Serialized Form
|
Package org.biojava.bibliography |
wrapped
Annotation wrapped
changer
ChangeTable changer
properties
Map<K,V> properties
wrapped
Annotation wrapped
mapper
PropertyChanger mapper
properties
Map<K,V> properties
properties
Map<K,V> properties
mergeSet
List<E> mergeSet
parent
Annotation parent
overlay
Map<K,V> overlay
properties
Map<K,V> properties
- The properties map. This may be null if no property values have
yet been set.
properties
Map<K,V> properties
|
Package org.biojava.bio.alignment |
|
Package org.biojava.bio.annodb |
method
Method method
|
Package org.biojava.bio.chromatogram |
|
Package org.biojava.bio.dist |
serialVersionUID: 1406135308618188893L
alphabet
Alphabet alphabet
firstA
Alphabet firstA
lastA
Alphabet lastA
nullModel
Distribution nullModel
writeReplace
private Object writeReplace()
throws ObjectStreamException
- Throws:
ObjectStreamException
serialVersionUID: 88622317L
alpha
Alphabet alpha
serialVersionUID: -1764931829553447679L
readObject
private void readObject(ObjectInputStream stream)
throws IOException,
ClassNotFoundException
- Throws:
IOException
ClassNotFoundException
writeObject
private void writeObject(ObjectOutputStream oos)
throws IOException
- Throws:
IOException
alpha
FiniteAlphabet alpha
first
Distribution first
second
Distribution second
alphabet
Alphabet alphabet
serialVersionUID: 7252850540926095728L
readObject
private void readObject(ObjectInputStream stream)
throws IOException,
ClassNotFoundException
- Throws:
IOException
ClassNotFoundException
writeObject
private void writeObject(ObjectOutputStream oos)
throws IOException
- Throws:
IOException
nullModel
Distribution nullModel
alpha
FiniteAlphabet alpha
dis
Distribution dis
- Deprecated.
c
Map<K,V> c
- Deprecated.
distToTrainer
Map<K,V> distToTrainer
trainers
Set<E> trainers
nullModelWeight
double nullModelWeight
other
Distribution other
delegate
Distribution delegate
table
ReversibleTranslationTable table
serialVersionUID: 88454038L
alphabet
FiniteAlphabet alphabet
nullModel
Distribution nullModel
|
Package org.biojava.bio.dp |
sym
SymbolList sym
index
int index
from
State from
to
State to
writeReplace
private Object writeReplace()
throws ObjectStreamException
- Throws:
ObjectStreamException
columns
int columns
- The number of columns in this model.
matchStates
EmissionState[] matchStates
- Match states array.
matchStates[0] == matchStates[columns+1] == magicalState().
insertStates
EmissionState[] insertStates
- Insert states array.
From 0 .. columns().
deleteStates
DotState[] deleteStates
- Delete states array.
From 0 .. columns()-1 corresponding to indexes 1..columns().
dis
Distribution dis
name
String name
ann
Annotation ann
advance
int[] advance
matches
Alphabet matches
serialVersionUID: -3043028839927615753L
emissionAlpha
Alphabet emissionAlpha
stateAlpha
FiniteAlphabet stateAlpha
magicalState
MagicalState magicalState
transFrom
Map<K,V> transFrom
transTo
Map<K,V> transTo
transWeights
Map<K,V> transWeights
model
MarkovModel model
models
Set<E> models
score
double score
delegate
Alignment delegate
serialVersionUID: 73394340224964858L
columns
Distribution[] columns
alpha
Alphabet alpha
trainer
TransitionTrainer trainer
from
State from
to
State to
from
State from
to
State to
matrix
WeightMatrix matrix
threshold
double threshold
scoreType
ScoreType scoreType
wmID
String wmID
wm
WeightMatrix wm
stateAlpha
FiniteAlphabet stateAlpha
magicalState
MagicalState magicalState
states
EmissionState[] states
transFrom
Map<K,V> transFrom
transTo
Map<K,V> transTo
transWeights
Map<K,V> transWeights
|
Package org.biojava.bio.dp.onehead |
emissionsProb
HashMap<K,V> emissionsProb
emissionsOdds
HashMap<K,V> emissionsOdds
emissionsNull
HashMap<K,V> emissionsNull
states
State[] states
model
MarkovModel model
symList
SymbolList[] symList
scores
double[][] scores
score
double score
|
Package org.biojava.bio.dp.twohead |
dp
DP dp
eMap
Map<K,V> eMap
alpha
Alphabet alpha
states
State[] states
dsi
int dsi
scoreType
ScoreType scoreType
gap
Symbol[] gap
states
State[] states
seqs
SymbolList[] seqs
scores
double[][][] scores
model
MarkovModel model
finalScore
double finalScore
emissionCache
HashMap<K,V> emissionCache
ccFactory
CellCalculatorFactory ccFactory
|
Package org.biojava.bio.gui |
dist
Distribution dist
- The dist to render.
logoPainter
LogoPainter logoPainter
- The logoPainter property.
style
SymbolStyle style
- The style property.
scaleByInformation
boolean scaleByInformation
- The information/plain property
blockPainter
BlockPainter blockPainter
renderingHints
RenderingHints renderingHints
root
String root
seqs
ArrayList<E> seqs
|
Package org.biojava.bio.gui.sequence |
beadDepth
double beadDepth
beadDisplacement
double beadDisplacement
beadOutline
Paint beadOutline
beadFill
Paint beadFill
beadStroke
Stroke beadStroke
delegates
Map<K,V> delegates
delegationCache
Map<K,V> delegationCache
source
FeatureSource source
digestFilter
FeatureFilter digestFilter
laneMap
Map<K,V> laneMap
laneCount
int laneCount
distanceBetween
int distanceBetween
label
Object label
renderer
BasicFeatureRenderer renderer
imageMap
ImageMap imageMap
urlFactory
URLFactory urlFactory
leadingPixles
int leadingPixles
trailingPixles
int trailingPixles
contextCache
CacheMap contextCache
flushers
Set<E> flushers
ctxt
CircularRendererContext ctxt
symList
SymbolList symList
radius
double radius
renderer
CircularRenderer renderer
offset
double offset
dimensionRatio
double dimensionRatio
filter
FeatureFilter filter
recurse
boolean recurse
contextCache
CacheMap contextCache
flushers
Set<E> flushers
serialVersionUID: 7005846487574725181L
depth
double depth
fList
List<E> fList
gList
List<E> gList
name
String name
hotSpots
List<E> hotSpots
type
String type
url
URL url
coordinates
Integer[] coordinates
userObject
Object userObject
hotSpots
List<E> hotSpots
renderers
List<E> renderers
renderer
SequenceRenderer renderer
padding
double padding
line
Line2D.Float line
line is the line to be drawn for each feature.
outline
Paint outline
outline is the line colour.
filter
FeatureFilter filter
filter is the filter applied to both
FeatureHolders.
recurse
boolean recurse
recurse indicates whether the filter should
recurse through any subfeatures.
subContextCache
CacheMap subContextCache
cacheFlushers
Set<E> cacheFlushers
renderer
PairwiseSequenceRenderer renderer
renderers
List<E> renderers
sequence
Sequence sequence
translation
int translation
direction
int direction
secSequence
Sequence secSequence
secTranslation
int secTranslation
secDirection
int secDirection
scale
double scale
renderer
PairwiseSequenceRenderer renderer
hints
RenderingHints hints
leadingBorder
SequenceRenderContext.Border leadingBorder
trailingBorder
SequenceRenderContext.Border trailingBorder
propertyListener
PropertyChangeListener propertyListener
repaintListener
ChangeListener repaintListener
layoutListener
ChangeListener layoutListener
svSupport
SequenceViewerSupport svSupport
mouseListener
MouseListener mouseListener
svmSupport
SequenceViewerMotionSupport svmSupport
mouseMotionListener
MouseMotionListener mouseMotionListener
defaultPaint
Paint defaultPaint
rect
Rectangle2D rect
scaleHeight
boolean scaleHeight
renderer
RectangularBeadRenderer renderer
imageMap
ImageMap imageMap
urlFactory
URLFactory urlFactory
rect
RoundRectangle2D rect
arcWidth
double arcWidth
arcHeight
double arcHeight
sequence
SymbolList sequence
range
RangeLocation range
direction
int direction
scale
double scale
pixelOffset
double pixelOffset
leadingBorder
SequenceRenderContext.Border leadingBorder
trailingBorder
SequenceRenderContext.Border trailingBorder
renderer
SequenceRenderer renderer
theMonitor
org.biojava.bio.gui.sequence.SequencePanel.RendererMonitor theMonitor
hints
RenderingHints hints
svSupport
SequenceViewerSupport svSupport
mouseListener
MouseListener mouseListener
svmSupport
SequenceViewerMotionSupport svmSupport
mouseMotionListener
MouseMotionListener mouseMotionListener
layoutListener
ChangeListener layoutListener
repaintListener
ChangeListener repaintListener
pcs
PropertyChangeSupport pcs
size
double size
alignment
int alignment
serialVersionUID: 8749249181471157230L
seqPanels
SequencePanel[] seqPanels
range
RangeLocation range
sequence
Sequence sequence
renderer
SequenceRenderer renderer
scale
double scale
hints
RenderingHints hints
direction
int direction
trackLayout
TrackLayout trackLayout
viewerListeners
List<E> viewerListeners
motionListeners
List<E> motionListeners
sequence
Sequence sequence
- Deprecated.
direction
int direction
- Deprecated.
scale
double scale
- Deprecated.
lines
int lines
- Deprecated.
spacer
int spacer
- Deprecated.
leadingBorder
SequenceRenderContext.Border leadingBorder
- Deprecated.
trailingBorder
SequenceRenderContext.Border trailingBorder
- Deprecated.
renderer
SequenceRenderer renderer
- Deprecated.
offsets
double[] offsets
- Deprecated.
realLines
int realLines
- Deprecated.
alongDim
double alongDim
- Deprecated.
acrossDim
double acrossDim
- Deprecated.
symbolsPerLine
int symbolsPerLine
- Deprecated.
theMonitor
org.biojava.bio.gui.sequence.SequencePoster.RendererMonitor theMonitor
- Deprecated.
renderingHints
RenderingHints renderingHints
- Deprecated.
svSupport
SequenceViewerSupport svSupport
- Deprecated.
mouseListener
MouseListener mouseListener
- Deprecated.
svmSupport
SequenceViewerMotionSupport svmSupport
- Deprecated.
mouseMotionListener
MouseMotionListener mouseMotionListener
- Deprecated.
layoutListener
ChangeListener layoutListener
- Deprecated.
repaintListener
ChangeListener repaintListener
- Deprecated.
pcs
PropertyChangeSupport pcs
size
double size
alignment
int alignment
size
double size
alignment
int alignment
renderer
SequenceRenderer renderer
path
List<E> path
target
Object target
mouseEvent
MouseEvent mouseEvent
pos
int pos
pane
SixFrameRenderer pane
serialVersionUID: 3269477379497205817L
sequence
SymbolList sequence
translation
int translation
direction
int direction
scale
double scale
renderer
SequenceRenderer renderer
rendererBorders
double rendererBorders
hints
RenderingHints hints
leadingBorder
SequenceRenderContext.Border leadingBorder
trailingBorder
SequenceRenderContext.Border trailingBorder
propertyListener
PropertyChangeListener propertyListener
repaintListener
ChangeListener repaintListener
layoutListener
ChangeListener layoutListener
svSupport
SequenceViewerSupport svSupport
mouseListener
MouseListener mouseListener
svmSupport
SequenceViewerMotionSupport svmSupport
mouseMotionListener
MouseMotionListener mouseMotionListener
outline
Paint outline
fill
Paint fill
blockDepth
double blockDepth
renderer
ZiggyFeatureRenderer renderer
imageMap
ImageMap imageMap
urlFactory
URLFactory urlFactory
|
Package org.biojava.bio.molbio |
name
String name
site
SymbolList site
cutType
int cutType
dsCutPositions
int[] dsCutPositions
usCutPositions
int[] usCutPositions
forwardRegex
String forwardRegex
reverseRegex
String reverseRegex
summary
String summary
enzyme
RestrictionEnzyme enzyme
enzyme RestrictionEnzyme field.
|
Package org.biojava.bio.program.abi |
|
Package org.biojava.bio.program.das.dasalignment |
|
Package org.biojava.bio.program.gff |
|
Package org.biojava.bio.program.hmmer |
j
EmissionState j
c
EmissionState c
n
EmissionState n
hmmState
ModelInState hmmState
|
Package org.biojava.bio.program.homologene |
|
Package org.biojava.bio.program.phred |
mListeners
Vector<E> mListeners
lineWidth
int lineWidth
- The line width for output.
|
Package org.biojava.bio.program.ssaha |
|
Package org.biojava.bio.proteomics |
readResolve
protected Object readResolve()
throws ObjectStreamException
- Prevent duplication of the object during Serialization
- Throws:
ObjectStreamException
cleavageResidues
SymbolList cleavageResidues
notCleaveResidues
SymbolList notCleaveResidues
endoProtease
boolean endoProtease
name
String name
|
Package org.biojava.bio.search |
cachedOutcome
TriState cachedOutcome
key
Object key
test
FilterTest test
key
Object key
test
FilterTest test
key
Object key
test
FilterTest test
filter
BlastLikeSearchFilter.AbstractBlastLikeSearchFilter filter
|
Package org.biojava.bio.seq |
componentSequenceName
String componentSequenceName
componentSequence
Sequence componentSequence
componentLocation
Location componentLocation
location
Location location
type
String type
source
String source
typeTerm
Term typeTerm
sourceTerm
Term sourceTerm
annotation
Annotation annotation
c1
FeatureFilter c1
c2
FeatureFilter c2
key
Object key
value
Object value
filter
FeatureFilter filter
key
Object key
value
Object value
type
AnnotationType type
filter
FeatureFilter filter
clazz
Class<T> clazz
cname
String cname
filter
FeatureFilter filter
feature
Feature feature
minScore
double minScore
maxScore
double maxScore
score
double score
hashCode
int hashCode
filter
FeatureFilter filter
seqName
String seqName
source
String source
type
String type
loc
Location loc
frame
FramedFeature.ReadingFrame frame
key
Object key
child
FeatureFilter child
filter
FeatureFilter filter
filter
FeatureFilter filter
c1
FeatureFilter c1
c2
FeatureFilter c2
loc
Location loc
loc
Location loc
loc
Location loc
strand
StrandedFeature.Strand strand
text
String text
frame
int frame
readingFrame
FramedFeature.ReadingFrame readingFrame
featureHolders
List<E> featureHolders
regions
List<E> regions
resolver
RemoteFeature.Resolver resolver
features
List<E> features
- The child features.
schema
FeatureFilter schema
templateToImpl
List<E> templateToImpl
fallBack
FeatureRealizer fallBack
writeReplace
private Object writeReplace()
throws ObjectStreamException
- Throws:
ObjectStreamException
text
String text
value
int value
token
char token
strand
StrandedFeature.Strand strand
|
Package org.biojava.bio.seq.db |
parent
SequenceDB parent
annotator
SequenceAnnotator annotator
readObject
private void readObject(ObjectInputStream in)
throws IOException,
ClassNotFoundException
- Throws:
IOException
ClassNotFoundException
sequenceByID
Map<K,V> sequenceByID
- The sequence-by-id map.
idMaker
IDMaker idMaker
- An object to extract an ID for a sequence.
name
String name
- The name of this sequence database.
writeReplace
private Object writeReplace()
throws IOException
- Throws:
IOException
writeReplace
private Object writeReplace()
throws IOException
- Throws:
IOException
idMaker
IDMaker idMaker
indexStore
IndexStore indexStore
parent
SequenceDB parent
ids
Set<E> ids
readObject
private void readObject(ObjectInputStream in)
throws IOException,
ClassNotFoundException
- Throws:
IOException
ClassNotFoundException
storeFile
File storeFile
indexFile
File indexFile
name
String name
files
Set<E> files
seqFileIndex
File[] seqFileIndex
format
SequenceFormat format
sbFactory
SequenceBuilderFactory sbFactory
symbolParser
SymbolTokenization symbolParser
|
Package org.biojava.bio.seq.homol |
homology
Homology homology
sibling
SimilarityPairFeature sibling
sibling SimilarityPairFeature
field. May be null if the reciprocal
SimilarityPairFeature has not yet been
created.
alignment
Alignment alignment
alignment Alignment field.
score
double score
score of the search which produced the
alignment.
|
Package org.biojava.bio.seq.impl |
pfh
ProjectedFeatureHolder pfh
origSeq
Sequence origSeq
featureHolder
SimpleFeatureHolder featureHolder
- The FeatureHolder that we will delegate the FeatureHolder interface too.
This is lazily instantiated.
loc
Location loc
- The location of this feature.
type
String type
- The type of this feature - something like Exon.
This is included for cheap interoperability with GFF.
source
String source
- The source of this feature - the program that generated it.
This is included for cheap interoperability with GFF.
parent
FeatureHolder parent
- Our parent FeatureHolder.
annotation
Annotation annotation
- The annotation object.
This is lazily instantiated.
typeTerm
Term typeTerm
sourceTerm
Term sourceTerm
readingFrame
FramedFeature.ReadingFrame readingFrame
sequence
Sequence sequence
features
MergeFeatureHolder features
localFeatures
SimpleFeatureHolder localFeatures
projectedFeatures
FeatureHolder projectedFeatures
createOnUnderlying
boolean createOnUnderlying
homology
Homology homology
regions
List<E> regions
resolver
RemoteFeature.Resolver resolver
enzyme
RestrictionEnzyme enzyme
position
int position
symList
SymbolList symList
- Delegate SymbolList.
urn
String urn
name
String name
annotation
Annotation annotation
featureHolder
SimpleFeatureHolder featureHolder
realizer
FeatureRealizer realizer
sibling
SimilarityPairFeature sibling
alignment
Alignment alignment
score
double score
strand
StrandedFeature.Strand strand
parent
Sequence parent
symbols
SymbolList symbols
name
String name
uri
String uri
annotation
Annotation annotation
parentLocation
RangeLocation parentLocation
parentLocation
RangeLocation parentLocation
remoteLocationFilter
FeatureFilter remoteLocationFilter
clippingFilter
FeatureFilter clippingFilter
serialVersionUID: 9866447L
readObject
private void readObject(ObjectInputStream s)
throws IOException,
ClassNotFoundException
- Throws:
IOException
ClassNotFoundException
seqDelegate
Sequence seqDelegate
- Delegate Sequence.
exposedFeatures
MergeFeatureHolder exposedFeatures
- FeatureHolder support
addedFeatures
SimpleFeatureHolder addedFeatures
name
String name
- IDs
urn
String urn
anno
Annotation anno
- Our annotation.
|
Package org.biojava.bio.seq.io |
alphabet
Alphabet alphabet
symbolsToStrings
Map<K,V> symbolsToStrings
caseSensitive
boolean caseSensitive
initiated
boolean initiated
width
int width
alphabet
Alphabet alphabet
symbolsToCharacters
Map<K,V> symbolsToCharacters
charactersToSymbols
Map<K,V> charactersToSymbols
caseSensitive
boolean caseSensitive
subTokenizations
List<E> subTokenizations
elideSymbols
boolean elideSymbols
- Deprecated.
mListeners
Vector<E> mListeners
- Deprecated.
delegateFactory
SequenceBuilderFactory delegateFactory
delegateFactory
SequenceBuilderFactory delegateFactory
mListeners
Vector<E> mListeners
- Deprecated.
lineWidth
int lineWidth
- Deprecated.
- The line width for output.
mListeners
Vector<E> mListeners
- Deprecated.
elideSymbols
boolean elideSymbols
- Deprecated.
delegateFactory
SequenceBuilderFactory delegateFactory
m_xmlParser
SAXParser m_xmlParser
- Deprecated.
m_handler
org.biojava.bio.seq.io.GenbankXmlFormat.GenbankXmlHandler m_handler
- Deprecated.
m_parsed
boolean m_parsed
- Deprecated.
m_sequenceIndex
int m_sequenceIndex
- Deprecated.
caseSensitive
boolean caseSensitive
delegateFactory
SequenceBuilderFactory delegateFactory
sciNameKey
String sciNameKey
commonNameKey
String commonNameKey
ncbiTaxonKey
String ncbiTaxonKey
taxonFactory
TaxonFactory taxonFactory
taxonParser
TaxonParser taxonParser
delegateFactory
SequenceBuilderFactory delegateFactory
properties
Map<K,V> properties
- Deprecated.
- The properties map. This may be null if no property values have
yet been set.
delegateFactory
SequenceBuilderFactory delegateFactory
alphabet
Alphabet alphabet
|
Package org.biojava.bio.seq.projection |
context
ProjectionContext context
topLevelFeatures
FeatureHolder topLevelFeatures
parent
FeatureHolder parent
wrapped
FeatureHolder wrapped
translation
int translation
oppositeStrand
boolean oppositeStrand
|
Package org.biojava.bio.structure |
serialVersionUID: 62946250941673093L
|
Package org.biojava.bio.structure.gui |
serialVersionUID: 0L
abortB
JButton abortB
tab1
PDBDirPanel tab1
tab2
PDBUploadPanel tab2
tab3
PDBServerPanel tab3
thread
Thread thread
alicalc
AlignmentCalc alicalc
tabPane
JTabbedPane tabPane
progress
JProgressBar progress
serialVersionUID: -1720879395453257846L
_bufImage
BufferedImage _bufImage
matrix
Matrix matrix
saturation
float saturation
scalevalue
float scalevalue
scale
float scale
fragmentPairs
FragmentPair[] fragmentPairs
aligs
AlternativeAlignment[] aligs
selectedAlignmentPos
int selectedAlignmentPos
params
StrucAligParameters params
serialVersionUID: -8082261434322968652L
mPanel
JMatrixPanel mPanel
slider
JSlider slider
scroll
JScrollPane scroll
serialVersionUID: -1829252532712454236L
structure1
Structure structure1
structure2
Structure structure2
alig
AlternativeAlignment alig
structurePairAligner
StructurePairAligner structurePairAligner
panel1
SequenceScalePanel panel1
panel2
SequenceScalePanel panel2
residueSizeSlider
JSlider residueSizeSlider
percentageDisplay
JLabel percentageDisplay
idx1
int[] idx1
idx2
int[] idx2
logger
Logger logger
apos
List<E> apos
scale
float scale
mouseListener1
SequenceMouseListener mouseListener1
mouseListener2
SequenceMouseListener mouseListener2
label1
JLabel label1
label2
JLabel label2
|
Package org.biojava.bio.structure.gui.util |
serialVersionUID: 0L
aligs
AlternativeAlignment[] aligs
panel
JPanel panel
structure1
Structure structure1
structure2
Structure structure2
structurePairAligner
StructurePairAligner structurePairAligner
serialVersionUID: -5682120627824627408L
debug
boolean debug
pdbDir
JTextField pdbDir
f1
JTextField f1
f2
JTextField f2
c1
JTextField c1
c2
JTextField c2
serialVersionUID: -5682120627824627408L
debug
boolean debug
pdbDir
JTextField pdbDir
f1
JTextField f1
f2
JTextField f2
c1
JTextField c1
c2
JTextField c2
serialVersionUID: 1L
filePath1
JTextField filePath1
filePath2
JTextField filePath2
serialVersionUID: 7893248902423L
logger
Logger logger
chain
Chain chain
chainLength
int chainLength
scale
float scale
seqArr
Character[] seqArr
coordManager
CoordManager coordManager
position
int position
apos
List<E> apos
|
Package org.biojava.bio.structure.io |
serialVersionUID: 219047230178423923L
|
Package org.biojava.bio.structure.jama |
serialVersionUID: 224348942390823L
L
double[][] L
- Array for internal storage of decomposition.
- internal array storage.
n
int n
- Row and column dimension (square matrix).
- matrix dimension.
isspd
boolean isspd
- Symmetric and positive definite flag.
- is symmetric and positive definite flag.
serialVersionUID: 93489734879234789L
n
int n
- Row and column dimension (square matrix).
- matrix dimension.
issymmetric
boolean issymmetric
- Symmetry flag.
- internal symmetry flag.
d
double[] d
- Arrays for internal storage of eigenvalues.
- internal storage of eigenvalues.
e
double[] e
- Arrays for internal storage of eigenvalues.
- internal storage of eigenvalues.
V
double[][] V
- Array for internal storage of eigenvectors.
- internal storage of eigenvectors.
H
double[][] H
- Array for internal storage of nonsymmetric Hessenberg form.
- internal storage of nonsymmetric Hessenberg form.
ort
double[] ort
- Working storage for nonsymmetric algorithm.
- working storage for nonsymmetric algorithm.
serialVersionUID: 9271028462937843L
LU
double[][] LU
- Array for internal storage of decomposition.
- internal array storage.
m
int m
- Row and column dimensions, and pivot sign.
- column dimension.
n
int n
- Row and column dimensions, and pivot sign.
- column dimension.
pivsign
int pivsign
- Row and column dimensions, and pivot sign.
- column dimension.
piv
int[] piv
- Internal storage of pivot vector.
- pivot vector.
serialVersionUID: 8492558293015348719L
A
double[][] A
- Array for internal storage of elements.
- internal array storage.
m
int m
- Row and column dimensions.
- row dimension.
n
int n
- Row and column dimensions.
- row dimension.
serialVersionUID: 10293720387423L
QR
double[][] QR
- Array for internal storage of decomposition.
- internal array storage.
m
int m
- Row and column dimensions.
- column dimension.
n
int n
- Row and column dimensions.
- column dimension.
Rdiag
double[] Rdiag
- Array for internal storage of diagonal of R.
- diagonal of R.
serialVersionUID: 640239472093534756L
U
double[][] U
- Arrays for internal storage of U and V.
- internal storage of U.
V
double[][] V
- Arrays for internal storage of U and V.
- internal storage of U.
s
double[] s
- Array for internal storage of singular values.
- internal storage of singular values.
m
int m
- Row and column dimensions.
- row dimension.
n
int n
- Row and column dimensions.
- row dimension.
|
Package org.biojava.bio.symbol |
serialVersionUID: -3043128839927615753L
readResolve
protected Object readResolve()
throws ObjectStreamException
- To prevent duplication of a what should be a
single instance of an existing alphabet. This method
was written as protected so that subclasses even from
other packages will inherit it. It should only be overridden
with care.
- Throws:
ObjectStreamException
tokenizationsByName
Map<K,V> tokenizationsByName
ambCache
Map<K,V> ambCache
registered
boolean registered
readObject
private void readObject(ObjectInputStream stream)
throws IOException,
ClassNotFoundException
- Throws:
IOException
ClassNotFoundException
chunks
SymbolList[] chunks
chunkSize
int chunkSize
alpha
Alphabet alpha
length
int length
syms
Symbol[] syms
placeHolder
byte placeHolder
writeReplace
private Object writeReplace()
throws ObjectStreamException
- Throws:
ObjectStreamException
alphabets
List<E> alphabets
doubleToSym
WeakValueHashMap doubleToSym
minVal
double minVal
maxVal
double maxVal
matches
Alphabet matches
val
double val
matches
Alphabet matches
readResolve
protected Object readResolve()
throws ObjectStreamException
- To prevent duplication of a what should be a
single instance of an existing alphabet. This method
was written as protected so that subclasses even from
other packages will inherit it. It should only be overridden
with care.
- Throws:
ObjectStreamException
min
double min
max
double max
name
String name
sym
Symbol sym
alpha
Alphabet alpha
length
int length
pos
int pos
length
int length
replacement
SymbolList replacement
name
String name
annotation
Annotation annotation
outerMin
int outerMin
innerMin
int innerMin
innerMax
int innerMax
outerMax
int outerMax
mIsMinFuzzy
boolean mIsMinFuzzy
mIsMaxFuzzy
boolean mIsMaxFuzzy
resolver
FuzzyLocation.RangeResolver resolver
min
int min
max
int max
resolver
FuzzyPointLocation.PointResolver resolver
sym
Symbol sym
writeReplace
private Object writeReplace()
throws ObjectStreamException
- Throws:
ObjectStreamException
intToSym
WeakValueHashMap intToSym
- Canonicalization map for ints and references to symbols.
val
int val
matches
Alphabet matches
min
int min
max
int max
name
String name
componentLocations
List<E> componentLocations
packing
Packing packing
syms
long[] syms
length
int length
symsPerElement
byte symsPerElement
mask
byte mask
currentMin
int currentMin
currentMax
int currentMax
currentWord
long currentWord
wordsize
int wordsize
point
int point
- The actual index contained.
min
int min
- The minimum point contained.
max
int max
- The maximum point contained.
serialVersionUID: -1760075176220928440L
labelToSymbolList
LinkedHashMap<K,V> labelToSymbolList
labels
List<E> labels
alphabet
Alphabet alphabet
length
int length
serialVersionUID: 216254146L
name
String name
annotation
Annotation annotation
symbols
Set<E> symbols
alphabets
List<E> alphabets
- A list of alphabets that make up this one - a singleton list containing
this.
writeReplace
private Object writeReplace()
serialVersionUID: 4258621048300499709L
alpha
Alphabet alpha
- The Alphabet - the same as source but guaranteed to include the gap character.
source
SymbolList source
- The SymbolList to view.
blocks
ArrayList<E> blocks
- The list of ungapped blocks that align between source and this view.
length
int length
- The total length of the alignment - necessary to allow leading & trailing gaps.
serialVersionUID: 4090888450309921439L
sourceStart
int sourceStart
sourceEnd
int sourceEnd
viewStart
int viewStart
viewEnd
int viewEnd
table_num
int table_num
description
String description
transMap
Map<K,V> transMap
revMap
Map<K,V> revMap
source
FiniteAlphabet source
target
Alphabet target
transMap
Map<K,V> transMap
revMap
Map<K,V> revMap
source
FiniteAlphabet source
target
Alphabet target
serialVersionUID: -9015317520644706924L
alphabet
Alphabet alphabet
symbols
Symbol[] symbols
length
int length
isView
boolean isView
viewOffset
int viewOffset
referenceSymbolList
SymbolList referenceSymbolList
transMap
Map<K,V> transMap
source
FiniteAlphabet source
target
Alphabet target
sym
AtomicSymbol sym
alphabets
List<E> alphabets
alphabet
FiniteAlphabet alphabet
root
SuffixTree.SuffixNode root
indexer
AlphabetIndex indexer
counts
List<E> counts
|
Package org.biojava.bio.taxa |
|
Package org.biojava.directory |
|
Package org.biojava.ontology |
serialVersionUID: -8064461497813727957L
terms
Map<K,V> terms
triples
Set<E> triples
subjectTriples
Map<K,V> subjectTriples
objectTriples
Map<K,V> objectTriples
relationTriples
Map<K,V> relationTriples
remoteTerms
Map<K,V> remoteTerms
localRemoteTerms
Set<E> localRemoteTerms
name
String name
description
String description
ops
OntologyOps ops
ontology
Ontology ontology
target
Ontology target
synonyms
Set<E> synonyms
serialVersionUID: 922700041939183676L
ontology
Ontology ontology
remoteTerm
Term remoteTerm
name
String name
synonyms
Set<E> synonyms
serialVersionUID: 6561668917514377417L
name
String name
ontology
Ontology ontology
annotation
Annotation annotation
synonyms
Set<E> synonyms
serialVersionUID: 3807331980372839221L
subject
Term subject
object
Term object
predicate
Term predicate
name
String name
description
String description
synonyms
Set<E> synonyms
|
Package org.biojava.stats.svm |
posClass
Set<E> posClass
negClass
Set<E> negClass
lambda
double lambda
- The scale vactor.
nested
SVMKernel nested
- The SVMKernel being wrapped.
order
double order
a
double a
c
double c
width
double width
size
int size
keys
int[] keys
values
double[] values
s
SparseVector s
- The sparse vector that performes the normalization.
|
Package org.biojava.stats.svm.tools |
target
SVMTarget target
model
SVMClassifierModel model
addPos
boolean addPos
posShape
Shape posShape
negShape
Shape negShape
svPaint
Paint svPaint
plainPaint
Paint plainPaint
posPaint
Paint posPaint
negPaint
Paint negPaint
kernel
SVMKernel kernel
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
BitSet bSet
|
Package org.biojava.utils |
type
ChangeType type
change
Object change
previous
Object previous
chain
ChangeEvent chain
writeReplace
private Object writeReplace()
- Make a placeholder for this object in a serialized stream.
name
String name
ourField
Field ourField
superType
ChangeType superType
change
ChangeEvent change
a
Object a
b
Object b
a
Object a
b
Object b
c
Object c
mMessage
String mMessage
locator
String locator
lineNumber
int lineNumber
character
int character
line
String line
returnCode
int returnCode
obj
Object obj
mappings
Object[] mappings
numMappings
int numMappings
readResolve
public Object readResolve()
throws ObjectStreamException
- Throws:
ObjectStreamException
className
String className
fieldName
String fieldName
|
Package org.biojava.utils.automata |
|
Package org.biojava.utils.candy |
|
Package org.biojava.utils.lsid |
serialVersionUID: 8478038493421763123L
authorityId
String authorityId
namespaceId
String namespaceId
objectId
String objectId
revisionId
String revisionId
|
Package org.biojava.utils.regex |
|
Package org.biojava.utils.xml |
writeReplace
private Object writeReplace()
throws ObjectStreamException
- Throws:
ObjectStreamException
emptyNotes
Note[] emptyNotes
|
Package org.biojavax.bio.db.biosql |
isNotNull
Method isNotNull
isNull
Method isNull
c1
BioSQLFeatureFilter c1
c2
BioSQLFeatureFilter c2
name
String name
note
Note note
term
ComparableTerm term
rank
int rank
seqName
String seqName
sourceTerm
ComparableTerm sourceTerm
sourceTermName
String sourceTermName
str
RichLocation.Strand str
typeTerm
ComparableTerm typeTerm
typeTermName
String typeTermName
loc
RichLocation loc
not
Method not
and
Method and
or
Method or
eq
Method eq
le
Method le
ge
Method ge
conjunction
Method conjunction
disjunction
Method disjunction
conjunctAdd
Method conjunctAdd
disjunctAdd
Method disjunctAdd
child
BioSQLFeatureFilter child
c1
BioSQLFeatureFilter c1
c2
BioSQLFeatureFilter c2
loc
RichLocation loc
|
Package org.biojavax.bio.seq |
featureRelationshipSet
Set<E> featureRelationshipSet
rankedCrossRefs
Set<E> rankedCrossRefs
|
Package org.biojavax.ga.exception |
|
Package org.biojavax.ga.util |
key2Weight
HashMap<K,V> key2Weight
totalWeight
double totalWeight