uk.ac.ebi.jmzidml.model.mzidml
Class SearchModification

java.lang.Object
  extended by uk.ac.ebi.jmzidml.model.MzIdentMLObject
      extended by uk.ac.ebi.jmzidml.model.mzidml.SearchModification
All Implemented Interfaces:
Serializable

public class SearchModification
extends MzIdentMLObject
implements Serializable

Specification of a search modification as parameter for a spectra search. Contains the name of the modification, the mass, the specificity and whether it is a static modification.

Java class for SearchModificationType complex type.

The following schema fragment specifies the expected content contained within this class.

 <complexType name="SearchModificationType">
   <complexContent>
     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
       <sequence>
         <element name="SpecificityRules" type="{http://psidev.info/psi/pi/mzIdentML/1.1}SpecificityRulesType" maxOccurs="unbounded" minOccurs="0"/>
         <element name="cvParam" type="{http://psidev.info/psi/pi/mzIdentML/1.1}CVParamType" maxOccurs="unbounded"/>
       </sequence>
       <attribute name="fixedMod" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
       <attribute name="massDelta" use="required" type="{http://www.w3.org/2001/XMLSchema}float" />
       <attribute name="residues" use="required" type="{http://psidev.info/psi/pi/mzIdentML/1.1}listOfCharsOrAny" />
     </restriction>
   </complexContent>
 </complexType>
 

See Also:
Serialized Form

Field Summary
protected  List<CvParam> cvParam
           
protected  boolean fixedMod
           
protected  float massDelta
           
protected  List<String> residues
           
protected  List<SpecificityRules> specificityRules
           
 
Constructor Summary
SearchModification()
           
 
Method Summary
 List<CvParam> getCvParam()
          Gets the value of the cvParam property.
 float getMassDelta()
          Gets the value of the massDelta property.
 List<String> getResidues()
          Gets the value of the residues property.
 List<SpecificityRules> getSpecificityRules()
          Gets the value of the specificityRules property.
 boolean isFixedMod()
          Gets the value of the fixedMod property.
 void setFixedMod(boolean value)
          Sets the value of the fixedMod property.
 void setMassDelta(float value)
          Sets the value of the massDelta property.
 
Methods inherited from class uk.ac.ebi.jmzidml.model.MzIdentMLObject
getHid
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

specificityRules

protected List<SpecificityRules> specificityRules

cvParam

protected List<CvParam> cvParam

fixedMod

protected boolean fixedMod

massDelta

protected float massDelta

residues

protected List<String> residues
Constructor Detail

SearchModification

public SearchModification()
Method Detail

getSpecificityRules

public List<SpecificityRules> getSpecificityRules()
Gets the value of the specificityRules 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 specificityRules property.

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

    getSpecificityRules().add(newItem);
 

Objects of the following type(s) are allowed in the list SpecificityRules


getCvParam

public List<CvParam> getCvParam()
Gets the value of the cvParam 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 cvParam property.

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

    getCvParam().add(newItem);
 

Objects of the following type(s) are allowed in the list CvParam


isFixedMod

public boolean isFixedMod()
Gets the value of the fixedMod property.


setFixedMod

public void setFixedMod(boolean value)
Sets the value of the fixedMod property.


getMassDelta

public float getMassDelta()
Gets the value of the massDelta property.


setMassDelta

public void setMassDelta(float value)
Sets the value of the massDelta property.


getResidues

public List<String> getResidues()
Gets the value of the residues 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 residues property.

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

    getResidues().add(newItem);
 

Objects of the following type(s) are allowed in the list String



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