|
||||||||||
PREV CLASS NEXT CLASS | FRAMES NO FRAMES | |||||||||
SUMMARY: NESTED | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |
java.lang.Objectuk.ac.ebi.jmzidml.model.MzIdentMLObject
uk.ac.ebi.jmzidml.model.mzidml.Modification
public class Modification
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>
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 |
---|
protected List<CvParam> cvParam
protected Integer location
protected List<String> residues
protected Double avgMassDelta
protected Double monoisotopicMassDelta
Constructor Detail |
---|
public Modification()
Method Detail |
---|
public List<CvParam> getCvParam()
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
getCvParam
in interface CvParamListCapable
public Integer getLocation()
Integer
public void setLocation(Integer value)
value
- allowed object is
Integer
public List<String> getResidues()
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
public Double getAvgMassDelta()
Double
public void setAvgMassDelta(Double value)
value
- allowed object is
Double
public Double getMonoisotopicMassDelta()
Double
public void setMonoisotopicMassDelta(Double value)
value
- allowed object is
Double
|
||||||||||
PREV CLASS NEXT CLASS | FRAMES NO FRAMES | |||||||||
SUMMARY: NESTED | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |