public class MsmsPipelineAnalysis 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_summary" 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/pepXML}nameValueType" maxOccurs="unbounded" 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="version" type="{http://www.w3.org/2001/XMLSchema}string" />
</restriction>
</complexContent>
</complexType>
</element>
<element name="dataset_derivation" minOccurs="0">
<complexType>
<complexContent>
<restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
<sequence>
<element name="data_filter" maxOccurs="unbounded" minOccurs="0">
<complexType>
<complexContent>
<restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
<attribute name="number" use="required" type="{http://www.w3.org/2001/XMLSchema}nonNegativeInteger" />
<attribute name="parent_file" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
<attribute name="windows_parent" type="{http://www.w3.org/2001/XMLSchema}string" />
<attribute name="description" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
</restriction>
</complexContent>
</complexType>
</element>
</sequence>
<attribute name="generation_no" use="required" type="{http://www.w3.org/2001/XMLSchema}nonNegativeInteger" />
</restriction>
</complexContent>
</complexType>
</element>
<element name="msms_run_summary" maxOccurs="unbounded">
<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>
</element>
</sequence>
<attribute name="name" type="{http://www.w3.org/2001/XMLSchema}string" />
<attribute name="date" use="required" type="{http://www.w3.org/2001/XMLSchema}dateTime" />
<attribute name="summary_xml" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
</restriction>
</complexContent>
</complexType>
| Modifier and Type | Field and Description |
|---|---|
protected List<AnalysisSummary> |
analysisSummary |
protected DatasetDerivation |
datasetDerivation |
protected XMLGregorianCalendar |
date |
protected List<MsmsRunSummary> |
msmsRunSummary |
protected String |
name |
protected String |
summaryXml |
| Constructor and Description |
|---|
MsmsPipelineAnalysis() |
| Modifier and Type | Method and Description |
|---|---|
List<AnalysisSummary> |
getAnalysisSummary()
Gets the value of the analysisSummary property.
|
DatasetDerivation |
getDatasetDerivation()
Gets the value of the datasetDerivation property.
|
XMLGregorianCalendar |
getDate()
Gets the value of the date property.
|
List<MsmsRunSummary> |
getMsmsRunSummary()
Gets the value of the msmsRunSummary property.
|
String |
getName()
Gets the value of the name property.
|
String |
getSummaryXml()
Gets the value of the summaryXml property.
|
void |
setDatasetDerivation(DatasetDerivation value)
Sets the value of the datasetDerivation property.
|
void |
setDate(XMLGregorianCalendar value)
Sets the value of the date property.
|
void |
setName(String value)
Sets the value of the name property.
|
void |
setSummaryXml(String value)
Sets the value of the summaryXml property.
|
protected List<AnalysisSummary> analysisSummary
protected DatasetDerivation datasetDerivation
protected List<MsmsRunSummary> msmsRunSummary
protected String name
protected XMLGregorianCalendar date
protected String summaryXml
public List<AnalysisSummary> getAnalysisSummary()
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 analysisSummary property.
For example, to add a new item, do as follows:
getAnalysisSummary().add(newItem);
Objects of the following type(s) are allowed in the list
AnalysisSummary
public DatasetDerivation getDatasetDerivation()
DatasetDerivationpublic void setDatasetDerivation(DatasetDerivation value)
value - allowed object is
DatasetDerivationpublic List<MsmsRunSummary> getMsmsRunSummary()
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 msmsRunSummary property.
For example, to add a new item, do as follows:
getMsmsRunSummary().add(newItem);
Objects of the following type(s) are allowed in the list
MsmsRunSummary
public String getName()
Stringpublic void setName(String value)
value - allowed object is
Stringpublic XMLGregorianCalendar getDate()
XMLGregorianCalendarpublic void setDate(XMLGregorianCalendar value)
value - allowed object is
XMLGregorianCalendarpublic String getSummaryXml()
StringCopyright © 2017. All rights reserved.