uk.ac.ebi.jmzidml
Enum MzIdentMLElement

java.lang.Object
  extended by java.lang.Enum<MzIdentMLElement>
      extended by uk.ac.ebi.jmzidml.MzIdentMLElement
All Implemented Interfaces:
Serializable, Comparable<MzIdentMLElement>

public enum MzIdentMLElement
extends Enum<MzIdentMLElement>

For performance reasons (Memory Overflow), all the reference auto-resolving have been switched off. Reference auto-resolving creates too many duplicated objects, one possible solution for this is to use caching.


Enum Constant Summary
AbstractContact
           
AbstractParam
           
Affiliation
           
AmbiguousResidue
           
AnalysisCollection
           
AnalysisData
           
AnalysisProtocolCollection
           
AnalysisSampleCollection
           
AnalysisSoftware
           
AnalysisSoftwareList
           
AuditCollection
           
BibliographicReference
           
ContactRole
           
CV
           
CvList
           
CvParam
           
DatabaseFilters
           
DatabaseTranslation
           
DataCollection
           
DBSequence
           
Enzyme
           
Enzymes
           
ExternalData
           
FileFormat
           
Filter
           
FragmentArray
           
Fragmentation
           
FragmentationTable
           
Identifiable
           
Inputs
           
InputSpectra
           
InputSpectrumIdentifications
           
IonType
           
MassTable
           
Measure
           
Modification
           
ModificationParams
           
MzIdentML
           
Organization
           
Param
           
ParamList
           
ParentOrganization
           
Peptide
           
PeptideEvidence
           
PeptideEvidenceRef
           
PeptideHypothesis
           
Person
           
ProteinAmbiguityGroup
           
ProteinDetection
           
ProteinDetectionHypothesis
           
ProteinDetectionList
           
ProteinDetectionProtocol
           
ProtocolApplication
           
Provider
           
Residue
           
Role
           
Sample
           
SearchDatabase
           
SearchDatabaseRef
           
SearchModification
           
SequenceCollection
           
SetupMzIdentMLElement
          Order is important - SetupMzIdentMLElement must appear first so that initialization of cfgMap happens before it is used in remaining constructors.
SourceFile
           
SpecificityRules
           
SpectraData
           
SpectrumIdentification
           
SpectrumIdentificationItem
           
SpectrumIdentificationItemRef
           
SpectrumIdentificationList
           
SpectrumIdentificationProtocol
           
SpectrumIdentificationResult
           
SpectrumIDFormat
           
SubSample
           
SubstitutionModification
           
Tolerance
           
TranslationTable
           
UserParam
           
 
Method Summary
<T extends MzIdentMLObject>
Class<T>
getClazz()
           
<C extends CvParam>
Class<C>
getCvParamClass()
           
<R extends AbstractReferenceResolver>
Class<R>
getRefResolverClass()
           
 String getTagName()
           
static MzIdentMLElement getType(Class clazz)
           
static MzIdentMLElement getType(String xpath)
           
<U extends UserParam>
Class<U>
getUserParamClass()
           
 String getXpath()
           
 boolean isAutoRefResolving()
           
 boolean isCached()
           
 boolean isIdMapped()
           
 boolean isIndexed()
           
static void loadProperties()
          Read the configuration info from the properties file.
 String toString()
           
static MzIdentMLElement valueOf(String name)
          Returns the enum constant of this type with the specified name.
static MzIdentMLElement[] values()
          Returns an array containing the constants of this enum type, in the order they are declared.
 
Methods inherited from class java.lang.Enum
clone, compareTo, equals, finalize, getDeclaringClass, hashCode, name, ordinal, valueOf
 
Methods inherited from class java.lang.Object
getClass, notify, notifyAll, wait, wait, wait
 

Enum Constant Detail

SetupMzIdentMLElement

public static final MzIdentMLElement SetupMzIdentMLElement
Order is important - SetupMzIdentMLElement must appear first so that initialization of cfgMap happens before it is used in remaining constructors.


AbstractContact

public static final MzIdentMLElement AbstractContact

AbstractParam

public static final MzIdentMLElement AbstractParam

Affiliation

public static final MzIdentMLElement Affiliation

AmbiguousResidue

public static final MzIdentMLElement AmbiguousResidue

AnalysisCollection

public static final MzIdentMLElement AnalysisCollection

AnalysisData

public static final MzIdentMLElement AnalysisData

AnalysisProtocolCollection

public static final MzIdentMLElement AnalysisProtocolCollection

AnalysisSampleCollection

public static final MzIdentMLElement AnalysisSampleCollection

AnalysisSoftware

public static final MzIdentMLElement AnalysisSoftware

AnalysisSoftwareList

public static final MzIdentMLElement AnalysisSoftwareList

AuditCollection

public static final MzIdentMLElement AuditCollection

BibliographicReference

public static final MzIdentMLElement BibliographicReference

ContactRole

public static final MzIdentMLElement ContactRole

CV

public static final MzIdentMLElement CV

CvList

public static final MzIdentMLElement CvList

CvParam

public static final MzIdentMLElement CvParam

DatabaseFilters

public static final MzIdentMLElement DatabaseFilters

DatabaseTranslation

public static final MzIdentMLElement DatabaseTranslation

DataCollection

public static final MzIdentMLElement DataCollection

DBSequence

public static final MzIdentMLElement DBSequence

Enzyme

public static final MzIdentMLElement Enzyme

Enzymes

public static final MzIdentMLElement Enzymes

ExternalData

public static final MzIdentMLElement ExternalData

FileFormat

public static final MzIdentMLElement FileFormat

Filter

public static final MzIdentMLElement Filter

FragmentArray

public static final MzIdentMLElement FragmentArray

Fragmentation

public static final MzIdentMLElement Fragmentation

FragmentationTable

public static final MzIdentMLElement FragmentationTable

Identifiable

public static final MzIdentMLElement Identifiable

Inputs

public static final MzIdentMLElement Inputs

InputSpectra

public static final MzIdentMLElement InputSpectra

InputSpectrumIdentifications

public static final MzIdentMLElement InputSpectrumIdentifications

IonType

public static final MzIdentMLElement IonType

MassTable

public static final MzIdentMLElement MassTable

Measure

public static final MzIdentMLElement Measure

Modification

public static final MzIdentMLElement Modification

ModificationParams

public static final MzIdentMLElement ModificationParams

MzIdentML

public static final MzIdentMLElement MzIdentML

Organization

public static final MzIdentMLElement Organization

Param

public static final MzIdentMLElement Param

ParamList

public static final MzIdentMLElement ParamList

ParentOrganization

public static final MzIdentMLElement ParentOrganization

Peptide

public static final MzIdentMLElement Peptide

PeptideEvidence

public static final MzIdentMLElement PeptideEvidence

PeptideEvidenceRef

public static final MzIdentMLElement PeptideEvidenceRef

PeptideHypothesis

public static final MzIdentMLElement PeptideHypothesis

Person

public static final MzIdentMLElement Person

ProteinAmbiguityGroup

public static final MzIdentMLElement ProteinAmbiguityGroup

ProteinDetection

public static final MzIdentMLElement ProteinDetection

ProteinDetectionHypothesis

public static final MzIdentMLElement ProteinDetectionHypothesis

ProteinDetectionList

public static final MzIdentMLElement ProteinDetectionList

ProteinDetectionProtocol

public static final MzIdentMLElement ProteinDetectionProtocol

ProtocolApplication

public static final MzIdentMLElement ProtocolApplication

Provider

public static final MzIdentMLElement Provider

Residue

public static final MzIdentMLElement Residue

Role

public static final MzIdentMLElement Role

Sample

public static final MzIdentMLElement Sample

SearchDatabase

public static final MzIdentMLElement SearchDatabase

SearchDatabaseRef

public static final MzIdentMLElement SearchDatabaseRef

SearchModification

public static final MzIdentMLElement SearchModification

SequenceCollection

public static final MzIdentMLElement SequenceCollection

SourceFile

public static final MzIdentMLElement SourceFile

SpecificityRules

public static final MzIdentMLElement SpecificityRules

SpectraData

public static final MzIdentMLElement SpectraData

SpectrumIdentification

public static final MzIdentMLElement SpectrumIdentification

SpectrumIdentificationItem

public static final MzIdentMLElement SpectrumIdentificationItem

SpectrumIdentificationItemRef

public static final MzIdentMLElement SpectrumIdentificationItemRef

SpectrumIdentificationList

public static final MzIdentMLElement SpectrumIdentificationList

SpectrumIdentificationProtocol

public static final MzIdentMLElement SpectrumIdentificationProtocol

SpectrumIdentificationResult

public static final MzIdentMLElement SpectrumIdentificationResult

SpectrumIDFormat

public static final MzIdentMLElement SpectrumIDFormat

SubSample

public static final MzIdentMLElement SubSample

SubstitutionModification

public static final MzIdentMLElement SubstitutionModification

Tolerance

public static final MzIdentMLElement Tolerance

TranslationTable

public static final MzIdentMLElement TranslationTable

UserParam

public static final MzIdentMLElement UserParam
Method Detail

values

public static MzIdentMLElement[] values()
Returns an array containing the constants of this enum type, in the order they are declared. This method may be used to iterate over the constants as follows:
for (MzIdentMLElement c : MzIdentMLElement.values())
    System.out.println(c);

Returns:
an array containing the constants of this enum type, in the order they are declared

valueOf

public static MzIdentMLElement valueOf(String name)
Returns the enum constant of this type with the specified name. The string must match exactly an identifier used to declare an enum constant in this type. (Extraneous whitespace characters are not permitted.)

Parameters:
name - the name of the enum constant to be returned.
Returns:
the enum constant with the specified name
Throws:
IllegalArgumentException - if this enum type has no constant with the specified name
NullPointerException - if the argument is null

getTagName

public String getTagName()

isIndexed

public boolean isIndexed()

isCached

public boolean isCached()

isIdMapped

public boolean isIdMapped()

isAutoRefResolving

public boolean isAutoRefResolving()

getXpath

public String getXpath()

getClazz

public <T extends MzIdentMLObject> Class<T> getClazz()

getCvParamClass

public <C extends CvParam> Class<C> getCvParamClass()

getUserParamClass

public <U extends UserParam> Class<U> getUserParamClass()

getRefResolverClass

public <R extends AbstractReferenceResolver> Class<R> getRefResolverClass()

getType

public static MzIdentMLElement getType(Class clazz)

getType

public static MzIdentMLElement getType(String xpath)

loadProperties

public static void loadProperties()
Read the configuration info from the properties file. Note: this simply loads the information into a hashmap. Actual setting of values is done through the constructors.


toString

public String toString()
Overrides:
toString in class Enum<MzIdentMLElement>


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