parameter

hitRank

peptide

peptidePrevAa

peptideNextAa

protein

numTotProteins

numMatchedIons

totNumIons

calcNeutralPepMass

massdiff

numTolTerm

numMissedCleavages

isRejected

proteinDescr

calcPI

proteinMw

Constructor Detail

MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit

Method Detail

getAlternativeProtein

getModificationInfo

setModificationInfo

getSearchScore

getAnalysisResult

getParameter

getHitRank

setHitRank

getPeptide

setPeptide

getPeptidePrevAa

setPeptidePrevAa

getPeptideNextAa

setPeptideNextAa

getProtein

setProtein

getNumTotProteins

setNumTotProteins

getNumMatchedIons

setNumMatchedIons

getTotNumIons

setTotNumIons

getCalcNeutralPepMass

setCalcNeutralPepMass

getMassdiff

setMassdiff

getNumTolTerm

setNumTolTerm

getNumMissedCleavages

setNumMissedCleavages

getIsRejected

setIsRejected

getProteinDescr

setProteinDescr

getCalcPI

setCalcPI

getProteinMw

setProteinMw