public static class MsmsPipelineAnalysis.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="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="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}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>
</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="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" />
</restriction>
</complexContent>
</complexType>
| Modifier and Type | Class and Description |
|---|---|
static class |
MsmsPipelineAnalysis.MsmsRunSummary.AnalysisTimestamp
Java class for anonymous complex type.
|
static class |
MsmsPipelineAnalysis.MsmsRunSummary.SampleEnzyme
Java class for anonymous complex type.
|
static class |
MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary
Java class for anonymous complex type.
|
static class |
MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery
Java class for anonymous complex type.
|
| Modifier and Type | Field and Description |
|---|---|
protected List<MsmsPipelineAnalysis.MsmsRunSummary.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 MsmsPipelineAnalysis.MsmsRunSummary.SampleEnzyme |
sampleEnzyme |
protected List<MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary> |
searchSummary |
protected List<MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery> |
spectrumQuery |
| Constructor and Description |
|---|
MsmsPipelineAnalysis.MsmsRunSummary() |
| Modifier and Type | Method and Description |
|---|---|
List<MsmsPipelineAnalysis.MsmsRunSummary.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.
|
MsmsPipelineAnalysis.MsmsRunSummary.SampleEnzyme |
getSampleEnzyme()
Gets the value of the sampleEnzyme property.
|
List<MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary> |
getSearchSummary()
Gets the value of the searchSummary property.
|
List<MsmsPipelineAnalysis.MsmsRunSummary.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(MsmsPipelineAnalysis.MsmsRunSummary.SampleEnzyme value)
Sets the value of the sampleEnzyme property.
|
protected MsmsPipelineAnalysis.MsmsRunSummary.SampleEnzyme sampleEnzyme
protected List<MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary> searchSummary
protected List<MsmsPipelineAnalysis.MsmsRunSummary.AnalysisTimestamp> analysisTimestamp
protected List<MsmsPipelineAnalysis.MsmsRunSummary.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
public MsmsPipelineAnalysis.MsmsRunSummary.SampleEnzyme getSampleEnzyme()
MsmsPipelineAnalysis.MsmsRunSummary.SampleEnzymepublic void setSampleEnzyme(MsmsPipelineAnalysis.MsmsRunSummary.SampleEnzyme value)
value - allowed object is
MsmsPipelineAnalysis.MsmsRunSummary.SampleEnzymepublic List<MsmsPipelineAnalysis.MsmsRunSummary.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
MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary
public List<MsmsPipelineAnalysis.MsmsRunSummary.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
MsmsPipelineAnalysis.MsmsRunSummary.AnalysisTimestamp
public List<MsmsPipelineAnalysis.MsmsRunSummary.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
MsmsPipelineAnalysis.MsmsRunSummary.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()
StringCopyright © 2016. All Rights Reserved.