Annotation wrapped
ChangeTable changer
java.util.Map<K,V> properties
Annotation wrapped
PropertyChanger mapper
java.util.Map<K,V> properties
java.util.Map<K,V> properties
java.util.List<E> mergeSet
Annotation parent
java.util.Map<K,V> overlay
java.util.Map<K,V> properties
java.util.Map<K,V> properties
java.lang.reflect.Method method
Alphabet alphabet
Alphabet firstA
Alphabet lastA
Distribution nullModel
private java.lang.Object writeReplace() throws java.io.ObjectStreamException
java.io.ObjectStreamException
Alphabet alpha
private void readObject(java.io.ObjectInputStream stream) throws java.io.IOException, java.lang.ClassNotFoundException
java.io.IOException
java.lang.ClassNotFoundException
private void writeObject(java.io.ObjectOutputStream oos) throws java.io.IOException
java.io.IOException
FiniteAlphabet alpha
Distribution first
Distribution second
Alphabet alphabet
private void readObject(java.io.ObjectInputStream stream) throws java.io.IOException, java.lang.ClassNotFoundException
java.io.IOException
java.lang.ClassNotFoundException
private void writeObject(java.io.ObjectOutputStream oos) throws java.io.IOException
java.io.IOException
Distribution nullModel
FiniteAlphabet alpha
Distribution dis
java.util.Map<K,V> c
java.util.Map<K,V> distToTrainer
java.util.Set<E> trainers
double nullModelWeight
Distribution other
Distribution delegate
ReversibleTranslationTable table
FiniteAlphabet alphabet
Distribution nullModel
SymbolList sym
int index
private java.lang.Object writeReplace() throws java.io.ObjectStreamException
java.io.ObjectStreamException
int columns
EmissionState[] matchStates
matchStates[0] == matchStates[columns+1] == magicalState().
EmissionState[] insertStates
From 0 .. columns().
DotState[] deleteStates
From 0 .. columns()-1 corresponding to indexes 1..columns().
Distribution dis
java.lang.String name
Annotation ann
int[] advance
Alphabet matches
Alphabet emissionAlpha
FiniteAlphabet stateAlpha
MagicalState magicalState
java.util.Map<K,V> transFrom
java.util.Map<K,V> transTo
java.util.Map<K,V> transWeights
MarkovModel model
java.util.Set<E> models
double score
Alignment delegate
Distribution[] columns
Alphabet alpha
TransitionTrainer trainer
State from
State to
WeightMatrix matrix
double threshold
ScoreType scoreType
java.lang.String wmID
WeightMatrix wm
FiniteAlphabet stateAlpha
MagicalState magicalState
EmissionState[] states
java.util.Map<K,V> transFrom
java.util.Map<K,V> transTo
java.util.Map<K,V> transWeights
java.util.HashMap<K,V> emissionsProb
java.util.HashMap<K,V> emissionsOdds
java.util.HashMap<K,V> emissionsNull
State[] states
MarkovModel model
SymbolList[] symList
double[][] scores
double score
DP dp
State[] states
SymbolList[] seqs
double[][][] scores
MarkovModel model
double finalScore
java.util.HashMap<K,V> emissionCache
CellCalculatorFactory ccFactory
Distribution dist
LogoPainter logoPainter
SymbolStyle style
boolean scaleByInformation
BlockPainter blockPainter
java.awt.RenderingHints renderingHints
java.lang.String root
java.util.ArrayList<E> seqs
double beadDepth
double beadDisplacement
java.awt.Paint beadOutline
java.awt.Paint beadFill
java.awt.Stroke beadStroke
java.util.Map<K,V> delegates
java.util.Map<K,V> delegationCache
FeatureSource source
FeatureFilter digestFilter
java.util.Map<K,V> laneMap
int laneCount
int distanceBetween
java.lang.Object label
BasicFeatureRenderer renderer
ImageMap imageMap
URLFactory urlFactory
int leadingPixles
int trailingPixles
CacheMap contextCache
java.util.Set<E> flushers
CircularRendererContext ctxt
SymbolList symList
double radius
CircularRenderer renderer
double offset
double dimensionRatio
FeatureFilter filter
boolean recurse
CacheMap contextCache
java.util.Set<E> flushers
double depth
java.util.List<E> fList
java.util.List<E> gList
java.lang.String name
java.util.List<E> hotSpots
java.lang.String type
java.net.URL url
java.lang.Integer[] coordinates
java.lang.Object userObject
java.util.List<E> hotSpots
java.util.List<E> renderers
SequenceRenderer renderer
double padding
java.awt.geom.Line2D.Float line
line
is the line to be drawn for each feature.java.awt.Paint outline
outline
is the line colour.FeatureFilter filter
filter
is the filter applied to both
FeatureHolder
s.boolean recurse
recurse
indicates whether the filter should
recurse through any subfeatures.CacheMap subContextCache
java.util.Set<E> cacheFlushers
PairwiseSequenceRenderer renderer
java.util.List<E> renderers
Sequence sequence
int translation
int direction
Sequence secSequence
int secTranslation
int secDirection
double scale
PairwiseSequenceRenderer renderer
java.awt.RenderingHints hints
SequenceRenderContext.Border leadingBorder
SequenceRenderContext.Border trailingBorder
java.beans.PropertyChangeListener propertyListener
ChangeListener repaintListener
ChangeListener layoutListener
SequenceViewerSupport svSupport
java.awt.event.MouseListener mouseListener
SequenceViewerMotionSupport svmSupport
java.awt.event.MouseMotionListener mouseMotionListener
java.awt.Paint defaultPaint
java.awt.geom.Rectangle2D rect
boolean scaleHeight
RectangularBeadRenderer renderer
ImageMap imageMap
URLFactory urlFactory
java.awt.geom.RoundRectangle2D rect
double arcWidth
double arcHeight
SymbolList sequence
RangeLocation range
int direction
double scale
double pixelOffset
SequenceRenderContext.Border leadingBorder
SequenceRenderContext.Border trailingBorder
SequenceRenderer renderer
org.biojava.bio.gui.sequence.SequencePanel.RendererMonitor theMonitor
java.awt.RenderingHints hints
SequenceViewerSupport svSupport
java.awt.event.MouseListener mouseListener
SequenceViewerMotionSupport svmSupport
java.awt.event.MouseMotionListener mouseMotionListener
ChangeListener layoutListener
ChangeListener repaintListener
java.beans.PropertyChangeSupport pcs
double size
int alignment
SequencePanel[] seqPanels
RangeLocation range
Sequence sequence
SequenceRenderer renderer
double scale
java.awt.RenderingHints hints
int direction
TrackLayout trackLayout
java.util.List<E> viewerListeners
java.util.List<E> motionListeners
Sequence sequence
int direction
double scale
int lines
int spacer
SequenceRenderContext.Border leadingBorder
SequenceRenderContext.Border trailingBorder
SequenceRenderer renderer
double[] offsets
int realLines
double alongDim
double acrossDim
int symbolsPerLine
org.biojava.bio.gui.sequence.SequencePoster.RendererMonitor theMonitor
java.awt.RenderingHints renderingHints
SequenceViewerSupport svSupport
java.awt.event.MouseListener mouseListener
SequenceViewerMotionSupport svmSupport
java.awt.event.MouseMotionListener mouseMotionListener
ChangeListener layoutListener
ChangeListener repaintListener
java.beans.PropertyChangeSupport pcs
double size
int alignment
double size
int alignment
SequenceRenderer renderer
java.util.List<E> path
java.lang.Object target
java.awt.event.MouseEvent mouseEvent
int pos
SixFrameRenderer pane
SymbolList sequence
int translation
int direction
double scale
SequenceRenderer renderer
double rendererBorders
java.awt.RenderingHints hints
SequenceRenderContext.Border leadingBorder
SequenceRenderContext.Border trailingBorder
java.beans.PropertyChangeListener propertyListener
ChangeListener repaintListener
ChangeListener layoutListener
SequenceViewerSupport svSupport
java.awt.event.MouseListener mouseListener
SequenceViewerMotionSupport svmSupport
java.awt.event.MouseMotionListener mouseMotionListener
java.awt.Paint outline
java.awt.Paint fill
double blockDepth
ZiggyFeatureRenderer renderer
ImageMap imageMap
URLFactory urlFactory
java.lang.String name
SymbolList site
int cutType
int[] dsCutPositions
int[] usCutPositions
java.lang.String forwardRegex
java.lang.String reverseRegex
java.lang.String summary
RestrictionEnzyme enzyme
enzyme
RestrictionEnzyme
field.EmissionState j
EmissionState c
EmissionState n
ModelInState hmmState
java.util.Vector<E> mListeners
int lineWidth
protected java.lang.Object readResolve() throws java.io.ObjectStreamException
java.io.ObjectStreamException
SymbolList cleavageResidues
SymbolList notCleaveResidues
boolean endoProtease
java.lang.String name
TriState cachedOutcome
java.lang.Object key
FilterTest test
java.lang.Object key
FilterTest test
java.lang.Object key
FilterTest test
BlastLikeSearchFilter.AbstractBlastLikeSearchFilter filter
Location location
java.lang.String type
java.lang.String source
Term typeTerm
Term sourceTerm
Annotation annotation
FeatureFilter c1
FeatureFilter c2
java.lang.Object key
java.lang.Object value
FeatureFilter filter
java.lang.Object key
java.lang.Object value
AnnotationType type
FeatureFilter filter
java.lang.Class<T> clazz
java.lang.String cname
FeatureFilter filter
Feature feature
double minScore
double maxScore
double score
int hashCode
FeatureFilter filter
java.lang.String seqName
java.lang.String source
java.lang.String type
Location loc
FramedFeature.ReadingFrame frame
java.lang.Object key
FeatureFilter child
FeatureFilter filter
FeatureFilter filter
FeatureFilter c1
FeatureFilter c2
Location loc
Location loc
Location loc
StrandedFeature.Strand strand
java.lang.String text
int frame
FramedFeature.ReadingFrame readingFrame
java.util.List<E> featureHolders
java.util.List<E> regions
RemoteFeature.Resolver resolver
java.util.List<E> features
FeatureFilter schema
java.util.List<E> templateToImpl
FeatureRealizer fallBack
private java.lang.Object writeReplace() throws java.io.ObjectStreamException
java.io.ObjectStreamException
java.lang.String text
int value
char token
StrandedFeature.Strand strand
SequenceDB parent
SequenceAnnotator annotator
private void readObject(java.io.ObjectInputStream in) throws java.io.IOException, java.lang.ClassNotFoundException
java.io.IOException
java.lang.ClassNotFoundException
java.util.Map<K,V> sequenceByID
IDMaker idMaker
java.lang.String name
private java.lang.Object writeReplace() throws java.io.IOException
java.io.IOException
private java.lang.Object writeReplace() throws java.io.IOException
java.io.IOException
IDMaker idMaker
IndexStore indexStore
SequenceDB parent
java.util.Set<E> ids
private void readObject(java.io.ObjectInputStream in) throws java.io.IOException, java.lang.ClassNotFoundException
java.io.IOException
java.lang.ClassNotFoundException
java.io.File storeFile
java.io.File indexFile
java.lang.String name
java.util.Set<E> files
java.io.File[] seqFileIndex
SequenceFormat format
SequenceBuilderFactory sbFactory
SymbolTokenization symbolParser
Homology homology
SimilarityPairFeature sibling
sibling
SimilarityPairFeature
field. May be null if the reciprocal
SimilarityPairFeature
has not yet been
created.Alignment alignment
alignment
Alignment
field.double score
score
of the search which produced the
alignment.ProjectedFeatureHolder pfh
Sequence origSeq
SimpleFeatureHolder featureHolder
Location loc
java.lang.String type
java.lang.String source
FeatureHolder parent
Annotation annotation
Term typeTerm
Term sourceTerm
FramedFeature.ReadingFrame readingFrame
Sequence sequence
MergeFeatureHolder features
SimpleFeatureHolder localFeatures
FeatureHolder projectedFeatures
boolean createOnUnderlying
Homology homology
java.util.List<E> regions
RemoteFeature.Resolver resolver
RestrictionEnzyme enzyme
int position
SymbolList symList
java.lang.String urn
java.lang.String name
Annotation annotation
SimpleFeatureHolder featureHolder
FeatureRealizer realizer
SimilarityPairFeature sibling
Alignment alignment
double score
StrandedFeature.Strand strand
Sequence parent
SymbolList symbols
java.lang.String name
java.lang.String uri
Annotation annotation
RangeLocation parentLocation
RangeLocation parentLocation
FeatureFilter remoteLocationFilter
FeatureFilter clippingFilter
private void readObject(java.io.ObjectInputStream s) throws java.io.IOException, java.lang.ClassNotFoundException
java.io.IOException
java.lang.ClassNotFoundException
Sequence seqDelegate
MergeFeatureHolder exposedFeatures
SimpleFeatureHolder addedFeatures
java.lang.String name
java.lang.String urn
Annotation anno
Alphabet alphabet
java.util.Map<K,V> symbolsToStrings
boolean caseSensitive
boolean initiated
int width
Alphabet alphabet
java.util.Map<K,V> symbolsToCharacters
java.util.Map<K,V> charactersToSymbols
boolean caseSensitive
java.util.List<E> subTokenizations
boolean elideSymbols
java.util.Vector<E> mListeners
SequenceBuilderFactory delegateFactory
SequenceBuilderFactory delegateFactory
java.util.Vector<E> mListeners
int lineWidth
java.util.Vector<E> mListeners
boolean elideSymbols
SequenceBuilderFactory delegateFactory
javax.xml.parsers.SAXParser m_xmlParser
org.biojava.bio.seq.io.GenbankXmlFormat.GenbankXmlHandler m_handler
boolean m_parsed
int m_sequenceIndex
boolean caseSensitive
SequenceBuilderFactory delegateFactory
java.lang.String sciNameKey
java.lang.String commonNameKey
java.lang.String ncbiTaxonKey
TaxonFactory taxonFactory
TaxonParser taxonParser
SequenceBuilderFactory delegateFactory
java.util.Map<K,V> properties
SequenceBuilderFactory delegateFactory
Alphabet alphabet
ProjectionContext context
FeatureHolder topLevelFeatures
FeatureHolder parent
FeatureHolder wrapped
int translation
boolean oppositeStrand
javax.swing.JButton abortB
PDBDirPanel tab1
PDBUploadPanel tab2
PDBServerPanel tab3
java.lang.Thread thread
AlignmentCalc alicalc
javax.swing.JTabbedPane tabPane
javax.swing.JProgressBar progress
java.awt.image.BufferedImage _bufImage
Matrix matrix
float saturation
float scalevalue
float scale
FragmentPair[] fragmentPairs
AlternativeAlignment[] aligs
int selectedAlignmentPos
StrucAligParameters params
JMatrixPanel mPanel
javax.swing.JSlider slider
javax.swing.JScrollPane scroll
Structure structure1
Structure structure2
AlternativeAlignment alig
StructurePairAligner structurePairAligner
SequenceScalePanel panel1
SequenceScalePanel panel2
javax.swing.JSlider residueSizeSlider
javax.swing.JLabel percentageDisplay
int[] idx1
int[] idx2
java.util.logging.Logger logger
java.util.List<E> apos
float scale
SequenceMouseListener mouseListener1
SequenceMouseListener mouseListener2
javax.swing.JLabel label1
javax.swing.JLabel label2
AlternativeAlignment[] aligs
javax.swing.JPanel panel
Structure structure1
Structure structure2
StructurePairAligner structurePairAligner
boolean debug
javax.swing.JTextField pdbDir
javax.swing.JTextField f1
javax.swing.JTextField f2
javax.swing.JTextField c1
javax.swing.JTextField c2
boolean debug
javax.swing.JTextField pdbDir
javax.swing.JTextField f1
javax.swing.JTextField f2
javax.swing.JTextField c1
javax.swing.JTextField c2
javax.swing.JTextField filePath1
javax.swing.JTextField filePath2
java.util.logging.Logger logger
Chain chain
int chainLength
float scale
java.lang.Character[] seqArr
CoordManager coordManager
int position
java.util.List<E> apos
double[][] L
int n
boolean isspd
int n
boolean issymmetric
double[] d
double[] e
double[][] V
double[][] H
double[] ort
double[][] LU
int m
int n
int pivsign
int[] piv
double[][] A
int m
int n
double[][] QR
int m
int n
double[] Rdiag
double[][] U
double[][] V
double[] s
int m
int n
protected java.lang.Object readResolve() throws java.io.ObjectStreamException
java.io.ObjectStreamException
java.util.Map<K,V> tokenizationsByName
java.util.Map<K,V> ambCache
boolean registered
private void readObject(java.io.ObjectInputStream stream) throws java.io.IOException, java.lang.ClassNotFoundException
java.io.IOException
java.lang.ClassNotFoundException
SymbolList[] chunks
int chunkSize
Alphabet alpha
int length
Symbol[] syms
byte placeHolder
private java.lang.Object writeReplace() throws java.io.ObjectStreamException
java.io.ObjectStreamException
java.util.List<E> alphabets
WeakValueHashMap doubleToSym
double minVal
double maxVal
Alphabet matches
double val
Alphabet matches
protected java.lang.Object readResolve() throws java.io.ObjectStreamException
java.io.ObjectStreamException
double min
double max
java.lang.String name
int pos
int length
SymbolList replacement
java.lang.String name
Annotation annotation
int outerMin
int innerMin
int innerMax
int outerMax
boolean mIsMinFuzzy
boolean mIsMaxFuzzy
FuzzyLocation.RangeResolver resolver
int min
int max
FuzzyPointLocation.PointResolver resolver
Symbol sym
private java.lang.Object writeReplace() throws java.io.ObjectStreamException
java.io.ObjectStreamException
WeakValueHashMap intToSym
int val
Alphabet matches
int min
int max
java.lang.String name
java.util.List<E> componentLocations
Packing packing
long[] syms
int length
byte symsPerElement
byte mask
int currentMin
int currentMax
long currentWord
int wordsize
int point
int min
int max
java.util.LinkedHashMap<K,V> labelToSymbolList
java.util.List<E> labels
Alphabet alphabet
int length
java.lang.String name
Annotation annotation
java.util.Set<E> symbols
java.util.List<E> alphabets
private java.lang.Object writeReplace()
Alphabet alpha
SymbolList source
java.util.ArrayList<E> blocks
int length
int sourceStart
int sourceEnd
int viewStart
int viewEnd
int table_num
java.lang.String description
java.util.Map<K,V> transMap
java.util.Map<K,V> revMap
FiniteAlphabet source
Alphabet target
java.util.Map<K,V> transMap
java.util.Map<K,V> revMap
FiniteAlphabet source
Alphabet target
Alphabet alphabet
Symbol[] symbols
int length
boolean isView
int viewOffset
SymbolList referenceSymbolList
java.util.Map<K,V> transMap
FiniteAlphabet source
Alphabet target
AtomicSymbol sym
java.util.List<E> alphabets
FiniteAlphabet alphabet
SuffixTree.SuffixNode root
AlphabetIndex indexer
java.util.List<E> counts
java.util.Map<K,V> terms
java.util.Set<E> triples
java.util.Map<K,V> subjectTriples
java.util.Map<K,V> objectTriples
java.util.Map<K,V> relationTriples
java.util.Map<K,V> remoteTerms
java.util.Set<E> localRemoteTerms
java.lang.String name
java.lang.String description
OntologyOps ops
java.lang.String name
Ontology ontology
Annotation annotation
java.util.Set<E> synonyms
java.util.Set<E> posClass
java.util.Set<E> negClass
double lambda
SVMKernel nested
double order
double a
double c
double width
int size
int[] keys
double[] values
SparseVector s
SVMTarget target
SVMClassifierModel model
boolean addPos
java.awt.Shape posShape
java.awt.Shape negShape
java.awt.Paint svPaint
java.awt.Paint plainPaint
java.awt.Paint posPaint
java.awt.Paint negPaint
SVMKernel kernel
SuffixTreeKernel.DepthScaler depthScaler
java.util.BitSet bSet
ChangeType type
java.lang.Object change
java.lang.Object previous
ChangeEvent chain
private java.lang.Object writeReplace()
java.lang.String name
java.lang.reflect.Field ourField
ChangeType superType
ChangeEvent change
java.lang.Object a
java.lang.Object b
java.lang.Object a
java.lang.Object b
java.lang.Object c
java.lang.String mMessage
java.lang.String locator
int lineNumber
int character
java.lang.String line
int returnCode
java.lang.Object obj
java.lang.Object[] mappings
int numMappings
public java.lang.Object readResolve() throws java.io.ObjectStreamException
java.io.ObjectStreamException
java.lang.String className
java.lang.String fieldName
java.lang.String authorityId
java.lang.String namespaceId
java.lang.String objectId
java.lang.String revisionId
private java.lang.Object writeReplace() throws java.io.ObjectStreamException
java.io.ObjectStreamException
Note[] emptyNotes
java.lang.reflect.Method isNotNull
java.lang.reflect.Method isNull
BioSQLFeatureFilter c1
BioSQLFeatureFilter c2
java.lang.String name
Note note
ComparableTerm term
int rank
java.lang.String seqName
ComparableTerm sourceTerm
java.lang.String sourceTermName
RichLocation.Strand str
ComparableTerm typeTerm
java.lang.String typeTermName
RichLocation loc
java.lang.reflect.Method not
java.lang.reflect.Method and
java.lang.reflect.Method or
java.lang.reflect.Method eq
java.lang.reflect.Method le
java.lang.reflect.Method ge
java.lang.reflect.Method conjunction
java.lang.reflect.Method disjunction
java.lang.reflect.Method conjunctAdd
java.lang.reflect.Method disjunctAdd
BioSQLFeatureFilter child
BioSQLFeatureFilter c1
BioSQLFeatureFilter c2
RichLocation loc
java.util.Set<E> featureRelationshipSet
java.util.Set<E> rankedCrossRefs
java.util.HashMap<K,V> key2Weight
double totalWeight