Serialized Form

Package org.biojava.bio.gui

Class org.biojava.bio.gui.DistributionLogo extends javax.swing.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

java.awt.RenderingHints renderingHints

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

Serialized Fields

root

java.lang.String root

seqs

java.util.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

java.awt.Paint beadOutline

beadFill

java.awt.Paint beadFill

beadStroke

java.awt.Stroke beadStroke

delegates

java.util.Map<K,V> delegates

delegationCache

java.util.Map<K,V> delegationCache

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

Serialized Fields

source

FeatureSource source

digestFilter

FeatureFilter digestFilter

laneMap

java.util.Map<K,V> laneMap

laneCount

int laneCount

distanceBetween

int distanceBetween

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

Serialized Fields

label

java.lang.String label

Class org.biojava.bio.gui.sequence.BasicImapRenderer extends java.lang.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

java.util.Set<E> flushers

Class org.biojava.bio.gui.sequence.CircularRendererPanel extends javax.swing.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

java.util.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

serialVersionUID:

7005846487574725181L

Serialized Fields

depth

double depth

fList

java.util.List<E> fList

gList

java.util.List<E> gList

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

Serialized Fields

name

java.lang.String name

hotSpots

java.util.List<E> hotSpots

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

Serialized Fields

type

java.lang.String type

url

java.net.URL url

coordinates

java.lang.Integer[] coordinates

userObject

java.lang.Object userObject

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

Serialized Fields

hotSpots

java.util.List<E> hotSpots

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

Serialized Fields

renderers

java.util.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

java.awt.geom.Line2D.Float line

line is the line to be drawn for each feature.

outline

java.awt.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

java.util.Set<E> cacheFlushers

renderer

PairwiseSequenceRenderer renderer

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

Serialized Fields

renderers

java.util.List<E> renderers

Class org.biojava.bio.gui.sequence.PairwiseSequencePanel extends javax.swing.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

java.awt.RenderingHints hints

leadingBorder

SequenceRenderContext.Border leadingBorder

trailingBorder

SequenceRenderContext.Border trailingBorder

propertyListener

java.beans.PropertyChangeListener propertyListener

repaintListener

ChangeListener repaintListener

layoutListener

ChangeListener layoutListener

svSupport

SequenceViewerSupport svSupport

mouseListener

java.awt.event.MouseListener mouseListener

svmSupport

SequenceViewerMotionSupport svmSupport

mouseMotionListener

java.awt.event.MouseMotionListener mouseMotionListener

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

Serialized Fields

defaultPaint

java.awt.Paint defaultPaint

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

Serialized Fields

rect

java.awt.geom.Rectangle2D rect

scaleHeight

boolean scaleHeight

Class org.biojava.bio.gui.sequence.RectangularImapRenderer extends java.lang.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

java.awt.geom.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 javax.swing.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

java.awt.RenderingHints hints

svSupport

SequenceViewerSupport svSupport

mouseListener

java.awt.event.MouseListener mouseListener

svmSupport

SequenceViewerMotionSupport svmSupport

mouseMotionListener

java.awt.event.MouseMotionListener mouseMotionListener

layoutListener

ChangeListener layoutListener

repaintListener

ChangeListener repaintListener

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

Serialized Fields

pcs

java.beans.PropertyChangeSupport pcs

size

double size

alignment

int alignment

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

serialVersionUID:

8749249181471157230L

Serialized Fields

seqPanels

SequencePanel[] seqPanels

range

RangeLocation range

sequence

Sequence sequence

renderer

SequenceRenderer renderer

scale

double scale

hints

java.awt.RenderingHints hints

direction

int direction

trackLayout

TrackLayout trackLayout

viewerListeners

java.util.List<E> viewerListeners

motionListeners

java.util.List<E> motionListeners

Class org.biojava.bio.gui.sequence.SequencePoster extends javax.swing.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

java.awt.RenderingHints renderingHints

Deprecated.

svSupport

SequenceViewerSupport svSupport

Deprecated.

mouseListener

java.awt.event.MouseListener mouseListener

Deprecated.

svmSupport

SequenceViewerMotionSupport svmSupport

Deprecated.

mouseMotionListener

java.awt.event.MouseMotionListener mouseMotionListener

Deprecated.

layoutListener

ChangeListener layoutListener

Deprecated.

repaintListener

ChangeListener repaintListener

Deprecated.

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

Serialized Fields

pcs

java.beans.PropertyChangeSupport pcs

size

double size

alignment

int alignment

Class org.biojava.bio.gui.sequence.SequenceRenderContext.Border extends java.lang.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 java.util.EventObject implements Serializable

Serialized Fields

path

java.util.List<E> path

target

java.lang.Object target

mouseEvent

java.awt.event.MouseEvent mouseEvent

pos

int pos

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

Serialized Fields

pane

SixFrameRenderer pane

Class org.biojava.bio.gui.sequence.TranslatedSequencePanel extends javax.swing.JComponent implements Serializable

serialVersionUID:

3269477379497205817L

Serialized Fields

sequence

SymbolList sequence

translation

int translation

direction

int direction

scale

double scale

renderer

SequenceRenderer renderer

rendererBorders

double rendererBorders

hints

java.awt.RenderingHints hints

leadingBorder

SequenceRenderContext.Border leadingBorder

trailingBorder

SequenceRenderContext.Border trailingBorder

propertyListener

java.beans.PropertyChangeListener propertyListener

repaintListener

ChangeListener repaintListener

layoutListener

ChangeListener layoutListener

svSupport

SequenceViewerSupport svSupport

mouseListener

java.awt.event.MouseListener mouseListener

svmSupport

SequenceViewerMotionSupport svmSupport

mouseMotionListener

java.awt.event.MouseMotionListener mouseMotionListener

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

Serialized Fields

outline

java.awt.Paint outline

fill

java.awt.Paint fill

blockDepth

double blockDepth

Class org.biojava.bio.gui.sequence.ZiggyImapRenderer extends java.lang.Object implements Serializable

Serialized Fields

renderer

ZiggyFeatureRenderer renderer

imageMap

ImageMap imageMap

urlFactory

URLFactory urlFactory