Serialized Form (pgatk-io 1.0.1-SNAPSHOT API)

Package io.github.bigbio.pgatk.io.apl
- Class io.github.bigbio.pgatk.io.apl.AplIndexedReader extends Object implements Serializable
  - Serialized Fields
    - sourceFile
```
File sourceFile
```
      The source file if this object was generated from a file
    - index
```
List<E> index
```
      Position from the "BEGIN IONS" fields in the file to the "END IONS"
    - peakLists
```
HashMap<K,V> peakLists
```
      MS2 peak lists. The index of the query in the file as key and the respective query as value.
    - useCache
```
boolean useCache
```
      Indicates whether the cache should be used
    - currentPosition
```
int currentPosition
```
    - keys
```
List<E> keys
```
- Class io.github.bigbio.pgatk.io.apl.AplSpectrum extends Object implements Serializable
  - Serialized Fields
    - peakList
```
Map<K,V> peakList
```
      The spectrum's peaks
    - header
```
String header
```
    - mz
```
Double mz
```
    - fragmentation
```
String fragmentation
```
    - chargeState
```
String chargeState
```
    - index
```
Long index
```
Package io.github.bigbio.pgatk.io.clustering
- Class io.github.bigbio.pgatk.io.clustering.ClusteringFileReader extends Object implements Serializable
  - Serialized Fields
    - clusteringFile
```
File clusteringFile
```
    - br
```
BufferedReader br
```
    - inCluster
```
boolean inCluster
```
    - index
```
Map<K,V> index
```
    - nextCluster
```
ICluster nextCluster
```
Package io.github.bigbio.pgatk.io.clustering.indexing
- Class io.github.bigbio.pgatk.io.clustering.indexing.ClusteringIndexElement extends Object implements Serializable
  - Serialized Fields
    - id
```
String id
```
    - start
```
long start
```
    - size
```
int size
```
    - precursorMz
```
float precursorMz
```
Package io.github.bigbio.pgatk.io.common
- Class io.github.bigbio.pgatk.io.common.CvParam extends Object implements Serializable
  - Serialized Fields
    - name
```
String name
```
    - value
```
String value
```
    - cv
```
String cv
```
    - accession
```
String accession
```
- Class io.github.bigbio.pgatk.io.common.DefaultSpectrum extends Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - id
```
String id
```
    - index
```
Long index
```
    - precursorCharge
```
int precursorCharge
```
    - precursorMz
```
Double precursorMz
```
    - precursorIntensity
```
Double precursorIntensity
```
    - peakList
```
Map<K,V> peakList
```
    - msLevel
```
Integer msLevel
```
    - params
```
List<E> params
```
- Class io.github.bigbio.pgatk.io.common.IndexElementImpl extends Object implements Serializable
  - Serialized Fields
    - start
```
long start
```
    - size
```
int size
```
- Class io.github.bigbio.pgatk.io.common.PgatkIOException extends Exception implements Serializable
- Class io.github.bigbio.pgatk.io.common.SpectrumProperty extends LongObject implements Serializable
  - Serialized Fields
    - key
```
String key
```
    - spectrumId
```
String spectrumId
```
    - propertyId
```
String propertyId
```
    - value
```
String value
```
Package io.github.bigbio.pgatk.io.common.cluster
- Class io.github.bigbio.pgatk.io.common.cluster.ClusteringFileCluster extends Object implements Serializable
  - Serialized Fields
    - avPrecursorMz
```
double avPrecursorMz
```
    - avPrecursorIntens
```
double avPrecursorIntens
```
    - sequenceCounts
```
List<E> sequenceCounts
```
    - spectrumRefs
```
List<E> spectrumRefs
```
    - maxSequence
```
String maxSequence
```
    - minSpecPrecursorMz
```
Double minSpecPrecursorMz
```
    - maxSpecPrecursorMz
```
Double maxSpecPrecursorMz
```
    - maxRatio
```
float maxRatio
```
    - totalPsms
```
int totalPsms
```
    - consensusMzValues
```
List<E> consensusMzValues
```
    - consensusIntensValues
```
List<E> consensusIntensValues
```
    - consensusCountValues
```
List<E> consensusCountValues
```
    - id
```
String id
```
    - identifiedSpecCount
```
int identifiedSpecCount
```
    - unidentifiedSpecCount
```
int unidentifiedSpecCount
```
    - countPerPsmSequence
```
Map<K,V> countPerPsmSequence
```
    - species
```
Set<E> species
```
    - fileName
```
String fileName
```
- Class io.github.bigbio.pgatk.io.common.cluster.ClusteringFileSpectrumReference extends Object implements Serializable
  - Serialized Fields
    - INDEX_ID
```
int INDEX_ID
```
    - INDEX_SEQUENCE
```
int INDEX_SEQUENCE
```
    - INDEX_PRECURSOR_MZ
```
int INDEX_PRECURSOR_MZ
```
    - INDEX_CHARGE
```
int INDEX_CHARGE
```
    - INDEX_SPECIES
```
int INDEX_SPECIES
```
    - INDEX_MODIFICATIONS
```
int INDEX_MODIFICATIONS
```
    - INDEX_SIMILARITY_SCORE
```
int INDEX_SIMILARITY_SCORE
```
    - SEPARATOR
```
String SEPARATOR
```
    - modificationPattern
```
Pattern modificationPattern
```
    - sequence
```
String sequence
```
    - charge
```
int charge
```
    - precursorMz
```
Double precursorMz
```
    - id
```
String id
```
    - similarityScore
```
float similarityScore
```
    - species
```
String species
```
    - modifications
```
String modifications
```
    - isIdentified
```
boolean isIdentified
```
    - hasPeaks
```
boolean hasPeaks
```
    - peaks
```
List<E> peaks
```
    - psms
```
List<E> psms
```
    - mostCommonPsm
```
IPeptideSpectrumMatch mostCommonPsm
```
Package io.github.bigbio.pgatk.io.common.spectra
Package io.github.bigbio.pgatk.io.mapcache
Package io.github.bigbio.pgatk.io.mgf
- Class io.github.bigbio.pgatk.io.mgf.MgfIndexedReader extends Object implements Serializable
  - Serialized Fields
    - accessions
```
List<E> accessions
```
      ---------- OPTIONAL PARAMETERS THAT CAN BE SET IN A MGF FILE --------------
    - charge
```
String charge
```
    - enzyme
```
String enzyme
```
    - searchTitle
```
String searchTitle
```
    - precursorRemoval
```
String precursorRemoval
```
    - database
```
String database
```
    - performDecoySearch
```
Boolean performDecoySearch
```
    - isErrorTolerant
```
Boolean isErrorTolerant
```
    - format
```
String format
```
    - frames
```
List<E> frames
```
    - instrument
```
String instrument
```
    - variableModifications
```
String variableModifications
```
    - fragmentIonTolerance
```
Double fragmentIonTolerance
```
    - fragmentIonToleranceUnit
```
MgfUtils.FragmentToleranceUnits fragmentIonToleranceUnit
```
    - massType
```
MgfUtils.MassType massType
```
    - fixedMofications
```
String fixedMofications
```
    - peptideIsotopeError
```
Double peptideIsotopeError
```
    - partials
```
Integer partials
```
    - precursor
```
Double precursor
```
    - quantitation
```
String quantitation
```
    - maxHitsToReport
```
String maxHitsToReport
```
    - reportType
```
MgfUtils.ReportType reportType
```
    - searchType
```
MgfUtils.SearchType searchType
```
    - proteinMass
```
String proteinMass
```
    - taxonomy
```
String taxonomy
```
    - peptideMassTolerance
```
Double peptideMassTolerance
```
    - peptideMassToleranceUnit
```
MgfUtils.PeptideToleranceUnit peptideMassToleranceUnit
```
    - userParameter
```
List<E> userParameter
```
    - userMail
```
String userMail
```
    - userName
```
String userName
```
    - sourceFile
```
File sourceFile
```
      The source file if this object was generated from a file
    - index
```
List<E> index
```
      Position from the "BEGIN IONS" fields in the file to the "END IONS"
    - ms2Queries
```
HashMap<K,V> ms2Queries
```
      MS2 queries. The index of the query in the file as key and the respective query as value.
    - useCache
```
boolean useCache
```
      Indicates whether the cache should be used
    - allowCustomTags
```
boolean allowCustomTags
```
      Indicates whether the parser will fail on unknown tags
    - disableCommentSupport
```
boolean disableCommentSupport
```
      If this option is set, comments are not removed from MGF files. This speeds up parsing considerably but causes problems if MGF files do contain comments.
    - ignoreWrongPeaks
```
boolean ignoreWrongPeaks
```
      This function helps to ignore peaks if the parser found parser errors in the peaks
    - currentPosition
```
int currentPosition
```
- Class io.github.bigbio.pgatk.io.mgf.MgfIterableReader extends MzIterableChannelReader implements Serializable
  - Serialized Fields
    - allowCustomTags
```
boolean allowCustomTags
```
    - disableCommentSupport
```
boolean disableCommentSupport
```
      If this option is set, comments are not removed from MGF files. This speeds up parsing considerably but causes problems if MGF files do contain comments.
    - ignoreWrongPeaks
```
boolean ignoreWrongPeaks
```
      This function helps to ignore peaks if the parser found parser errors in the peaks
    - sourceFile
```
File sourceFile
```
      Source File containing all the spectra.
    - channelCursor
```
int channelCursor
```
    - specIndex
```
long specIndex
```
    - spectrum
```
Ms2Query spectrum
```
- Class io.github.bigbio.pgatk.io.mgf.Ms2Query extends Object implements Serializable
  - Serialized Fields
    - DEFAULT_MS_LEVEL
```
int DEFAULT_MS_LEVEL
```
    - title
```
String title
```
    - chargeState
```
String chargeState
```
    - tolerance
```
Double tolerance
```
    - toleranceUnit
```
MgfUtils.PeptideToleranceUnit toleranceUnit
```
    - sequenceQualifiers
```
List<E> sequenceQualifiers
```
    - composition
```
String composition
```
    - tags
```
List<E> tags
```
    - errorTolerantTags
```
List<E> errorTolerantTags
```
    - scan
```
String scan
```
    - rawScan
```
String rawScan
```
    - retentionTime
```
String retentionTime
```
    - instrument
```
String instrument
```
    - variableModifications
```
String variableModifications
```
    - peakList
```
Map<K,V> peakList
```
    - peptideMass
```
Double peptideMass
```
    - peptideIntensity
```
Double peptideIntensity
```
    - index
```
Long index
```
    - userTags
```
Map<K,V> userTags
```
    - disableCommentSupport
```
boolean disableCommentSupport
```
    - msLevel
```
Integer msLevel
```
Package io.github.bigbio.pgatk.io.msp
- Class io.github.bigbio.pgatk.io.msp.MspIterableReader extends MzIterableChannelReader implements Serializable
  - Serialized Fields
    - sourceFile
```
File sourceFile
```
    - channelCursor
```
int channelCursor
```
    - specIndex
```
long specIndex
```
    - spectrum
```
MspSpectrum spectrum
```
    - builder
```
LibrarySpectrumBuilder builder
```
- Class io.github.bigbio.pgatk.io.msp.MspSpectrum extends Object implements Serializable
  - Serialized Fields
    - index
```
long index
```
    - peakList
```
Map<K,V> peakList
```
    - msLevel
```
Integer msLevel
```
    - precursorIntensity
```
Double precursorIntensity
```
    - precursorMz
```
Double precursorMz
```
    - precursorCharge
```
Integer precursorCharge
```
    - usi
```
String usi
```
    - peptideSequence
```
String peptideSequence
```
    - ptms
```
List<E> ptms
```
    - properties
```
Map<K,V> properties
```
    - scores
```
Map<K,V> scores
```
    - proteins
```
List<E> proteins
```
Package io.github.bigbio.pgatk.io.mzml
- Class io.github.bigbio.pgatk.io.mzml.MzMlIndexedReader extends Object implements Serializable
  - Serialized Fields
    - idToIndexElementMap
```
HashMap<K,V> idToIndexElementMap
```
    - msNScans
```
HashMap<K,V> msNScans
```
    - idIterator
```
Iterator<E> idIterator
```
    - unmarshaller
```
uk.ac.ebi.jmzml.xml.io.MzMLUnmarshaller unmarshaller
```
      The unmarshaller to use to unmarshall the mzML objects.
    - spectraIds
```
List<E> spectraIds
```
      List of spectra found in the mzML file.
- Class io.github.bigbio.pgatk.io.mzml.MzMLSpectrum extends Object implements Serializable
  - Serialized Fields
    - id
```
String id
```
    - index
```
Long index
```
    - charge
```
Integer charge
```
    - mz
```
Double mz
```
    - intensity
```
Double intensity
```
    - msLevel
```
Integer msLevel
```
    - peakList
```
Map<K,V> peakList
```
    - paramGroup
```
Collection<E> paramGroup
```
Package io.github.bigbio.pgatk.io.mzxml
- Class io.github.bigbio.pgatk.io.mzxml.MzXMLIndexedReader extends Object implements Serializable
  - Serialized Fields
    - sourcefile
```
File sourcefile
```
      The mzXML source file.
    - accessFile
```
RandomAccessFile accessFile
```
      The random access file object is used to read the file. This object is only opened once.
    - index
```
psidev.psi.tools.xxindex.index.XpathIndex index
```
      The actual XPath index to use.
    - xpathAccess
```
psidev.psi.tools.xxindex.StandardXpathAccess xpathAccess
```
      The XPath access to use.
    - level1ScanIndexes
```
List<E> level1ScanIndexes
```
      The indexes of all level 1 scans in the mzXML file.
    - level2ScanIndexes
```
List<E> level2ScanIndexes
```
      The indexes of all level 2 scans in the mzXML file.
    - msNScans
```
Map<K,V> msNScans
```
      A Map with the ms level as key and the list with associated index elements as values.
    - runAttributes
```
HashMap<K,V> runAttributes
```
      Holds the attributes of the run attribute.
    - numToIndexMap
```
Map<K,V> numToIndexMap
```
      Map with the spectra's num attribute as key and the corresponding IndexElement as value.
    - unmarshaller
```
MzXMLUnmarshaller unmarshaller
```
      The unmarshaller to use.
- Class io.github.bigbio.pgatk.io.mzxml.MzXMLIterableReader extends MzIterableChannelReader implements Serializable
  - Serialized Fields
    - sourceFile
```
File sourceFile
```
      Source File containing all the spectra.
    - channelCursor
```
int channelCursor
```
    - specIndex
```
int specIndex
```
    - spectrum
```
MzXMLSpectrum spectrum
```
- Class io.github.bigbio.pgatk.io.mzxml.MzXMLParsingException extends Exception implements Serializable
  
  serialVersionUID:
  
  1L
- Class io.github.bigbio.pgatk.io.mzxml.MzXMLSpectrum extends Object implements Serializable
  - Serialized Fields
    - id
```
String id
```
      The scan id
    - charge
```
Integer charge
```
      The spectrum's charge
    - precursorMz
```
Double precursorMz
```
      The precursor's m/z
    - precursorIntensity
```
Double precursorIntensity
```
      The precursor's intensity
    - peakList
```
Map<K,V> peakList
```
      The actual peak list
    - paramGroup
```
List<E> paramGroup
```
      ParamGroup holding additional information about the spectrum.
    - msLevel
```
int msLevel
```
      The spectrum's ms level
    - index
```
Long index
```
    - retentionTime
```
String retentionTime
```
Package io.github.bigbio.pgatk.io.mzxml.mzxml.model
- Class io.github.bigbio.pgatk.io.mzxml.mzxml.model.DataProcessing extends Object implements Serializable
  
  serialVersionUID:
  
  320L
  - Serialized Fields
    - software
```
Software software
```
    - processingOperationAndComment
```
List<E> processingOperationAndComment
```
    - intensityCutoff
```
Float intensityCutoff
```
    - centroided
```
Boolean centroided
```
    - deisotoped
```
Boolean deisotoped
```
    - chargeDeconvoluted
```
Boolean chargeDeconvoluted
```
    - spotIntegration
```
Boolean spotIntegration
```
- Class io.github.bigbio.pgatk.io.mzxml.mzxml.model.Maldi extends Object implements Serializable
  
  serialVersionUID:
  
  320L
  - Serialized Fields
    - plateID
```
String plateID
```
    - spotID
```
String spotID
```
    - laserShootCount
```
Long laserShootCount
```
    - laserFrequency
```
Duration laserFrequency
```
    - laserIntensity
```
Long laserIntensity
```
    - collisionGas
```
Boolean collisionGas
```
- Class io.github.bigbio.pgatk.io.mzxml.mzxml.model.MsInstrument extends Object implements Serializable
  
  serialVersionUID:
  
  320L
  - Serialized Fields
    - msManufacturer
```
MsManufacturer msManufacturer
```
    - msModel
```
OntologyEntry msModel
```
    - msIonisation
```
OntologyEntry msIonisation
```
    - msMassAnalyzer
```
MsMassAnalyzer msMassAnalyzer
```
    - msDetector
```
OntologyEntry msDetector
```
    - software
```
Software software
```
    - msResolution
```
OntologyEntry msResolution
```
    - operator
```
Operator operator
```
    - nameValueAndComment
```
List<E> nameValueAndComment
```
    - msInstrumentID
```
Integer msInstrumentID
```
- Class io.github.bigbio.pgatk.io.mzxml.mzxml.model.MsManufacturer extends OntologyEntry implements Serializable
  
  serialVersionUID:
  
  320L
- Class io.github.bigbio.pgatk.io.mzxml.mzxml.model.MsMassAnalyzer extends OntologyEntry implements Serializable
  
  serialVersionUID:
  
  320L
- Class io.github.bigbio.pgatk.io.mzxml.mzxml.model.MsRun extends Object implements Serializable
  
  serialVersionUID:
  
  320L
  - Serialized Fields
    - parentFile
```
List<E> parentFile
```
    - msInstrument
```
List<E> msInstrument
```
    - dataProcessing
```
List<E> dataProcessing
```
    - separation
```
Separation separation
```
    - spotting
```
Spotting spotting
```
    - scan
```
List<E> scan
```
    - sha1
```
String sha1
```
    - scanCount
```
Long scanCount
```
    - startTime
```
Duration startTime
```
    - endTime
```
Duration endTime
```
- Class io.github.bigbio.pgatk.io.mzxml.mzxml.model.NameValue extends Object implements Serializable
  
  serialVersionUID:
  
  320L
  - Serialized Fields
    - value
```
String value
```
    - name
```
String name
```
    - theValue
```
String theValue
```
    - type
```
String type
```
- Class io.github.bigbio.pgatk.io.mzxml.mzxml.model.OntologyEntry extends Object implements Serializable
  
  serialVersionUID:
  
  320L
  - Serialized Fields
    - category
```
String category
```
    - theValue
```
String theValue
```
- Class io.github.bigbio.pgatk.io.mzxml.mzxml.model.Operator extends Object implements Serializable
  
  serialVersionUID:
  
  320L
  - Serialized Fields
    - value
```
String value
```
    - first
```
String first
```
    - last
```
String last
```
    - phone
```
String phone
```
    - email
```
String email
```
    - uri
```
String uri
```
- Class io.github.bigbio.pgatk.io.mzxml.mzxml.model.Orientation extends Object implements Serializable
  
  serialVersionUID:
  
  320L
  - Serialized Fields
    - firstSpotID
```
String firstSpotID
```
    - secondSpotID
```
String secondSpotID
```
- Class io.github.bigbio.pgatk.io.mzxml.mzxml.model.ParentFile extends Object implements Serializable
  
  serialVersionUID:
  
  320L
  - Serialized Fields
    - value
```
String value
```
    - fileName
```
String fileName
```
    - fileType
```
String fileType
```
    - fileSha1
```
String fileSha1
```
- Class io.github.bigbio.pgatk.io.mzxml.mzxml.model.Pattern extends Object implements Serializable
  
  serialVersionUID:
  
  320L
  - Serialized Fields
    - spottingPattern
```
OntologyEntry spottingPattern
```
    - orientation
```
Orientation orientation
```
- Class io.github.bigbio.pgatk.io.mzxml.mzxml.model.Peaks extends Object implements Serializable
  
  serialVersionUID:
  
  320L
  - Serialized Fields
    - value
```
byte[] value
```
    - precision
```
Long precision
```
    - byteOrder
```
String byteOrder
```
    - contentType
```
String contentType
```
    - compressionType
```
String compressionType
```
    - compressedLen
```
int compressedLen
```
- Class io.github.bigbio.pgatk.io.mzxml.mzxml.model.Plate extends Object implements Serializable
  
  serialVersionUID:
  
  320L
  - Serialized Fields
    - plateManufacturer
```
OntologyEntry plateManufacturer
```
    - plateModel
```
OntologyEntry plateModel
```
    - pattern
```
Pattern pattern
```
    - spot
```
List<E> spot
```
    - plateID
```
Long plateID
```
    - spotXCount
```
Long spotXCount
```
    - spotYCount
```
Long spotYCount
```
- Class io.github.bigbio.pgatk.io.mzxml.mzxml.model.PrecursorMz extends Object implements Serializable
  
  serialVersionUID:
  
  320L
  - Serialized Fields
    - value
```
float value
```
    - precursorScanNum
```
Long precursorScanNum
```
    - precursorIntensity
```
float precursorIntensity
```
    - precursorCharge
```
Long precursorCharge
```
    - possibleCharges
```
String possibleCharges
```
    - windowWideness
```
Float windowWideness
```
    - activationMethod
```
String activationMethod
```
- Class io.github.bigbio.pgatk.io.mzxml.mzxml.model.Robot extends Object implements Serializable
  
  serialVersionUID:
  
  320L
  - Serialized Fields
    - robotManufacturer
```
OntologyEntry robotManufacturer
```
    - robotModel
```
OntologyEntry robotModel
```
    - timePerSpot
```
Duration timePerSpot
```
    - deadVolume
```
Long deadVolume
```
- Class io.github.bigbio.pgatk.io.mzxml.mzxml.model.Scan extends Object implements Serializable
  
  serialVersionUID:
  
  320L
  - Serialized Fields
    - scanOrigin
```
List<E> scanOrigin
```
    - precursorMz
```
List<E> precursorMz
```
    - maldi
```
Maldi maldi
```
    - peaks
```
List<E> peaks
```
    - nameValueAndComment
```
List<E> nameValueAndComment
```
    - scan
```
List<E> scan
```
    - num
```
Long num
```
    - msLevel
```
Long msLevel
```
    - peaksCount
```
Long peaksCount
```
    - polarity
```
String polarity
```
    - scanType
```
String scanType
```
    - filterLine
```
String filterLine
```
    - centroided
```
Boolean centroided
```
    - deisotoped
```
Boolean deisotoped
```
    - chargeDeconvoluted
```
Boolean chargeDeconvoluted
```
    - retentionTime
```
Duration retentionTime
```
    - ionisationEnergy
```
Float ionisationEnergy
```
    - collisionEnergy
```
Float collisionEnergy
```
    - cidGasPressure
```
Float cidGasPressure
```
    - startMz
```
Float startMz
```
    - endMz
```
Float endMz
```
    - lowMz
```
Float lowMz
```
    - highMz
```
Float highMz
```
    - basePeakMz
```
Float basePeakMz
```
    - basePeakIntensity
```
Float basePeakIntensity
```
    - totIonCurrent
```
Float totIonCurrent
```
    - msInstrumentID
```
Integer msInstrumentID
```
    - compensationVoltage
```
Float compensationVoltage
```
- Class io.github.bigbio.pgatk.io.mzxml.mzxml.model.ScanOrigin extends Object implements Serializable
  
  serialVersionUID:
  
  320L
  - Serialized Fields
    - parentFileID
```
String parentFileID
```
    - num
```
Long num
```
- Class io.github.bigbio.pgatk.io.mzxml.mzxml.model.Separation extends Object implements Serializable
  
  serialVersionUID:
  
  320L
  - Serialized Fields
    - separationTechnique
```
List<E> separationTechnique
```
- Class io.github.bigbio.pgatk.io.mzxml.mzxml.model.SeparationTechnique extends Object implements Serializable
  
  serialVersionUID:
  
  320L
- Class io.github.bigbio.pgatk.io.mzxml.mzxml.model.Software extends Object implements Serializable
  
  serialVersionUID:
  
  320L
  - Serialized Fields
    - value
```
String value
```
    - type
```
String type
```
    - name
```
String name
```
    - version
```
String version
```
    - completionTime
```
XMLGregorianCalendar completionTime
```
- Class io.github.bigbio.pgatk.io.mzxml.mzxml.model.Spot extends Object implements Serializable
  
  serialVersionUID:
  
  320L
  - Serialized Fields
    - maldiMatrix
```
OntologyEntry maldiMatrix
```
    - spotID
```
String spotID
```
    - spotXPosition
```
String spotXPosition
```
    - spotYPosition
```
String spotYPosition
```
    - spotDiameter
```
Long spotDiameter
```
- Class io.github.bigbio.pgatk.io.mzxml.mzxml.model.Spotting extends Object implements Serializable
  
  serialVersionUID:
  
  320L
  - Serialized Fields
    - plate
```
List<E> plate
```
    - robot
```
Robot robot
```
Package io.github.bigbio.pgatk.io.objectdb
- Class io.github.bigbio.pgatk.io.objectdb.DbObject extends org.zoodb.api.impl.ZooPC implements Serializable
  - Serialized Fields
    - id
```
long id
```
    - firstLevel
```
boolean firstLevel
```
- Class io.github.bigbio.pgatk.io.objectdb.LongObject extends DbObject implements Serializable
  - Serialized Fields
    - urParams
```
HashMap<K,V> urParams
```
Package io.github.bigbio.pgatk.io.pride
- Class io.github.bigbio.pgatk.io.pride.AnnotatedSpectrum extends Object implements Serializable
  - Serialized Fields
    - usi
```
String usi
```
      USI of the spectra. The USI is the accession of the project that originate the dataset, the collection (RAW file) that contains the spectrum and the scan number of the spectra.
    - pepSequence
```
String pepSequence
```
      The peptide sequence.
    - peptidoform
```
String peptidoform
```
      The peptidoform information. The combination of peptide Sequence + modification in position.
    - proteinAccessions
```
List<E> proteinAccessions
```
      Protein accessions. A List of protein accessions from Uniprot, ENSEMBL, or other major databases.
    - geneAccessions
```
List<E> geneAccessions
```
      Gene related accessions, including: Transcript, Exon Accessions from multiple databases.
    - proteinLocalizations
```
List<E> proteinLocalizations
```
      Protein localization including: - Accession of the protein - start: start in the sequence 1-based - end: end in the sequence (start + length (peptideSequence))
    - geneLocalizations
```
List<E> geneLocalizations
```
      Gene Coordinates are more complex than Protein localizations, it contains, Transcript position, Gene positions and exon information.
    - sampleAccession
```
String sampleAccession
```
    - organism
```
String organism
```
      The organism where the peptide has been found/identified. In PRIDE some peptides are associated to more than one species, a unique species/organism should be selected.
    - sample
```
List<E> sample
```
      Sample information from SDRF, the sample information a a list of key value pairs from samples, for example: - organism:homo sapiens - organism part: brain
    - biologicalAnnotations
```
List<E> biologicalAnnotations
```
      Additional biological annotations for the peptide as keywords, for example: - non-canonical - unique peptide - variant
    - precursorMz
```
double precursorMz
```
      Precursor Mz
    - precursorCharge
```
Integer precursorCharge
```
      Precursor charge
    - modifications
```
List<E> modifications
```
      Structure of Post-translational modifications as position+name-modification+score of the quality of PTM.
    - binaryPeaks
```
BinaryPeaks binaryPeaks
```
    - retentionTime
```
Double retentionTime
```
      Spectrum retention time.
    - msLevel
```
Integer msLevel
```
      Spectrum retention time.
    - missedCleavages
```
Integer missedCleavages
```
      Number of missclevages for the peptide, this is related with the cleavage agent used to generate the peptide
    - qualityScores
```
List<E> qualityScores
```
      List of spectrum identification scores and statistical assessment scores such as q-value, posterior error probabilities, or p-values.
    - msAnnotations
```
List<E> msAnnotations
```
      A list of String values that to characterize the MS information, example: - pass FDR threshold - Orbitrap LTQ - Label-free
    - pxAccession
```
String pxAccession
```
      A list of ProteomeXchange projects that has been used to generate the following peptide.
    - isDecoy
```
Boolean isDecoy
```
      A list of ProteomeXchange projects that has been used to generate the following peptide.
    - peptideIntensity
```
Double peptideIntensity
```
      Raw peptide intensity in the sample
- Class io.github.bigbio.pgatk.io.pride.ArchiveSpectrum extends Object implements Serializable
  - Serialized Fields
    - usi
```
String usi
```
    - projectAccession
```
String projectAccession
```
    - assayAccession
```
String assayAccession
```
    - spectrumFile
```
String spectrumFile
```
    - sourceID
```
String sourceID
```
    - spectrumTitle
```
String spectrumTitle
```
    - masses
```
Double[] masses
```
    - intensities
```
Double[] intensities
```
    - numPeaks
```
Integer numPeaks
```
    - msLevel
```
Integer msLevel
```
    - precursorCharge
```
Integer precursorCharge
```
    - precursorMz
```
Double precursorMz
```
    - retentionTime
```
Double retentionTime
```
    - properties
```
Set<E> properties
```
    - peptideSequence
```
String peptideSequence
```
      Interpretation of the Spectra
    - missedCleavages
```
Integer missedCleavages
```
    - modifications
```
Collection<E> modifications
```
    - annotations
```
List<E> annotations
```
    - isDecoy
```
Boolean isDecoy
```
    - qualityEstimationMethods
```
Set<E> qualityEstimationMethods
```
    - isValid
```
Boolean isValid
```
    - proteinAccessions
```
List<E> proteinAccessions
```
    - geneAccessions
```
List<E> geneAccessions
```
- Class io.github.bigbio.pgatk.io.pride.PrideJsonIndexedReader extends Object implements Serializable
  - Serialized Fields
    - source
```
File source
```
    - index
```
List<E> index
```
      Index Spectra in the Json file
    - indexSpectra
```
HashMap<K,V> indexSpectra
```
      Index in the file to ArchiveSpectrum
    - peakLists
```
HashMap<K,V> peakLists
```
      Usi to ArchiveSpectrum
    - useCache
```
boolean useCache
```
      Indicates whether the cache should be used
    - keys
```
Map<K,V> keys
```
- Class io.github.bigbio.pgatk.io.pride.PrideJsonIterableReader extends Object implements Serializable
  - Serialized Fields
    - classMapper
```
Class<T> classMapper
```
    - source
```
File source
```
    - braf
```
BufferedRandomAccessFile braf
```
    - line
```
String line
```
Package io.github.bigbio.pgatk.io.properties
- Class io.github.bigbio.pgatk.io.properties.BinaryPropertyStorage extends Object implements Serializable
  - Serialized Fields
    - key
```
String key
```
    - value
```
String value
```
    - propertyName
```
String propertyName
```
- Class io.github.bigbio.pgatk.io.properties.ChronicleMapPropertyStorage extends InMemoryPropertyStorage implements Serializable
  - Serialized Fields
    - dbDirectory
```
File dbDirectory
```
    - numberProperties
```
long numberProperties
```
- Class io.github.bigbio.pgatk.io.properties.EcachePropertyStorage extends InMemoryPropertyStorage implements Serializable
  - Serialized Fields
    - cacheManager
```
org.ehcache.PersistentCacheManager cacheManager
```
    - cacheStorage
```
org.ehcache.Cache<K,V> cacheStorage
```
    - dbDirectory
```
File dbDirectory
```
    - entryCounter
```
long entryCounter
```
- Class io.github.bigbio.pgatk.io.properties.InMemoryPropertyStorage extends Object implements Serializable
  - Serialized Fields
    - propertyStorage
```
Map<K,V> propertyStorage
```
    - propertyNames
```
Set<E> propertyNames
```
- Class io.github.bigbio.pgatk.io.properties.LevelDBPropertyStorage extends InMemoryPropertyStorage implements Serializable
  - Serialized Fields
    - levelDB
```
org.iq80.leveldb.DB levelDB
```
    - levelDBSize
```
int levelDBSize
```
    - dbDirectory
```
File dbDirectory
```
- Class io.github.bigbio.pgatk.io.properties.MapDBPropertyStorage extends InMemoryPropertyStorage implements Serializable
  - Serialized Fields
    - directoryPath
```
File directoryPath
```
    - db
```
org.mapdb.DB db
```
    - dbFile
```
File dbFile
```
- Class io.github.bigbio.pgatk.io.properties.ObjectDBPropertyStorage extends LongObject implements Serializable
  - Serialized Fields
    - dbDirectory
```
String dbDirectory
```
    - objectsDB
```
ObjectsDB objectsDB
```
- Class io.github.bigbio.pgatk.io.properties.SparkeyPropertyStorage extends InMemoryPropertyStorage implements Serializable
  - Serialized Fields
    - dbDirectory
```
File dbDirectory
```
    - dbFile
```
File dbFile
```
    - writerSet
```
HashSet<E> writerSet
```
    - readerSet
```
HashSet<E> readerSet
```
    - entryCounter
```
long entryCounter
```
    - DEFAULT_CHARSET
```
Charset DEFAULT_CHARSET
```
    - writers
```
ThreadLocal<T> writers
```
    - readers
```
ThreadLocal<T> readers
```
Package io.github.bigbio.pgatk.io.utils
- Class io.github.bigbio.pgatk.io.utils.Triple extends Object implements Serializable
  - Serialized Fields
    - first
```
Object first
```
    - second
```
Object second
```
    - third
```
Object third
```
- Class io.github.bigbio.pgatk.io.utils.Tuple extends Object implements Serializable
  - Serialized Fields
    - key
```
Object key
```
    - value
```
Object value
```
    - hashCode
```
int hashCode
```

Serialized Form

Package io.github.bigbio.pgatk.io.apl

Class io.github.bigbio.pgatk.io.apl.AplIndexedReader extends Object implements Serializable

Serialized Fields

sourceFile

index

peakLists

useCache

currentPosition

keys

Class io.github.bigbio.pgatk.io.apl.AplSpectrum extends Object implements Serializable

Serialized Fields

peakList

header

mz

fragmentation

chargeState

index

Package io.github.bigbio.pgatk.io.clustering

Class io.github.bigbio.pgatk.io.clustering.ClusteringFileReader extends Object implements Serializable

Serialized Fields

clusteringFile

br

inCluster

index

nextCluster

Package io.github.bigbio.pgatk.io.clustering.indexing

Class io.github.bigbio.pgatk.io.clustering.indexing.ClusteringIndexElement extends Object implements Serializable

Serialized Fields

id

start

size

precursorMz

Package io.github.bigbio.pgatk.io.common

Class io.github.bigbio.pgatk.io.common.CvParam extends Object implements Serializable

Serialized Fields

name

value

cv

accession

Class io.github.bigbio.pgatk.io.common.DefaultSpectrum extends Object implements Serializable

Serialized Fields

id

index

precursorCharge

precursorMz

precursorIntensity

peakList

msLevel

params

Class io.github.bigbio.pgatk.io.common.IndexElementImpl extends Object implements Serializable

Serialized Fields

start

size

Class io.github.bigbio.pgatk.io.common.PgatkIOException extends Exception implements Serializable

Class io.github.bigbio.pgatk.io.common.SpectrumProperty extends LongObject implements Serializable

Serialized Fields

key

spectrumId

propertyId

value

Package io.github.bigbio.pgatk.io.common.cluster

Class io.github.bigbio.pgatk.io.common.cluster.ClusteringFileCluster extends Object implements Serializable

Serialized Fields

avPrecursorMz

avPrecursorIntens

sequenceCounts

spectrumRefs

maxSequence

minSpecPrecursorMz

maxSpecPrecursorMz

maxRatio

totalPsms

consensusMzValues

consensusIntensValues

consensusCountValues

id

identifiedSpecCount

unidentifiedSpecCount

countPerPsmSequence