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# 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

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