Serialized Form


Package contextFold.features

Class contextFold.features.AbstractFeatureVector extends java.lang.Object implements Serializable

serialVersionUID: 2795966210352590105L

Serialized Fields

featureNames

java.util.Map<K,V> featureNames

Class contextFold.features.BinnedLengthFeatureExtractor extends FeatureExtractor implements Serializable

serialVersionUID: 359725666704635808L

Serialized Fields

firstBinSize

int firstBinSize

binSize

int binSize

Class contextFold.features.Context extends java.lang.Object implements Serializable

serialVersionUID: 852430395486899819L

Serialized Fields

offsets

int[] offsets

alphabetSize

byte alphabetSize

alphabet

byte[] alphabet

length

int length

reverseArray

int[] reverseArray

OUT_OF_RANGE

byte OUT_OF_RANGE

cardinality

int cardinality

id

int id

Class contextFold.features.ContextFeatureExtractor extends FeatureExtractor implements Serializable

serialVersionUID: -7686018620402519501L

Serialized Fields

length

int length

reversedContext

ContextFeatureExtractor reversedContext

Class contextFold.features.DenseFeatureVector extends AbstractFeatureVector implements Serializable

serialVersionUID: 5653817811624274914L

Serialized Fields

weights

float[] weights

acc

float[] acc

upd

int[] upd

intWeights

int[] intWeights

dimension

int dimension

updateTime

int updateTime

floatMin

float floatMin

floatMax

float floatMax

isCompressed

boolean isCompressed

Class contextFold.features.DoublePosContext extends ContextFeatureExtractor implements Serializable

serialVersionUID: 3047027062261976385L

Serialized Fields

firstPosContext

ContextFeatureExtractor firstPosContext

secondPosContext

ContextFeatureExtractor secondPosContext

Class contextFold.features.FeatureExtractor extends java.lang.Object implements Serializable

serialVersionUID: -1005827948851607113L

Serialized Fields

cardinality

int cardinality

seqFeatures

int[] seqFeatures

currProcessedSeq

byte[] currProcessedSeq

Class contextFold.features.FeatureManager extends java.lang.Object implements Serializable

serialVersionUID: 527046066222200738L

Serialized Fields

featuresNum

int featuresNum

baseFeatures

int[][] baseFeatures

edgeFeatures

int[][] edgeFeatures

lengthFeatures

int[][] lengthFeatures

seqFeatures

int[][][] seqFeatures

elementScores

int[][][] elementScores

featureTemplates

java.util.List<E> featureTemplates
Contains an array contexts that corresponds to this template. The array either contains a single context, or a context and its reverse context.


baseFeatureExtractors

java.util.List<E> baseFeatureExtractors
All base contexts.


repBaseFeatureExtractors

java.util.List<E> repBaseFeatureExtractors
A subset of representative baseContexts that covers all base contexts.


edgeFeatureExtractors

java.util.List<E> edgeFeatureExtractors
All base-pair contexts.


repEdgeFeatureExtractors

java.util.List<E> repEdgeFeatureExtractors
A subset of representative basepairContexts that covers all base-pair contexts.


weightVector

DenseFeatureVector weightVector

scoresUpdateTime

int scoresUpdateTime

maxLengthVal

int maxLengthVal

sr

StructureRecognizer sr

elementTypeToFeatureTemplates

java.util.List<E>[] elementTypeToFeatureTemplates

elementTypeToTemplateReverseFlags

java.util.List<E>[] elementTypeToTemplateReverseFlags

featuresMap

java.util.HashMap<K,V> featuresMap

representativeMap

java.util.HashMap<K,V> representativeMap

tempFeatureVector

AbstractFeatureVector tempFeatureVector

scoreFactor

float scoreFactor

Class contextFold.features.FeatureTemplate extends java.lang.Object implements Serializable

serialVersionUID: 1724149770194889341L

Serialized Fields

firstVectorIx

int firstVectorIx

name

java.lang.String name

featureExtractor

FeatureExtractor featureExtractor

valueCalculator

ValueCalculator valueCalculator

initWeights

java.util.Map<K,V> initWeights

Class contextFold.features.HpLengthCalculator extends java.lang.Object implements Serializable

serialVersionUID: 1759845472683487330L

Class contextFold.features.IlLengthCalculator extends java.lang.Object implements Serializable

serialVersionUID: 1863819475190201714L

Class contextFold.features.IntervalLengthCalculator extends java.lang.Object implements Serializable

serialVersionUID: 2732051356303135122L

Class contextFold.features.LogLengthValueFeature extends java.lang.Object implements Serializable

serialVersionUID: 6037397681940822811L

Serialized Fields

elementTypeToLengthCalculator

java.util.Map<K,V> elementTypeToLengthCalculator

Class contextFold.features.SinglePosContext extends ContextFeatureExtractor implements Serializable

serialVersionUID: -5234559063914379876L

Serialized Fields

offsets

int[] offsets

alphabetIx

int alphabetIx

currWord

byte[] currWord

effectiveCardinality

int effectiveCardinality

Class contextFold.features.SparseFeatureVector extends AbstractFeatureVector implements Serializable

serialVersionUID: -8553992343906370592L

Serialized Fields

weights

java.util.Map<K,V> weights

Class contextFold.features.ValueCalculator extends java.lang.Object implements Serializable

serialVersionUID: 6589412360512776664L


Package contextFold.rnaFolding

Class contextFold.rnaFolding.StructureRecognizerImpl extends java.lang.Object implements Serializable

serialVersionUID: -3466539402528122226L

Serialized Fields

numTypes

int numTypes

typeNames

java.util.Map<K,V> typeNames

FIRST_BASE_TYPE

int FIRST_BASE_TYPE

LAST_BASE_TYPE

int LAST_BASE_TYPE

BASE_TYPES_NUM

int BASE_TYPES_NUM

HP_BASE

int HP_BASE

IL_BASE

int[][] IL_BASE

ML_BASE

int ML_BASE

XI_BASE_5

int XI_BASE_5

XI_BASE_3

int XI_BASE_3

XI_BASE_MID

int XI_BASE_MID

IL_MEDIUM

int[] IL_MEDIUM

IL_LONG

int[] IL_LONG

IL_MEDIUM_MAX_TOTAL_LENGTH

int IL_MEDIUM_MAX_TOTAL_LENGTH

FIRST_LOOP_TERMINATION_TYPE

int FIRST_LOOP_TERMINATION_TYPE

LAST_LOOP_TERMINATION_TYPE

int LAST_LOOP_TERMINATION_TYPE

LOOP_TERMINATION_TYPES_NUM

int LOOP_TERMINATION_TYPES_NUM

HP_CLOSE

int[] HP_CLOSE

IL_CLOSE

int[][] IL_CLOSE

IL_OPEN

int[][] IL_OPEN

ML_CLOSE

int ML_CLOSE

ML_OPEN

int ML_OPEN

XL_OPEN

int XL_OPEN

HP_MAX_IX

int HP_MAX_IX

IL_SHORT_MAX_IX

int IL_SHORT_MAX_IX

IL_MAX_IX

int IL_MAX_IX

FIRST_LENGTH_TYPE

int FIRST_LENGTH_TYPE

LAST_LENGTH_TYPE

int LAST_LENGTH_TYPE

LENGTH_TYPES_NUM

int LENGTH_TYPES_NUM

HP_LENGTH

int HP_LENGTH

IL_MEDIUM_LENGTH

int[] IL_MEDIUM_LENGTH

XI_LENGTH_5

int XI_LENGTH_5

XI_LENGTH_3

int XI_LENGTH_3

XI_LENGTH_MID

int XI_LENGTH_MID