Serialized Form (MiLib 1.8.3 API)

Package com.milaboratory.cli
- Class com.milaboratory.cli.ProcessException extends RuntimeException implements Serializable
Package com.milaboratory.core
- Class com.milaboratory.core.Range extends Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - lower
```
int lower
```
    - upper
```
int upper
```
    - reversed
```
boolean reversed
```
Package com.milaboratory.core.alignment
- Class com.milaboratory.core.alignment.AbstractAlignmentScoring extends Object implements Serializable
  - Serialized Fields
    - alphabet
```
Alphabet<S extends Sequence<S>> alphabet
```
      Link to alphabet
    - subsMatrix
```
com.milaboratory.core.alignment.SubstitutionMatrix subsMatrix
```
      Stores information about how the object was created. AbstractAlignmentScoring.subsMatrixActual used for actual calculations
    - subsMatrixActual
```
int[] subsMatrixActual
```
      Actual substitution matrix
    - uniformBasicMatch
```
boolean uniformBasicMatch
```
      Flag indicating whether substitution matrix has the same value on main diagonal or not
- Class com.milaboratory.core.alignment.AffineGapAlignmentScoring extends AbstractAlignmentScoring<S extends Sequence<S>> implements Serializable
  - Serialization Methods
    - writeReplace
```
protected Object writeReplace()
                       throws ObjectStreamException
```
      Throws:
      
      ObjectStreamException
  - Serialized Fields
    - gapOpenPenalty
```
int gapOpenPenalty
```
      Penalty value for opening gap
    - gapExtensionPenalty
```
int gapExtensionPenalty
```
      Penalty for extending gap
- Class com.milaboratory.core.alignment.AffineGapAlignmentScoring.SerializationObject extends Object implements Serializable
  - Serialization Methods
    - readResolve
```
private Object readResolve()
                    throws ObjectStreamException
```
      Throws:
      
      ObjectStreamException
  - Serialized Fields
    - alphabet
```
Alphabet<S extends Sequence<S>> alphabet
```
    - matrix
```
com.milaboratory.core.alignment.SubstitutionMatrix matrix
```
    - gapOpenPenalty
```
int gapOpenPenalty
```
    - gapExtensionPenalty
```
int gapExtensionPenalty
```
- Class com.milaboratory.core.alignment.Alignment extends Object implements Serializable
  - Serialized Fields
    - sequence1
```
Sequence<S extends Sequence<S>> sequence1
```
      Initial sequence. (upper sequence in alignment; sequence1)
    - mutations
```
Mutations<S extends Sequence<S>> mutations
```
      Mutations
    - sequence1Range
```
Range sequence1Range
```
      Range in initial sequence (sequence1)
    - sequence2Range
```
Range sequence2Range
```
      Range in mutated sequence (sequence2)
    - score
```
float score
```
      Alignment score
- Class com.milaboratory.core.alignment.AlignmentHelper extends Object implements Serializable
  - Serialized Fields
    - seq1String
```
String seq1String
```
    - seq2String
```
String seq2String
```
    - markup
```
String markup
```
    - seq1Position
```
int[] seq1Position
```
    - seq2Position
```
int[] seq2Position
```
    - match
```
BitArray match
```
    - offset
```
int offset
```
- Class com.milaboratory.core.alignment.BandedAlignerParameters extends Object implements Serializable
  - Serialized Fields
    - scoring
```
AlignmentScoring<S extends Sequence<S>> scoring
```
    - width
```
int width
```
    - stopPenalty
```
int stopPenalty
```
- Class com.milaboratory.core.alignment.BandedMatrix extends Object implements Serializable
  - Serialized Fields
    - matrix
```
int[] matrix
```
      Main alignment matrix
    - rowFactor
```
int rowFactor
```
      Row length
    - columnDelta
```
int columnDelta
```
      Negative offset value of first row
- Class com.milaboratory.core.alignment.BandedSemiLocalResult extends Object implements Serializable
  - Serialized Fields
    - sequence1Stop
```
int sequence1Stop
```
      Positions at which alignment terminates.
      If BandedSemiLocalLeft alignment was performed, second sequence is aligned to the left part of first sequence. If BandedSemiLocalRight alignment was performed, second sequence is aligned to the right part of first sequence.
    - sequence2Stop
```
int sequence2Stop
```
      Positions at which alignment terminates.
      If BandedSemiLocalLeft alignment was performed, second sequence is aligned to the left part of first sequence. If BandedSemiLocalRight alignment was performed, second sequence is aligned to the right part of first sequence.
    - score
```
int score
```
      Score
- Class com.milaboratory.core.alignment.CachedIntArray extends Object implements Serializable
  - Serialized Fields
    - array
```
int[] array
```
- Class com.milaboratory.core.alignment.LinearGapAlignmentScoring extends AbstractAlignmentScoring<S extends Sequence<S>> implements Serializable
  - Serialization Methods
    - writeReplace
```
protected Object writeReplace()
                       throws ObjectStreamException
```
      Throws:
      
      ObjectStreamException
  - Serialized Fields
    - gapPenalty
```
int gapPenalty
```
      Penalty for gap, must be < 0
- Class com.milaboratory.core.alignment.LinearGapAlignmentScoring.SerializationObject extends Object implements Serializable
  - Serialization Methods
    - readResolve
```
private Object readResolve()
                    throws ObjectStreamException
```
      Throws:
      
      ObjectStreamException
  - Serialized Fields
    - alphabet
```
Alphabet<S extends Sequence<S>> alphabet
```
    - matrix
```
com.milaboratory.core.alignment.SubstitutionMatrix matrix
```
    - gapPenalty
```
int gapPenalty
```
Package com.milaboratory.core.alignment.kaligner1
- Class com.milaboratory.core.alignment.kaligner1.KAligner extends Object implements Serializable
  - Serialized Fields
    - mapper
```
KMapper mapper
```
      Link to KMapper
    - parameters
```
KAlignerParameters parameters
```
      Parameters of alignment
    - sequences
```
List<E> sequences
```
      Base records for reference sequences
    - payloads
```
gnu.trove.map.hash.TIntObjectHashMap<V> payloads
```
      Record payloads.
    - lazyResults
```
boolean lazyResults
```
      Flag indicating how to load final alignments - at first request or immediately after obtaining KAlignmentResult
    - threads
```
int threads
```
      Number fo threads to use in piped processing.
- Class com.milaboratory.core.alignment.kaligner1.KAlignerParameters extends Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - mapperKValue
```
int mapperKValue
```
      Nucleotides in kMer (value of k; kMer length)
    - floatingLeftBound
```
boolean floatingLeftBound
```
      Defines floating bounds of alignment
    - floatingRightBound
```
boolean floatingRightBound
```
      Defines floating bounds of alignment
    - mapperAbsoluteMinScore
```
float mapperAbsoluteMinScore
```
      Minimal allowed absolute hit score obtained by KMapper to consider hit as reliable candidate
    - mapperRelativeMinScore
```
float mapperRelativeMinScore
```
      Minimal allowed absolute hit score obtained by KMapper to consider hit as reliable candidate
    - mapperMatchScore
```
float mapperMatchScore
```
      Minimal allowed absolute hit score obtained by KMapper to consider hit as reliable candidate
    - mapperMismatchPenalty
```
float mapperMismatchPenalty
```
      Minimal allowed absolute hit score obtained by KMapper to consider hit as reliable candidate
    - mapperOffsetShiftPenalty
```
float mapperOffsetShiftPenalty
```
      Minimal allowed absolute hit score obtained by KMapper to consider hit as reliable candidate
    - mapperMinSeedsDistance
```
int mapperMinSeedsDistance
```
      Minimal and maximal distance between kMer seed positions in target sequence
    - mapperMaxSeedsDistance
```
int mapperMaxSeedsDistance
```
      Minimal and maximal distance between kMer seed positions in target sequence
    - minAlignmentLength
```
int minAlignmentLength
```
      Minimal allowed alignment length
    - maxAdjacentIndels
```
int maxAdjacentIndels
```
      Maximal allowed number of insertions and deletions between 2 kMers
    - alignmentStopPenalty
```
int alignmentStopPenalty
```
      Penalty score to stop alignment extension.
    - absoluteMinScore
```
float absoluteMinScore
```
      Minimal allowed score value to consider hit as reliable candidate
    - relativeMinScore
```
float relativeMinScore
```
      Minimal allowed score value to consider hit as reliable candidate
    - maxHits
```
int maxHits
```
      Maximal number of hits to be stored as result
    - scoring
```
LinearGapAlignmentScoring<S extends Sequence<S>> scoring
```
      Scoring system
- Class com.milaboratory.core.alignment.kaligner1.KAlignmentHit extends Object implements Serializable
  - Serialized Fields
    - result
```
KAlignmentResult<P> result
```
      Link to result container
    - index
```
int index
```
      According hit index in KMappingResult.hits array
    - alignment
```
Alignment<S extends Sequence<S>> alignment
```
      Actual alignment
- Class com.milaboratory.core.alignment.kaligner1.KAlignmentResult extends Object implements Serializable
  - Serialized Fields
    - aligner
```
KAligner<P> aligner
```
      Link to KAligner
    - mappingResult
```
KMappingResult mappingResult
```
      Link to according KMappingResult
    - hits
```
List<E> hits
```
      List of hits
    - target
```
NucleotideSequence target
```
      Target sequence to be aligned
    - targetFrom
```
int targetFrom
```
      Range of target sequence to be aligned
    - targetTo
```
int targetTo
```
      Range of target sequence to be aligned
- Class com.milaboratory.core.alignment.kaligner1.KAlignmentResultP extends KAlignmentResult<P> implements Serializable
  - Serialized Fields
    - query
```
Object query
```
- Class com.milaboratory.core.alignment.kaligner1.KMapper extends Object implements Serializable
  - Serialized Fields
    - bitsForOffset
```
int bitsForOffset
```
      Number of bits in base record for offset value
    - offsetMask
```
int offsetMask
```
      Mask to extract offset value (= 0xFFFFFFFF >>> (32 - bitsForOffset))
    - kValue
```
int kValue
```
      Nucleotides in kMer (value of k)
    - base
```
int[][] base
```
      Base of records for individual kMers
    - lengths
```
int[] lengths
```
      Number of records for each individual kMer (used only for building of base)
    - absoluteMinScore
```
float absoluteMinScore
```
      Minimal absolute score value
    - relativeMinScore
```
float relativeMinScore
```
      Minimal absolute score value
    - matchScore
```
float matchScore
```
      Minimal absolute score value
    - mismatchPenalty
```
float mismatchPenalty
```
      Minimal absolute score value
    - offsetShiftPenalty
```
float offsetShiftPenalty
```
      Minimal absolute score value
    - minAlignmentLength
```
int minAlignmentLength
```
      Minimal alignment length
    - maxIndels
```
int maxIndels
```
      Maximal number of insertions and deletions
    - floatingLeftBound
```
boolean floatingLeftBound
```
      Determines boundaries type: floating(only part of sequence should be aligned) or fixed (whole sequence should be aligned).
    - floatingRightBound
```
boolean floatingRightBound
```
      Determines boundaries type: floating(only part of sequence should be aligned) or fixed (whole sequence should be aligned).
    - minDistance
```
int minDistance
```
      Minimal and maximal distance between kMer seed positions in target sequence
    - maxDistance
```
int maxDistance
```
      Minimal and maximal distance between kMer seed positions in target sequence
    - built
```
boolean built
```
    - refFrom
```
int[] refFrom
```
    - refLength
```
int[] refLength
```
    - maxReferenceLength
```
int maxReferenceLength
```
    - minReferenceLength
```
int minReferenceLength
```
    - sequencesInBase
```
int sequencesInBase
```
    - allFilter
```
BitArray allFilter
```
      Length = sequencesInBase, all bits set
- Class com.milaboratory.core.alignment.kaligner1.KMappingHit extends Object implements Serializable
  - Serialized Fields
    - offset
```
int offset
```
      Best offset value (most popular offset)
    - id
```
int id
```
      Best offset value (most popular offset)
    - from
```
int from
```
      Intersection range of target and reference sequences, where they are supposed to be aligned From and to are indices of seeds in seeds array of KMappingResult
    - to
```
int to
```
      Intersection range of target and reference sequences, where they are supposed to be aligned From and to are indices of seeds in seeds array of KMappingResult
    - score
```
float score
```
      Alignment score value
    - seedOffsets
```
int[] seedOffsets
```
      Offset values for according seeds inside intersection
- Class com.milaboratory.core.alignment.kaligner1.KMappingResult extends Object implements Serializable
  - Serialized Fields
    - seeds
```
IntArrayList seeds
```
      Seeds used to align target sequence
    - hits
```
List<E> hits
```
      List of hits (potential candidates) for target sequence
Package com.milaboratory.core.alignment.kaligner2
- Class com.milaboratory.core.alignment.kaligner2.KAlignerParameters2 extends Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - mapperNValue
```
int mapperNValue
```
      Nucleotides in kMer (value of k; kMer length)
    - mapperKValue
```
int mapperKValue
```
      Allowed mutations in kMers
    - floatingLeftBound
```
boolean floatingLeftBound
```
      Defines floating bounds of alignment
    - floatingRightBound
```
boolean floatingRightBound
```
      Defines floating bounds of alignment
    - mapperAbsoluteMinClusterScore
```
int mapperAbsoluteMinClusterScore
```
      Minimal allowed absolute hit score obtained by KMapper to consider hit as reliable candidate
    - mapperExtraClusterScore
```
int mapperExtraClusterScore
```
      Minimal allowed absolute hit score obtained by KMapper to consider hit as reliable candidate
    - mapperMatchScore
```
int mapperMatchScore
```
      Minimal allowed absolute hit score obtained by KMapper to consider hit as reliable candidate
    - mapperMismatchScore
```
int mapperMismatchScore
```
      Minimal allowed absolute hit score obtained by KMapper to consider hit as reliable candidate
    - mapperOffsetShiftScore
```
int mapperOffsetShiftScore
```
      Minimal allowed absolute hit score obtained by KMapper to consider hit as reliable candidate
    - mapperSlotCount
```
int mapperSlotCount
```
      Minimal allowed absolute hit score obtained by KMapper to consider hit as reliable candidate
    - mapperMaxClusters
```
int mapperMaxClusters
```
      Minimal allowed absolute hit score obtained by KMapper to consider hit as reliable candidate
    - mapperMaxClusterIndels
```
int mapperMaxClusterIndels
```
      Minimal allowed absolute hit score obtained by KMapper to consider hit as reliable candidate
    - mapperKMersPerPosition
```
int mapperKMersPerPosition
```
      Minimal allowed absolute hit score obtained by KMapper to consider hit as reliable candidate
    - mapperAbsoluteMinScore
```
int mapperAbsoluteMinScore
```
      Minimal value of total mapping score (sum of cluster scores and mapperExtraClusterScore * (nClusters - 1))
    - mapperRelativeMinScore
```
float mapperRelativeMinScore
```
      Minimal allowed ratio between best hit score and other hits obtained by KMapper to consider hit as reliable candidate
    - mapperMinSeedsDistance
```
int mapperMinSeedsDistance
```
      Minimal and maximal distance between kMer seed positions in target sequence
    - mapperMaxSeedsDistance
```
int mapperMaxSeedsDistance
```
      Minimal and maximal distance between kMer seed positions in target sequence
    - alignmentStopPenalty
```
int alignmentStopPenalty
```
      Penalty score to stop alignment extension.
    - absoluteMinScore
```
int absoluteMinScore
```
      Minimal allowed score value to consider hit as reliable candidate
    - relativeMinScore
```
float relativeMinScore
```
      Maximal ratio between best hit score and other hits scores in returned result to consider hit as reliable candidate
    - maxHits
```
int maxHits
```
      Maximal number of hits to be stored as result
    - scoring
```
AffineGapAlignmentScoring<S extends Sequence<S>> scoring
```
      Scoring system
- Class com.milaboratory.core.alignment.kaligner2.KMapper2 extends Object implements Serializable
  - Serialized Fields
    - nValue
```
int nValue
```
      Nucleotides in kMer (value of k)
    - kValue
```
int kValue
```
      Allowed number of mutations in kMer
    - kMersPerPosition
```
int kMersPerPosition
```
      Iterations for each kMer
    - base
```
int[][][] base
```
      Base of records for individual kMers
    - lengths
```
int[][] lengths
```
      Number of records for each individual kMer (used only for building of base)
    - absoluteMinClusterScore
```
int absoluteMinClusterScore
```
      Minimal absolute score value
    - extraClusterScore
```
int extraClusterScore
```
      Minimal absolute score value
    - matchScore
```
int matchScore
```
      Minimal absolute score value
    - mismatchScore
```
int mismatchScore
```
      Minimal absolute score value
    - offsetShiftScore
```
int offsetShiftScore
```
      Minimal absolute score value
    - slotCount
```
int slotCount
```
      Minimal absolute score value
    - maxClusterIndels
```
int maxClusterIndels
```
      Minimal absolute score value
    - maxClusters
```
int maxClusters
```
    - absoluteMinScore
```
int absoluteMinScore
```
      Minimal absolute score.
    - relativeMinScore
```
float relativeMinScore
```
      Minimal score in fractions of top score.
    - floatingLeftBound
```
boolean floatingLeftBound
```
      Determines boundaries type: floating(only part of sequence should be aligned) or fixed (whole sequence should be aligned).
    - floatingRightBound
```
boolean floatingRightBound
```
      Determines boundaries type: floating(only part of sequence should be aligned) or fixed (whole sequence should be aligned).
    - minDistance
```
int minDistance
```
      Minimal and maximal distance between kMer seed positions in target sequence
    - maxDistance
```
int maxDistance
```
      Minimal and maximal distance between kMer seed positions in target sequence
    - built
```
boolean built
```
    - maxReferenceLength
```
int maxReferenceLength
```
    - minReferenceLength
```
int minReferenceLength
```
    - sequencesInBase
```
int sequencesInBase
```
    - allFilter
```
BitArray allFilter
```
      Length = sequencesInBase, all bits set
    - memoryCache
```
ThreadLocal<T> memoryCache
```
      Cache to prevent excessive memory allocation
    - stat
```
KAligner2Statistics stat
```
      Statistics aggregator
- Class com.milaboratory.core.alignment.kaligner2.KMappingHit2 extends Object implements Serializable
  - Serialized Fields
    - id
```
int id
```
      Reference id (in storage)
    - seedRecords
```
int[] seedRecords
```
      Offset values for according seeds inside intersection. each record = (offset << bitsForIndex) | seedIndex
    - boundaries
```
int[] boundaries
```
      Islands boundaries. count = countOfIslands - 1
    - score
```
int score
```
      Mapping score value
    - result
```
KMappingResult2 result
```
- Class com.milaboratory.core.alignment.kaligner2.KMappingResult2 extends Object implements Serializable
  - Serialized Fields
    - seeds
```
IntArrayList seeds
```
      Seeds used to align target sequence
    - hits
```
List<E> hits
```
      List of hits (potential candidates) for target sequence
Package com.milaboratory.core.clustering
- Class com.milaboratory.core.clustering.Cluster extends Object implements Serializable
  - Serialized Fields
    - head
```
Object head
```
    - parent
```
Cluster<T> parent
```
    - children
```
ArrayList<E> children
```
Package com.milaboratory.core.io.sequence
- Class com.milaboratory.core.io.sequence.IllegalFileFormatException extends RuntimeException implements Serializable
- Class com.milaboratory.core.io.sequence.MultiRead extends Object implements Serializable
  - Serialized Fields
    - data
```
SingleRead[] data
```
- Class com.milaboratory.core.io.sequence.PairedRead extends MultiRead implements Serializable
- Class com.milaboratory.core.io.sequence.SingleReadImpl extends Object implements Serializable
  - Serialized Fields
    - id
```
long id
```
    - sequenceWithQuality
```
NSequenceWithQuality sequenceWithQuality
```
    - description
```
String description
```
- Class com.milaboratory.core.io.sequence.SingleReadLazy extends Object implements Serializable
  - Serialized Fields
    - id
```
long id
```
    - buffer
```
byte[] buffer
```
    - descriptionFrom
```
int descriptionFrom
```
    - sequenceOffset
```
short sequenceOffset
```
    - qualityOffset
```
short qualityOffset
```
    - dataLength
```
short dataLength
```
    - descriptionLength
```
short descriptionLength
```
    - replaceWildcards
```
boolean replaceWildcards
```
    - sequenceWithQuality
```
NSequenceWithQuality sequenceWithQuality
```
    - description
```
String description
```
Package com.milaboratory.core.io.sequence.fasta
- Class com.milaboratory.core.io.sequence.fasta.RandomAccessFastaIndex.MultipleMatchingRecordsException extends RuntimeException implements Serializable
- Class com.milaboratory.core.io.sequence.fasta.RandomAccessFastaIndex.NoSuchRecordException extends RuntimeException implements Serializable
Package com.milaboratory.core.io.sequence.fastq
- Class com.milaboratory.core.io.sequence.fastq.WrongQualityFormat extends IllegalFileFormatException implements Serializable
Package com.milaboratory.core.merger
- Class com.milaboratory.core.merger.MergerParameters extends Object implements Serializable
  - Serialized Fields
    - qualityMergingAlgorithm
```
QualityMergingAlgorithm qualityMergingAlgorithm
```
    - partsLayout
```
PairedEndReadsLayout partsLayout
```
    - minimalOverlap
```
int minimalOverlap
```
    - maxQuality
```
int maxQuality
```
    - minimalIdentity
```
double minimalIdentity
```
    - identityType
```
MergerParameters.IdentityType identityType
```
- Class com.milaboratory.core.merger.MismatchOnlyPairedReadMerger extends Object implements Serializable
  - Serialized Fields
    - minOverlap
```
int minOverlap
```
    - minimalIdentity
```
double minimalIdentity
```
    - identityType
```
MergerParameters.IdentityType identityType
```
    - maxMismatchesPart
```
double maxMismatchesPart
```
    - maxScoreValue
```
int maxScoreValue
```
    - strands
```
boolean[] strands
```
    - motifLength
```
int motifLength
```
    - maxMismatchesInMotif
```
int maxMismatchesInMotif
```
    - qualityMergingAlgorithm
```
QualityMergingAlgorithm qualityMergingAlgorithm
```
    - pairedEndReadsLayout
```
PairedEndReadsLayout pairedEndReadsLayout
```
- Class com.milaboratory.core.merger.PairedReadMergingResult extends Object implements Serializable
  - Serialized Fields
    - originalRead
```
PairedRead originalRead
```
    - overlappedSequence
```
NSequenceWithQuality overlappedSequence
```
    - overlap
```
int overlap
```
    - errors
```
int errors
```
    - reversed
```
boolean reversed
```
    - offset
```
int offset
```
    - identityType
```
MergerParameters.IdentityType identityType
```
    - identity
```
double identity
```
Package com.milaboratory.core.motif
- Class com.milaboratory.core.motif.BitapMatcherFilter extends Object implements Serializable
  - Serialized Fields
    - nestedMatcher
```
BitapMatcher nestedMatcher
```
    - positionsBuffer
```
int[] positionsBuffer
```
    - errorsBuffer
```
int[] errorsBuffer
```
- Class com.milaboratory.core.motif.BitapMatcherImpl extends Object implements Serializable
  - Serialized Fields
    - errors
```
int errors
```
    - R
```
long[] R
```
    - to
```
int to
```
    - current
```
int current
```
- Class com.milaboratory.core.motif.BitapPattern extends Object implements Serializable
  - Serialized Fields
    - size
```
int size
```
    - patternMask
```
long[] patternMask
```
    - reversePatternMask
```
long[] reversePatternMask
```
- Class com.milaboratory.core.motif.Motif extends Object implements Serializable
  - Serialized Fields
    - alphabet
```
Alphabet<S extends Sequence<S>> alphabet
```
    - size
```
int size
```
    - data
```
BitArray data
```
      data.get(code * size + position)
    - bitapPattern
```
BitapPattern bitapPattern
```
Package com.milaboratory.core.mutations
- Class com.milaboratory.core.mutations.Mutations extends Object implements Serializable
  - Serialized Fields
    - alphabet
```
Alphabet<S extends Sequence<S>> alphabet
```
    - mutations
```
int[] mutations
```
Package com.milaboratory.core.mutations.generator
- Class com.milaboratory.core.mutations.generator.GenericNucleotideMutationModel extends Object implements Serializable
  - Serialized Fields
    - generator
```
org.apache.commons.math3.random.RandomGenerator generator
```
    - events
```
double[] events
```
    - insertionProbability
```
double insertionProbability
```
- Class com.milaboratory.core.mutations.generator.SubstitutionModel extends Object implements Serializable
  - Serialized Fields
    - size
```
int size
```
    - probabilities
```
double[] probabilities
```
    - cdf
```
double[] cdf
```
Package com.milaboratory.core.sequence
- Class com.milaboratory.core.sequence.Alphabet extends Object implements Serializable
  - Serialization Methods
    - writeReplace
```
protected Object writeReplace()
                       throws ObjectStreamException
```
      Throws:
      
      ObjectStreamException
  - Serialized Fields
    - alphabetId
```
byte alphabetId
```
      Alphabet id
    - alphabetName
```
String alphabetName
```
      Alphabet name
    - hashCode
```
int hashCode
```
    - countOfBasicLetters
```
int countOfBasicLetters
```
      Every code below this threshold represents definite letter, codes >= countOfPureLetters represents wildcards
    - codeToSymbol
```
char[] codeToSymbol
```
      Code to char upper case symbol mapping
    - codeToWildcard
```
Wildcard[] codeToWildcard
```
      Code to wildcard object mapping
    - wildcardsList
```
List<E> wildcardsList
```
      Unmodifiable list of wildcards
    - symbolToCode
```
gnu.trove.map.hash.TCharByteHashMap symbolToCode
```
      Backward mapping for both cases
    - wildcardForAnyLetter
```
Wildcard wildcardForAnyLetter
```
      Wildcard for any letter (e.g. N for nucleotides, X for amino acids)
    - basicMaskToWildcard
```
gnu.trove.map.TLongObjectMap<V> basicMaskToWildcard
```
      Mapping between wildcard basicMask representation (bit representation) and wildcard object
    - empty
```
Sequence<S extends Sequence<S>> empty
```
      Singleton empty sequence
- Class com.milaboratory.core.sequence.Alphabet.AlphabetSerialization extends Object implements Serializable
  - Serialization Methods
    - readResolve
```
private Object readResolve()
                    throws ObjectStreamException
```
      Throws:
      
      ObjectStreamException
  - Serialized Fields
    - id
```
byte id
```
- Class com.milaboratory.core.sequence.AminoAcidAlphabet extends com.milaboratory.core.sequence.AbstractArrayAlphabet<AminoAcidSequence> implements Serializable
- Class com.milaboratory.core.sequence.AminoAcidSequence extends com.milaboratory.core.sequence.AbstractArraySequence<AminoAcidSequence> implements Serializable
- Class com.milaboratory.core.sequence.NSequenceWithQuality extends SequenceWithQuality<NucleotideSequence> implements Serializable
- Class com.milaboratory.core.sequence.NucleotideAlphabet extends com.milaboratory.core.sequence.AbstractArrayAlphabet<NucleotideSequence> implements Serializable
- Class com.milaboratory.core.sequence.NucleotideSequence extends com.milaboratory.core.sequence.AbstractArraySequence<NucleotideSequence> implements Serializable
  
  serialVersionUID:
  
  2L
- Class com.milaboratory.core.sequence.SequenceQuality extends AbstractSeq<SequenceQuality> implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - data
```
byte[] data
```
- Class com.milaboratory.core.sequence.SequenceWithQuality extends Object implements Serializable
  - Serialized Fields
    - sequence
```
Sequence<S extends Sequence<S>> sequence
```
    - quality
```
SequenceQuality quality
```
Package com.milaboratory.core.sequence.provider
- Class com.milaboratory.core.sequence.provider.SequenceProviderIndexOutOfBoundsException extends IndexOutOfBoundsException implements Serializable
  - Serialized Fields
    - availableRange
```
Range availableRange
```
Package com.milaboratory.core.tree
- Class com.milaboratory.core.tree.SequenceTreeMap extends Object implements Serializable
  - Serialized Fields
    - alphabet
```
Alphabet<S extends Sequence<S>> alphabet
```
    - root
```
SequenceTreeMap.Node<O> root
```
- Class com.milaboratory.core.tree.SequenceTreeMap.Node extends Object implements Serializable
  - Serialized Fields
    - links
```
SequenceTreeMap.Node<O>[] links
```
    - object
```
Object object
```
- Class com.milaboratory.core.tree.SequenceTreeMap.NodeIterator extends cc.redberry.pipe.CUtils.OPIterator<SequenceTreeMap.Node<O>> implements Serializable
- Class com.milaboratory.core.tree.SequenceTreeMap.NodeOp extends Object implements Serializable
  - Serialized Fields
    - pointer
```
int pointer
```
    - wrappers
```
com.milaboratory.core.tree.SequenceTreeMap.NodeWrapper<O>[] wrappers
```
- Class com.milaboratory.core.tree.SequenceTreeMap.ValuesOp extends Object implements Serializable
  - Serialized Fields
    - nodeOp
```
SequenceTreeMap.NodeOp nodeOp
```
- Class com.milaboratory.core.tree.TreeSearchParameters extends Object implements Serializable
  - Serialized Fields
    - maxErrors
```
int[] maxErrors
```
    - penalty
```
double[] penalty
```
    - maxPenalty
```
double maxPenalty
```
    - differencesCombination
```
byte[][] differencesCombination
```
    - greedy
```
boolean greedy
```
Package com.milaboratory.util
- Class com.milaboratory.util.Bit2Array extends Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - data
```
byte[] data
```
    - size
```
int size
```
- Class com.milaboratory.util.BitArray extends Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - data
```
byte[] data
```
    - size
```
int size
```
- Class com.milaboratory.util.GlobalObjectMappers.DefaultPrettyPrinter1 extends com.fasterxml.jackson.core.util.DefaultPrettyPrinter implements Serializable
- Class com.milaboratory.util.IntArrayList extends Object implements Serializable
  - Serialized Fields
    - data
```
int[] data
```
    - size
```
int size
```
- Class com.milaboratory.util.ParserException extends RuntimeException implements Serializable
- Class com.milaboratory.util.RangeMap extends Object implements Serializable
  - Serialized Fields
    - map
```
TreeMap<K,V> map
```
- Class com.milaboratory.util.RangeMap.IntersectingRangesException extends IllegalArgumentException implements Serializable

Serialized Form

Package com.milaboratory.cli

Class com.milaboratory.cli.ProcessException extends RuntimeException implements Serializable

Package com.milaboratory.core

Class com.milaboratory.core.Range extends Object implements Serializable

Serialized Fields

lower

upper

reversed

Package com.milaboratory.core.alignment

Class com.milaboratory.core.alignment.AbstractAlignmentScoring extends Object implements Serializable

Serialized Fields

alphabet

subsMatrix

subsMatrixActual

uniformBasicMatch

Class com.milaboratory.core.alignment.AffineGapAlignmentScoring extends AbstractAlignmentScoring<S extends Sequence<S>> implements Serializable

Serialization Methods

writeReplace

Serialized Fields

gapOpenPenalty

gapExtensionPenalty

Class com.milaboratory.core.alignment.AffineGapAlignmentScoring.SerializationObject extends Object implements Serializable

Serialization Methods

readResolve

Serialized Fields

alphabet

matrix

gapOpenPenalty

gapExtensionPenalty

Class com.milaboratory.core.alignment.Alignment extends Object implements Serializable

Serialized Fields

sequence1

mutations

sequence1Range

sequence2Range

score

Class com.milaboratory.core.alignment.AlignmentHelper extends Object implements Serializable

Serialized Fields

seq1String

seq2String

markup

seq1Position

seq2Position

match

offset

Class com.milaboratory.core.alignment.BandedAlignerParameters extends Object implements Serializable

Serialized Fields

scoring

width

stopPenalty

Class com.milaboratory.core.alignment.BandedMatrix extends Object implements Serializable

Serialized Fields

matrix

rowFactor

columnDelta

Class com.milaboratory.core.alignment.BandedSemiLocalResult extends Object implements Serializable

Serialized Fields

sequence1Stop

sequence2Stop

score

Class com.milaboratory.core.alignment.CachedIntArray extends Object implements Serializable

Serialized Fields

array

Class com.milaboratory.core.alignment.LinearGapAlignmentScoring extends AbstractAlignmentScoring<S extends Sequence<S>> implements Serializable

Serialization Methods

writeReplace

Serialized Fields

gapPenalty

Class com.milaboratory.core.alignment.LinearGapAlignmentScoring.SerializationObject extends Object implements Serializable

Serialization Methods

readResolve

Serialized Fields

alphabet

matrix

gapPenalty

Package com.milaboratory.core.alignment.kaligner1

Class com.milaboratory.core.alignment.kaligner1.KAligner extends Object implements Serializable

Serialized Fields

mapper