Serialized Form
Package uk.ac.man.bioinf.apps.cinema.group |
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 |
alignment
SequenceAlignment alignment
Package uk.ac.man.bioinf.apps.cinema.utils |
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 |
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 |
e
Exception e
Package uk.ac.man.bioinf.apps.optionable |
Package uk.ac.man.bioinf.apps.systemevents |
option
SystemEventOption option
event
SystemEvent event
Package uk.ac.man.bioinf.gui.color |
Package uk.ac.man.bioinf.gui.misc |
delegate
Vector delegate
Package uk.ac.man.bioinf.gui.optionable |
optionableName
String optionableName
optionHandler
OptionHandler optionHandler
sizeSetAsOption
boolean sizeSetAsOption
locationSetAsOption
boolean locationSetAsOption
haveOptioned
boolean haveOptioned
optionableName
String optionableName
optionHandler
OptionHandler optionHandler
locationSetAsOption
boolean locationSetAsOption
haveOptioned
boolean haveOptioned
Package uk.ac.man.bioinf.gui.util |
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
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 |
format
NumberFormat format
format
Format format
toolkit
Toolkit toolkit
integerFormatter
NumberFormat integerFormatter
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
toolkit
Toolkit toolkit
integerFormatter
NumberFormat integerFormatter
Package uk.ac.man.bioinf.gui.viewer |
titleLabel
JLabel titleLabel
currentSequence
GappedSequence currentSequence
green
Border green
red
Border red
black
Border black
empty
Border empty
itemListener
ItemListener itemListener
prototypicalCellHeight
int prototypicalCellHeight
buttonMap
Map buttonMap
colorMap
Map colorMap
msa
SequenceAlignment msa
preferredSize
Dimension preferredSize
widthPerBase
int widthPerBase
preferredHeight
int preferredHeight
seq
SequenceAlignment seq
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
viewer
JAlignmentViewer viewer
Package uk.ac.man.bioinf.gui.viewer.event |
rectangle
SequenceAlignmentRectangle rectangle
isAdjusting
boolean isAdjusting
Package uk.ac.man.bioinf.gui.viewer.test |
blinkOn
JMenuItem blinkOn
blinkOff
JMenuItem blinkOff
viewer
JAlignmentViewer viewer
Package uk.ac.man.bioinf.io |
expectedSequenceType
SequenceType expectedSequenceType
position
int position
sequence
String sequence
identifier
Identifier identifier
Package uk.ac.man.bioinf.module |
id
ModuleExceptionType id
throwable
Throwable throwable
ident
ModuleIdentifier ident
Package uk.ac.man.bioinf.sequence |
Package uk.ac.man.bioinf.sequence.alignment |
source
GappedSequence source
index
int index
Package uk.ac.man.bioinf.sequence.alignment.event |
start
int start
end
int end
type
AlignmentEventType type
event
AlignmentEvent event
Package uk.ac.man.bioinf.sequence.event |
start
int start
length
int length
type
SequenceEventType type
event
SequenceEvent event
Package uk.ac.man.bioinf.sequence.complex |
Package uk.ac.man.bioinf.sequence.identifier |
Package uk.ac.man.bioinf.util |