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

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

public class Modification
extends MzIdentMLObject
implements Serializable, CvParamListCapable

A molecule modification specification. If n modifications have been found on a peptide, there should be n instances of Modification. If multiple modifications are provided as cvParams, it is assumed that the modification is ambiguous i.e. one modification or another. A cvParam must be provided with the identification of the modification sourced from a suitable CV e.g. UNIMOD. If the modification is not present in the CV (and this will be checked by the semantic validator within a given tolerance window), there is a “unknown modification� CV term that must be used instead. A neutral loss should be defined as an additional CVParam within Modification. If more complex information should be given about neutral losses (such as presence/absence on particular product ions), this can additionally be encoded within the FragmentationArray.

Java class for ModificationType complex type.

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

 <complexType name="ModificationType">
   <complexContent>
     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
       <sequence>
         <element name="cvParam" type="{http://psidev.info/psi/pi/mzIdentML/1.1}CVParamType" maxOccurs="unbounded"/>
       </sequence>
       <attribute name="location" type="{http://www.w3.org/2001/XMLSchema}int" />
       <attribute name="residues" type="{http://psidev.info/psi/pi/mzIdentML/1.1}listOfChars" />
       <attribute name="avgMassDelta" type="{http://www.w3.org/2001/XMLSchema}double" />
       <attribute name="monoisotopicMassDelta" type="{http://www.w3.org/2001/XMLSchema}double" />
     </restriction>
   </complexContent>
 </complexType>
 

See Also:
Serialized Form

Field Summary
protected  Double avgMassDelta
           
protected  List<CvParam> cvParam
           
protected  Integer location
           
protected  Double monoisotopicMassDelta
           
protected  List<String> residues
           
 
Constructor Summary
Modification()
           
 
Method Summary
 Double getAvgMassDelta()
          Gets the value of the avgMassDelta property.
 List<CvParam> getCvParam()
          Gets the value of the cvParam property.
 Integer getLocation()
          Gets the value of the location property.
 Double getMonoisotopicMassDelta()
          Gets the value of the monoisotopicMassDelta property.
 List<String> getResidues()
          Gets the value of the residues property.
 void setAvgMassDelta(Double value)
          Sets the value of the avgMassDelta property.
 void setLocation(Integer value)
          Sets the value of the location property.
 void setMonoisotopicMassDelta(Double value)
          Sets the value of the monoisotopicMassDelta 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

cvParam

protected List<CvParam> cvParam

location

protected Integer location

residues

protected List<String> residues

avgMassDelta

protected Double avgMassDelta

monoisotopicMassDelta

protected Double monoisotopicMassDelta
Constructor Detail

Modification

public Modification()
Method Detail

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

Specified by:
getCvParam in interface CvParamListCapable
Returns:
A List of CvParam objects.

getLocation

public Integer getLocation()
Gets the value of the location property.

Returns:
possible object is Integer

setLocation

public void setLocation(Integer value)
Sets the value of the location property.

Parameters:
value - allowed object is Integer

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


getAvgMassDelta

public Double getAvgMassDelta()
Gets the value of the avgMassDelta property.

Returns:
possible object is Double

setAvgMassDelta

public void setAvgMassDelta(Double value)
Sets the value of the avgMassDelta property.

Parameters:
value - allowed object is Double

getMonoisotopicMassDelta

public Double getMonoisotopicMassDelta()
Gets the value of the monoisotopicMassDelta property.

Returns:
possible object is Double

setMonoisotopicMassDelta

public void setMonoisotopicMassDelta(Double value)
Sets the value of the monoisotopicMassDelta property.

Parameters:
value - allowed object is Double


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