Serialized Form
serialVersionUID: 1L
pane
javax.swing.JTabbedPane pane
start
java.lang.Integer start
end
java.lang.Integer end
strand
java.lang.Integer strand
fl
FeatureList fl
serialVersionUID: 1L
serialVersionUID: 1L
seqAnalysis
SeqAnalysisI seqAnalysis
op
org.bdgp.io.IOOperation op
pathList
javax.swing.JComboBox pathList
typeLabel
javax.swing.JLabel typeLabel
filePaths
java.util.Vector<E> filePaths
browseButton
javax.swing.JButton browseButton
props
java.util.Properties props
jboxes
java.util.Hashtable<K,V> jboxes
|
Package apollo.analysis.filter |
filterConfigurationPanel
javax.swing.JPanel filterConfigurationPanel
showFilterConfiguration
javax.swing.JButton showFilterConfiguration
min_expect
javax.swing.JTextField min_expect
use_expect
javax.swing.JCheckBox use_expect
min_score
javax.swing.JTextField min_score
use_score
javax.swing.JCheckBox use_score
min_identity
javax.swing.JTextField min_identity
use_identity
javax.swing.JCheckBox use_identity
min_length
javax.swing.JTextField min_length
length_units
javax.swing.JComboBox length_units
use_length
javax.swing.JToggleButton use_length
min_coincidence
javax.swing.JTextField min_coincidence
use_coincidence
javax.swing.JCheckBox use_coincidence
max_coverage
javax.swing.JTextField max_coverage
limit_coverage
javax.swing.JCheckBox limit_coverage
word_size
javax.swing.JTextField word_size
compress_threshold
javax.swing.JTextField compress_threshold
remove_lowinfo
javax.swing.JCheckBox remove_lowinfo
remove_twilight
javax.swing.JCheckBox remove_twilight
remove_shadows
javax.swing.JCheckBox remove_shadows
split_frames
javax.swing.JCheckBox split_frames
split_dups
javax.swing.JCheckBox split_dups
split_HSPs
javax.swing.JCheckBox split_HSPs
queryIsGenomic
javax.swing.JCheckBox queryIsGenomic
- Before, query==genomic was the default. Now query != genomic is the default.
parent
AnalysisPanel parent
keep_polyA
javax.swing.JCheckBox keep_polyA
keep_promoter
javax.swing.JCheckBox keep_promoter
filterConfigurationPanel
javax.swing.JPanel filterConfigurationPanel
showFilterConfiguration
javax.swing.JButton showFilterConfiguration
filterConfigurationPanel
javax.swing.JPanel filterConfigurationPanel
showFilterConfiguration
javax.swing.JButton showFilterConfiguration
min_score
javax.swing.JTextField min_score
min_length
javax.swing.JTextField min_length
length_units
javax.swing.JComboBox length_units
use_length
javax.swing.JToggleButton use_length
max_coverage
javax.swing.JTextField max_coverage
limit_coverage
javax.swing.JCheckBox limit_coverage
use_score
javax.swing.JCheckBox use_score
join_reads
javax.swing.JCheckBox join_reads
revcomp3
javax.swing.JCheckBox revcomp3
suffix
javax.swing.JTextField suffix
remove_polyA
javax.swing.JCheckBox remove_polyA
limit_exons
javax.swing.JCheckBox limit_exons
exon_max
javax.swing.JTextField exon_max
limit_gaps
javax.swing.JCheckBox limit_gaps
gap_max
javax.swing.JTextField gap_max
heading
java.lang.String heading
preferredWidth
int preferredWidth
columns
java.util.Vector<E> columns
sortProperty
java.lang.String sortProperty
reverseSort
boolean reverseSort
type
java.lang.String type
tiername
java.lang.String tiername
tier
TierProperty tier
analysis_types
java.util.Vector<E> analysis_types
style
java.lang.String style
colour
java.awt.Color colour
utrColor
java.awt.Color utrColor
problematicColor
java.awt.Color problematicColor
finishedColor
java.awt.Color finishedColor
usescore
boolean usescore
minScore
float minScore
maxScore
float maxScore
minWidth
int minWidth
thresholdScore
float thresholdScore
URLString
java.lang.String URLString
groupFlag
java.lang.Integer groupFlag
recentDate
java.util.Date recentDate
comments
java.util.Vector<E> comments
idFormat
java.lang.String idFormat
idPrefix
java.lang.String idPrefix
chromosomeFormat
java.lang.String chromosomeFormat
annotType
java.lang.String annotType
nameAdapterString
java.lang.String nameAdapterString
overlapper
OverlapI overlapper
nameAdapterWasSet
boolean nameAdapterWasSet
overlapperWasSet
boolean overlapperWasSet
groupFlagSet
boolean groupFlagSet
linkType
LinkType linkType
- linkType indicates type of link it is. Default is NO_LINK
linkSpecies1
java.lang.String linkSpecies1
- Species that are linked
linkSpecies2
java.lang.String linkSpecies2
warnOnEdit
boolean warnOnEdit
- warnOnEdit can be set at the Tier level and also at the Feature level (here)
warnOnEditWasSet
boolean warnOnEditWasSet
numberOfLevels
int numberOfLevels
- Number of levels to the annotation - default is now 1 except for
gene/pseudogene, which have 3 levels (gene-transcript-exon).
Normally the number of levels for a result doesn't matter; it
only matters if you're flipping the result to the other strand,
so I made DrawableUtil.createDrawable do the special "make it a
one-level glyph" thing only for one-level annotations; results
are treated as DrawableFeatureSets, as before.
# of levels can be explicitly set in tiers file with "number_of_levels : 1"
tiersVect
java.util.Vector<E> tiersVect
- vector of TierProperties (which hold FeatureProperties)
tiersHash
java.util.Hashtable<K,V> tiersHash
fpTypeToPropHash
CaseInsensitiveStringHash fpTypeToPropHash
fpAnalNameToPropHash
CaseInsensitiveStringHash fpAnalNameToPropHash
cachesNeedUpdate
boolean cachesNeedUpdate
groupedUpdate
boolean groupedUpdate
comments
java.util.Vector<E> comments
propSchemeChangeListeners
java.util.Vector<E> propSchemeChangeListeners
changed
boolean changed
annotationFeatureProps
java.util.Vector<E> annotationFeatureProps
defaultFeatureProperty
FeatureProperty defaultFeatureProperty
linkedFeatProps
java.util.List<E> linkedFeatProps
- list of linked props - presently this doesnt change over lifetime of prop scheme
if that changes this can no longer be cached - or has to be invalidated. One
possible scenario would be doing a layover with lined features.
linkedTierProps
java.util.List<E> linkedTierProps
- list of all TierProperties that contain at least one linked FeatureProperty
properties
PropertyScheme properties
label
java.lang.String label
expanded
boolean expanded
visible
boolean visible
sorted
boolean sorted
labeled
boolean labeled
maxRow
int maxRow
curated
boolean curated
warnOnEdit
boolean warnOnEdit
- warnOnEdit can be set at the Tier level (here) or at the individual FeatureProperty level
comments
java.util.Vector<E> comments
analysis_types
CaseInsensitiveStringHash analysis_types
typesHash
CaseInsensitiveStringHash typesHash
propertyScheme
PropertyScheme propertyScheme
featProps
java.util.Vector<E> featProps
- A list of FeatureProperties
isFirstTier
boolean isFirstTier
isProtein
boolean isProtein
|
Package apollo.dataadapter |
parentException
java.lang.Exception parentException
type
int type
curationSet
CurationSet curationSet
regionList
javax.swing.JComboBox regionList
pathList
javax.swing.JComboBox pathList
chrStartEndList
javax.swing.JComboBox chrStartEndList
chrTextBox
javax.swing.JTextField chrTextBox
startTextBox
javax.swing.JTextField startTextBox
endTextBox
javax.swing.JTextField endTextBox
regionLabel
javax.swing.JLabel regionLabel
chrLabel
javax.swing.JLabel chrLabel
startLabel
javax.swing.JLabel startLabel
endLabel
javax.swing.JLabel endLabel
pathLabel
javax.swing.JLabel pathLabel
chrStartEndLabel
javax.swing.JLabel chrStartEndLabel
pane
javax.swing.JTabbedPane pane
rangePanel
javax.swing.JPanel rangePanel
regionPanel
javax.swing.JPanel regionPanel
proxyButton
javax.swing.JButton proxyButton
chrAction
java.awt.event.ActionListener chrAction
pathVector
java.util.Vector<E> pathVector
regionVector
java.util.Vector<E> regionVector
chrStartEndVector
java.util.Vector<E> chrStartEndVector
driver
org.bdgp.io.DataAdapter driver
op
org.bdgp.io.IOOperation op
props
java.util.Properties props
parentComponent
java.awt.Component parentComponent
chrStartEndList
javax.swing.JComboBox chrStartEndList
chrTextBox
javax.swing.JTextField chrTextBox
startTextBox
javax.swing.JTextField startTextBox
endTextBox
javax.swing.JTextField endTextBox
chrLabel
javax.swing.JLabel chrLabel
startLabel
javax.swing.JLabel startLabel
endLabel
javax.swing.JLabel endLabel
chrStartEndLabel
javax.swing.JLabel chrStartEndLabel
rangePanel
javax.swing.JPanel rangePanel
proxyButton
javax.swing.JButton proxyButton
chrAction
java.awt.event.ActionListener chrAction
chrStartEndVector
java.util.Vector<E> chrStartEndVector
driver
org.bdgp.io.DataAdapter driver
op
org.bdgp.io.IOOperation op
props
java.util.Properties props
seqButton
javax.swing.JButton seqButton
seqFileList
javax.swing.JComboBox seqFileList
seqFilePaths
java.util.Vector<E> seqFilePaths
label
java.lang.String label
inputType
DataInputType inputType
comboBox
javax.swing.JComboBox comboBox
history
java.util.Vector<E> history
innerPanel
javax.swing.JPanel innerPanel
example
java.lang.String example
dbComboBox
javax.swing.JComboBox dbComboBox
colorScheme
java.lang.String colorScheme
constraints
GuiTabPanel.ApolloGridBagConstraints constraints
allowedSet
java.util.Set<E> allowedSet
queryField
javax.swing.JTextField queryField
responseField
javax.swing.JTextArea responseField
executeButton
javax.swing.JButton executeButton
returnButton
javax.swing.JButton returnButton
executeListener
java.awt.event.ActionListener executeListener
- Responds to the "execute" button being pressed by sending the query string
as a GET to the specified URL.
returnListener
java.awt.event.ActionListener returnListener
- Responds to the "Return" button by disposing of this dialogue
|
Package apollo.dataadapter.analysis |
op
org.bdgp.io.IOOperation op
analysisDriver
AnalysisAdapter analysisDriver
- The only driver that works with this is the BlastAdapter
tabbedPane
javax.swing.JTabbedPane tabbedPane
curation_set
CurationSet curation_set
analysisPanels
AnalysisPanel[] analysisPanels
- The order of this array is the order that the panels will appear in
the JTabbedPane
label
java.lang.String label
fileBox
javax.swing.JComboBox fileBox
seqField
javax.swing.JTextField seqField
displayTierBox
javax.swing.JComboBox displayTierBox
displayTypeBox
javax.swing.JComboBox displayTypeBox
offsetField
javax.swing.JTextField offsetField
box
javax.swing.Box box
example
java.lang.String example
parent
AnalysisAdapterGUI parent
curation
CurationSet curation
tier_history
java.util.HashMap<K,V> tier_history
file_history
java.util.HashMap<K,V> file_history
most_recent_tier
java.lang.String most_recent_tier
most_recent_file
java.lang.String most_recent_file
historic_file
java.lang.String historic_file
history_is_initialized
boolean history_is_initialized
parser
AnalysisParserI parser
filter
AnalysisFilterI filter
filterPanel
FilterPanel filterPanel
|
Package apollo.dataadapter.chado |
operation
org.bdgp.io.IOOperation operation
- The IOOperation (e.g. reading/writing) that this object was created to support.
chado_dbs
ChadoDatabase[] chado_dbs
- List of Chado databases read by the ChadoAdapter from its configuration file.
- See Also:
ChadoAdapter.readConfigFile
userPanel
javax.swing.JPanel userPanel
- GUI panel for database login and password
seqQueryPanel
javax.swing.JPanel seqQueryPanel
- Gui panel for read operation, for querying db. Not needed for write.
databaseChoicePrompt
javax.swing.JLabel databaseChoicePrompt
databaseComboBox
javax.swing.JComboBox databaseComboBox
driverClassPrompt
javax.swing.JLabel driverClassPrompt
driverClassComboBox
javax.swing.JComboBox driverClassComboBox
jdbcUrlPrompt
javax.swing.JLabel jdbcUrlPrompt
jdbcUrlTextField
javax.swing.JTextField jdbcUrlTextField
chadoDbPrompt
javax.swing.JLabel chadoDbPrompt
chadoDbTextField
javax.swing.JTextField chadoDbTextField
usernamePrompt
javax.swing.JLabel usernamePrompt
usernameTextField
javax.swing.JTextField usernameTextField
- Where logins are entered - make this a dropdown history list
passwordPrompt
javax.swing.JLabel passwordPrompt
passwordTextField
javax.swing.JPasswordField passwordTextField
seqTypes
java.lang.String[] seqTypes
seqTypePrompt
javax.swing.JLabel seqTypePrompt
seqTypeComboBox
javax.swing.JComboBox seqTypeComboBox
seqChoicePrompt
javax.swing.JLabel seqChoicePrompt
seqChoiceComboBox
javax.swing.JComboBox seqChoiceComboBox
seqChoiceButton
javax.swing.JButton seqChoiceButton
seqIdPrompt
javax.swing.JLabel seqIdPrompt
seqIdTextField
javax.swing.JTextField seqIdTextField
- Where seq ids are entered - this should be changed to a drop down list of
history
startLabel
javax.swing.JLabel startLabel
startField
javax.swing.JTextField startField
endLabel
javax.swing.JLabel endLabel
endField
javax.swing.JTextField endField
chromosomeLabel
javax.swing.JLabel chromosomeLabel
chromosomeComboBox
javax.swing.JComboBox chromosomeComboBox
sequenceUniquenames
java.lang.String[] sequenceUniquenames
- A list of chado feature.uniquenames read from the current database by the ChadoAdapter.
|
Package apollo.dataadapter.chadoxml |
driver
ChadoXmlAdapter driver
saveAnnots
javax.swing.JCheckBox saveAnnots
saveResults
javax.swing.JCheckBox saveResults
|
Package apollo.dataadapter.das |
server
DASServerI server
dsn
DASDsn dsn
segment
DASSegment segment
|
Package apollo.dataadapter.das.simple |
serverList
javax.swing.JComboBox serverList
dsnList
javax.swing.JComboBox dsnList
segList
javax.swing.JComboBox segList
lowTextBox
javax.swing.JTextField lowTextBox
hiTextBox
javax.swing.JTextField hiTextBox
historyList
javax.swing.JComboBox historyList
serverLabel
javax.swing.JLabel serverLabel
dsnLabel
javax.swing.JLabel dsnLabel
segLabel
javax.swing.JLabel segLabel
lowLabel
javax.swing.JLabel lowLabel
hiLabel
javax.swing.JLabel hiLabel
historyLabel
javax.swing.JLabel historyLabel
proxyLabel
javax.swing.JLabel proxyLabel
pane
javax.swing.JPanel pane
proxyTextField
javax.swing.JTextField proxyTextField
proxyButton
javax.swing.JButton proxyButton
dsnVector
java.util.Vector<E> dsnVector
serverVector
java.util.Vector<E> serverVector
historyVector
java.util.Vector<E> historyVector
segmentVector
java.util.Vector<E> segmentVector
emptyVector
java.util.Vector<E> emptyVector
driver
org.bdgp.io.DataAdapter driver
op
org.bdgp.io.IOOperation op
props
java.util.Properties props
server_listener
SimpleDASAdapterGUI.ServerListener server_listener
dsn_listener
SimpleDASAdapterGUI.DSNListener dsn_listener
history_listener
SimpleDASAdapterGUI.HistoryListener history_listener
posValidator
apollo.dataadapter.das.simple.SimpleDASAdapterGUI.LongValidator posValidator
dasServer
DASServerI dasServer
|
Package apollo.dataadapter.das2 |
serverList
javax.swing.JComboBox serverList
versionedSourcesList
javax.swing.JComboBox versionedSourcesList
segList
javax.swing.JComboBox segList
lowTextBox
javax.swing.JTextField lowTextBox
hiTextBox
javax.swing.JTextField hiTextBox
historyList
javax.swing.JComboBox historyList
serverLabel
javax.swing.JLabel serverLabel
dsnLabel
javax.swing.JLabel dsnLabel
segLabel
javax.swing.JLabel segLabel
lowLabel
javax.swing.JLabel lowLabel
hiLabel
javax.swing.JLabel hiLabel
historyLabel
javax.swing.JLabel historyLabel
proxyLabel
javax.swing.JLabel proxyLabel
pane
javax.swing.JPanel pane
proxyTextField
javax.swing.JTextField proxyTextField
proxyButton
javax.swing.JButton proxyButton
versionedSourcesVector
java.util.Vector<E> versionedSourcesVector
serverVector
java.util.Vector<E> serverVector
historyVector
java.util.Vector<E> historyVector
segmentVector
java.util.Vector<E> segmentVector
emptyVector
java.util.Vector<E> emptyVector
driver
DAS2Adapter driver
op
org.bdgp.io.IOOperation op
props
java.util.Properties props
server_listener
DAS2AdapterGUI.ServerListener server_listener
dsn_listener
DAS2AdapterGUI.DSNListener dsn_listener
history_listener
DAS2AdapterGUI.HistoryListener history_listener
posValidator
apollo.dataadapter.das2.DAS2AdapterGUI.LongValidator posValidator
dasServer
DAS2Request dasServer
|
Package apollo.dataadapter.ensj |
_location
org.ensembl.datamodel.Location _location
_driverProperties
java.util.Properties _driverProperties
_operation
org.bdgp.io.IOOperation _operation
_view
View _view
_model
Model _model
_controller
Controller _controller
|
Package apollo.dataadapter.ensj.view |
_view
View _view
_fileLabel
javax.swing.JLabel _fileLabel
_serverLabel
javax.swing.JLabel _serverLabel
_serverPortLabel
javax.swing.JLabel _serverPortLabel
_dataSetLabel
javax.swing.JLabel _dataSetLabel
_annotationUserLabel
javax.swing.JLabel _annotationUserLabel
_annotationUserEmailLabel
javax.swing.JLabel _annotationUserEmailLabel
_annotationUserTextField
javax.swing.JTextField _annotationUserTextField
_serverTextField
javax.swing.JTextField _serverTextField
_serverPortTextField
javax.swing.JTextField _serverPortTextField
_annotationUserEmailTextField
javax.swing.JTextField _annotationUserEmailTextField
_editingEnabledCheckBox
javax.swing.JCheckBox _editingEnabledCheckBox
_dataSetDropdown
javax.swing.JComboBox _dataSetDropdown
_fileDropdown
javax.swing.JComboBox _fileDropdown
_fileChooseButton
javax.swing.JButton _fileChooseButton
_fileChooser
javax.swing.JFileChooser _fileChooser
_hostLabel
javax.swing.JLabel _hostLabel
_portLabel
javax.swing.JLabel _portLabel
_userLabel
javax.swing.JLabel _userLabel
_passwordLabel
javax.swing.JLabel _passwordLabel
_ensemblDatabaseLabel
javax.swing.JLabel _ensemblDatabaseLabel
_hostTextField
javax.swing.JTextField _hostTextField
_portTextField
javax.swing.JTextField _portTextField
_userTextField
javax.swing.JTextField _userTextField
_passwordTextField
javax.swing.JPasswordField _passwordTextField
_ensemblDatabaseDropdown
UpdateWorkRoundComboBox _ensemblDatabaseDropdown
_sequenceHostLabel
javax.swing.JLabel _sequenceHostLabel
_sequencePortLabel
javax.swing.JLabel _sequencePortLabel
_sequenceUserLabel
javax.swing.JLabel _sequenceUserLabel
_sequencePasswordLabel
javax.swing.JLabel _sequencePasswordLabel
_sequenceEnsemblDatabaseLabel
javax.swing.JLabel _sequenceEnsemblDatabaseLabel
_sequenceHostTextField
javax.swing.JTextField _sequenceHostTextField
_sequencePortTextField
javax.swing.JTextField _sequencePortTextField
_sequenceUserTextField
javax.swing.JTextField _sequenceUserTextField
_sequencePasswordTextField
javax.swing.JPasswordField _sequencePasswordTextField
_sequenceEnsemblDatabaseDropdown
javax.swing.JComboBox _sequenceEnsemblDatabaseDropdown
_view
View _view
_view
View _view
_stableIDLabel
javax.swing.JLabel _stableIDLabel
_coordSystemLabel
javax.swing.JLabel _coordSystemLabel
_seqRegionLabel
javax.swing.JLabel _seqRegionLabel
_startLabel
javax.swing.JLabel _startLabel
_stableIDDropdown
UpdateWorkRoundComboBox _stableIDDropdown
_coordSystemDropdown
UpdateWorkRoundComboBox _coordSystemDropdown
_seqRegionDropdown
UpdateWorkRoundComboBox _seqRegionDropdown
_startField
javax.swing.JTextField _startField
_endField
javax.swing.JTextField _endField
_historyLabel
javax.swing.JLabel _historyLabel
_historyDropdown
UpdateWorkRoundComboBox _historyDropdown
_view
View _view
_ssResetCheckBox
javax.swing.JCheckBox _ssResetCheckBox
_namingCheckBox
javax.swing.JCheckBox _namingCheckBox
_geneAddCheckBox
javax.swing.JCheckBox _geneAddCheckBox
_supportAddCheckBox
javax.swing.JCheckBox _supportAddCheckBox
_typePrefixLabel
javax.swing.JLabel _typePrefixLabel
_typePrefixTextField
javax.swing.JTextField _typePrefixTextField
_view
View _view
_genesCheckBox
javax.swing.JCheckBox _genesCheckBox
_geneTypesButton
javax.swing.JButton _geneTypesButton
_dnaProteinAlignmentsCheckBox
javax.swing.JCheckBox _dnaProteinAlignmentsCheckBox
_dnaProteinAlignmentTypesButton
javax.swing.JButton _dnaProteinAlignmentTypesButton
_dnaDnaAlignmentsCheckBox
javax.swing.JCheckBox _dnaDnaAlignmentsCheckBox
_dnaDnaAlignmentTypesButton
javax.swing.JButton _dnaDnaAlignmentTypesButton
_simpleFeaturesCheckBox
javax.swing.JCheckBox _simpleFeaturesCheckBox
_simpleFeaturesTypesButton
javax.swing.JButton _simpleFeaturesTypesButton
_ditagFeaturesCheckBox
javax.swing.JCheckBox _ditagFeaturesCheckBox
_ditagFeaturesTypesButton
javax.swing.JButton _ditagFeaturesTypesButton
_proteinAnnotationsCheckBox
javax.swing.JCheckBox _proteinAnnotationsCheckBox
_repeatsCheckBox
javax.swing.JCheckBox _repeatsCheckBox
_contigsCheckBox
javax.swing.JCheckBox _contigsCheckBox
_abInitioPredictionsCheckBox
javax.swing.JCheckBox _abInitioPredictionsCheckBox
_predictionTypesButton
javax.swing.JButton _predictionTypesButton
_geneTypesList
javax.swing.JList _geneTypesList
_dnaTypesList
javax.swing.JList _dnaTypesList
_proteinTypesList
javax.swing.JList _proteinTypesList
_simpleTypesList
javax.swing.JList _simpleTypesList
_abInitioTypesList
javax.swing.JList _abInitioTypesList
_ditagTypesList
javax.swing.JList _ditagTypesList
_geneTypesPane
javax.swing.JScrollPane _geneTypesPane
_dnaTypesPane
javax.swing.JScrollPane _dnaTypesPane
_proteinTypesPane
javax.swing.JScrollPane _proteinTypesPane
_simpleTypesPane
javax.swing.JScrollPane _simpleTypesPane
_abInitioTypesPane
javax.swing.JScrollPane _abInitioTypesPane
_ditagTypesPane
javax.swing.JScrollPane _ditagTypesPane
_adapterGUI
EnsJAdapterGUI _adapterGUI
_locationPanel
LocationPanel _locationPanel
_optionsPanel
OptionsPanel _optionsPanel
_typesPanel
TypesPanel _typesPanel
_databasePanel
DatabasePanel _databasePanel
_annotationsPanel
AnnotationsPanel _annotationsPanel
_typesButton
javax.swing.JButton _typesButton
_optionsButton
javax.swing.JButton _optionsButton
_databaseButton
javax.swing.JButton _databaseButton
_annotationsButton
javax.swing.JButton _annotationsButton
|
Package apollo.dataadapter.ensj19 |
location
org.ensembl19.datamodel.LinearLocation location
driverProperties
java.util.Properties driverProperties
testButton
javax.swing.JButton testButton
showTypes
javax.swing.JButton showTypes
showDataSourceConfiguration
javax.swing.JButton showDataSourceConfiguration
showAnnotation
javax.swing.JButton showAnnotation
typesPanel
javax.swing.JPanel typesPanel
dataSourceConfigurationPanel
javax.swing.JPanel dataSourceConfigurationPanel
annotationPanel
javax.swing.JPanel annotationPanel
annotationSourceChooser
AnnotationSourceChooser annotationSourceChooser
includePanel
javax.swing.JPanel includePanel
dataConfigChooser
CompositeDataSourceConfigurationPanel dataConfigChooser
dbInitialised
boolean dbInitialised
logicalSpeciesName
java.lang.String logicalSpeciesName
inputFileLabel
javax.swing.JLabel inputFileLabel
inputServerLabel
javax.swing.JLabel inputServerLabel
inputDataSetLabel
javax.swing.JLabel inputDataSetLabel
outputFileLabel
javax.swing.JLabel outputFileLabel
outputDataSetLabel
javax.swing.JLabel outputDataSetLabel
serverPortLabel
javax.swing.JLabel serverPortLabel
annotationUserTextField
javax.swing.JTextField annotationUserTextField
annotationUserLabel
javax.swing.JLabel annotationUserLabel
annotationUserEmailTextField
javax.swing.JTextField annotationUserEmailTextField
serverPortTextField
javax.swing.JTextField serverPortTextField
annotationUserEmailLabel
javax.swing.JLabel annotationUserEmailLabel
editingEnabledCheckBox
javax.swing.JCheckBox editingEnabledCheckBox
inputFileTextField
org.ensembl19.gui.FileChooserWithHistory inputFileTextField
inputServerTextField
SourceChooserWithHistory inputServerTextField
inputDataSetList
javax.swing.JComboBox inputDataSetList
outputFileTextField
org.ensembl19.gui.FileChooserWithHistory outputFileTextField
outputDataSetList
javax.swing.JComboBox outputDataSetList
findButton
javax.swing.JButton findButton
choosers
java.util.HashMap<K,V> choosers
chooserDropdown
javax.swing.JComboBox chooserDropdown
chooserActionListener
java.awt.event.ActionListener chooserActionListener
previousChooserKey
java.lang.String previousChooserKey
chooserNames
java.lang.String[] chooserNames
defaultChooserName
java.lang.String defaultChooserName
interactionListener
java.awt.event.ActionListener interactionListener
linkChooserInteractions
boolean linkChooserInteractions
hostLabel
javax.swing.JLabel hostLabel
portLabel
javax.swing.JLabel portLabel
userLabel
javax.swing.JLabel userLabel
passwordLabel
javax.swing.JLabel passwordLabel
ensemblDatabaseLabel
javax.swing.JLabel ensemblDatabaseLabel
jdbcDriverTextField
javax.swing.JTextField jdbcDriverTextField
hostTextField
javax.swing.JTextField hostTextField
portTextField
javax.swing.JTextField portTextField
userTextField
javax.swing.JTextField userTextField
passwordTextField
javax.swing.JPasswordField passwordTextField
ensemblDriverTextField
javax.swing.JTextField ensemblDriverTextField
ensemblDatabaseDropdown
javax.swing.JComboBox ensemblDatabaseDropdown
findButton
javax.swing.JButton findButton
hostListener
java.awt.event.ActionListener hostListener
interactionListener
java.awt.event.ActionListener interactionListener
ensemblDBDropdownSelectionListener
java.awt.event.ActionListener ensemblDBDropdownSelectionListener
prefix
java.lang.String prefix
externalDataChangeListener
java.awt.event.ActionListener externalDataChangeListener
useCustom
boolean useCustom
seqDriverConfigPanel
org.ensembl19.gui.DriverConfigPanel seqDriverConfigPanel
customBox
javax.swing.JCheckBox customBox
ok
javax.swing.JButton ok
cancel
javax.swing.JButton cancel
stateInformation
java.util.Properties stateInformation
chrButton
javax.swing.JRadioButton chrButton
chrStartEndList
javax.swing.JComboBox chrStartEndList
chrDropdown
javax.swing.JComboBox chrDropdown
startTextBox
javax.swing.JTextField startTextBox
endTextBox
javax.swing.JTextField endTextBox
chrAction
java.awt.event.ActionListener chrAction
chrStartEndVector
java.util.Vector<E> chrStartEndVector
cloneFragmentButton
javax.swing.JRadioButton cloneFragmentButton
cloneFragmentList
javax.swing.JComboBox cloneFragmentList
cloneFragmentTextBox
javax.swing.JTextField cloneFragmentTextBox
cloneFragmentAction
java.awt.event.ActionListener cloneFragmentAction
cloneFragmentHistory
java.util.Vector<E> cloneFragmentHistory
stableIDButton
javax.swing.JRadioButton stableIDButton
stableIDList
javax.swing.JComboBox stableIDList
stableIDHistory
java.util.Vector<E> stableIDHistory
dataTypeButtons
EnsJAdapterGUI.DataTypeButton[] dataTypeButtons
cloneFragmentPanel
javax.swing.Box cloneFragmentPanel
adapter
org.bdgp.io.DataAdapter adapter
op
org.bdgp.io.IOOperation op
initialSettings
java.util.Properties initialSettings
loggingFile
java.lang.String loggingFile
- Holds the logging file parameter passed in from the history file. An
exception will be thrown in createStateInformation() if this is null.
locationPanel
javax.swing.JPanel locationPanel
chromosomeListInitialised
boolean chromosomeListInitialised
propertyName
java.lang.String propertyName
adaptorName
java.lang.String adaptorName
location
org.ensembl19.datamodel.Location location
driverPath
java.lang.String driverPath
sourceHistoryList
javax.swing.JComboBox sourceHistoryList
sourceHistory
java.util.Vector<E> sourceHistory
historyListAction
java.awt.event.ItemListener historyListAction
listenerList
java.util.List<E> listenerList
|
Package apollo.dataadapter.exception |
stackTraceAtCreate
java.lang.String stackTraceAtCreate
|
Package apollo.dataadapter.flychadoxml |
ioOperation
org.bdgp.io.IOOperation ioOperation
driver
FlyChadoXmlAdapter driver
tabbedPane
javax.swing.JTabbedPane tabbedPane
panels
GuiTabPanel[] panels
- The order of this array is the order that the panels will appear in
the JTabbedPane
FileTabIndex
int FileTabIndex
grayBackgroundColor
java.awt.Color grayBackgroundColor
saveAnnots
javax.swing.JCheckBox saveAnnots
saveResults
javax.swing.JCheckBox saveResults
chrField
ChromosomeField chrField
startField
javax.swing.JTextField startField
endField
javax.swing.JTextField endField
|
Package apollo.dataadapter.flygamexml |
ioOperation
org.bdgp.io.IOOperation ioOperation
gameDriver
FlyGAMEAdapter gameDriver
- The only driver that works with this is the FlyGAMEAdapter
tabbedPane
javax.swing.JTabbedPane tabbedPane
gamePanels
GuiTabPanel[] gamePanels
- The order of this array is the order that the panels will appear in
the JTabbedPane
FileTabIndex
int FileTabIndex
grayBackgroundColor
java.awt.Color grayBackgroundColor
saveAnnots
javax.swing.JCheckBox saveAnnots
saveResults
javax.swing.JCheckBox saveResults
chrField
ChromosomeField chrField
startField
javax.swing.JTextField startField
endField
javax.swing.JTextField endField
|
Package apollo.dataadapter.gamexml |
driver
GAMEAdapter driver
saveAnnots
javax.swing.JCheckBox saveAnnots
saveResults
javax.swing.JCheckBox saveResults
|
Package apollo.dataadapter.genbank |
tabbedPane
javax.swing.JTabbedPane tabbedPane
pubPanels
GuiTabPanel[] pubPanels
FileTabIndex
int FileTabIndex
filePanelColor
java.awt.Color filePanelColor
genbankPanelColor
java.awt.Color genbankPanelColor
|
Package apollo.dataadapter.gff3 |
seqButton
javax.swing.JButton seqButton
seqFileList
javax.swing.JComboBox seqFileList
seqFilePaths
java.util.Vector<E> seqFilePaths
fastaFromGff
javax.swing.JCheckBox fastaFromGff
|
Package apollo.dataadapter.graph |
color
java.awt.Color color
|
Package apollo.dataadapter.otter |
driver
org.bdgp.io.DataAdapter driver
op
org.bdgp.io.IOOperation op
inputFileLabel
javax.swing.JLabel inputFileLabel
inputFileField
javax.swing.JTextField inputFileField
outputFileLabel
javax.swing.JLabel outputFileLabel
outputFileField
javax.swing.JTextField outputFileField
props
java.util.Properties props
seqButton
javax.swing.JButton seqButton
seqFileList
javax.swing.JComboBox seqFileList
seqFilePaths
java.util.Vector<E> seqFilePaths
gffButton
javax.swing.JButton gffButton
gffFileList
javax.swing.JComboBox gffFileList
gffFilePaths
java.util.Vector<E> gffFilePaths
|
Package apollo.dataadapter.sample |
operation
org.bdgp.io.IOOperation operation
numberLabel
javax.swing.JLabel numberLabel
lastChosenLabel
javax.swing.JLabel lastChosenLabel
numberTextField
javax.swing.JTextField numberTextField
|
Package apollo.dataadapter.synteny |
alignHash
java.util.HashMap<K,V> alignHash
locationHash
java.util.HashMap<K,V> locationHash
oKButton
javax.swing.JButton oKButton
labels
javax.swing.JLabel[] labels
buttonGroup
javax.swing.ButtonGroup buttonGroup
buttonList
java.util.ArrayList<E> buttonList
parent
javax.swing.JComponent parent
chr
Chromosome chr
regions
java.util.Vector<E> regions
colours
java.util.Hashtable<K,V> colours
hitChrs
java.util.Vector<E> hitChrs
hitRegions
java.util.Hashtable<K,V> hitRegions
drawers
java.util.Vector<E> drawers
hitOrder
java.util.Vector<E> hitOrder
sb
StatusBar sb
callback
org.bdgp.swing.AbstractDataAdapterUI callback
logicalQuerySpecies
java.lang.String logicalQuerySpecies
logicalHitSpecies
java.lang.String logicalHitSpecies
org1
java.lang.String org1
org2
java.lang.String org2
chrPanel
javax.swing.JPanel chrPanel
sb
StatusBar sb
sa
SyntenyAdapterI sa
ka
KaryotypeAdapterI ka
callback
org.bdgp.swing.AbstractDataAdapterUI callback
logicalQuerySpecies
java.lang.String logicalQuerySpecies
logicalHitSpecies
java.lang.String logicalHitSpecies
adapterGUIs
java.util.Map<K,V> adapterGUIs
adapterLabelList
java.util.List<E> adapterLabelList
sharedData
java.util.HashMap<K,V> sharedData
driver
SyntenyAdapter driver
op
org.bdgp.io.IOOperation op
props
java.util.Properties props
fullPanelButton
javax.swing.JButton fullPanelButton
thePanel
FullEnsJDBCSyntenyPanel thePanel
tabbedPane
javax.swing.JTabbedPane tabbedPane
speciesNumberDropdownList
javax.swing.JComboBox speciesNumberDropdownList
- Dropdown list of how many species to query for - max is configged
numberOfSpeciesToLoad
int numberOfSpeciesToLoad
querySpecies
java.lang.String querySpecies
hitSpecies
java.lang.String hitSpecies
logicalQuerySpecies
java.lang.String logicalQuerySpecies
logicalHitSpecies
java.lang.String logicalHitSpecies
frame
javax.swing.JDialog frame
fullPanelButton
javax.swing.JButton fullPanelButton
parent
SyntenyAdapterGUI parent
adapter
org.bdgp.io.DataAdapter adapter
thePanel
FullEnsJDBCSyntenyPanel thePanel
dataConfigChooser
CompositeDataSourceConfigurationPanel dataConfigChooser
dataSourceConfigurationPanel
javax.swing.JPanel dataSourceConfigurationPanel
showDataSourceConfiguration
javax.swing.JButton showDataSourceConfiguration
addHighConservationDnaAligns
javax.swing.JCheckBox addHighConservationDnaAligns
addDnaAligns
javax.swing.JCheckBox addDnaAligns
dnaAlignTypesButton
javax.swing.JButton dnaAlignTypesButton
dnaAlignTypesList
javax.swing.JList dnaAlignTypesList
addProteinAligns
javax.swing.JCheckBox addProteinAligns
addDnaAlignsToSingleSpeciesPanes
javax.swing.JCheckBox addDnaAlignsToSingleSpeciesPanes
methodLinksVisible
boolean methodLinksVisible
methodLinksInitialised
boolean methodLinksInitialised
region1
javax.swing.JMenuItem region1
region2
javax.swing.JMenuItem region2
cp
ChromosomePanel cp
- ChromosomePanel not actually used - delete?
region
SyntenyRegion region
species1
java.lang.String species1
species2
java.lang.String species2
callback
org.bdgp.swing.AbstractDataAdapterUI callback
logicalQuerySpecies
java.lang.String logicalQuerySpecies
logicalHitSpecies
java.lang.String logicalHitSpecies
|
Package apollo.dataadapter.synteny.builder |
properties
java.util.Properties properties
operation
org.bdgp.io.IOOperation operation
controller
Controller controller
view
View view
treeToAdapterSplitPane
javax.swing.JSplitPane treeToAdapterSplitPane
adapterToGUISplitPane
javax.swing.JSplitPane adapterToGUISplitPane
treeScrollPane
javax.swing.JScrollPane treeScrollPane
tree
javax.swing.JTree tree
treeHash
java.util.Hashtable<K,V> treeHash
rootNode
javax.swing.tree.DefaultMutableTreeNode rootNode
adapterPanel
javax.swing.JPanel adapterPanel
setPanel
javax.swing.JPanel setPanel
setAndAdapterPanel
javax.swing.JPanel setAndAdapterPanel
adapterPropertiesScrollPane
javax.swing.JScrollPane adapterPropertiesScrollPane
propertiesTable
javax.swing.JTable propertiesTable
propertiesTableModel
javax.swing.table.DefaultTableModel propertiesTableModel
setDropDown
javax.swing.JComboBox setDropDown
createSetButton
javax.swing.JButton createSetButton
deleteSetButton
javax.swing.JButton deleteSetButton
setLabel
javax.swing.JLabel setLabel
nameTextField
javax.swing.JTextField nameTextField
nameLabel
javax.swing.JLabel nameLabel
adapterClassDropdown
javax.swing.JComboBox adapterClassDropdown
adapterClassLabel
javax.swing.JLabel adapterClassLabel
adapterTypeDropdown
javax.swing.JComboBox adapterTypeDropdown
adapterTypeLabel
javax.swing.JLabel adapterTypeLabel
controller
Controller controller
createButton
javax.swing.JButton createButton
updateButton
javax.swing.JButton updateButton
deleteButton
javax.swing.JButton deleteButton
guiPanel
javax.swing.JPanel guiPanel
name
java.lang.String name
accession
java.lang.String accession
description
java.lang.String description
dbxrefs
java.util.Vector<E> dbxrefs
residue_type
java.lang.String residue_type
checksum
java.lang.String checksum
length
int length
genomicRange
RangeI genomicRange
genomic_errors
java.util.HashMap<K,V> genomic_errors
- allow for some adjustments if the genomic sequence has
sequencing errors
update_date
java.util.Date update_date
organism
java.lang.String organism
needShiftFromOneToZeroBasedCoords
boolean needShiftFromOneToZeroBasedCoords
evidenceSet
EvidenceSet evidenceSet
finder
EvidenceFinder finder
comment_list
java.util.Vector<E> comment_list
isProblematic
boolean isProblematic
annotationRoot
boolean annotationRoot
owner
java.lang.String owner
fragmentOffset
int fragmentOffset
chromosome
java.lang.String chromosome
accession
java.lang.String accession
version
int version
keywords
java.util.Vector<E> keywords
remarks
java.util.Vector<E> remarks
id
java.lang.String id
text
java.lang.String text
person
java.lang.String person
timestamp
long timestamp
isInternal
boolean isInternal
childCurationSets
java.util.HashMap<K,V> childCurationSets
childSetOrderedNames
java.util.Vector<E> childSetOrderedNames
results
StrandedFeatureSetI results
annots
StrandedFeatureSetI annots
sequence_vect
java.util.Vector<E> sequence_vect
sequence_hash
java.util.Hashtable<K,V> sequence_hash
assemblyType
java.lang.String assemblyType
tranManager
TransactionManager tranManager
inputFile
java.lang.String inputFile
idtype
java.lang.String idtype
idvalue
java.lang.String idvalue
dbname
java.lang.String dbname
version
java.lang.String version
current
short current
description
java.lang.String description
isPrimary
boolean isPrimary
isSecondary
boolean isSecondary
isOntology
boolean isOntology
type
int type
featureId
java.lang.String featureId
setId
java.lang.String setId
dbType
java.lang.String dbType
dbXref
DbXref dbXref
fset
FeatureSetI fset
nameHash
java.util.Hashtable<K,V> nameHash
evidence_hash
java.util.Hashtable<K,V> evidence_hash
evidence
java.util.Vector<E> evidence
query
SeqFeatureI query
- query feature, do we really need to store query separately, couldnt query
just be this and just the associated hit would be a separate SeqFeatureI?
Thats really the way to go. how hard a change would this be?
hit
SeqFeatureI hit
- hit feature
cigar
java.lang.String cigar
- Genuine Sequence of the hit to query , the aligned sequence
is still stored as a property of the hit feature
features
java.util.Vector<E> features
hitSequence
SequenceI hitSequence
flags
byte flags
- This flag is just for the use of bop to indicate that the
feature has already had a an exon removed. Or for other
simple flags that we don't want to allocate an entire boolean
to.
translation_start
int translation_start
translation_end
int translation_end
plus1_frameshift
int plus1_frameshift
minus1_frameshift
int minus1_frameshift
readthrough_stop
java.lang.String readthrough_stop
genericReadThroughStopResidue
java.lang.String genericReadThroughStopResidue
readthrough_pos
int readthrough_pos
trans_spliced
boolean trans_spliced
missing_5prime
boolean missing_5prime
missing_3prime
boolean missing_3prime
start_codon
java.lang.String start_codon
isProteinCodingGene
boolean isProteinCodingGene
- See Also:
FeatureSet.setProteinCodingGene(boolean)
chromosome
java.lang.String chromosome
description
java.lang.String description
synonyms
java.util.Vector<E> synonyms
dbXrefs
java.util.TreeMap<K,V> dbXrefs
transcript
Transcript transcript
low
int low
high
int high
strand
byte strand
name
java.lang.String name
type
java.lang.String type
refSeq
SequenceI refSeq
name
java.lang.String name
value
double value
id
java.lang.String id
refId
java.lang.String refId
identifier
Identifier identifier
refFeature
SeqFeatureI refFeature
ref_features
java.util.Hashtable<K,V> ref_features
analogousOppositeStrandFeature
SeqFeatureI analogousOppositeStrandFeature
biotype
java.lang.String biotype
scores
java.util.Hashtable<K,V> scores
score
double score
properties
java.util.Hashtable<K,V> properties
phase
byte phase
alignment
java.lang.String alignment
- alignment either comes from explicitAlignment or a cigar. null if there is no
alignment. alignments are only for leaf features. alignment has peptide padding
if a peptide alignment.
unpaddedAlignment
java.lang.String unpaddedAlignment
- alignment with no padding
explicitAlignment
java.lang.String explicitAlignment
edit_offset_adjust
int edit_offset_adjust
- When translating the offset for the stop codon in genome
coordinates needs to be adjusted to account for edits to
the mRNA that alter the relative position of the Stop codon
on the mRNA vs. the genome (e.g. from translational frame
shift, or genomic sequencing errors
userObject
java.lang.Object userObject
syntenyLinkInfo
java.lang.String syntenyLinkInfo
cloneSource
SeqFeatureI cloneSource
queryFeature
SeqFeatureI queryFeature
alignmentResidueType
java.lang.String alignmentResidueType
readObject
private void readObject(java.io.ObjectInputStream in)
throws java.io.IOException,
java.lang.ClassNotFoundException
- Throws:
java.io.IOException
java.lang.ClassNotFoundException
writeObject
private void writeObject(java.io.ObjectOutputStream out)
throws java.io.IOException
- Throws:
java.io.IOException
dna_chars
char[] dna_chars
residues
java.lang.String residues
refSeq
SequenceI refSeq
residue
java.lang.String residue
forward
FeatureSetI forward
reverse
FeatureSetI reverse
name
java.lang.String name
properties
java.util.Hashtable<K,V> properties
owner
java.lang.String owner
ownerId
int ownerId
cDNA
SequenceI cDNA
peptide
SequenceI peptide
peptideValidity
boolean peptideValidity
allow_nonconsensus_splicing
boolean allow_nonconsensus_splicing
proteinFeat
Protein proteinFeat
|
Package apollo.datamodel.seq |
readObject
private void readObject(java.io.ObjectInputStream in)
throws java.io.IOException,
java.lang.ClassNotFoundException
- Throws:
java.io.IOException
java.lang.ClassNotFoundException
writeObject
private void writeObject(java.io.ObjectOutputStream out)
throws java.io.IOException
- Throws:
java.io.IOException
llco
AbstractLazySequence.LazyLoadControlledObject llco
cacher
CacheSequenceLoader cacher
residues
java.lang.String residues
server
java.lang.String server
range_residues
java.lang.String range_residues
header
java.lang.String header
properties
java.util.Hashtable<K,V> properties
isPeptide
boolean isPeptide
residues
java.lang.String residues
annotFeature
AnnotatedFeatureI annotFeature
deletedAnnot
AnnotatedFeatureI deletedAnnot
subpartRank
int subpartRank
- For subparts that are lists, like comments and synoyms we need to know which
item in the list is being operated on. FeatCngEv?
oldString
java.lang.String oldString
deletedComment
Comment deletedComment
oldId
java.lang.String oldId
transaction
Transaction transaction
isUndo
boolean isUndo
transactions
java.util.List<E> transactions
compoundTransaction
CompoundTransaction compoundTransaction
controller
Controller controller
- The controller to which AnnotationChangeEvents are sent.
annotCngListener
AnnotationChangeListener annotCngListener
- Who to fire AnnotationChangeEvents to
annotationCollection
FeatureSetI annotationCollection
- The top of the annotations AnnotatedFeatureI. This is model NOT drawable.
This is AnnotViews dfset.getFeature. It is the top model object for
the AnnotView being edited. It is the holder of genes of a strand, of
all genes in an AnnotView.
curation
CurationSet curation
- The entire curation set, not just the portion on one strand
(as above in the annotationCollection
cursorSet
apollo.editor.SelectionSet cursorSet
- One of the four SelectionSets. This one is made up of the features
under the cursor (for the default edits at least).
annotSet
apollo.editor.SelectionSet annotSet
- One of the four SelectionSets. This one is made up of the features from
the selection in the current view (for the default edits at least).
evidenceSet
apollo.editor.SelectionSet evidenceSet
- One of the four SelectionSets. This one is made up of the features
from the selection in the result view (for the default edits at least).
siteSet
apollo.editor.SelectionSet siteSet
- One of the four SelectionSets. This one is made up of the features from
the selection in the start-stop codon view (for the default edits at
least).
basePosition
int basePosition
- The base position at which the current edit is occuring.
endBasePosition
int endBasePosition
- endBasePosition specifies the end of the feature to be added????
defaultStrand
int defaultStrand
- This strand is used if no information is available from features.
strandSet
boolean strandSet
- Indicates whether the defaultStrand has been set.
parentComponent
java.awt.Component parentComponent
- The parentComponent is needed for displaying messages in a dialog box.
annotationView
AnnotationView annotationView
- We need access to annotationView later on when we
select the newly-created thing
curationState
GuiCurationState curationState
- should just be CurationState - eventually
oldTranscripts
FeatureList oldTranscripts
newTranscripts
FeatureList newTranscripts
oldAnnots
FeatureList oldAnnots
oldParent
SeqFeatureI oldParent
oldRange
RangeI oldRange
isIntUpdate
boolean isIntUpdate
oldInt
int oldInt
oldComment
Comment oldComment
newSequencingErrorPosition
int newSequencingErrorPosition
changes
java.util.Vector<E> changes
- List of AnnotationChangeEvents
controller
Controller controller
annotEditor
AnnotationEditor annotEditor
childTransactions
java.util.List<E> childTransactions
newSplitFeature
AnnotatedFeatureI newSplitFeature
compoundType
int compoundType
operation
int operation
- Update means only one part of the feature has changed as hopefully
described by ObjectClass or SubObjectClass or something like that
changeTop
SeqFeatureI changeTop
changedFeature
SeqFeatureI changedFeature
parentFeature
SeqFeatureI parentFeature
- parent only explictly set for deletes
replacedFeature
AnnotatedFeatureI replacedFeature
- Until we get rid of REPLACE - artifact of annot info doing undo kluge
transaction
Transaction transaction
transactionSubpart
TransactionSubpart transactionSubpart
isSingularEvent
boolean isSingularEvent
- If true, event is not part of a series of events, its stand alone,
and isEndOfEditSession returns true - dont need separate end of session event
should this be called endOfSession - and be used by real events at the end of
a session? that might be murky territory - i think compound events will solve
a lot of these issues - which will be needed for undo
objectClass
int objectClass
readObject
private void readObject(java.io.ObjectInputStream in)
throws java.io.IOException,
java.lang.ClassNotFoundException
- Throws:
java.io.IOException
java.lang.ClassNotFoundException
date
java.util.Date date
author
java.lang.String author
transactionClass
TransactionClass transactionClass
transactionOperation
TransactionOperation transactionOperation
transactionSubpart
TransactionSubpart transactionSubpart
- Enumeration/value class that captures the subpart of the feature that is
effected by the transaction. This is optional as some transactions effect
the whole feature (e.g. delete transcript)
newSubpartValue
java.lang.Object newSubpartValue
- The touched subpart value. For example, A comment is deleted, updated
// or added, this Comment object is subpartValue. It can also be a String
// (e.g. for synonym). This is the post/new value. Rename newValue?
oldSubpartValue
java.lang.Object oldSubpartValue
oldProperties
java.util.Hashtable<K,V> oldProperties
newProperties
java.util.Hashtable<K,V> newProperties
parentTransaction
CompoundTransaction parentTransaction
- If this is a child of a compound transactions, parentTransaction is a ref to
that parent, null if no parent.
feature
SeqFeatureI feature
- do we need more than one feature?
featureClone
SeqFeatureI featureClone
- A clone of
feature, this allows us to know the original state
of the SeqFeature as it was affected by the transaction, even if it has
subsequently been modified. Will not be set unless
Config.getSaveClonedFeaturesInTransactions == true.
parentFeature
SeqFeatureI parentFeature
parentFeatureClone
SeqFeatureI parentFeatureClone
subpartRank
int subpartRank
rank
int rank
oldId
java.lang.String oldId
newId
java.lang.String newId
classString
java.lang.String classString
unflattenedTransactions
java.util.List<E> unflattenedTransactions
- Hold all unflattened Transaction instances, includes compound trans
flattenedTransactions
java.util.List<E> flattenedTransactions
- Holds all transactions in flattened form, compound trans have been flattened
out to children
author
java.lang.String author
needCoalescence
boolean needCoalescence
isCoalescedDone
boolean isCoalescedDone
operationString
java.lang.String operationString
subpartString
java.lang.String subpartString
type
java.lang.Class<T> type
child
SeqFeatureI child
oldParent
SeqFeatureI oldParent
newParent
SeqFeatureI newParent
previousValue
java.lang.Object previousValue
evidenceSzapSplitPane
UnBorderedSplitPane evidenceSzapSplitPane
- UnBorderedSplitPane to split evp and szap.
syntenyPanel
SyntenyPanel syntenyPanel
- SyntenyPanel holds all the szaps and link panels (rename?)
ld
javax.swing.JDialog ld
beforeLazyLoad
java.lang.Runnable beforeLazyLoad
afterLazyLoad
java.lang.Runnable afterLazyLoad
localArrayListFlavor
java.awt.datatransfer.DataFlavor localArrayListFlavor
serialArrayListFlavor
java.awt.datatransfer.DataFlavor serialArrayListFlavor
localArrayListType
java.lang.String localArrayListType
source
javax.swing.JList source
target
javax.swing.JList target
indices
int[] indices
addIndex
int addIndex
addCount
int addCount
jp
javax.swing.JPanel jp
frame
javax.swing.JFrame frame
ap
ApolloPanel ap
featureProperty
FeatureProperty featureProperty
seqField
javax.swing.JTextField seqField
nameField
javax.swing.JTextField nameField
positionField
javax.swing.JTextField positionField
seqLabel
javax.swing.JLabel seqLabel
nameLabel
javax.swing.JLabel nameLabel
positionLabel
javax.swing.JLabel positionLabel
seqButton
javax.swing.JButton seqButton
nameButton
javax.swing.JButton nameButton
positionButton
javax.swing.JButton positionButton
clearButton
javax.swing.JButton clearButton
cancelButton
javax.swing.JButton cancelButton
revStrand
javax.swing.JCheckBox revStrand
regExp
javax.swing.JCheckBox regExp
seqValidator
apollo.gui.FindPanel.BaseValidator seqValidator
curationState
GuiCurationState curationState
resultTable
javax.swing.JTable resultTable
resultTableScroller
javax.swing.JScrollPane resultTableScroller
mainPanel
javax.swing.JPanel mainPanel
closePanel
javax.swing.JPanel closePanel
columns
java.util.Vector<E> columns
sf
SeqFeatureI sf
features
java.util.Vector<E> features
currentFeatureType
int currentFeatureType
resultsPane
StatusPane resultsPane
org1
java.lang.String org1
org2
java.lang.String org2
fileStub
java.lang.String fileStub
chrPanel
javax.swing.JPanel chrPanel
sb
StatusBar sb
panels
java.util.Vector<E> panels
driver
org.bdgp.io.DataAdapter driver
op
org.bdgp.io.IOOperation op
pathList
javax.swing.JComboBox pathList
panel
javax.swing.JPanel panel
panel2
javax.swing.JPanel panel2
typeLabel
javax.swing.JLabel typeLabel
filePaths
java.util.Vector<E> filePaths
browseButton
javax.swing.JButton browseButton
props
java.util.Properties props
filter
javax.swing.filechooser.FileFilter filter
pathListWidth
int pathListWidth
- How much space to display file names - changed from 300 to 500 as
300 was just too small for really long path-filenames. Readjust if need be.
Maybe it could even be smart and grow itself according to the size of the
pathname. wouldnt that be nifty
arrayListHandler
ArrayListTransferHandler arrayListHandler
featureProperty
FeatureProperty featureProperty
glyphChoiceList
javax.swing.JComboBox glyphChoiceList
applyButton
javax.swing.JButton applyButton
includedProps
javax.swing.DefaultListModel includedProps
excludedProps
javax.swing.DefaultListModel excludedProps
writeObject
private void writeObject(java.io.ObjectOutputStream out)
throws java.io.IOException
- Throws:
java.io.IOException
controller
Controller controller
helpButton
javax.swing.JButton helpButton
restoreButton
javax.swing.JButton restoreButton
saveButton
javax.swing.JButton saveButton
cancelButton
javax.swing.JButton cancelButton
prefsPanel
PrefsPanel prefsPanel
bgColor
java.awt.Color bgColor
origText
java.lang.String origText
defaultStyleFile
java.lang.String defaultStyleFile
styleFileName
java.lang.String styleFileName
controller
Controller controller
tabbedPane
javax.swing.JTabbedPane tabbedPane
styleWizard
StyleWizard styleWizard
typesWizard
TypesWizard typesWizard
previewButton
javax.swing.JButton previewButton
cancelButton
javax.swing.JButton cancelButton
saveButton
javax.swing.JButton saveButton
defaultTextArea
javax.swing.JTextArea defaultTextArea
personalTextArea
javax.swing.JTextArea personalTextArea
bgColor
java.awt.Color bgColor
defaultHeader
javax.swing.JLabel defaultHeader
personalHeader
javax.swing.JLabel personalHeader
progressListener
org.bdgp.util.ProgressListener progressListener
progressBar
javax.swing.JProgressBar progressBar
adapter
org.bdgp.io.VisualDataAdapter adapter
visible
javax.swing.JCheckBox visible
expanded
javax.swing.JCheckBox expanded
sorted
javax.swing.JCheckBox sorted
labeled
javax.swing.JCheckBox labeled
jp
javax.swing.JPanel jp
ap
ApolloPanel ap
tierProperty
TierProperty tierProperty
beginFlash
boolean beginFlash
flashTimer
javax.swing.Timer flashTimer
proxyServer
java.lang.String proxyServer
proxyPort
java.lang.String proxyPort
userName
java.lang.String userName
userPassword
java.lang.String userPassword
hasAuthentication
boolean hasAuthentication
hasProxy
boolean hasProxy
server
javax.swing.JTextField server
port
javax.swing.JTextField port
name
javax.swing.JTextField name
password
javax.swing.JPasswordField password
authBox
javax.swing.JCheckBox authBox
proxyBox
javax.swing.JCheckBox proxyBox
authP
javax.swing.JPanel authP
ok
javax.swing.JButton ok
cancel
javax.swing.JButton cancel
selectionItems
java.util.Vector<E> selectionItems
- Vector of SelectionItems
currentlySelected
Selection currentlySelected
controller
Controller controller
szap
StrandedZoomableApolloPanel szap
reverseComplement
boolean reverseComplement
controller
Controller controller
table
javax.swing.JTable table
model
javax.swing.table.DefaultTableModel model
seqString
java.lang.String seqString
refSeqString
java.lang.String refSeqString
searchString
java.lang.String searchString
slp
javax.swing.JPanel slp
tableData
java.util.Vector<E> tableData
data
java.util.Vector<E> data
columns
java.util.Vector<E> columns
slider
javax.swing.JSlider slider
field
javax.swing.JTextField field
labelStr
java.lang.String labelStr
title
java.lang.String title
model
javax.swing.BoundedRangeModel model
frame
javax.swing.JFrame frame
isAdjusting
boolean isAdjusting
actionPane
StatusPane actionPane
featurePane
StatusPane featurePane
positionPane
StatusPane positionPane
label
javax.swing.JLabel label
tb
javax.swing.JTextField tb
defaultColor
java.awt.Color defaultColor
tiersFileField
javax.swing.JTextField tiersFileField
showAnnotationsCheckBox
javax.swing.JCheckBox showAnnotationsCheckBox
showResultsCheckBox
javax.swing.JCheckBox showResultsCheckBox
enableEditingCheckBox
javax.swing.JCheckBox enableEditingCheckBox
annotationBackgroundColorButton
javax.swing.JButton annotationBackgroundColorButton
featureBackgroundColorButton
javax.swing.JButton featureBackgroundColorButton
annotationLabelColorButton
javax.swing.JButton annotationLabelColorButton
featureLabelColorButton
javax.swing.JButton featureLabelColorButton
annotationBackgroundColorButtonPanel
javax.swing.JPanel annotationBackgroundColorButtonPanel
featureBackgroundColorButtonPanel
javax.swing.JPanel featureBackgroundColorButtonPanel
annotationLabelColorButtonPanel
javax.swing.JPanel annotationLabelColorButtonPanel
featureLabelColorButtonPanel
javax.swing.JPanel featureLabelColorButtonPanel
annotationCommentsArea
javax.swing.JTextArea annotationCommentsArea
transcriptCommentsArea
javax.swing.JTextArea transcriptCommentsArea
annotationCommentsAreaScrollPane
javax.swing.JScrollPane annotationCommentsAreaScrollPane
transcriptCommentsAreaScrollPane
javax.swing.JScrollPane transcriptCommentsAreaScrollPane
origOptions
apollo.gui.StyleWizard.ConfigurableStyleOptions origOptions
arrayListHandler
ArrayListTransferHandler arrayListHandler
featureProperty
FeatureProperty featureProperty
includedProps
javax.swing.DefaultListModel includedProps
excludedProps
javax.swing.DefaultListModel excludedProps
tiers
java.util.Vector<E> tiers
- Vector of Tiers (FeatureTiers for FeatureTierManager)
This is not set in this class, a subclass has to set this and there
is no set method(perhaps there should be) only way to set is to use
the variable itself.
visibleLimits
int[] visibleLimits
viewHeight
int viewHeight
offsetPixelHeight
int offsetPixelHeight
aggregateSizeChange
int aggregateSizeChange
charHeight
int charHeight
view
ViewI view
controller
Controller controller
tierManagerListeners
java.util.Vector<E> tierManagerListeners
ignoreScoreThresholds
boolean ignoreScoreThresholds
properties
PropertyScheme properties
panels
java.util.Vector<E> panels
ap
ApolloPanel ap
controller
Controller controller
sp
javax.swing.JScrollPane sp
mainP
javax.swing.JPanel mainP
autoRaise
boolean autoRaise
autoBox
javax.swing.JCheckBox autoBox
doneInit
boolean doneInit
frame
javax.swing.JFrame frame
styleFileName
java.lang.String styleFileName
tierComboBox
javax.swing.JComboBox tierComboBox
visibleCheckBox
javax.swing.JCheckBox visibleCheckBox
labeledCheckBox
javax.swing.JCheckBox labeledCheckBox
expandedCheckBox
javax.swing.JCheckBox expandedCheckBox
typeComboBox
javax.swing.JComboBox typeComboBox
shapeComboBox
javax.swing.JComboBox shapeComboBox
colorButton
javax.swing.JButton colorButton
colorButtonPanel
javax.swing.JPanel colorButtonPanel
scaleCheckBox
javax.swing.JCheckBox scaleCheckBox
minScoreField
javax.swing.JTextField minScoreField
maxScoreField
javax.swing.JTextField maxScoreField
urlField
javax.swing.JTextField urlField
dataTypeArea
javax.swing.JTextArea dataTypeArea
newTierButton
javax.swing.JButton newTierButton
newTypeButton
javax.swing.JButton newTypeButton
matchUtrColorToBackgroundCheckBox
javax.swing.JCheckBox matchUtrColorToBackgroundCheckBox
matchUtrColorToBackgroundLabel
javax.swing.JLabel matchUtrColorToBackgroundLabel
separator
javax.swing.JSeparator separator
origFeatureProperties
java.util.Map<K,V> origFeatureProperties
|
Package apollo.gui.annotinfo |
controller
Controller controller
selectionManager
SelectionManager selectionManager
selectIsFromTree
boolean selectIsFromTree
buttonPanel
javax.swing.Box buttonPanel
cancelButton
javax.swing.JButton cancelButton
undoButton
javax.swing.JButton undoButton
followSelectionCheckBox
javax.swing.JCheckBox followSelectionCheckBox
genePanel
GeneEditPanel genePanel
treePanel
FeatureTreePanel treePanel
annots
StrandedFeatureSetI annots
orig_feature
SeqFeatureI orig_feature
orig_annot
AnnotatedFeatureI orig_annot
curationState
GuiCurationState curationState
- Has state related to species/szap that fed has sprung from
isUndoing
boolean isUndoing
- true if amidst undo
originalFeature
AnnotatedFeatureI originalFeature
featureEditorDialog
FeatureEditorDialog featureEditorDialog
featureBox
javax.swing.Box featureBox
- box for whole panel
isProblematicCheckbox
javax.swing.JCheckBox isProblematicCheckbox
fieldsPanel
javax.swing.JPanel fieldsPanel
- fields panel holds all the "fields" (check boxes, names,...
bgColor
java.awt.Color bgColor
border
javax.swing.border.TitledBorder border
featureNameField
apollo.gui.annotinfo.ReadWriteField featureNameField
featureIDField
apollo.gui.annotinfo.ReadWriteField featureIDField
featureSynonymField
apollo.gui.annotinfo.ReadWriteField featureSynonymField
synGuiList
javax.swing.JList synGuiList
guiListModel
javax.swing.DefaultListModel guiListModel
synScrollPane
javax.swing.JScrollPane synScrollPane
delSynButton
javax.swing.JButton delSynButton
addSynButton
javax.swing.JButton addSynButton
lockFocus
boolean lockFocus
goodUser
boolean goodUser
isReadOnly
boolean isReadOnly
row
int row
synonymEditor
apollo.gui.annotinfo.FeatureEditPanel.SynonymEditor synonymEditor
SYN_SUBPART
TransactionSubpart SYN_SUBPART
transcriptPanel
apollo.gui.annotinfo.TranscriptEditPanel transcriptPanel
featureTypeList
apollo.gui.annotinfo.ReadWriteField featureTypeList
bigCommentField
javax.swing.JTextArea bigCommentField
- bigCommentField is where all the comments from gene and trans
are displayed, not edited
peptideStatus
apollo.gui.annotinfo.ReadWriteField peptideStatus
sequencingComments
javax.swing.JTextArea sequencingComments
isDicistronicCheckbox
javax.swing.JCheckBox isDicistronicCheckbox
table_row_selected
int table_row_selected
annotFeatureProps
java.util.Vector<E> annotFeatureProps
- Vector of feature properties for type field, not used for readOnly
dbXRefModel
apollo.gui.annotinfo.GeneEditPanel.DbxRefTableModel dbXRefModel
dataBox
javax.swing.Box dataBox
addAnnotComment
javax.swing.JButton addAnnotComment
addTransComment
javax.swing.JButton addTransComment
commentator
apollo.gui.annotinfo.Commentator commentator
GO_URL
java.lang.String GO_URL
warnedAboutEditingIDs
boolean warnedAboutEditingIDs
idFocusListener
apollo.gui.annotinfo.GeneEditPanel.IDFocusListener idFocusListener
geneNameListener
apollo.gui.annotinfo.GeneEditPanel.GeneNameListener geneNameListener
dbxrefTable
javax.swing.JTable dbxrefTable
|
Package apollo.gui.detailviewers.exonviewer |
bgcolor
java.awt.Color bgcolor
disabled
java.awt.Color disabled
phase
int phase
regularFont
java.awt.Font regularFont
boldFont
java.awt.Font boldFont
panel
SeqAlignPanel panel
hatchColor
java.awt.Color hatchColor
padAmt
int padAmt
selectedFeature
SeqFeatureI selectedFeature
selectedTier
int selectedTier
annotationEditor
AnnotationEditor annotationEditor
baseFineEditor
BaseFineEditor baseFineEditor
locationLabel
javax.swing.JLabel locationLabel
relativeLocationLabel
javax.swing.JLabel relativeLocationLabel
rightClickMenu
javax.swing.JPopupMenu rightClickMenu
makeIntronMenuItem
javax.swing.JMenuItem makeIntronMenuItem
createExonMenuItem
javax.swing.JMenuItem createExonMenuItem
merge5PrimeMenuItem
javax.swing.JMenuItem merge5PrimeMenuItem
merge3PrimeMenuItem
javax.swing.JMenuItem merge3PrimeMenuItem
set5PrimeMenuItem
javax.swing.JMenuItem set5PrimeMenuItem
set3PrimeMenuItem
javax.swing.JMenuItem set3PrimeMenuItem
deleteExonMenuItem
javax.swing.JMenuItem deleteExonMenuItem
startTranslationMenuItem
javax.swing.JMenuItem startTranslationMenuItem
translationSlipMenuItem
javax.swing.JMenuItem translationSlipMenuItem
translationStutterMenuItem
javax.swing.JMenuItem translationStutterMenuItem
insertionMenuItem
javax.swing.JMenuItem insertionMenuItem
deletionMenuItem
javax.swing.JMenuItem deletionMenuItem
substitutionMenuItem
javax.swing.JMenuItem substitutionMenuItem
noAdjustmentMenuItem
javax.swing.JMenuItem noAdjustmentMenuItem
sequencingErrorSubMenu
javax.swing.JMenu sequencingErrorSubMenu
findSequenceMenuItem
javax.swing.JMenuItem findSequenceMenuItem
sequenceMenuItem
javax.swing.JMenuItem sequenceMenuItem
seqSelectColor
java.awt.Color seqSelectColor
selectionBoxColor
java.awt.Color selectionBoxColor
refSeq
SequenceI refSeq
frame
SequenceI[] frame
mouseListener
apollo.gui.detailviewers.exonviewer.BaseMouseListener mouseListener
rightClickListener
apollo.gui.detailviewers.exonviewer.BaseEditorPanel.RightClickActionListener rightClickListener
selectBeginPos
int selectBeginPos
selectCurrentPos
int selectCurrentPos
splices
int[] splices
hitZones
java.util.Vector<E> hitZones
translatedHitZones
java.util.Vector<E> translatedHitZones
showHitZones
boolean showHitZones
curationState
GuiCurationState curationState
baseEditorSelectionListener
apollo.gui.detailviewers.exonviewer.BaseEditorPanel.BaseEditorSelectionListener baseEditorSelectionListener
- inner class that listens for selection events
editorPanel
BaseEditorPanel editorPanel
translationViewer
apollo.gui.detailviewers.exonviewer.TranslationViewer translationViewer
viewport
javax.swing.JViewport viewport
lengthLabel
javax.swing.JLabel lengthLabel
transcriptComboBox
javax.swing.JComboBox transcriptComboBox
szap
StrandedZoomableApolloPanel szap
transformer
Transformer transformer
scrollListener
apollo.gui.detailviewers.exonviewer.BaseFineEditor.FineEditorScrollListener scrollListener
indicatorColor
java.awt.Color indicatorColor
colorSwatch
javax.swing.JPanel colorSwatch
selection_manager
SelectionManager selection_manager
findButton
javax.swing.JButton findButton
clearFindsButton
javax.swing.JButton clearFindsButton
goToButton
javax.swing.JButton goToButton
showIntronBox
javax.swing.JCheckBox showIntronBox
followSelectionCheckBox
javax.swing.JCheckBox followSelectionCheckBox
upstream_button
javax.swing.JButton upstream_button
downstream_button
javax.swing.JButton downstream_button
currentAnnot
AnnotatedFeatureI currentAnnot
neighbor_up
Transcript neighbor_up
neighbor_down
Transcript neighbor_down
curationState
GuiCurationState curationState
transItemListener
apollo.gui.detailviewers.exonviewer.BaseFineEditor.TranscriptComboBoxItemListener transItemListener
baseEditorPanel
BaseEditorPanel baseEditorPanel
textMargin
int textMargin
c
char c
pos
int pos
tier
int tier
seq
SequenceI seq
metrics
java.awt.FontMetrics metrics
transcriptColorList
java.awt.Color[][] transcriptColorList
transcriptColorIndex
int transcriptColorIndex
exonColorIndex
int exonColorIndex
baseEditor
SeqAlignPanel baseEditor
currentRange
double[] currentRange
transcriptRange
double[] transcriptRange
oldRange
double[] oldRange
currentFeature
SeqFeatureI currentFeature
currentFeatureSet
FeatureSetI currentFeatureSet
type
int type
isIntron
boolean isIntron
isExon
boolean isExon
targetNucleotide
int targetNucleotide
targetTier
int targetTier
hitIndex
int hitIndex
targetColor
java.awt.Color targetColor
seqSelectColor
java.awt.Color seqSelectColor
hatchColor
java.awt.Color hatchColor
shiftColor
java.awt.Color shiftColor
sequences
java.util.Vector<E> sequences
- Holds a sequence (SeqWrapper) for every tier, element # is tier number
defaultRowHeader
javax.swing.JComponent defaultRowHeader
cols
int cols
stripeWidth
int stripeWidth
rowMargin
int rowMargin
horizontalMode
boolean horizontalMode
reverseStrand
boolean reverseStrand
horizontalScrollThread
SeqAlignPanel.AutoscrollThread horizontalScrollThread
verticalScrollThread
SeqAlignPanel.AutoscrollThread verticalScrollThread
autoscroll
boolean autoscroll
lowestBase
int lowestBase
- The base pair the sequence starts at in outside world(chromosomal)
highestBase
int highestBase
longest_seq
int longest_seq
renderer
BaseRenderer renderer
low
int low
|
Package apollo.gui.detailviewers.seqexport |
features
FeatureList features
seqScrollPane
javax.swing.JScrollPane seqScrollPane
seqTextArea
javax.swing.JTextArea seqTextArea
- text area displaying sequence
currentlySelectedButton
javax.swing.JRadioButton currentlySelectedButton
resultSequenceButton
javax.swing.JRadioButton resultSequenceButton
cdsButton
javax.swing.JRadioButton cdsButton
aminoAcidsButton
javax.swing.JRadioButton aminoAcidsButton
cdnaButton
javax.swing.JRadioButton cdnaButton
genomicButton
javax.swing.JRadioButton genomicButton
genomicPlusMinusButton
javax.swing.JRadioButton genomicPlusMinusButton
genomicPlusMinusField
javax.swing.JTextField genomicPlusMinusField
genomicPlusMinus
int genomicPlusMinus
followSelectionCheckBox
javax.swing.JCheckBox followSelectionCheckBox
selection
Selection selection
controller
Controller controller
offset
int offset
|
Package apollo.gui.detailviewers.sequencealigner |
bgcolor
java.awt.Color bgcolor
disabled
java.awt.Color disabled
phase
int phase
regularFont
java.awt.Font regularFont
boldFont
java.awt.Font boldFont
panel
SeqAlignPanel panel
hatchColor
java.awt.Color hatchColor
panel
MultiTierPanel panel
- This should be the Annotation window
curationState
GuiCurationState curationState
- The curation state
scrollableObject
BaseScrollable scrollableObject
- This should be reference to the main MultiSequenceAlignerPanel
createIntronAction
CreateIntronAction createIntronAction
createExonAction
CreateExonAction createExonAction
deleteExonAction
DeleteExonAction deleteExonAction
plus1FrameShiftAction
FrameShiftAction plus1FrameShiftAction
minus1FrameShiftAction
FrameShiftAction minus1FrameShiftAction
setTranslationStartAction
SetTranslationStartAction setTranslationStartAction
merge5PrimeAction
MergeExonAction merge5PrimeAction
merge3PrimeAction
MergeExonAction merge3PrimeAction
set5PrimeAction
SetEndAction set5PrimeAction
set3PrimeAction
SetEndAction set3PrimeAction
insertionAction
SequenceEditAction insertionAction
deletionAction
SequenceEditAction deletionAction
substitutionAction
SequenceEditAction substitutionAction
removeAdjustmentAction
SequenceEditAction removeAdjustmentAction
displaySequenceAction
DisplaySequenceAction displaySequenceAction
displayFindAction
javax.swing.AbstractAction displayFindAction
displayGoToAction
javax.swing.AbstractAction displayGoToAction
locationLabel
javax.swing.JLabel locationLabel
relativeLocationLabel
javax.swing.JLabel relativeLocationLabel
creaateIntronMenuItem
javax.swing.JMenuItem creaateIntronMenuItem
createExonMenuItem
javax.swing.JMenuItem createExonMenuItem
merge5PrimeMenuItem
javax.swing.JMenuItem merge5PrimeMenuItem
merge3PrimeMenuItem
javax.swing.JMenuItem merge3PrimeMenuItem
set5PrimeMenuItem
javax.swing.JMenuItem set5PrimeMenuItem
set3PrimeMenuItem
javax.swing.JMenuItem set3PrimeMenuItem
deleteExonMenuItem
javax.swing.JMenuItem deleteExonMenuItem
setTranslationStartMenuItem
javax.swing.JMenuItem setTranslationStartMenuItem
plus1FrameShiftMenuItem
javax.swing.JMenuItem plus1FrameShiftMenuItem
minus1FrameShiftMenuItem
javax.swing.JMenuItem minus1FrameShiftMenuItem
insertionMenuItem
javax.swing.JMenuItem insertionMenuItem
deletionMenuItem
javax.swing.JMenuItem deletionMenuItem
substitutionMenuItem
javax.swing.JMenuItem substitutionMenuItem
removeAdjustmentMenuItem
javax.swing.JMenuItem removeAdjustmentMenuItem
sequencingErrorSubMenu
javax.swing.JMenu sequencingErrorSubMenu
findSequenceMenuItem
javax.swing.JMenuItem findSequenceMenuItem
displaySequenceMenuItem
javax.swing.JMenuItem displaySequenceMenuItem
goToMenuItem
javax.swing.JMenuItem goToMenuItem
padAmt
int padAmt
selectedFeature
SeqFeatureI selectedFeature
selectedTier
int selectedTier
annotationEditor
AnnotationEditor annotationEditor
baseFineEditor
BaseFineEditor baseFineEditor
locationLabel
javax.swing.JLabel locationLabel
relativeLocationLabel
javax.swing.JLabel relativeLocationLabel
rightClickMenu
javax.swing.JPopupMenu rightClickMenu
makeIntronMenuItem
javax.swing.JMenuItem makeIntronMenuItem
createExonMenuItem
javax.swing.JMenuItem createExonMenuItem
merge5PrimeMenuItem
javax.swing.JMenuItem merge5PrimeMenuItem
merge3PrimeMenuItem
javax.swing.JMenuItem merge3PrimeMenuItem
set5PrimeMenuItem
javax.swing.JMenuItem set5PrimeMenuItem
set3PrimeMenuItem
javax.swing.JMenuItem set3PrimeMenuItem
deleteExonMenuItem
javax.swing.JMenuItem deleteExonMenuItem
startTranslationMenuItem
javax.swing.JMenuItem startTranslationMenuItem
translationSlipMenuItem
javax.swing.JMenuItem translationSlipMenuItem
translationStutterMenuItem
javax.swing.JMenuItem translationStutterMenuItem
insertionMenuItem
javax.swing.JMenuItem insertionMenuItem
deletionMenuItem
javax.swing.JMenuItem deletionMenuItem
substitutionMenuItem
javax.swing.JMenuItem substitutionMenuItem
noAdjustmentMenuItem
javax.swing.JMenuItem noAdjustmentMenuItem
sequencingErrorSubMenu
javax.swing.JMenu sequencingErrorSubMenu
findSequenceMenuItem
javax.swing.JMenuItem findSequenceMenuItem
sequenceMenuItem
javax.swing.JMenuItem sequenceMenuItem
seqSelectColor
java.awt.Color seqSelectColor
selectionBoxColor
java.awt.Color selectionBoxColor
refSeq
SequenceI refSeq
frame
SequenceI[] frame
mouseListener
apollo.gui.detailviewers.sequencealigner.BaseMouseListener mouseListener
rightClickListener
apollo.gui.detailviewers.sequencealigner.BaseEditorPanel.RightClickActionListener rightClickListener
selectBeginPos
int selectBeginPos
selectCurrentPos
int selectCurrentPos
splices
int[] splices
hitZones
java.util.Vector<E> hitZones
translatedHitZones
java.util.Vector<E> translatedHitZones
showHitZones
boolean showHitZones
curationState
GuiCurationState curationState
baseEditorSelectionListener
apollo.gui.detailviewers.sequencealigner.BaseEditorPanel.BaseEditorSelectionListener baseEditorSelectionListener
- inner class that listens for selection events
editorPanel
BaseEditorPanel editorPanel
- RAY: This is where the annotations get added
resultPanel
BaseEditorPanel resultPanel
translationViewer
apollo.gui.detailviewers.sequencealigner.TranslationViewer translationViewer
- RAY: The box at the bottom of the EDE which shows the selected transcript
viewport
javax.swing.JViewport viewport
- RAY: This is the box that holds the Scrollable part of the EDE
lengthLabel
javax.swing.JLabel lengthLabel
transcriptComboBox
javax.swing.JComboBox transcriptComboBox
- RAY: The drop down menu with the list of transcripts in it
szap
StrandedZoomableApolloPanel szap
transformer
Transformer transformer
scrollListener
apollo.gui.detailviewers.sequencealigner.BaseFineEditor.FineEditorScrollListener scrollListener
indicatorColor
java.awt.Color indicatorColor
colorSwatch
javax.swing.JPanel colorSwatch
selection_manager
SelectionManager selection_manager
findButton
javax.swing.JButton findButton
clearFindsButton
javax.swing.JButton clearFindsButton
goToButton
javax.swing.JButton goToButton
showIntronBox
javax.swing.JCheckBox showIntronBox
followSelectionCheckBox
javax.swing.JCheckBox followSelectionCheckBox
upstream_button
javax.swing.JButton upstream_button
downstream_button
javax.swing.JButton downstream_button
currentAnnot
AnnotatedFeatureI currentAnnot
neighbor_up
Transcript neighbor_up
neighbor_down
Transcript neighbor_down
curationState
GuiCurationState curationState
transItemListener
apollo.gui.detailviewers.sequencealigner.BaseFineEditor.TranscriptComboBoxItemListener transItemListener
baseEditorPanel
BaseEditorPanel baseEditorPanel
height
int height
width
int width
margin
int margin
baseEditorPanel
BaseEditorPanel baseEditorPanel
textMargin
int textMargin
c
char c
pos
int pos
tier
int tier
seq
SequenceI seq
metrics
java.awt.FontMetrics metrics
seqLabel
javax.swing.JLabel seqLabel
seqField
javax.swing.JTextField seqField
isAminoAcidButton
javax.swing.JRadioButton isAminoAcidButton
isGenomicButton
javax.swing.JRadioButton isGenomicButton
posTable
javax.swing.JTable posTable
searchButton
javax.swing.JButton searchButton
colNames
java.util.Vector<E> colNames
reverseStrand
boolean reverseStrand
- What type of sequence is being displayed
refSeq
SequenceI refSeq
frame
SequenceI[] frame
translatedHitZones
java.util.Vector<E> translatedHitZones
hitZones
java.util.Vector<E> hitZones
showHitZones
boolean showHitZones
transformer
MultiTierPanel transformer
scrollableObject
BaseScrollable scrollableObject
- Object that will be scrolled
scrollableObject
BaseScrollable scrollableObject
- Object that will be scrolled
posLabel
javax.swing.JLabel posLabel
- Visual components
posField
javax.swing.JTextField posField
goButton
javax.swing.JButton goButton
panel
MultiSequenceAlignerPanel panel
curationState
GuiCurationState curationState
- The curation state
selectedAnnotation
AnnotatedFeatureI selectedAnnotation
- The currently selected annotation
indicatorColor
java.awt.Color indicatorColor
- The color from colorList used to identify this instance
noExternalSelection
boolean noExternalSelection
- The state of external selection acceptance
placeFinder
FeaturePlaceFinder placeFinder
tierMap
java.util.Map<K,V> tierMap
tiers
java.util.List<E> tiers
multiTierPanel
MultiTierPanel multiTierPanel
view
javax.swing.JViewport view
model
SeqFeatureTableModel model
strand
Strand strand
baseEditor
SeqAlignPanel baseEditor
colorMap
java.util.Map<K,V> colorMap
state
java.lang.Integer state
panel
MultiTierPanel panel
- This should be the Result window
curationState
GuiCurationState curationState
- The curation state
multiSequenceAlignerPanel
MultiSequenceAlignerPanel multiSequenceAlignerPanel
insertion
java.lang.String insertion
viewInsertion
javax.swing.AbstractAction viewInsertion
filterName
AddResultFilterAction filterName
filterType
AddResultFilterAction filterType
filterFrame
AddResultFilterAction filterFrame
transcriptColorList
java.awt.Color[][] transcriptColorList
transcriptColorIndex
int transcriptColorIndex
exonColorIndex
int exonColorIndex
baseEditor
SeqAlignPanel baseEditor
currentRange
double[] currentRange
transcriptRange
double[] transcriptRange
oldRange
double[] oldRange
currentFeature
SeqFeatureI currentFeature
currentFeatureSet
FeatureSetI currentFeatureSet
type
int type
isIntron
boolean isIntron
isExon
boolean isExon
targetNucleotide
int targetNucleotide
targetTier
int targetTier
hitIndex
int hitIndex
targetColor
java.awt.Color targetColor
seqSelectColor
java.awt.Color seqSelectColor
hatchColor
java.awt.Color hatchColor
shiftColor
java.awt.Color shiftColor
sequences
java.util.Vector<E> sequences
- Holds a sequence (SeqWrapper) for every tier, element # is tier number
cols
int cols
- The number of base pairs displayed in a single row
stripeWidth
int stripeWidth
- The default size of the background color stripes, in number of bases
rowMargin
int rowMargin
- Maybe this controls the space between rows when in vertical mode?
horizontalMode
boolean horizontalMode
- Related to the scroll policy. Controls how display is generated
reverseStrand
boolean reverseStrand
- What type of sequence is being displayed
horizontalScrollThread
SeqAlignPanel.AutoscrollThread horizontalScrollThread
- Related to scroll handling
verticalScrollThread
SeqAlignPanel.AutoscrollThread verticalScrollThread
autoscroll
boolean autoscroll
- More Scrolling... not really sure.
lowestBase
int lowestBase
- The base pair the panel starts at in outside world(chromosomal)
highestBase
int highestBase
- The base pair the panel ends at in outside world(chromosomal)
features
java.util.List<E> features
cols
java.util.List<E> cols
tier
TierI tier
- the tier that will be rendered by this panel
orientation
Orientation orientation
- the orientation of this panel
renderer
BaseRendererI renderer
- the renderer for this panel
tierPanel
MultiTierPanel tierPanel
height
int height
width
int width
margin
int margin
tickInterval
int tickInterval
|
Package apollo.gui.detailviewers.sequencealigner.AAPanel |
annotationPanel
MultiTierPanel annotationPanel
addressComponent
AbstractScrollablePanel addressComponent
referencePanel
MultiTierPanel referencePanel
resultPanel
MultiTierPanel resultPanel
annotationPane
javax.swing.JScrollPane annotationPane
addressPane
javax.swing.JScrollPane addressPane
referencePane
javax.swing.JScrollPane referencePane
resultPane
javax.swing.JScrollPane resultPane
annotationHeader
MultiTierPanelHeaderTable annotationHeader
addressHeader
java.awt.Component addressHeader
referenceHeader
java.awt.Component referenceHeader
resultHeaderHeading
java.awt.Component resultHeaderHeading
resultHeader
MultiTierPanelHeaderTable resultHeader
resultPaneHeading
java.awt.Component resultPaneHeading
nextAnnotation
javax.swing.JButton nextAnnotation
prevAnnotation
javax.swing.JButton prevAnnotation
frameSwitchButtons
javax.swing.ButtonGroup frameSwitchButtons
f1Button
javax.swing.JRadioButton f1Button
f2Button
javax.swing.JRadioButton f2Button
f3Button
javax.swing.JRadioButton f3Button
externalSelection
javax.swing.JCheckBox externalSelection
annotationHeaderView
javax.swing.JViewport annotationHeaderView
resultHeaderView
javax.swing.JViewport resultHeaderView
overview
Overview overview
horizontalSplitPane
javax.swing.JSplitPane horizontalSplitPane
leftPane
javax.swing.JPanel leftPane
rightPane
javax.swing.JSplitPane rightPane
topPanel
javax.swing.JPanel topPanel
bottomPanel
javax.swing.JPanel bottomPanel
menu
javax.swing.JMenu menu
horizontalScrollBar
javax.swing.JScrollBar horizontalScrollBar
annotationMouseListener
AnnotationEditorMouseListener annotationMouseListener
resultMouseListener
ResultMouseListener resultMouseListener
annotations
java.util.List<E> annotations
results
java.util.List<E> results
annotationComparator
MultiComparator<T> annotationComparator
resultComparator
MultiComparator<T> resultComparator
annotationFilter
MultiFilter<T> annotationFilter
resultFilter
MultiFilter<T> resultFilter
strand
Strand strand
frame
ReadingFrame frame
referenceFactory
ReferenceFactoryI referenceFactory
easyRead
boolean easyRead
resultRendererFactory
ResultRendererFactory resultRendererFactory
referenceFactory
ReferenceFactoryI referenceFactory
annotationPanel
MultiTierPanel annotationPanel
dnaColor
java.awt.Color dnaColor
|
Package apollo.gui.detailviewers.sequencealigner.actions |
alignerPanel
MultiSequenceAlignerPanel alignerPanel
type
AddFilterPanel.TYPES type
multiSequenceAlignerPanel
MultiSequenceAlignerPanel multiSequenceAlignerPanel
filter
Filter<T> filter
curationState
GuiCurationState curationState
annotationEditor
AnnotationEditor annotationEditor
feature
SeqFeatureI feature
basepair
int basepair
curationState
GuiCurationState curationState
annotationEditor
AnnotationEditor annotationEditor
basepair
int basepair
feature
SeqFeatureI feature
feature
SeqFeatureI feature
curationState
GuiCurationState curationState
annotationEditor
AnnotationEditor annotationEditor
curationState
GuiCurationState curationState
feature
SeqFeatureI feature
curationState
GuiCurationState curationState
annotationEditor
AnnotationEditor annotationEditor
feature
SeqFeatureI feature
basepair
int basepair
shiftType
FrameShiftAction.FrameShiftType shiftType
curationState
GuiCurationState curationState
annotationEditor
AnnotationEditor annotationEditor
feature
SeqFeatureI feature
mergeFeature
SeqFeatureI mergeFeature
curationState
GuiCurationState curationState
- Instance Variables
annotationEditor
AnnotationEditor annotationEditor
feature
SeqFeatureI feature
basepair
int basepair
type
java.lang.String type
parent
javax.swing.JComponent parent
curationState
GuiCurationState curationState
annotationEditor
AnnotationEditor annotationEditor
feature
SeqFeatureI feature
basepair
int basepair
terminus
int terminus
curationState
GuiCurationState curationState
annotationEditor
AnnotationEditor annotationEditor
feature
SeqFeatureI feature
basepair
int basepair
|
Package apollo.gui.detailviewers.sequencealigner.comparators |
|
Package apollo.gui.detailviewers.sequencealigner.DNAPanel |
aminoAcidPanel
MultiTierPanel aminoAcidPanel
annotationPanel
MultiTierPanel annotationPanel
addressComponent
AbstractScrollablePanel addressComponent
referencePanel
MultiTierPanel referencePanel
resultPanel
MultiTierPanel resultPanel
aminoAcidPane
javax.swing.JScrollPane aminoAcidPane
annotationPane
javax.swing.JScrollPane annotationPane
addressPane
javax.swing.JScrollPane addressPane
referencePane
javax.swing.JScrollPane referencePane
resultPane
javax.swing.JScrollPane resultPane
resultPaneHeading
java.awt.Component resultPaneHeading
nextAnnotation
javax.swing.JButton nextAnnotation
prevAnnotation
javax.swing.JButton prevAnnotation
externalSelection
javax.swing.JCheckBox externalSelection
aminoAcidHeader
java.awt.Component aminoAcidHeader
annotationHeader
MultiTierPanelHeaderTable annotationHeader
addressHeader
java.awt.Component addressHeader
referenceHeader
java.awt.Component referenceHeader
resultHeaderHeading
java.awt.Component resultHeaderHeading
resultHeader
MultiTierPanelHeaderTable resultHeader
annotationHeaderView
javax.swing.JViewport annotationHeaderView
resultHeaderView
javax.swing.JViewport resultHeaderView
overview
Overview overview
horizontalScrollBar
javax.swing.JScrollBar horizontalScrollBar
horizontalSplitPane
javax.swing.JSplitPane horizontalSplitPane
leftPane
javax.swing.JPanel leftPane
rightPane
javax.swing.JSplitPane rightPane
topPanel
javax.swing.JPanel topPanel
bottomPanel
javax.swing.JPanel bottomPanel
menu
javax.swing.JMenu menu
annotationMouseListener
AnnotationEditorMouseListener annotationMouseListener
resultMouseListener
ResultMouseListener resultMouseListener
annotations
java.util.List<E> annotations
results
java.util.List<E> results
annotationComparator
MultiComparator<T> annotationComparator
resultComparator
MultiComparator<T> resultComparator
annotationFilter
MultiFilter<T> annotationFilter
resultFilter
MultiFilter<T> resultFilter
strand
Strand strand
referenceFactory
ReferenceFactoryI referenceFactory
easyRead
boolean easyRead
resultRendererFactory
ResultRendererFactory resultRendererFactory
panelFactory
PanelFactory panelFactory
referenceFactory
ReferenceFactoryI referenceFactory
annotationPanel
MultiTierPanel annotationPanel
resultPanel
MultiTierPanel resultPanel
|
Package apollo.gui.detailviewers.sequencealigner.filters |
|
Package apollo.gui.detailviewers.sequencealigner.menus |
panel
MultiSequenceAlignerPanel panel
values
java.util.List<E> values
type
AddFilterPanel.TYPES type
label
javax.swing.JLabel label
textField
javax.swing.JTextField textField
|
Package apollo.gui.detailviewers.sequencealigner.overview |
serialVersionUID: -8127066813604422951L
intervalHeight
java.util.TreeMap<K,V> intervalHeight
colors
java.util.HashMap<K,V> colors
direction
apollo.gui.detailviewers.sequencealigner.overview.IntervalComponent.Directions direction
length
int length
vAlignment
IntervalComponent.Valignment vAlignment
primaryColor
java.awt.Color primaryColor
top
IntervalComponent top
bottom
IntervalComponent bottom
editorPanel
MultiSequenceAlignerPanel editorPanel
transcript
Transcript transcript
tier
int tier
strand
Strand strand
isForward
boolean isForward
rh
org.bdgp.util.RangeHash rh
drawIntrons
boolean drawIntrons
margin
int margin
barHeight
int barHeight
resultInflection
int resultInflection
shiftColor
java.awt.Color shiftColor
transcript
Transcript transcript
drawIntrons
boolean drawIntrons
tran
IntervalComponent tran
barHeight
int barHeight
shiftColor
java.awt.Color shiftColor
|
Package apollo.gui.detailviewers.sequencealigner.renderers |
offset
int offset
orientation
Orientation orientation
frame
ReadingFrame frame
phase
int phase
state
apollo.gui.detailviewers.sequencealigner.renderers.AnnotationRenderer.State state
selectionStart
int selectionStart
selectionEnd
int selectionEnd
curationState
GuiCurationState curationState
currentParent
Transcript currentParent
currentParentClone
Transcript currentParentClone
currentParentClone2
Transcript currentParentClone2
currentStart
int currentStart
featureStart
int featureStart
featureEnd
int featureEnd
transcript
Transcript transcript
state
java.lang.Integer state
outlineType
int outlineType
feature
SeqFeatureI feature
easyRead
boolean easyRead
character
char character
focusPosition
int focusPosition
feature
SeqFeatureI feature
isPosition
boolean isPosition
- base focus can either be for a position (single base to center on - scroll) or a
range (set view to range - zoom & scroll). If this is too much to load onto
base focus event, then a new range event could be made
rangeStart
int rangeStart
rangeEnd
int rangeEnd
selected
Selection selected
force_selection
boolean force_selection
- whether this event requires attention. some of the i/fs
have a checkbox to ignore changes to selection, but if
the change to the selection is a delete or a replace then
the change must not be ignored
type
int type
type
int type
dataType
int dataType
id
java.lang.String id
names
java.lang.String[] names
bandBounds
java.awt.Rectangle bandBounds
value
double value
source
java.lang.Object source
oldActiveCurState
GuiCurationState oldActiveCurState
newActiveCurState
GuiCurationState newActiveCurState
type
int type
tierManagerSource
TierManager tierManagerSource
type
int type
viewSource
ViewI viewSource
removeElement
boolean removeElement
propagated
boolean propagated
zoomFactor
java.lang.String zoomFactor
factorMultiplier
double factorMultiplier
|
Package apollo.gui.evidencepanel |
setDetailPanel
SetDetailPanel setDetailPanel
split
UnBorderedSplitPane split
featureSelectionListener
apollo.gui.evidencepanel.EvidencePanel.ApolloFeatureSelectionListener featureSelectionListener
initialDividerPercentage
double initialDividerPercentage
- should we have public getter and setter for this variable? Is 50% a good initial
setting?
firstPaint
boolean firstPaint
evidencePanels
java.util.Vector<E> evidencePanels
orientation
int orientation
labelBox
javax.swing.JLabel labelBox
descPane
javax.swing.JScrollPane descPane
descBox
javax.swing.JTextArea descBox
headerPanel
javax.swing.JPanel headerPanel
fset
SeqFeatureI fset
controller
Controller controller
table
apollo.gui.evidencepanel.TablePanel.EvidenceTable table
pane
javax.swing.JScrollPane pane
model
TablePanel.FilteredFeatureModel model
selectionManager
SelectionManager selectionManager
listSelectionComesFromSelf
boolean listSelectionComesFromSelf
rowSelectionListener
TablePanel.RowSelectionListener rowSelectionListener
- Made it an instance variable as it is a source of selection events that
needs to be tested for
propertyList
java.util.Vector<E> propertyList
data
java.util.Vector<E> data
sortKey
java.lang.String sortKey
reverseSort
boolean reverseSort
type
java.lang.String type
keysWithDefaultSortingDescending
java.util.Vector<E> keysWithDefaultSortingDescending
|
Package apollo.gui.featuretree |
panel
FeatureTreePanel panel
curationState
GuiCurationState curationState
tree
javax.swing.JTree tree
feature_set
FeatureSetI feature_set
parent
FeatureNavigationI parent
remote_update
boolean remote_update
treeHash
java.util.Hashtable<K,V> treeHash
endToggle
boolean endToggle
curationState
GuiCurationState curationState
|
Package apollo.gui.genomemap |
resultView
ResultView resultView
- The ResultView linked to this AnnotationView for edit purposes.
finder
EvidenceFinder finder
- Essentially a hash table of all the results in the affiliated
ResultView linked to this AnnotationView for edit purposes.
Initialized when resultView is set. is this still used?
siteView
SiteView siteView
- The SiteView linked to this AnnotationView for edit purposes.
editor
AnnotationEditor editor
- The AnnotationEditor for performing edits in this view.
curationState
GuiCurationState curationState
- Species this annotation view is for, has all the state for that species/szap
editingEnabled
boolean editingEnabled
- Whether editing is enabled, default true
annotMenu
AnnotationMenu annotMenu
free
java.awt.Component free
freeBounds
java.awt.Rectangle freeBounds
viewmap
java.util.Hashtable<K,V> viewmap
backBuffer
java.awt.Image backBuffer
backBufferWidth
int backBufferWidth
backBufferHeight
int backBufferHeight
views
java.util.Vector<E> views
linearViews
java.util.Vector<E> linearViews
pickViews
java.util.Vector<E> pickViews
scaleView
ScaleView scaleView
layout_manager
ApolloLayoutManager layout_manager
controller
Controller controller
focus
ViewI focus
name
java.lang.String name
syncLimits
boolean syncLimits
rubberband
RubberbandRectangle rubberband
inDrag
boolean inDrag
pressEvent
java.awt.event.MouseEvent pressEvent
inTierDrag
boolean inTierDrag
dragTierView
TierViewI dragTierView
statusBar
StatusBar statusBar
layoutBounds
java.awt.Rectangle layoutBounds
invalid
boolean invalid
allowsMovement
boolean allowsMovement
showEdgeMatches
boolean showEdgeMatches
mouseManager
apollo.gui.genomemap.MouseManager mouseManager
selectionManager
SelectionManager selectionManager
curationState
GuiCurationState curationState
count
int count
- Overidden doLayout to handle View layout
controller
Controller controller
views
java.util.Vector<E> views
drawables
java.util.Vector<E> drawables
tierhash
java.util.Hashtable<K,V> tierhash
transformer
Transformer transformer
tier_properties
java.util.Vector<E> tier_properties
debug
boolean debug
textTransform
Transformer textTransform
fm
java.awt.FontMetrics fm
textAvoidance
boolean textAvoidance
pickSize
java.awt.Dimension pickSize
dfset
DrawableSetI dfset
edges
int[] edges
lastTierNum
int lastTierNum
startTierNum
int startTierNum
inTierDrag
boolean inTierDrag
tierColour
java.awt.Color tierColour
drawables
java.util.Vector<E> drawables
selectedDrawables
java.util.Vector<E> selectedDrawables
lastBPP
double lastBPP
layout
ColumnApolloLayout layout
font
java.awt.Font font
curationState
GuiCurationState curationState
leftButton
javax.swing.JButton leftButton
rightButton
javax.swing.JButton rightButton
startField
javax.swing.JTextField startField
endField
javax.swing.JTextField endField
chrField
ChromosomeField chrField
loadButton
javax.swing.JButton loadButton
expandButton
javax.swing.JButton expandButton
navigatorManager
apollo.gui.genomemap.NavigationBar.NavigatorManager navigatorManager
annotationView
AnnotationView annotationView
tierPopupMenu
TierPopupMenu tierPopupMenu
sites
Sites[] sites
stopCodons
apollo.gui.genomemap.SiteView.Codon[] stopCodons
height
int height
sitesArray
Sites[] sitesArray
- [0,1,2] start sites, [3,4,5] for stop sites (3 frames for each)
curation
CurationSet curation
resultView
ResultView resultView
- For TranslationStartStopSelectionListener
v1
ViewI v1
v2
ViewI v2
splitPoly
java.awt.Polygon splitPoly
splitSelectPoly
java.awt.Polygon splitSelectPoly
splitBoundary
java.awt.Polygon splitBoundary
splitFract
double splitFract
triangleColor
java.awt.Color triangleColor
triangleSize
int triangleSize
currentV1Vis
boolean currentV1Vis
currentV2Vis
boolean currentV2Vis
start
int start
startFract
double startFract
panel2
javax.swing.JPanel panel2
apolloPanel
ApolloPanel apolloPanel
hScroll
javax.swing.JScrollBar hScroll
zoomin
javax.swing.JButton zoomin
- ShiftAwareButton is an inner class
zoomout
javax.swing.JButton zoomout
zoomin2
javax.swing.JButton zoomin2
zoomout2
javax.swing.JButton zoomout2
reset
javax.swing.JButton reset
statusBar
StatusBar statusBar
HSCROLLABLE
boolean HSCROLLABLE
ZOOMABLE
boolean ZOOMABLE
ZOOMPOSITION
java.lang.String ZOOMPOSITION
name
java.lang.String name
forwardVisible
boolean forwardVisible
- Whether forward strand is visible
reverseVisible
boolean reverseVisible
forwardSitesVisibleAtZoomLevel
boolean forwardSitesVisibleAtZoomLevel
- Whether forward sites are at present zoom level
reverseSitesVisibleAtZoomLevel
boolean reverseSitesVisibleAtZoomLevel
- Whether reverse sites are at present zoom level
sitesVisibleOnZoom
boolean sitesVisibleOnZoom
- Whether sites are visible at all, zoomed in or not
reverseComplement
boolean reverseComplement
forwardResultView
ResultView forwardResultView
reverseResultView
ResultView reverseResultView
forwardAnnotView
AnnotationView forwardAnnotView
reverseAnnotView
AnnotationView reverseAnnotView
forwardSplitterView
SplitterView forwardSplitterView
reverseSplitterView
SplitterView reverseSplitterView
forwardContainerView
LaidoutViewContainer forwardContainerView
reverseContainerView
LaidoutViewContainer reverseContainerView
graphContainerView
LaidoutViewContainer graphContainerView
strandSplitter
SplitterView strandSplitter
forwardSv
SplitterView forwardSv
forwardSplitterScaleContainer
LaidoutViewContainer forwardSplitterScaleContainer
scaleView
ScaleView scaleView
forwardSiteView
SiteView forwardSiteView
reverseSiteView
SiteView reverseSiteView
controller
Controller controller
selectionManager
SelectionManager selectionManager
xscale
double xscale
settingScroller
boolean settingScroller
zoomLabel
javax.swing.JLabel zoomLabel
highlightRegions
java.util.Vector<E> highlightRegions
guide
GuideLine guide
graphs
java.util.List<E> graphs
curationSet
CurationSet curationSet
haveSequence
boolean haveSequence
revCompListener
RevCompListener revCompListener
organismLabel
javax.swing.JLabel organismLabel
useScrollHack
boolean useScrollHack
annotationViewsVisible
boolean annotationViewsVisible
resultViewsVisible
boolean resultViewsVisible
scaleViewVisible
boolean scaleViewVisible
scrollingPropagated
boolean scrollingPropagated
- This is for synteny where a scroll propigates from one
szap to the other("locked scrolling").
shiftForLockedZooming
boolean shiftForLockedZooming
- Synteny zoom propagate with shift if true, false without
previousStyle
Style previousStyle
- Used to track whether a new curation set has brought in a new style,
which affects layout issues
styleChanged
boolean styleChanged
curationState
GuiCurationState curationState
- curation that szap is for. has all state info for species
activeColor
java.awt.Color activeColor
mousePressShifted
boolean mousePressShifted
vScroll
javax.swing.JScrollBar vScroll
vscrollable
boolean vscrollable
rightSide
boolean rightSide
controller
Controller controller
dragSources
java.util.Vector<E> dragSources
rowCoordHeight
int rowCoordHeight
- Height of row in coordinate space (TierManager.Y_PIXELS_PER_FEATURE)
selectionManager
SelectionManager selectionManager
scrollHack
boolean scrollHack
drag_low
int drag_low
drag_high
int drag_high
gcplot
javax.swing.JMenuItem gcplot
restriction
javax.swing.JMenuItem restriction
analyze
javax.swing.JMenuItem analyze
tweekerFrame
Tweeker tweekerFrame
ap
ApolloPanelI ap
delete
javax.swing.JMenuItem delete
annotInfo
javax.swing.JMenuItem annotInfo
baseedit
javax.swing.JMenuItem baseedit
sequenceAligner
javax.swing.JMenuItem sequenceAligner
sequence
javax.swing.JMenuItem sequence
mergeExons
javax.swing.JMenuItem mergeExons
moveExonsToTranscript
javax.swing.JMenuItem moveExonsToTranscript
mergeTran
javax.swing.JMenuItem mergeTran
splitExon
javax.swing.JMenuItem splitExon
splitTran
javax.swing.JMenuItem splitTran
fivePrime
javax.swing.JMenuItem fivePrime
threePrime
javax.swing.JMenuItem threePrime
orf
javax.swing.JMenuItem orf
setEnds
javax.swing.JMenuItem setEnds
typesMenu
TypesMenu typesMenu
duplicateTranscript
javax.swing.JMenuItem duplicateTranscript
showGeneReport
javax.swing.JMenuItem showGeneReport
assignName
javax.swing.JMenuItem assignName
takeOwnership
javax.swing.JMenuItem takeOwnership
toggleCompleted
javax.swing.JMenuItem toggleCompleted
peptideStatusMenu
PeptideMenu peptideStatusMenu
collapseTier
javax.swing.JMenuItem collapseTier
expandTier
javax.swing.JMenuItem expandTier
changeColor
javax.swing.JMenuItem changeColor
typeSettings
javax.swing.JMenuItem typeSettings
cancel
javax.swing.JMenuItem cancel
preferences
javax.swing.JMenuItem preferences
analysis
javax.swing.JMenuItem analysis
annotView
AnnotationView annotView
curationState
GuiCurationState curationState
selection
Selection selection
transcripts
java.util.Vector<E> transcripts
annots
java.util.Vector<E> annots
selectedAnnots
java.util.Vector<E> selectedAnnots
- Selected Annotations in annotView
holder
FeatureSetI holder
- The feature set that holds all the top level annots(eg genes),
the top model for the annot view
pos
java.awt.Point pos
editor
AnnotationEditor editor
haveResidues
boolean haveResidues
haveWholeSeq
boolean haveWholeSeq
strand
int strand
addBookmark
javax.swing.JMenuItem addBookmark
removeBookmark
javax.swing.JMenuItem removeBookmark
featureComparator
apollo.gui.menus.BookmarkMenu.FeatureComparator featureComparator
bookmarks
java.util.Vector<E> bookmarks
frame
ApolloFrame frame
undo
javax.swing.JMenuItem undo
redo
javax.swing.JMenuItem redo
find
javax.swing.JMenuItem find
newPrefs
javax.swing.JMenuItem newPrefs
findDialog
javax.swing.JDialog findDialog
open
javax.swing.JMenuItem open
addon
javax.swing.JMenuItem addon
save
javax.swing.JMenuItem save
saveAll
javax.swing.JMenuItem saveAll
saveAs
javax.swing.JMenuItem saveAs
saveLayout
javax.swing.JMenuItem saveLayout
loadLayout
javax.swing.JMenuItem loadLayout
saveFasta
javax.swing.JMenuItem saveFasta
writeTypes
javax.swing.JMenuItem writeTypes
print
javax.swing.JMenuItem print
quit
javax.swing.JMenuItem quit
frame
ApolloFrame frame
view
GraphView view
ap
ApolloPanel ap
colour
javax.swing.JMenuItem colour
windowSize
javax.swing.JMenuItem windowSize
pos
java.awt.Point pos
about
javax.swing.JMenuItem about
help
javax.swing.JMenuItem help
bug
javax.swing.JMenuItem bug
update
javax.swing.JMenuItem update
frame
ApolloFrame frame
aboutBox
javax.swing.JDialog aboutBox
namesToURLs
java.util.Hashtable<K,V> namesToURLs
menuItemsToNames
java.util.Hashtable<K,V> menuItemsToNames
igbLink
javax.swing.JCheckBoxMenuItem igbLink
gene
AnnotatedFeatureI gene
curationState
GuiCurationState curationState
type_panel
PropertyPanel type_panel
tier_prop
TierProperty tier_prop
color_items
java.util.Hashtable<K,V> color_items
collapseTier
javax.swing.JMenuItem collapseTier
pos
java.awt.Point pos
adapter
ApolloDataAdapterI adapter
view
ScaleView view
pos
java.awt.Point pos
colouring
javax.swing.JMenuItem colouring
guideline
javax.swing.JMenuItem guideline
view
ViewI view
typeItems
javax.swing.JMenuItem[] typeItems
activationItems
java.util.Set<E> activationItems
frame
CompositeApolloFrame frame
useOpaqueLinks
boolean useOpaqueLinks
shadeByPercId
boolean shadeByPercId
lockScrolling
boolean lockScrolling
- Lock scrolling initial value from style. Not picking up lock scrolling
change on style change - this is ok for now because presently synteny's
style cant change. When synteny style can change, will have to either listen
for style changes or query an szap.
shiftLockZoom
boolean shiftLockZoom
- Whether shift needed for loack zooming - same issues as lockScrolling on
style change
useOpaqueLinksItem
javax.swing.JCheckBoxMenuItem useOpaqueLinksItem
shadeLinksByPercIdItem
javax.swing.JCheckBoxMenuItem shadeLinksByPercIdItem
lockScrollingItem
javax.swing.JCheckBoxMenuItem lockScrollingItem
shiftLockZoomMenuItem
javax.swing.JCheckBoxMenuItem shiftLockZoomMenuItem
synLinkPanel
SyntenyLinkPanel synLinkPanel
scale
javax.swing.JMenuItem scale
autoStraighten
javax.swing.JCheckBoxMenuItem autoStraighten
showJustDnaLinks
javax.swing.JMenuItem showJustDnaLinks
showJustProteinLinks
javax.swing.JMenuItem showJustProteinLinks
showBothLinkTypes
javax.swing.JMenuItem showBothLinkTypes
showAllStrands
javax.swing.JRadioButtonMenuItem showAllStrands
plusPlusStrands
javax.swing.JRadioButtonMenuItem plusPlusStrands
minusMinusStrands
javax.swing.JRadioButtonMenuItem minusMinusStrands
plusMinusStrands
javax.swing.JRadioButtonMenuItem plusMinusStrands
minusPlusStrands
javax.swing.JRadioButtonMenuItem minusPlusStrands
clearStrandsInvisibleButton
javax.swing.JRadioButtonMenuItem clearStrandsInvisibleButton
homeIn
javax.swing.JMenuItem homeIn
selectedLinks
LinkSet selectedLinks
collapse
javax.swing.JMenuItem collapse
expand
javax.swing.JMenuItem expand
zoom
javax.swing.JMenuItem zoom
orientation
javax.swing.JMenuItem orientation
navigator
javax.swing.JMenuItem navigator
invertcolours
javax.swing.JMenuItem invertcolours
reverseComplement
javax.swing.JCheckBoxMenuItem reverseComplement
textAvoid
javax.swing.JCheckBoxMenuItem textAvoid
types
javax.swing.JCheckBoxMenuItem types
gcplot
javax.swing.JCheckBoxMenuItem gcplot
threeD
javax.swing.JCheckBoxMenuItem threeD
outline
javax.swing.JCheckBoxMenuItem outline
showEdgeMatches
javax.swing.JCheckBoxMenuItem showEdgeMatches
showAllTiers
javax.swing.JMenuItem showAllTiers
hideAllTiers
javax.swing.JMenuItem hideAllTiers
frame
javax.swing.JFrame frame
sp
SyntenyPanel sp
type_panel
PropertyPanel type_panel
tier_prop
TierProperty tier_prop
threshItems
java.util.Hashtable<K,V> threshItems
collapseTier
javax.swing.JMenuItem collapseTier
adapter
ApolloDataAdapterI adapter
resultView
ResultView resultView
ap
ApolloPanelI ap
collapseTier
javax.swing.JMenuItem collapseTier
expandTier
javax.swing.JMenuItem expandTier
showLabel
javax.swing.JMenuItem showLabel
hideLabel
javax.swing.JMenuItem hideLabel
hideTier
javax.swing.JMenuItem hideTier
changeColor
javax.swing.JMenuItem changeColor
typeSettings
javax.swing.JMenuItem typeSettings
editor
AnnotationEditor editor
selection
Selection selection
dnaBlixem
javax.swing.JMenuItem dnaBlixem
protBlixem
javax.swing.JMenuItem protBlixem
getData
javax.swing.JMenuItem getData
set5Prime
javax.swing.JMenuItem set5Prime
set3Prime
javax.swing.JMenuItem set3Prime
setEnds
javax.swing.JMenuItem setEnds
createGeneTrans
javax.swing.JMenuItem createGeneTrans
typesMenu
TypesMenu typesMenu
addTranscript
javax.swing.JMenuItem addTranscript
flipResult
javax.swing.JMenuItem flipResult
sequence
javax.swing.JMenuItem sequence
props
javax.swing.JMenuItem props
loadSyntenyLink
javax.swing.JMenuItem loadSyntenyLink
cancel
javax.swing.JMenuItem cancel
resultTags
java.util.Hashtable<K,V> resultTags
jalviewMenus
apollo.gui.menus.AlignMenuItems jalviewMenus
pos
java.awt.Point pos
preferences
javax.swing.JMenuItem preferences
tag_group
javax.swing.ButtonGroup tag_group
collapse
javax.swing.JMenuItem collapse
expand
javax.swing.JMenuItem expand
showAllTiers
javax.swing.JMenuItem showAllTiers
hideAllTiers
javax.swing.JMenuItem hideAllTiers
invertTiers
javax.swing.JMenuItem invertTiers
shrinkTiers
javax.swing.JMenuItem shrinkTiers
growTiers
javax.swing.JMenuItem growTiers
frame
ApolloFrame frame
ftp
FeatureTreePanel ftp
show
javax.swing.JMenuItem show
hide
javax.swing.JMenuItem hide
edit
javax.swing.JMenuItem edit
pos
java.awt.Point pos
annot
AnnotatedFeatureI annot
curationState
GuiCurationState curationState
editor
AnnotationEditor editor
orientation
javax.swing.JMenuItem orientation
navigator
javax.swing.JMenuItem navigator
navigatorPosition
int navigatorPosition
- Index of navigator menu item
invertcolours
javax.swing.JMenuItem invertcolours
zoom
javax.swing.JMenuItem zoom
flip
javax.swing.JMenuItem flip
resetViews
javax.swing.JMenuItem resetViews
forward
javax.swing.JCheckBoxMenuItem forward
reverse
javax.swing.JCheckBoxMenuItem reverse
annotations
javax.swing.JCheckBoxMenuItem annotations
controls
javax.swing.JCheckBoxMenuItem controls
results
javax.swing.JCheckBoxMenuItem results
showSites
javax.swing.JCheckBoxMenuItem showSites
scale
javax.swing.JCheckBoxMenuItem scale
reverseComplement
javax.swing.JCheckBoxMenuItem reverseComplement
textAvoid
javax.swing.JCheckBoxMenuItem textAvoid
guide
javax.swing.JCheckBoxMenuItem guide
showEdgeMatches
javax.swing.JCheckBoxMenuItem showEdgeMatches
newSequenceWindowMenuItem
javax.swing.JMenuItem newSequenceWindowMenuItem
frame
ApolloFrame frame
frame
ApolloFrame frame
|
Package apollo.gui.synteny |
compositeAdapter
ApolloDataAdapterI compositeAdapter
linkPanels
java.util.HashMap<K,V> linkPanels
normalLabelColor
java.awt.Color normalLabelColor
selectedLabelColor
java.awt.Color selectedLabelColor
links
LinkSet links
trans1
Transformer trans1
trans2
Transformer trans2
autoStraighten
boolean autoStraighten
rubberband
RubberbandRectangle rubberband
szap1
StrandedZoomableApolloPanel szap1
szap2
StrandedZoomableApolloPanel szap2
linkHash
java.util.Hashtable<K,V> linkHash
polyHolder
java.util.Vector<E> polyHolder
drawables
java.util.ArrayList<E> drawables
useOpaqueLinks
boolean useOpaqueLinks
shadeByPercId
boolean shadeByPercId
statusbar
StatusBar statusbar
selectedLinks
LinkSet selectedLinks
- A LinkSet which are the selected links
syntenyPanel
SyntenyPanel syntenyPanel
- The SyntenyPanel that holds this SyntenyLinkPanel
colorToScorePaint
java.util.HashMap<K,V> colorToScorePaint
- Maps color to PropertyScorePaints
polygonComparator
java.util.Comparator<T> polygonComparator
speciesPanels
java.util.Vector<E> speciesPanels
linkPanels
java.util.Vector<E> linkPanels
dividers
java.util.Vector<E> dividers
sb
StatusBar sb
compositeApolloFrame
CompositeApolloFrame compositeApolloFrame
curNumCuration
int curNumCuration
|
Package apollo.gui.tweeker |
enzyme
RestrictionEnzyme enzyme
palindrome
boolean palindrome
export
boolean export
|
Class apollo.gui.tweeker.RestrictionEnzymeSelector.CutSiteModel extends javax.swing.table.AbstractTableModel implements Serializable |
data
java.util.Vector<E> data
columns
java.util.Vector<E> columns
|
Class apollo.gui.tweeker.RestrictionEnzymeSelector.RestrictionCell extends javax.swing.JLabel implements Serializable |
|
Class apollo.gui.tweeker.RestrictionEnzymeSelector.SiteSelectorTable extends javax.swing.JTable implements Serializable |
gcplot
javax.swing.JCheckBox gcplot
changeColour
javax.swing.JButton changeColour
gcSliderPanel
javax.swing.JPanel gcSliderPanel
resEnzSel
apollo.gui.tweeker.RestrictionEnzymeSelector resEnzSel
tabbedPane
javax.swing.JTabbedPane tabbedPane
winControl
apollo.gui.tweeker.Tweeker.TweekerWindowControl winControl
threshold
int threshold
loadFactor
float loadFactor
featurePairsOnly
boolean featurePairsOnly
alignablesOnly
boolean alignablesOnly
doUniqueCheck
boolean doUniqueCheck
- if unique check is true, check that feat doesnt already exist on adding
true by default