Serialized Form


Package uk.ac.man.bioinf.apps.cinema.group

Class uk.ac.man.bioinf.apps.cinema.group.CinemaGroupFrame implements Serializable

Serialized Fields

groupsList

JList groupsList

module

CinemaGroupModule module

groupsListModel

ChunkyListModel groupsListModel

sequencesListModel

ChunkyListModel sequencesListModel

viewGroupAlignment

JMenuItem viewGroupAlignment

editGroupName

JMenuItem editGroupName

addToConsensus

JMenuItem addToConsensus

createNewGroup

JMenuItem createNewGroup

addAllAsGroup

JMenuItem addAllAsGroup

anchor

JMenuItem anchor

unanchor

JMenuItem unanchor

anchorAll

JMenuItem anchorAll

unanchorAll

JMenuItem unanchorAll

lastSelectedGroup

CinemaGroup lastSelectedGroup


Package uk.ac.man.bioinf.apps.cinema.core

Class uk.ac.man.bioinf.apps.cinema.core.AlignmentToListCellRenderer implements Serializable

Class uk.ac.man.bioinf.apps.cinema.core.AlignmentToListModel implements Serializable

Serialized Fields

alignment

SequenceAlignment alignment


Package uk.ac.man.bioinf.apps.cinema.utils

Class uk.ac.man.bioinf.apps.cinema.utils.CinemaAlignmentFrame implements Serializable

Serialized Fields

mainPanel

JPanel mainPanel

rulerPanel

JPanel rulerPanel

rowHeadersPanel

JPanel rowHeadersPanel

viewer

JAlignmentViewer viewer

scrollPane

JScrollPane scrollPane

rowHeaders

JAlignmentButtonPanel rowHeaders

ruler

JAlignmentRuler ruler

initialCellSize

Dimension initialCellSize


Package uk.ac.man.bioinf.apps.cinema.motif

Class uk.ac.man.bioinf.apps.cinema.motif.CinemaMotifFrame implements Serializable

Serialized Fields

selectionList

JList selectionList

sequencesList

JList sequencesList

selectionListModel

DefaultListModel selectionListModel

sequencesListModel

DefaultListModel sequencesListModel

plusNorth

JButton plusNorth

plusEast

JButton plusEast

plusSouth

JButton plusSouth

plusWest

JButton plusWest

minusNorth

JButton minusNorth

minusEast

JButton minusEast

minusSouth

JButton minusSouth

minusWest

JButton minusWest

quit

JButton quit

clearAll

JButton clearAll

clearSelected

JButton clearSelected

saveSelected

JButton saveSelected

save

JButton save

sortMotifs

JCheckBox sortMotifs

motifName

JTextField motifName

selectionRegion

JTextField selectionRegion

motifNameBorder

TitledBorder motifNameBorder

model

NamedAlignmentSelectionModel model

module

CinemaMotifModule module

abst

AbstractSequenceOutput abst

exceptionHandler

ParserExceptionHandler exceptionHandler

dirChooser

CinemaMotifFrame.MotifFormatFileChooser dirChooser

fileChooser

CinemaMotifFrame.MotifFormatFileChooser fileChooser


Package uk.ac.man.bioinf.apps.invoker

Class uk.ac.man.bioinf.apps.invoker.InvokerInternalEventQueueException implements Serializable

Serialized Fields

e

Exception e

Class uk.ac.man.bioinf.apps.invoker.InvokerInternalQueueException implements Serializable


Package uk.ac.man.bioinf.apps.optionable

Class uk.ac.man.bioinf.apps.optionable.OptionableSourceNotFoundException implements Serializable

Class uk.ac.man.bioinf.apps.optionable.OptionableStateException implements Serializable


Package uk.ac.man.bioinf.apps.systemevents

Class uk.ac.man.bioinf.apps.systemevents.SystemEvent implements Serializable

Serialized Fields

option

SystemEventOption option

Class uk.ac.man.bioinf.apps.systemevents.SystemVetoException implements Serializable

Serialized Fields

event

SystemEvent event


Package uk.ac.man.bioinf.gui.color

Class uk.ac.man.bioinf.gui.color.ColorMapException implements Serializable


Package uk.ac.man.bioinf.gui.misc

Class uk.ac.man.bioinf.gui.misc.ChunkyListModel implements Serializable

Serialized Fields

delegate

Vector delegate


Package uk.ac.man.bioinf.gui.optionable

Class uk.ac.man.bioinf.gui.optionable.OptionableJFrame implements Serializable

Serialized Fields

optionableName

String optionableName

optionHandler

OptionHandler optionHandler

sizeSetAsOption

boolean sizeSetAsOption

locationSetAsOption

boolean locationSetAsOption

haveOptioned

boolean haveOptioned

Class uk.ac.man.bioinf.gui.optionable.OptionableJSplitPane implements Serializable

Serialized Fields

optionableName

String optionableName

optionHandler

OptionHandler optionHandler

locationSetAsOption

boolean locationSetAsOption

haveOptioned

boolean haveOptioned


Package uk.ac.man.bioinf.gui.util

Class uk.ac.man.bioinf.gui.util.ApplicationFrame implements Serializable

Serialized Fields

ra

PackageResourceAdapter ra

appName

String appName

mb

JMenuBar mb

tb

JToolBar tb

messages

JLabel messages

menuMapping

HashMap menuMapping

menuItemLocation

HashMap menuItemLocation

menuItemMapping

HashMap menuItemMapping

buttonMapping

HashMap buttonMapping

contentPane

JPanel contentPane

contents

JComponent contents

Class uk.ac.man.bioinf.gui.util.TripletPanel implements Serializable

Serialized Fields

leftRightSplit

JSplitPane leftRightSplit

upDownSplit

JSplitPane upDownSplit

mainWindow

JPanel mainWindow

topLeft

JPanel topLeft

bottomLeft

JPanel bottomLeft

tlt

JComponent tlt

blt

JComponent blt

rht

JComponent rht

tlp

JScrollPane tlp

blp

JScrollPane blp

rhp

JScrollPane rhp


Package uk.ac.man.bioinf.gui.util.forms

Class uk.ac.man.bioinf.gui.util.forms.DecimalField implements Serializable

Serialized Fields

format

NumberFormat format

Class uk.ac.man.bioinf.gui.util.forms.FormattedDocument implements Serializable

Serialized Fields

format

Format format

Class uk.ac.man.bioinf.gui.util.forms.IntegerField implements Serializable

Serialized Fields

toolkit

Toolkit toolkit

integerFormatter

NumberFormat integerFormatter

Class uk.ac.man.bioinf.gui.util.forms.IntegerField.IntegerDocument implements Serializable

Class uk.ac.man.bioinf.gui.util.forms.ValidatedForm implements Serializable

Serialized Fields

labels

HashMap labels

fields

HashMap fields

modifiers

HashMap modifiers

changes

HashMap changes

c

GridBagConstraints c

gridbag

GridBagLayout gridbag

currentRow

int currentRow

myDocumentListener

ValidatedForm.MyDocumentListener myDocumentListener

Class uk.ac.man.bioinf.gui.util.forms.WholeNumberField implements Serializable

Serialized Fields

toolkit

Toolkit toolkit

integerFormatter

NumberFormat integerFormatter

Class uk.ac.man.bioinf.gui.util.forms.WholeNumberField.WholeNumberDocument implements Serializable


Package uk.ac.man.bioinf.gui.viewer

Class uk.ac.man.bioinf.gui.viewer.ButtonViewerPopupMenu implements Serializable

Serialized Fields

titleLabel

JLabel titleLabel

currentSequence

GappedSequence currentSequence

Class uk.ac.man.bioinf.gui.viewer.DefaultAlignmentViewerCellRenderer implements Serializable

Serialized Fields

green

Border green

red

Border red

black

Border black

empty

Border empty

Class uk.ac.man.bioinf.gui.viewer.InvertedScrollPaneLayout implements Serializable

Class uk.ac.man.bioinf.gui.viewer.JAlignmentButtonPanel implements Serializable

Serialized Fields

itemListener

ItemListener itemListener

prototypicalCellHeight

int prototypicalCellHeight

buttonMap

Map buttonMap

colorMap

Map colorMap

msa

SequenceAlignment msa

preferredSize

Dimension preferredSize

Class uk.ac.man.bioinf.gui.viewer.JAlignmentRuler implements Serializable

Serialized Fields

widthPerBase

int widthPerBase

preferredHeight

int preferredHeight

seq

SequenceAlignment seq

Class uk.ac.man.bioinf.gui.viewer.JAlignmentViewer implements Serializable

Serialized Fields

alignment

SequenceAlignment alignment

prototypicalCellSize

Dimension prototypicalCellSize

renderer

AlignmentViewerCellRenderer renderer

fastRenderer

FastAlignmentViewerCellRenderer fastRenderer

selectionRenderer

AlignmentSelectionRenderer selectionRenderer

cursor

SequenceCursor cursor

viewerUI

AlignmentViewerUI viewerUI

selectionModel

AlignmentSelectionModel selectionModel

colorMap

ColorMap colorMap

preferredSize

Dimension preferredSize

cacheRect

Rectangle cacheRect

readonly

boolean readonly

viewerRect

Rectangle viewerRect

previousSelection

SequenceAlignmentRectangle previousSelection

Class uk.ac.man.bioinf.gui.viewer.JChangedScrollPane implements Serializable

Class uk.ac.man.bioinf.gui.viewer.JLayableScrollPane implements Serializable

Class uk.ac.man.bioinf.gui.viewer.PrintableAlignmentPanel implements Serializable

Class uk.ac.man.bioinf.gui.viewer.PrintableJAlignmentViewer implements Serializable

Class uk.ac.man.bioinf.gui.viewer.ReadonlyException implements Serializable

Serialized Fields

viewer

JAlignmentViewer viewer


Package uk.ac.man.bioinf.gui.viewer.event

Class uk.ac.man.bioinf.gui.viewer.event.AlignmentSelectionEvent implements Serializable

Serialized Fields

rectangle

SequenceAlignmentRectangle rectangle

isAdjusting

boolean isAdjusting


Package uk.ac.man.bioinf.gui.viewer.test

Class uk.ac.man.bioinf.gui.viewer.test.AlignmentViewerTest implements Serializable

Serialized Fields

blinkOn

JMenuItem blinkOn

blinkOff

JMenuItem blinkOff

viewer

JAlignmentViewer viewer

Class uk.ac.man.bioinf.gui.viewer.test.CellRendererPaneReplacement implements Serializable

Class uk.ac.man.bioinf.gui.viewer.test.SliderExample implements Serializable


Package uk.ac.man.bioinf.io

Class uk.ac.man.bioinf.io.InvalidSequenceTypeParserException implements Serializable

Serialized Fields

expectedSequenceType

SequenceType expectedSequenceType

Class uk.ac.man.bioinf.io.ParserException implements Serializable

Serialized Fields

position

int position

sequence

String sequence

identifier

Identifier identifier

Class uk.ac.man.bioinf.io.SequenceWriterException implements Serializable

Class uk.ac.man.bioinf.io.UnknownElementException implements Serializable


Package uk.ac.man.bioinf.module

Class uk.ac.man.bioinf.module.ModuleException implements Serializable

Serialized Fields

id

ModuleExceptionType id

throwable

Throwable throwable

Class uk.ac.man.bioinf.module.NoSuchRequiredModule implements Serializable

Serialized Fields

ident

ModuleIdentifier ident


Package uk.ac.man.bioinf.sequence

Class uk.ac.man.bioinf.sequence.InvalidSequenceTypeException implements Serializable

Class uk.ac.man.bioinf.sequence.NoSuchSequenceElementException implements Serializable

Class uk.ac.man.bioinf.sequence.SequenceException implements Serializable


Package uk.ac.man.bioinf.sequence.alignment

Class uk.ac.man.bioinf.sequence.alignment.NoGapAtThisPositionException implements Serializable

Serialized Fields

source

GappedSequence source

index

int index

Class uk.ac.man.bioinf.sequence.alignment.NoSuchSequenceException implements Serializable


Package uk.ac.man.bioinf.sequence.alignment.event

Class uk.ac.man.bioinf.sequence.alignment.event.AlignmentEvent implements Serializable

Serialized Fields

start

int start

end

int end

type

AlignmentEventType type

Class uk.ac.man.bioinf.sequence.alignment.event.AlignmentVetoException implements Serializable

Serialized Fields

event

AlignmentEvent event

Class uk.ac.man.bioinf.sequence.alignment.event.VetoableAlignmentEvent implements Serializable


Package uk.ac.man.bioinf.sequence.event

Class uk.ac.man.bioinf.sequence.event.SequenceEvent implements Serializable

Serialized Fields

start

int start

length

int length

type

SequenceEventType type

Class uk.ac.man.bioinf.sequence.event.SequenceVetoException implements Serializable

Serialized Fields

event

SequenceEvent event

Class uk.ac.man.bioinf.sequence.event.VetoableSequenceEvent implements Serializable


Package uk.ac.man.bioinf.sequence.complex

Class uk.ac.man.bioinf.sequence.complex.IllegalDuplicateModificationException implements Serializable

Class uk.ac.man.bioinf.sequence.complex.NoSuchModificationException implements Serializable


Package uk.ac.man.bioinf.sequence.identifier

Class uk.ac.man.bioinf.sequence.identifier.MalformedAccessionException implements Serializable


Package uk.ac.man.bioinf.util

Class uk.ac.man.bioinf.util.ChangeableEvent implements Serializable