Serialized Form

Package org.biojava.bibliography

Class org.biojava.bibliography.BibRefException extends Exception implements Serializable

Package org.biojava.bio

Class org.biojava.bio.AbstractAnnotation extends AbstractChangeable implements Serializable

Class org.biojava.bio.AnnotationChanger extends AbstractAnnotation implements Serializable

Serialized Fields

wrapped

Annotation wrapped

changer

ChangeTable changer

properties

Map<K,V> properties

Class org.biojava.bio.AnnotationRenamer extends AbstractAnnotation implements Serializable

Serialized Fields

wrapped

Annotation wrapped

mapper

PropertyChanger mapper

properties

Map<K,V> properties

Class org.biojava.bio.BeanAsAnnotation extends AbstractAnnotation implements Serializable

Serialized Fields

properties

Map<K,V> properties

Class org.biojava.bio.BioError extends Error implements Serializable

Class org.biojava.bio.BioException extends Exception implements Serializable

Class org.biojava.bio.BioRuntimeException extends RuntimeException implements Serializable

Class org.biojava.bio.MergeAnnotation extends AbstractChangeable implements Serializable

Serialized Fields

mergeSet

List<E> mergeSet

Class org.biojava.bio.OverlayAnnotation extends AbstractChangeable implements Serializable

Serialized Fields

parent

Annotation parent

overlay

Map<K,V> overlay

Class org.biojava.bio.SimpleAnnotation extends AbstractAnnotation implements Serializable

Serialized Fields

properties

Map<K,V> properties

The properties map. This may be null if no property values have yet been set.

Class org.biojava.bio.SmallAnnotation extends AbstractAnnotation implements Serializable

Serialized Fields

properties

Map<K,V> properties

Package org.biojava.bio.alignment

Class org.biojava.bio.alignment.IllegalAlignmentEditException extends BioRuntimeException implements Serializable

Package org.biojava.bio.annodb

Class org.biojava.bio.annodb.IndexedAnnotationDB.StaticMethodRPFactory extends Object implements Serializable

Serialized Fields

method

Method method

Package org.biojava.bio.chromatogram

Class org.biojava.bio.chromatogram.UnsupportedChromatogramFormatException extends BioException implements Serializable

Package org.biojava.bio.dist

Class org.biojava.bio.dist.AbstractOrderNDistribution extends AbstractDistribution implements Serializable

serialVersionUID: 1406135308618188893L

Serialized Fields

alphabet

Alphabet alphabet

firstA

Alphabet firstA

lastA

Alphabet lastA

nullModel

Distribution nullModel

Class org.biojava.bio.dist.DistributionFactory.DefaultDistributionFactory extends Object implements Serializable

Serialization Methods

writeReplace

private Object writeReplace()
                     throws ObjectStreamException

Throws:

ObjectStreamException

Class org.biojava.bio.dist.GapDistribution extends Unchangeable implements Serializable

serialVersionUID: 88622317L

Serialized Fields

alpha

Alphabet alpha

Class org.biojava.bio.dist.IndexedCount extends AbstractChangeable implements Serializable

serialVersionUID: -1764931829553447679L

Serialization Methods

readObject

private void readObject(ObjectInputStream stream)
                 throws IOException,
                        ClassNotFoundException

Throws:

IOException

ClassNotFoundException

writeObject

private void writeObject(ObjectOutputStream oos)
                  throws IOException

Throws:

IOException

Serialized Fields

alpha

FiniteAlphabet alpha

Class org.biojava.bio.dist.PairDistribution extends AbstractChangeable implements Serializable

Serialized Fields

first

Distribution first

second

Distribution second

alphabet

Alphabet alphabet

Class org.biojava.bio.dist.SimpleDistribution extends AbstractDistribution implements Serializable

serialVersionUID: 7252850540926095728L

Serialization Methods

readObject

private void readObject(ObjectInputStream stream)
                 throws IOException,
                        ClassNotFoundException

Throws:

IOException

ClassNotFoundException

writeObject

private void writeObject(ObjectOutputStream oos)
                  throws IOException

Throws:

IOException

Serialized Fields

nullModel

Distribution nullModel

alpha

FiniteAlphabet alpha

Class org.biojava.bio.dist.SimpleDistributionTrainer extends Object implements Serializable

Serialized Fields

dis

Distribution dis

Deprecated.

c

Map<K,V> c

Deprecated.

Class org.biojava.bio.dist.SimpleDistributionTrainerContext extends Object implements Serializable

Serialized Fields

distToTrainer

Map<K,V> distToTrainer

trainers

Set<E> trainers

nullModelWeight

double nullModelWeight

Class org.biojava.bio.dist.TranslatedDistribution extends AbstractChangeable implements Serializable

Serialized Fields

other

Distribution other

delegate

Distribution delegate

table

ReversibleTranslationTable table

Class org.biojava.bio.dist.UniformDistribution extends AbstractDistribution implements Serializable

serialVersionUID: 88454038L

Serialized Fields

alphabet

FiniteAlphabet alphabet

nullModel

Distribution nullModel

Class org.biojava.bio.dist.UntrainableDistribution extends SimpleDistribution implements Serializable

Package org.biojava.bio.dp

Class org.biojava.bio.dp.BaumWelchSampler extends AbstractTrainer implements Serializable

Class org.biojava.bio.dp.BaumWelchTrainer extends AbstractTrainer implements Serializable

Class org.biojava.bio.dp.DP.ReverseIterator extends Object implements Serializable

Serialized Fields

sym

SymbolList sym

index

int index

Class org.biojava.bio.dp.IllegalTransitionException extends BioException implements Serializable

Serialized Fields

from

State from

to

State to

Class org.biojava.bio.dp.MagicalState extends SimpleEmissionState implements Serializable

Serialization Methods

writeReplace

private Object writeReplace()
                     throws ObjectStreamException

Throws:

ObjectStreamException

Class org.biojava.bio.dp.ProfileHMM extends SimpleMarkovModel implements Serializable

Serialized Fields

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().

Class org.biojava.bio.dp.ScoreType.NullModel extends Object implements Serializable

Class org.biojava.bio.dp.ScoreType.Odds extends Object implements Serializable

Class org.biojava.bio.dp.ScoreType.Probability extends Object implements Serializable

Class org.biojava.bio.dp.SimpleDotState extends FundamentalAtomicSymbol implements Serializable

Class org.biojava.bio.dp.SimpleEmissionState extends AbstractChangeable implements Serializable

Serialized Fields

dis

Distribution dis

name

String name

ann

Annotation ann

advance

int[] advance

matches

Alphabet matches

Class org.biojava.bio.dp.SimpleMarkovModel extends AbstractChangeable implements Serializable

serialVersionUID: -3043028839927615753L

Serialized Fields

emissionAlpha

Alphabet emissionAlpha

stateAlpha

FiniteAlphabet stateAlpha

magicalState

MagicalState magicalState

transFrom

Map<K,V> transFrom

transTo

Map<K,V> transTo

transWeights

Map<K,V> transWeights

Class org.biojava.bio.dp.SimpleModelInState extends FundamentalAtomicSymbol implements Serializable

Serialized Fields

model

MarkovModel model

Class org.biojava.bio.dp.SimpleModelTrainer extends SimpleDistributionTrainerContext implements Serializable

Serialized Fields

models

Set<E> models

Class org.biojava.bio.dp.SimpleStatePath extends Unchangeable implements Serializable

Serialized Fields

score

double score

delegate

Alignment delegate

Class org.biojava.bio.dp.SimpleWeightMatrix extends Object implements Serializable

serialVersionUID: 73394340224964858L

Serialized Fields

columns

Distribution[] columns

alpha

Alphabet alpha

Class org.biojava.bio.dp.TrainerTransition extends Object implements Serializable

Serialized Fields

trainer

TransitionTrainer trainer

from

State from

to

State to

Class org.biojava.bio.dp.Transition extends Object implements Serializable

Serialized Fields

from

State from

to

State to

Class org.biojava.bio.dp.WeightMatrixAnnotator extends Object implements Serializable

Serialized Fields

matrix

WeightMatrix matrix

threshold

double threshold

scoreType

ScoreType scoreType

wmID

String wmID

Class org.biojava.bio.dp.WMAsMM extends AbstractChangeable implements Serializable

Serialized Fields

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

Class org.biojava.bio.dp.onehead.SingleDP extends DP implements Serializable

Serialized Fields

emissionsProb

HashMap<K,V> emissionsProb

emissionsOdds

HashMap<K,V> emissionsOdds

emissionsNull

HashMap<K,V> emissionsNull

Class org.biojava.bio.dp.onehead.SingleDPMatrix extends Object implements Serializable

Serialized Fields

states

State[] states

model

MarkovModel model

symList

SymbolList[] symList

scores

double[][] scores

score

double score

Package org.biojava.bio.dp.twohead

Class org.biojava.bio.dp.twohead.DPInterpreter extends Object implements Serializable

Serialized Fields

dp

DP dp

Class org.biojava.bio.dp.twohead.EmissionCache extends Object implements Serializable

Serialized Fields

eMap

Map<K,V> eMap

alpha

Alphabet alpha

states

State[] states

dsi

int dsi

scoreType

ScoreType scoreType

gap

Symbol[] gap

Class org.biojava.bio.dp.twohead.PairDPMatrix extends Object implements Serializable

Serialized Fields

states

State[] states

seqs

SymbolList[] seqs

scores

double[][][] scores

model

MarkovModel model

finalScore

double finalScore

Class org.biojava.bio.dp.twohead.PairwiseDP extends DP implements Serializable

Serialized Fields

emissionCache

HashMap<K,V> emissionCache

ccFactory

CellCalculatorFactory ccFactory

Package org.biojava.bio.gui

Class org.biojava.bio.gui.DistributionLogo extends JComponent implements Serializable

Serialized Fields

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

Class org.biojava.bio.gui.FeatureTree extends JTree implements Serializable

Serialized Fields

root

String root

seqs

ArrayList<E> seqs

Package org.biojava.bio.gui.sequence

Class org.biojava.bio.gui.sequence.AbstractBeadRenderer extends AbstractChangeable implements Serializable

Serialized Fields

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

Class org.biojava.bio.gui.sequence.AbstractPeptideDigestRenderer extends MultiLineRenderer implements Serializable

Serialized Fields

source

FeatureSource source

digestFilter

FeatureFilter digestFilter

laneMap

Map<K,V> laneMap

laneCount

int laneCount

distanceBetween

int distanceBetween

Class org.biojava.bio.gui.sequence.AlignmentRenderer extends SequenceRendererWrapper implements Serializable

Serialized Fields

label

Object label

Class org.biojava.bio.gui.sequence.BasicImapRenderer extends Object implements Serializable

Serialized Fields

renderer

BasicFeatureRenderer renderer

imageMap

ImageMap imageMap

urlFactory

URLFactory urlFactory

Class org.biojava.bio.gui.sequence.BumpedRenderer extends SequenceRendererWrapper implements Serializable

Serialized Fields

leadingPixles

int leadingPixles

trailingPixles

int trailingPixles

contextCache

CacheMap contextCache

flushers

Set<E> flushers

Class org.biojava.bio.gui.sequence.CircularRendererPanel extends JComponent implements Serializable

Serialized Fields

ctxt

CircularRendererContext ctxt

symList

SymbolList symList

radius

double radius

renderer

CircularRenderer renderer

offset

double offset

Class org.biojava.bio.gui.sequence.EllipticalBeadRenderer extends AbstractBeadRenderer implements Serializable

Serialized Fields

dimensionRatio

double dimensionRatio

Class org.biojava.bio.gui.sequence.FilteringRenderer extends SequenceRendererWrapper implements Serializable

Serialized Fields

filter

FeatureFilter filter

recurse

boolean recurse

contextCache

CacheMap contextCache

flushers

Set<E> flushers

Class org.biojava.bio.gui.sequence.GappedRenderer extends SequenceRendererWrapper implements Serializable

Class org.biojava.bio.gui.sequence.GlyphFeatureRenderer extends FilteringRenderer implements Serializable

Serialized Fields

depth

double depth

fList

List<E> fList

gList

List<E> gList

Class org.biojava.bio.gui.sequence.ImageMap.ClientSide extends Object implements Serializable

Serialized Fields

name

String name

hotSpots

List<E> hotSpots

Class org.biojava.bio.gui.sequence.ImageMap.HotSpot extends Object implements Serializable

Serialized Fields

type

String type

url

URL url

coordinates

Integer[] coordinates

userObject

Object userObject

Class org.biojava.bio.gui.sequence.ImageMap.ServerSide extends Object implements Serializable

Serialized Fields

hotSpots

List<E> hotSpots

Class org.biojava.bio.gui.sequence.MultiLineRenderer extends AbstractChangeable implements Serializable

Serialized Fields

renderers

List<E> renderers

Class org.biojava.bio.gui.sequence.OverlayRendererWrapper extends AbstractChangeable implements Serializable

Serialized Fields

renderer

SequenceRenderer renderer

Class org.biojava.bio.gui.sequence.PaddingRenderer extends SequenceRendererWrapper implements Serializable

Serialized Fields

padding

double padding

Class org.biojava.bio.gui.sequence.PairwiseDiagonalRenderer extends AbstractChangeable implements Serializable

Serialized Fields

line

Line2D.Float line

line is the line to be drawn for each feature.

outline

Paint outline

outline is the line colour.

Class org.biojava.bio.gui.sequence.PairwiseFilteringRenderer extends AbstractChangeable implements Serializable

Serialized Fields

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

Class org.biojava.bio.gui.sequence.PairwiseOverlayRenderer extends AbstractChangeable implements Serializable

Serialized Fields

renderers

List<E> renderers

Class org.biojava.bio.gui.sequence.PairwiseSequencePanel extends JComponent implements Serializable

Serialized Fields

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

Class org.biojava.bio.gui.sequence.PeptideDigestRenderer extends AbstractPeptideDigestRenderer implements Serializable

Serialized Fields

defaultPaint

Paint defaultPaint

Class org.biojava.bio.gui.sequence.RectangularBeadRenderer extends AbstractBeadRenderer implements Serializable

Serialized Fields

rect

Rectangle2D rect

scaleHeight

boolean scaleHeight

Class org.biojava.bio.gui.sequence.RectangularImapRenderer extends Object implements Serializable

Serialized Fields

renderer

RectangularBeadRenderer renderer

imageMap

ImageMap imageMap

urlFactory

URLFactory urlFactory

Class org.biojava.bio.gui.sequence.RoundRectangularBeadRenderer extends AbstractBeadRenderer implements Serializable

Serialized Fields

rect

RoundRectangle2D rect

arcWidth

double arcWidth

arcHeight

double arcHeight

Class org.biojava.bio.gui.sequence.SecondaryStructureFeatureRenderer extends GlyphFeatureRenderer implements Serializable

Class org.biojava.bio.gui.sequence.SequencePanel extends JComponent implements Serializable

Serialized Fields

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

Class org.biojava.bio.gui.sequence.SequencePanel.Border extends Object implements Serializable

Serialized Fields

pcs

PropertyChangeSupport pcs

size

double size

alignment

int alignment

Class org.biojava.bio.gui.sequence.SequencePanelWrapper extends JPanel implements Serializable

Serialized Fields

range

RangeLocation range

sequence

Sequence sequence

seqPanels

SequencePanel[] seqPanels

renderer

SequenceRenderer renderer

scale

double scale

hints

RenderingHints hints

direction

int direction

trackLayout

TrackLayout trackLayout

viewerListeners

List<E> viewerListeners

motionListeners

List<E> motionListeners

Class org.biojava.bio.gui.sequence.SequencePoster extends JComponent implements Serializable

Serialized Fields

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.

Class org.biojava.bio.gui.sequence.SequencePoster.Border extends Object implements Serializable

Serialized Fields

pcs

PropertyChangeSupport pcs

size

double size

alignment

int alignment

Class org.biojava.bio.gui.sequence.SequenceRenderContext.Border extends Object implements Serializable

Serialized Fields

size

double size

alignment

int alignment

Class org.biojava.bio.gui.sequence.SequenceRendererWrapper extends AbstractChangeable implements Serializable

Serialized Fields

renderer

SequenceRenderer renderer

Class org.biojava.bio.gui.sequence.SequenceViewerEvent extends EventObject implements Serializable

Serialized Fields

path

List<E> path

target

Object target

mouseEvent

MouseEvent mouseEvent

pos

int pos

Class org.biojava.bio.gui.sequence.SixFrameZiggyRenderer extends AbstractChangeable implements Serializable

Serialized Fields

pane