public class ProteinSummary 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="protein_summary_header">
<complexType>
<complexContent>
<restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
<sequence>
<element name="program_details">
<complexType>
<complexContent>
<restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
<sequence>
<any processContents='lax' minOccurs="0"/>
</sequence>
<attribute name="analysis" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
<attribute name="time" use="required" type="{http://www.w3.org/2001/XMLSchema}dateTime" />
<attribute name="version" type="{http://www.w3.org/2001/XMLSchema}string" />
</restriction>
</complexContent>
</complexType>
</element>
</sequence>
<attribute name="reference_database" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
<attribute name="win-cyg_reference_database" type="{http://www.w3.org/2001/XMLSchema}string" />
<attribute name="residue_substitution_list" type="{http://www.w3.org/2001/XMLSchema}string" />
<attribute name="organism" type="{http://www.w3.org/2001/XMLSchema}string" />
<attribute name="source_files" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
<attribute name="source_files_alt" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
<attribute name="win-cyg_source_files" type="{http://www.w3.org/2001/XMLSchema}string" />
<attribute name="source_file_xtn" type="{http://www.w3.org/2001/XMLSchema}string" />
<attribute name="min_peptide_probability" use="required" type="{http://www.w3.org/2001/XMLSchema}double" />
<attribute name="min_peptide_weight" use="required" type="{http://www.w3.org/2001/XMLSchema}double" />
<attribute name="num_predicted_correct_prots" use="required" type="{http://www.w3.org/2001/XMLSchema}double" />
<attribute name="num_input_1_spectra" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
<attribute name="num_input_2_spectra" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
<attribute name="num_input_3_spectra" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
<attribute name="num_input_4_spectra" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
<attribute name="num_input_5_spectra" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
<attribute name="initial_min_peptide_prob" use="required" type="{http://www.w3.org/2001/XMLSchema}double" />
<attribute name="total_no_spectrum_ids" type="{http://www.w3.org/2001/XMLSchema}double" />
<attribute name="sample_enzyme" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
</restriction>
</complexContent>
</complexType>
</element>
<element name="analysis_summary" maxOccurs="unbounded" minOccurs="0">
<complexType>
<complexContent>
<restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
<sequence>
<any processContents='lax' maxOccurs="unbounded" minOccurs="0"/>
</sequence>
<attribute name="analysis" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
<attribute name="time" use="required" type="{http://www.w3.org/2001/XMLSchema}dateTime" />
<attribute name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}nonNegativeInteger" />
</restriction>
</complexContent>
</complexType>
</element>
<element name="dataset_derivation">
<complexType>
<complexContent>
<restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
<sequence maxOccurs="unbounded" minOccurs="0">
<element name="data_filter">
<complexType>
<complexContent>
<restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
<attribute name="number" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
<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}string" />
</restriction>
</complexContent>
</complexType>
</element>
<element name="protein_group" maxOccurs="unbounded">
<complexType>
<complexContent>
<restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
<sequence>
<element name="protein" maxOccurs="unbounded">
<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>
</element>
</sequence>
<attribute name="group_number" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
<attribute name="pseudo_name" type="{http://www.w3.org/2001/XMLSchema}string" />
<attribute name="probability" use="required" type="{http://www.w3.org/2001/XMLSchema}double" />
</restriction>
</complexContent>
</complexType>
</element>
</sequence>
<attribute name="summary_xml" 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 List<ProteinGroup> |
proteinGroup |
protected ProteinSummaryHeader |
proteinSummaryHeader |
protected String |
summaryXml |
| Constructor and Description |
|---|
ProteinSummary() |
| 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.
|
List<ProteinGroup> |
getProteinGroup()
Gets the value of the proteinGroup property.
|
ProteinSummaryHeader |
getProteinSummaryHeader()
Gets the value of the proteinSummaryHeader property.
|
String |
getSummaryXml()
Gets the value of the summaryXml property.
|
void |
setDatasetDerivation(DatasetDerivation value)
Sets the value of the datasetDerivation property.
|
void |
setProteinSummaryHeader(ProteinSummaryHeader value)
Sets the value of the proteinSummaryHeader property.
|
void |
setSummaryXml(String value)
Sets the value of the summaryXml property.
|
protected ProteinSummaryHeader proteinSummaryHeader
protected List<AnalysisSummary> analysisSummary
protected DatasetDerivation datasetDerivation
protected List<ProteinGroup> proteinGroup
protected String summaryXml
public ProteinSummaryHeader getProteinSummaryHeader()
ProteinSummaryHeaderpublic void setProteinSummaryHeader(ProteinSummaryHeader value)
value - allowed object is
ProteinSummaryHeaderpublic 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<ProteinGroup> getProteinGroup()
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 proteinGroup property.
For example, to add a new item, do as follows:
getProteinGroup().add(newItem);
Objects of the following type(s) are allowed in the list
ProteinGroup
public String getSummaryXml()
StringCopyright © 2017. All rights reserved.