public class MsmsRunSummary 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="sample_enzyme">
<complexType>
<complexContent>
<restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
<sequence>
<element name="specificity" maxOccurs="unbounded" minOccurs="0">
<complexType>
<complexContent>
<restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
<attribute name="sense" use="required">
<simpleType>
<restriction base="{http://www.w3.org/2001/XMLSchema}string">
<enumeration value="C"/>
<enumeration value="N"/>
</restriction>
</simpleType>
</attribute>
<attribute name="min_spacing" type="{http://www.w3.org/2001/XMLSchema}nonNegativeInteger" default="1" />
<attribute name="cut" use="required">
<simpleType>
<restriction base="{http://www.w3.org/2001/XMLSchema}string">
<minLength value="1"/>
<maxLength value="20"/>
<pattern value="[A,C-I,K-N,P-T,VWY]+"/>
</restriction>
</simpleType>
</attribute>
<attribute name="no_cut">
<simpleType>
<restriction base="{http://www.w3.org/2001/XMLSchema}string">
<minLength value="0"/>
<maxLength value="20"/>
</restriction>
</simpleType>
</attribute>
</restriction>
</complexContent>
</complexType>
</element>
</sequence>
<attribute name="name" use="required">
<simpleType>
<restriction base="{http://www.w3.org/2001/XMLSchema}string">
<minLength value="1"/>
</restriction>
</simpleType>
</attribute>
<attribute name="description" type="{http://www.w3.org/2001/XMLSchema}string" />
<attribute name="fidelity" default="specific">
<simpleType>
<restriction base="{http://www.w3.org/2001/XMLSchema}string">
<enumeration value="specific"/>
<enumeration value="semispecific"/>
<enumeration value="nonspecific"/>
</restriction>
</simpleType>
</attribute>
<attribute name="independent" type="{http://www.w3.org/2001/XMLSchema}boolean" default="1" />
</restriction>
</complexContent>
</complexType>
</element>
<element name="search_summary" maxOccurs="unbounded">
<complexType>
<complexContent>
<restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
<sequence>
<element name="search_database" minOccurs="0">
<complexType>
<complexContent>
<restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
<attribute name="local_path" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
<attribute name="URL" type="{http://www.w3.org/2001/XMLSchema}string" />
<attribute name="database_name" type="{http://www.w3.org/2001/XMLSchema}string" />
<attribute name="orig_database_url" type="{http://www.w3.org/2001/XMLSchema}string" />
<attribute name="database_release_date" type="{http://www.w3.org/2001/XMLSchema}dateTime" />
<attribute name="database_release_identifier" type="{http://www.w3.org/2001/XMLSchema}string" />
<attribute name="size_in_db_entries" type="{http://www.w3.org/2001/XMLSchema}nonNegativeInteger" />
<attribute name="size_of_residues" type="{http://www.w3.org/2001/XMLSchema}nonNegativeInteger" />
<attribute name="type" use="required">
<simpleType>
<restriction base="{http://www.w3.org/2001/XMLSchema}string">
<enumeration value="AA"/>
<enumeration value="NA"/>
</restriction>
</simpleType>
</attribute>
</restriction>
</complexContent>
</complexType>
</element>
<element name="enzymatic_search_constraint" minOccurs="0">
<complexType>
<complexContent>
<restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
<attribute name="enzyme" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
<attribute name="max_num_internal_cleavages" use="required" type="{http://www.w3.org/2001/XMLSchema}nonNegativeInteger" />
<attribute name="min_number_termini" use="required" type="{http://www.w3.org/2001/XMLSchema}nonNegativeInteger" />
</restriction>
</complexContent>
</complexType>
</element>
<element name="sequence_search_constraint" maxOccurs="unbounded" minOccurs="0">
<complexType>
<complexContent>
<restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
<attribute name="sequence" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
</restriction>
</complexContent>
</complexType>
</element>
<element name="aminoacid_modification" maxOccurs="unbounded" minOccurs="0">
<complexType>
<complexContent>
<restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
<attribute name="aminoacid" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
<attribute name="massdiff" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
<attribute name="mass" use="required" type="{http://www.w3.org/2001/XMLSchema}float" />
<attribute name="variable" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
<attribute name="peptide_terminus" type="{http://www.w3.org/2001/XMLSchema}string" />
<attribute name="protein_terminus" type="{http://www.w3.org/2001/XMLSchema}string" />
<attribute name="symbol" type="{http://regis-web.systemsbiology.net/pepXML}aa_symbolType" />
<attribute name="binary" type="{http://www.w3.org/2001/XMLSchema}string" />
<attribute name="description" type="{http://www.w3.org/2001/XMLSchema}string" />
</restriction>
</complexContent>
</complexType>
</element>
<element name="terminal_modification" maxOccurs="unbounded" minOccurs="0">
<complexType>
<complexContent>
<restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
<attribute name="terminus" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
<attribute name="massdiff" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
<attribute name="mass" use="required" type="{http://www.w3.org/2001/XMLSchema}float" />
<attribute name="variable" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
<attribute name="symbol" type="{http://regis-web.systemsbiology.net/pepXML}term_symbolType" />
<attribute name="protein_terminus" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
<attribute name="description" type="{http://www.w3.org/2001/XMLSchema}string" />
</restriction>
</complexContent>
</complexType>
</element>
<element name="parameter" type="{http://regis-web.systemsbiology.net/pepXML}nameValueType" maxOccurs="unbounded" minOccurs="0"/>
</sequence>
<attribute name="base_name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
<attribute name="search_engine" use="required" type="{http://regis-web.systemsbiology.net/pepXML}engineType" />
<attribute name="search_engine_version" type="{http://www.w3.org/2001/XMLSchema}string" />
<attribute name="precursor_mass_type" use="required" type="{http://regis-web.systemsbiology.net/pepXML}massType" />
<attribute name="fragment_mass_type" use="required" type="{http://regis-web.systemsbiology.net/pepXML}massType" />
<attribute name="out_data_type" type="{http://www.w3.org/2001/XMLSchema}string" />
<attribute name="out_data" type="{http://www.w3.org/2001/XMLSchema}string" />
<attribute name="search_id" use="required" type="{http://regis-web.systemsbiology.net/pepXML}positiveInt" />
</restriction>
</complexContent>
</complexType>
</element>
<element name="analysis_timestamp" maxOccurs="unbounded" minOccurs="0">
<complexType>
<complexContent>
<restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
<sequence>
<any processContents='lax' minOccurs="0"/>
</sequence>
<attribute name="time" use="required" type="{http://www.w3.org/2001/XMLSchema}dateTime" />
<attribute name="analysis" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
<attribute name="id" use="required" type="{http://regis-web.systemsbiology.net/pepXML}positiveInt" />
</restriction>
</complexContent>
</complexType>
</element>
<element name="spectrum_query" maxOccurs="unbounded" minOccurs="0">
<complexType>
<complexContent>
<restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
<sequence>
<element name="search_result" maxOccurs="unbounded" minOccurs="0">
<complexType>
<complexContent>
<restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
<sequence>
<element name="search_hit" maxOccurs="unbounded" minOccurs="0">
<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}float" />
<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="num_matched_peptides" 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>
</element>
</sequence>
<attribute name="search_id" type="{http://regis-web.systemsbiology.net/pepXML}positiveInt" default="1" />
</restriction>
</complexContent>
</complexType>
</element>
</sequence>
<attribute name="spectrum" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
<attribute name="spectrumNativeID" type="{http://www.w3.org/2001/XMLSchema}string" />
<attribute name="start_scan" use="required" type="{http://www.w3.org/2001/XMLSchema}unsignedInt" />
<attribute name="end_scan" use="required" type="{http://www.w3.org/2001/XMLSchema}unsignedInt" />
<attribute name="retention_time_sec" type="{http://www.w3.org/2001/XMLSchema}float" />
<attribute name="collision_energy" type="{http://www.w3.org/2001/XMLSchema}float" />
<attribute name="compensation_voltage" type="{http://www.w3.org/2001/XMLSchema}float" />
<attribute name="precursor_intensity" type="{http://www.w3.org/2001/XMLSchema}float" />
<attribute name="activation_method" type="{http://regis-web.systemsbiology.net/pepXML}activationMethodType" />
<attribute name="precursor_neutral_mass" use="required" type="{http://www.w3.org/2001/XMLSchema}float" />
<attribute name="assumed_charge" use="required" type="{http://www.w3.org/2001/XMLSchema}nonNegativeInteger" />
<attribute name="search_specification" type="{http://www.w3.org/2001/XMLSchema}string" />
<attribute name="index" use="required" type="{http://regis-web.systemsbiology.net/pepXML}positiveInt" />
</restriction>
</complexContent>
</complexType>
</element>
</sequence>
<attribute name="base_name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
<attribute name="raw_data_type" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
<attribute name="raw_data" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
<attribute name="msManufacturer" type="{http://www.w3.org/2001/XMLSchema}string" />
<attribute name="msModel" type="{http://www.w3.org/2001/XMLSchema}string" />
<attribute name="msIonization" type="{http://www.w3.org/2001/XMLSchema}string" />
<attribute name="msMassAnalyzer" type="{http://www.w3.org/2001/XMLSchema}string" />
<attribute name="msDetector" type="{http://www.w3.org/2001/XMLSchema}string" />
<attribute name="search_engine" type="{http://regis-web.systemsbiology.net/pepXML}engineType" />
</restriction>
</complexContent>
</complexType>
| Modifier and Type | Field and Description |
|---|---|
protected List<AnalysisTimestamp> |
analysisTimestamp |
protected String |
baseName |
protected String |
msDetector |
protected String |
msIonization |
protected String |
msManufacturer |
protected String |
msMassAnalyzer |
protected String |
msModel |
protected String |
rawData |
protected String |
rawDataType |
protected SampleEnzyme |
sampleEnzyme |
protected EngineType |
searchEngine |
protected List<SearchSummary> |
searchSummary |
protected List<SpectrumQuery> |
spectrumQuery |
| Constructor and Description |
|---|
MsmsRunSummary() |
| Modifier and Type | Method and Description |
|---|---|
List<AnalysisTimestamp> |
getAnalysisTimestamp()
Gets the value of the analysisTimestamp property.
|
String |
getBaseName()
Gets the value of the baseName property.
|
String |
getMsDetector()
Gets the value of the msDetector property.
|
String |
getMsIonization()
Gets the value of the msIonization property.
|
String |
getMsManufacturer()
Gets the value of the msManufacturer property.
|
String |
getMsMassAnalyzer()
Gets the value of the msMassAnalyzer property.
|
String |
getMsModel()
Gets the value of the msModel property.
|
String |
getRawData()
Gets the value of the rawData property.
|
String |
getRawDataType()
Gets the value of the rawDataType property.
|
SampleEnzyme |
getSampleEnzyme()
Gets the value of the sampleEnzyme property.
|
EngineType |
getSearchEngine()
Gets the value of the searchEngine property.
|
List<SearchSummary> |
getSearchSummary()
Gets the value of the searchSummary property.
|
List<SpectrumQuery> |
getSpectrumQuery()
Gets the value of the spectrumQuery property.
|
void |
setBaseName(String value)
Sets the value of the baseName property.
|
void |
setMsDetector(String value)
Sets the value of the msDetector property.
|
void |
setMsIonization(String value)
Sets the value of the msIonization property.
|
void |
setMsManufacturer(String value)
Sets the value of the msManufacturer property.
|
void |
setMsMassAnalyzer(String value)
Sets the value of the msMassAnalyzer property.
|
void |
setMsModel(String value)
Sets the value of the msModel property.
|
void |
setRawData(String value)
Sets the value of the rawData property.
|
void |
setRawDataType(String value)
Sets the value of the rawDataType property.
|
void |
setSampleEnzyme(SampleEnzyme value)
Sets the value of the sampleEnzyme property.
|
void |
setSearchEngine(EngineType value)
Sets the value of the searchEngine property.
|
protected SampleEnzyme sampleEnzyme
protected List<SearchSummary> searchSummary
protected List<AnalysisTimestamp> analysisTimestamp
protected List<SpectrumQuery> spectrumQuery
protected String baseName
protected String rawDataType
protected String rawData
protected String msManufacturer
protected String msModel
protected String msIonization
protected String msMassAnalyzer
protected String msDetector
protected EngineType searchEngine
public SampleEnzyme getSampleEnzyme()
SampleEnzymepublic void setSampleEnzyme(SampleEnzyme value)
value - allowed object is
SampleEnzymepublic List<SearchSummary> getSearchSummary()
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 searchSummary property.
For example, to add a new item, do as follows:
getSearchSummary().add(newItem);
Objects of the following type(s) are allowed in the list
SearchSummary
public List<AnalysisTimestamp> getAnalysisTimestamp()
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 analysisTimestamp property.
For example, to add a new item, do as follows:
getAnalysisTimestamp().add(newItem);
Objects of the following type(s) are allowed in the list
AnalysisTimestamp
public List<SpectrumQuery> getSpectrumQuery()
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 spectrumQuery property.
For example, to add a new item, do as follows:
getSpectrumQuery().add(newItem);
Objects of the following type(s) are allowed in the list
SpectrumQuery
public String getBaseName()
Stringpublic void setBaseName(String value)
value - allowed object is
Stringpublic String getRawDataType()
Stringpublic void setRawDataType(String value)
value - allowed object is
Stringpublic String getRawData()
Stringpublic void setRawData(String value)
value - allowed object is
Stringpublic String getMsManufacturer()
Stringpublic void setMsManufacturer(String value)
value - allowed object is
Stringpublic String getMsModel()
Stringpublic void setMsModel(String value)
value - allowed object is
Stringpublic String getMsIonization()
Stringpublic void setMsIonization(String value)
value - allowed object is
Stringpublic String getMsMassAnalyzer()
Stringpublic void setMsMassAnalyzer(String value)
value - allowed object is
Stringpublic String getMsDetector()
Stringpublic void setMsDetector(String value)
value - allowed object is
Stringpublic EngineType getSearchEngine()
EngineTypepublic void setSearchEngine(EngineType value)
value - allowed object is
EngineTypeCopyright © 2017. All rights reserved.