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maltcms.io.xml.bindings.openms.featurexml
Class FeatureMap

java.lang.Object
  extended by maltcms.io.xml.bindings.openms.featurexml.FeatureMap

public class FeatureMap
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="dataProcessing" maxOccurs="unbounded" minOccurs="0">
           <complexType>
             <complexContent>
               <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
                 <sequence>
                   <element name="software">
                     <complexType>
                       <complexContent>
                         <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
                           <attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
                           <attribute name="version" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
                         </restriction>
                       </complexContent>
                     </complexType>
                   </element>
                   <element name="processingAction" maxOccurs="unbounded" minOccurs="0">
                     <complexType>
                       <complexContent>
                         <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
                           <attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
                         </restriction>
                       </complexContent>
                     </complexType>
                   </element>
                   <element name="userParam" maxOccurs="unbounded" minOccurs="0">
                     <complexType>
                       <complexContent>
                         <extension base="{}userParam">
                         </extension>
                       </complexContent>
                     </complexType>
                   </element>
                 </sequence>
                 <attribute name="completion_time" use="required" type="{http://www.w3.org/2001/XMLSchema}dateTime" />
               </restriction>
             </complexContent>
           </complexType>
         </element>
         <element name="IdentificationRun" maxOccurs="unbounded" minOccurs="0">
           <complexType>
             <complexContent>
               <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
                 <sequence>
                   <element name="SearchParameters">
                     <complexType>
                       <complexContent>
                         <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
                           <sequence>
                             <element name="FixedModification" maxOccurs="unbounded" minOccurs="0">
                               <complexType>
                                 <complexContent>
                                   <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
                                     <sequence minOccurs="0">
                                       <element name="userParam" type="{}userParam" maxOccurs="unbounded" minOccurs="0"/>
                                     </sequence>
                                     <attribute name="name" use="required">
                                       <simpleType>
                                         <restriction base="{http://www.w3.org/2001/XMLSchema}string">
                                           <minLength value="1"/>
                                         </restriction>
                                       </simpleType>
                                     </attribute>
                                   </restriction>
                                 </complexContent>
                               </complexType>
                             </element>
                             <element name="VariableModification" maxOccurs="unbounded" minOccurs="0">
                               <complexType>
                                 <complexContent>
                                   <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
                                     <sequence minOccurs="0">
                                       <element name="userParam" type="{}userParam" maxOccurs="unbounded" minOccurs="0"/>
                                     </sequence>
                                     <attribute name="name" use="required">
                                       <simpleType>
                                         <restriction base="{http://www.w3.org/2001/XMLSchema}string">
                                           <minLength value="1"/>
                                         </restriction>
                                       </simpleType>
                                     </attribute>
                                   </restriction>
                                 </complexContent>
                               </complexType>
                             </element>
                             <element name="userParam" type="{}userParam" maxOccurs="unbounded" minOccurs="0"/>
                           </sequence>
                           <attribute name="db" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
                           <attribute name="db_version" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
                           <attribute name="taxonomy" type="{http://www.w3.org/2001/XMLSchema}string" />
                           <attribute name="mass_type" use="required" type="{}MassType" />
                           <attribute name="charges" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
                           <attribute name="enzyme" type="{}DigestionEnzyme" />
                           <attribute name="missed_cleavages" type="{http://www.w3.org/2001/XMLSchema}unsignedInt" />
                           <attribute name="precursor_peak_tolerance" use="required" type="{http://www.w3.org/2001/XMLSchema}float" />
                           <attribute name="peak_mass_tolerance" use="required" type="{http://www.w3.org/2001/XMLSchema}float" />
                         </restriction>
                       </complexContent>
                     </complexType>
                   </element>
                   <element name="ProteinIdentification" minOccurs="0">
                     <complexType>
                       <complexContent>
                         <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
                           <sequence>
                             <element name="ProteinHit" maxOccurs="unbounded" minOccurs="0">
                               <complexType>
                                 <complexContent>
                                   <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
                                     <sequence minOccurs="0">
                                       <element name="userParam" type="{}userParam" maxOccurs="unbounded" minOccurs="0"/>
                                     </sequence>
                                     <attribute name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}ID" />
                                     <attribute name="accession" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
                                     <attribute name="score" use="required" type="{http://www.w3.org/2001/XMLSchema}float" />
                                     <attribute name="sequence" type="{http://www.w3.org/2001/XMLSchema}string" />
                                   </restriction>
                                 </complexContent>
                               </complexType>
                             </element>
                             <element name="userParam" type="{}userParam" maxOccurs="unbounded" minOccurs="0"/>
                           </sequence>
                           <attribute name="score_type" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
                           <attribute name="higher_score_better" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
                           <attribute name="significance_threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
                         </restriction>
                       </complexContent>
                     </complexType>
                   </element>
                 </sequence>
                 <attribute name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}ID" />
                 <attribute name="search_engine" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
                 <attribute name="search_engine_version" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
                 <attribute name="date" use="required" type="{http://www.w3.org/2001/XMLSchema}dateTime" />
               </restriction>
             </complexContent>
           </complexType>
         </element>
         <element name="UnassignedPeptideIdentification" maxOccurs="unbounded" minOccurs="0">
           <complexType>
             <complexContent>
               <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
                 <sequence>
                   <element name="PeptideHit" maxOccurs="unbounded" minOccurs="0">
                     <complexType>
                       <complexContent>
                         <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
                           <sequence minOccurs="0">
                             <element name="userParam" type="{}userParam" maxOccurs="unbounded" minOccurs="0"/>
                           </sequence>
                           <attribute name="sequence" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
                           <attribute name="charge" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
                           <attribute name="score" use="required" type="{http://www.w3.org/2001/XMLSchema}float" />
                           <attribute name="aa_before">
                             <simpleType>
                               <restriction base="{http://www.w3.org/2001/XMLSchema}string">
                                 <minLength value="0"/>
                                 <maxLength value="1"/>
                               </restriction>
                             </simpleType>
                           </attribute>
                           <attribute name="aa_after">
                             <simpleType>
                               <restriction base="{http://www.w3.org/2001/XMLSchema}string">
                                 <minLength value="0"/>
                                 <maxLength value="1"/>
                               </restriction>
                             </simpleType>
                           </attribute>
                           <attribute name="protein_refs" type="{http://www.w3.org/2001/XMLSchema}IDREFS" />
                         </restriction>
                       </complexContent>
                     </complexType>
                   </element>
                   <element name="userParam" type="{}userParam" maxOccurs="unbounded" minOccurs="0"/>
                 </sequence>
                 <attribute name="identification_run_ref" use="required" type="{http://www.w3.org/2001/XMLSchema}IDREF" />
                 <attribute name="score_type" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
                 <attribute name="higher_score_better" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
                 <attribute name="significance_threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
                 <attribute name="spectrum_reference" type="{http://www.w3.org/2001/XMLSchema}unsignedInt" />
                 <attribute name="RT" type="{http://www.w3.org/2001/XMLSchema}float" />
                 <attribute name="MZ" type="{http://www.w3.org/2001/XMLSchema}float" />
               </restriction>
             </complexContent>
           </complexType>
         </element>
         <element name="featureList">
           <complexType>
             <complexContent>
               <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
                 <sequence>
                   <element name="feature" type="{}featureType" maxOccurs="unbounded" minOccurs="0"/>
                 </sequence>
                 <attribute name="count" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
               </restriction>
             </complexContent>
           </complexType>
         </element>
       </sequence>
       <attribute name="version" type="{http://www.w3.org/2001/XMLSchema}float" />
       <attribute name="document_id" type="{http://www.w3.org/2001/XMLSchema}string" />
       <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" />
     </restriction>
   </complexContent>
 </complexType>

Nested Class Summary
static class FeatureMap.DataProcessing
          Java class for anonymous complex type.
static class FeatureMap.FeatureList
          Java class for anonymous complex type.
static class FeatureMap.IdentificationRun
          Java class for anonymous complex type.
static class FeatureMap.UnassignedPeptideIdentification
          Java class for anonymous complex type.
 
Constructor Summary
FeatureMap()
           
 
Method Summary
 List<FeatureMap.DataProcessing> getDataProcessing()
          Gets the value of the dataProcessing property.
 String getDocumentId()
          Gets the value of the documentId property.
 FeatureMap.FeatureList getFeatureList()
          Gets the value of the featureList property.
 String getId()
          Gets the value of the id property.
 List<FeatureMap.IdentificationRun> getIdentificationRun()
          Gets the value of the identificationRun property.
 List<FeatureMap.UnassignedPeptideIdentification> getUnassignedPeptideIdentification()
          Gets the value of the unassignedPeptideIdentification property.
 Float getVersion()
          Gets the value of the version property.
 void setDocumentId(String value)
          Sets the value of the documentId property.
 void setFeatureList(FeatureMap.FeatureList value)
          Sets the value of the featureList property.
 void setId(String value)
          Sets the value of the id property.
 void setVersion(Float value)
          Sets the value of the version property.
 
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

FeatureMap

public FeatureMap()
Method Detail

getDataProcessing

public List<FeatureMap.DataProcessing> getDataProcessing()
Gets the value of the dataProcessing 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 dataProcessing property.

For example, to add a new item, do as follows: 

    getDataProcessing().add(newItem);

Objects of the following type(s) are allowed in the list FeatureMap.DataProcessing

getIdentificationRun

public List<FeatureMap.IdentificationRun> getIdentificationRun()
Gets the value of the identificationRun 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 identificationRun property.

For example, to add a new item, do as follows: 

    getIdentificationRun().add(newItem);

Objects of the following type(s) are allowed in the list FeatureMap.IdentificationRun

getUnassignedPeptideIdentification

public List<FeatureMap.UnassignedPeptideIdentification> getUnassignedPeptideIdentification()
Gets the value of the unassignedPeptideIdentification 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 unassignedPeptideIdentification property.

For example, to add a new item, do as follows: 

    getUnassignedPeptideIdentification().add(newItem);

Objects of the following type(s) are allowed in the list FeatureMap.UnassignedPeptideIdentification

getFeatureList

public FeatureMap.FeatureList getFeatureList()
Gets the value of the featureList property.

Returns:
possible object is FeatureMap.FeatureList

setFeatureList

public void setFeatureList(FeatureMap.FeatureList value)
Sets the value of the featureList property.

Parameters:
value - allowed object is FeatureMap.FeatureList

getVersion

public Float getVersion()
Gets the value of the version property.

Returns:
possible object is Float

setVersion

public void setVersion(Float value)
Sets the value of the version property.

Parameters:
value - allowed object is Float

getDocumentId

public String getDocumentId()
Gets the value of the documentId property.

Returns:
possible object is String

setDocumentId

public void setDocumentId(String value)
Sets the value of the documentId property.

Parameters:
value - allowed object is String

getId

public String getId()
Gets the value of the id property.

Returns:
possible object is String

setId

public void setId(String value)
Sets the value of the id property.

Parameters:
value - allowed object is String
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