Serialized Form
servant
_Unknown_Operations servant
recoverable
boolean recoverable
Package org.Biocorba.Seqcore |
servant
_AnonymousSeq_Operations servant
servant
_PrimarySeq_Operations servant
servant
_PrimarySeqDB_Operations servant
servant
_PrimarySeqIterator_Operations servant
servant
_Seq_Operations servant
servant
_SeqDB_Operations servant
servant
_SeqFeature_Operations servant
servant
_SeqFeatureIterator_Operations servant
name
java.lang.String name
values
java.lang.String[] values
reason
java.lang.String reason
reason
java.lang.String reason
suggested_size
int suggested_size
_value
int _value
reason
java.lang.String reason
subException
java.lang.Throwable subException
- The wrapped Throwable object
subThrowable
java.lang.Throwable subThrowable
properties
java.util.Map properties
- The properties map.
This may be null if no property values have yet been set.
Package org.biojava.bio.dist |
other
Distribution other
nullModel
Distribution nullModel
scores
double[] scores
alphabet
CrossProductAlphabet alphabet
first
Distribution first
nullModel
Distribution nullModel
second
Distribution second
alphabet
FiniteAlphabet alphabet
nullModel
Distribution nullModel
weight
java.util.Map weight
c
java.util.Map c
dis
Distribution dis
distToTrainer
java.util.Map distToTrainer
nullModel
Distribution nullModel
nullModelWeight
double nullModelWeight
trainers
java.util.Set trainers
alphabet
FiniteAlphabet alphabet
nullModel
Distribution nullModel
weight
double weight
Package org.biojava.bio.dp |
index
int index
res
SymbolList res
from
State from
to
State to
mce
ModelChangeEvent mce
this$0
ModelView this$0
finalScore
double finalScore
model
MarkovModel model
scores
double[][][] scores
seqs
SymbolList[] seqs
states
State[] states
emissions
java.util.HashMap emissions
gopher
AlphabetManager.ListWrapper gopher
magicalState
EmissionState magicalState
columns
int columns
- The number of columns in this model.
deleteStates
DotState[] deleteStates
- Delete states array.
From 0 .. columns()-1 corresponding to indexes 1..columns().
insertStates
EmissionState[] insertStates
- Insert states array.
From 0 .. columns().
matchStates
EmissionState[] matchStates
- Match states array.
matchStates[0] == matchStates[columns+1] == magicalState().
advance
int[] advance
ann
Annotation ann
dis
Distribution dis
matches
Alphabet matches
name
java.lang.String name
_tran
Transition _tran
emissionAlpha
Alphabet emissionAlpha
magicalState
MagicalState magicalState
stateAlpha
FiniteAlphabet stateAlpha
transFrom
java.util.Map transFrom
transitionScores
java.util.Map transitionScores
transTo
java.util.Map transTo
_tran
Transition _tran
allTransitionTrainers
java.util.Set allTransitionTrainers
- The set of all TransitionTrainers.
model
MarkovModel model
modelToTrainer
java.util.Map modelToTrainer
- MarkovModel -> TransitionTrainer
nullModel
Distribution nullModel
nullModelWeight
double nullModelWeight
transCounts
double transCounts
transCountWeight
double transCountWeight
transitionToCount
java.util.Map transitionToCount
- Transition -> Double count
Optimization so that transition counts only need be distributed to all
listeners just prior to training.
transitionToTrainer
java.util.Map transitionToTrainer
- Transition -> Set
delegate
Alignment delegate
score
double score
_tran
Transition _tran
model
MarkovModel model
transCounts
java.util.Map transCounts
alpha
Alphabet alpha
columns
Distribution[] columns
from
State from
to
State to
trainer
TransitionTrainer trainer
from
State from
to
State to
end
State end
newScore
double newScore
oldScore
double oldScore
start
State start
matrix
WeightMatrix matrix
threshold
double threshold
magicalState
MagicalState magicalState
stateAlpha
FiniteAlphabet stateAlpha
states
EmissionState[] states
wm
WeightMatrix wm
Package org.biojava.bio.gui |
dist
Distribution dist
- The dist to render.
logoPainter
LogoPainter logoPainter
- The logoPainter property.
style
SymbolStyle style
- The style property.
acrossDim
double acrossDim
alongDim
double alongDim
depths
java.util.Map depths
direction
int direction
leadingBorder
SequencePanel.Border leadingBorder
lineDepth
double lineDepth
lines
int lines
realLines
int realLines
scale
double scale
sequence
Sequence sequence
spacer
int spacer
theMonitor
org.biojava.bio.gui.SequencePanel.RendererMonitor theMonitor
trailingBorder
SequencePanel.Border trailingBorder
views
java.util.List views
alignment
int alignment
pcs
java.beans.PropertyChangeSupport pcs
size
double size
this$0
SequencePanel this$0
Package org.biojava.bio.program.gff |
Package org.biojava.bio.seq |
annotation
Annotation annotation
location
Location location
source
java.lang.String source
type
java.lang.String type
c1
FeatureFilter c1
c2
FeatureFilter c2
source
java.lang.String source
type
java.lang.String type
loc
Location loc
child
FeatureFilter child
c1
FeatureFilter c1
c2
FeatureFilter c2
loc
Location loc
fallBack
FeatureRealizer fallBack
templateToImpl
java.util.List templateToImpl
realizer
FeatureRealizer realizer
text
java.lang.String text
token
char token
value
int value
strand
StrandedFeature.Strand strand
Package org.biojava.bio.seq.db |
annotator
SequenceAnnotator annotator
parent
SequenceDB parent
parent
SequenceDB parent
idMaker
IDMaker idMaker
- An object to extract an ID for a sequence.
name
java.lang.String name
- The name of this sequence database.
sequenceByID
java.util.Map sequenceByID
- The sequence-by-id map.
files
java.util.Set files
format
SequenceFormat format
idMaker
IDMaker idMaker
idToSource
java.util.Map idToSource
indexFile
java.io.File indexFile
name
java.lang.String name
sFact
SequenceFactory sFact
symParser
SymbolParser symParser
Package org.biojava.bio.seq.io |
featureBuilder
FeatureBuilder featureBuilder
fdr
FastaDescriptionReader fdr
- The description reader.
lineWidth
int lineWidth
- The line width for output.
featureBuilder
FeatureBuilder featureBuilder
Package org.biojava.bio.symbol |
annotation
Annotation annotation
name
java.lang.String name
nameToSymbol
java.util.Map nameToSymbol
symbols
java.util.Set symbols
tokenToSymbol
java.util.Map tokenToSymbol
locations
java.util.List locations
- The list of child locations in order. Should contain only RangeLocation
instances.
max
int max
- Maximum index contained.
min
int min
- Minimum index contained.
alpha
CrossProductAlphabet alpha
parser
SymbolParser[] parser
matches
Alphabet matches
val
double val
alpha
Alphabet alpha
- The alphabet for this parser.
tokenLength
int tokenLength
- The length of each token.
tokenToSymbol
java.util.Map tokenToSymbol
- Map from token to Symbol.
alpha
Alphabet alpha
- The Alphabet - the same as source but guaranteed to include the gap character.
blocks
java.util.ArrayList blocks
- The list of ungapped blocks that align between source and this view.
length
int length
- The total length of the alignment - necisary to allow leading & trailing gaps.
source
SymbolList source
- The SymbolList to view.
res
Symbol res
matches
Alphabet matches
val
int val
alphabet
FiniteAlphabet alphabet
- The alphabet to parse names to.
nameToSymbol
java.util.Map nameToSymbol
- The map of name to symbols.
alpha
CrossProductAlphabet alpha
- The alphabet for each overlapping tuple.
order
int order
- The view order.
source
SymbolList source
- The source sequence that we will transliterate.
point
int point
- The actual index contained.
max
int max
- The maximum point contained.
min
int min
- The minimum point contained.
source
SymbolList source
- The source sequence that we will transliterate.
alphabet
CrossProductAlphabet alphabet
labels
java.util.List labels
labelToSymbolList
java.util.Map labelToSymbolList
length
int length
ambig
java.util.Set ambig
- A set of well-known ambiguity symbols.
annotation
Annotation annotation
- The annotation associated with this alphabet.
name
java.lang.String name
- The name of this alphabet.
symbols
java.util.Set symbols
- A set of the non-ambiguity symbols within the alphabet.
annotation
Annotation annotation
matches
Alphabet matches
name
java.lang.String name
token
char token
alphabet
Alphabet alphabet
length
int length
symbols
Symbol[] symbols
source
FiniteAlphabet source
target
Alphabet target
transMap
java.util.Map transMap
sym
AtomicSymbol sym
alphabet
FiniteAlphabet alphabet
counts
java.util.List counts
resList
java.util.List resList
root
SuffixTree.SuffixNode root
alphabet
FiniteAlphabet alphabet
- The alphabet to parse into.
tokenToSymbol
java.util.Map tokenToSymbol
- The map from token to symbol.
alpha
CrossProductAlphabet alpha
- The alphabet of window Symbols.
source
SymbolList source
- The source sequence that we will transliterate.
width
int width
- The width of the window.
Package org.biojava.stats.svm |
lambda
double lambda
- The scale vactor.
negClass
java.util.Set negClass
posClass
java.util.Set posClass
nested
SVMKernel nested
- The SVMKernel being wrapped.
a
double a
c
double c
order
double order
width
double width
keys
int[] keys
size
int size
values
double[] values
s
SparseVector s
- The sparse vector that performes the normalization.
Package org.biojava.stats.svm.tools |
addPos
boolean addPos
kernel
SVMKernel kernel
model
SVMClassifierModel model
negPaint
java.awt.Paint negPaint
negShape
java.awt.Shape negShape
plainPaint
java.awt.Paint plainPaint
posPaint
java.awt.Paint posPaint
posShape
java.awt.Shape posShape
svPaint
java.awt.Paint svPaint
target
SVMTarget target
depthScaler
SuffixTreeKernel.DepthScaler depthScaler
- The DepthScaler that will scale each sub-space.
This defaults to UniformScaler.
a
SuffixTreeKernel.DepthScaler a
b
SuffixTreeKernel.DepthScaler b
bSet
java.util.BitSet bSet
Package org.biojava.utils |
character
int character
line
java.lang.String line
lineNumber
int lineNumber
locator
java.lang.String locator
className
java.lang.String className
fieldName
java.lang.String fieldName
Package org.biojava.utils.contract |