Serialized Form
Package contextFold.features |
serialVersionUID: 2795966210352590105L
featureNames
java.util.Map<K,V> featureNames
serialVersionUID: 359725666704635808L
firstBinSize
int firstBinSize
binSize
int binSize
serialVersionUID: 852430395486899819L
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
serialVersionUID: -7686018620402519501L
length
int length
reversedContext
ContextFeatureExtractor reversedContext
serialVersionUID: 5653817811624274914L
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
serialVersionUID: 3047027062261976385L
firstPosContext
ContextFeatureExtractor firstPosContext
secondPosContext
ContextFeatureExtractor secondPosContext
serialVersionUID: -1005827948851607113L
cardinality
int cardinality
seqFeatures
int[] seqFeatures
currProcessedSeq
byte[] currProcessedSeq
serialVersionUID: 527046066222200738L
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
serialVersionUID: 1724149770194889341L
firstVectorIx
int firstVectorIx
name
java.lang.String name
featureExtractor
FeatureExtractor featureExtractor
valueCalculator
ValueCalculator valueCalculator
initWeights
java.util.Map<K,V> initWeights
serialVersionUID: 1759845472683487330L
serialVersionUID: 1863819475190201714L
serialVersionUID: 2732051356303135122L
serialVersionUID: 6037397681940822811L
elementTypeToLengthCalculator
java.util.Map<K,V> elementTypeToLengthCalculator
serialVersionUID: -5234559063914379876L
offsets
int[] offsets
alphabetIx
int alphabetIx
currWord
byte[] currWord
effectiveCardinality
int effectiveCardinality
serialVersionUID: -8553992343906370592L
weights
java.util.Map<K,V> weights
serialVersionUID: 6589412360512776664L
Package contextFold.rnaFolding |
serialVersionUID: -3466539402528122226L
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