Serialized Form
Package fr.orsay.lri.varna |
serialVersionUID: 8194421570308956001L
_RNA
RNA _RNA
_debug
boolean _debug
_conf
VARNAConfig _conf
_VARNAListeners
ArrayList<E> _VARNAListeners
_selectionListeners
ArrayList<E> _selectionListeners
_RNAListeners
ArrayList<E> _RNAListeners
_manager
UndoManager _manager
_realCoords
Point2D.Double[] _realCoords
_realCenters
Point2D.Double[] _realCenters
_scaleFactor
double _scaleFactor
_offsetPanel
Point2D.Double _offsetPanel
_offsetRNA
Point2D.Double _offsetRNA
_offX
double _offX
_offY
double _offY
_blink
fr.orsay.lri.varna.controlers.ControleurBlinkingThread _blink
_selectedBases
BaseList _selectedBases
_backupSelection
ArrayList<E> _backupSelection
_nearestBase
Integer _nearestBase
_lastSelectedCoord
Point2D.Double _lastSelectedCoord
_linkOrigin
Point2D.Double _linkOrigin
_linkDestination
Point2D.Double _linkDestination
_selectionRectangle
Rectangle _selectionRectangle
_highlightAnnotation
boolean _highlightAnnotation
_titleHeight
int _titleHeight
_border
Dimension _border
_drawBBox
boolean _drawBBox
_drawBorder
boolean _drawBorder
_translation
Point _translation
_horsCadre
boolean _horsCadre
_premierAffichage
boolean _premierAffichage
_interpolator
fr.orsay.lri.varna.controlers.ControleurInterpolator _interpolator
_popup
VueMenu _popup
- If comparison mode is TRUE (ON), then the application will be used to
display a super-structure resulting on an RNA secondary structure
comparison. Else, the application is used by default.
_UI
VueUI _UI
_selectedAnnotation
TextAnnotation _selectedAnnotation
_hoveredBase
ModeleBase _hoveredBase
Package fr.orsay.lri.varna.components |
_btn
JButton _btn
serialVersionUID: 1L
serialVersionUID: 1L
columnNames
String[] columnNames
data
ArrayList<E> data
serialVersionUID: 1L
currentColor
Color currentColor
button
JButton button
colorChooser
JColorChooser colorChooser
dialog
JDialog dialog
_vueBases
VueBases _vueBases
_controleurSpecialColorEditor
fr.orsay.lri.varna.controlers.ControleurBaseSpecialColorEditor _controleurSpecialColorEditor
serialVersionUID: 1L
columnNames
String[] columnNames
data
ArrayList<E> data
outlineColor
Color outlineColor
innerColor
Color innerColor
baseColor
Color baseColor
numberColor
Color numberColor
serialVersionUID: 1L
unselectedBorder
Border unselectedBorder
selectedBorder
Border selectedBorder
isBordered
boolean isBordered
_mcm
ModeleColorMap _mcm
EDGES
Color EDGES
BUTTONS
Color BUTTONS
_selectedIndex
int _selectedIndex
dragSource
DragSource dragSource
dropTarget
DropTarget dropTarget
dropTargetIndex
int dropTargetIndex
draggedIndex
int draggedIndex
_vp
VARNAPanel _vp
_quitButton
JButton _quitButton
_contentPanel
JPanel _contentPanel
_quitPanel
JPanel _quitPanel
_input
JTextField _input
_output
JEditorPane _output
_scrolls
JScrollPane _scrolls
_firstFocus
boolean _firstFocus
Package fr.orsay.lri.varna.models |
serialVersionUID: -5468893731117925140L
config
VARNAConfig config
rna
RNA rna
name
String name
serialVersionUID: 2853916694420964233L
_colorMapHeight
double _colorMapHeight
- Various options.
_colorMapWidth
double _colorMapWidth
_colorMapXOffset
double _colorMapXOffset
_colorMapYOffset
double _colorMapYOffset
_mainBPStyle
VARNAConfig.BP_STYLE _mainBPStyle
_zoom
double _zoom
_zoomAmount
double _zoomAmount
_bpThickness
double _bpThickness
_baseThickness
double _baseThickness
_backboneColor
Color _backboneColor
_drawBackbone
boolean _drawBackbone
_hoverColor
Color _hoverColor
_backgroundColor
Color _backgroundColor
_drawBackground
boolean _drawBackground
_bondColor
Color _bondColor
_titleColor
Color _titleColor
_specialBasesColor
Color _specialBasesColor
_dashBasesColor
Color _dashBasesColor
_titleFont
Font _titleFont
_numbersFont
Font _numbersFont
_fontBasesGeneral
Font _fontBasesGeneral
_title
String _title
_numPeriod
int _numPeriod
_drawOutlineBase
boolean _drawOutlineBase
_fillBase
boolean _fillBase
_autoFit
boolean _autoFit
_autoCenter
boolean _autoCenter
_modifiable
boolean _modifiable
_errorsOn
boolean _errorsOn
_colorSpecialBases
boolean _colorSpecialBases
_colorDashBases
boolean _colorDashBases
_useBaseColorsForBPs
boolean _useBaseColorsForBPs
_drawnNonCanonicalBP
boolean _drawnNonCanonicalBP
_drawnNonPlanarBP
boolean _drawnNonPlanarBP
_showWarnings
boolean _showWarnings
_comparisonMode
boolean _comparisonMode
_flatExteriorLoop
boolean _flatExteriorLoop
_distNumbers
double _distNumbers
_cm
ModeleColorMap _cm
_colorMapCaption
String _colorMapCaption
_drawColorMap
boolean _drawColorMap
_msbp
ModeleBP _msbp
_i
int _i
_j
int _j
_vp
VARNAPanel _vp
_indices
ArrayList<E> _indices
_dx
double _dx
_dy
double _dy
_vp
VARNAPanel _vp
_h
Point _h
_vp
VARNAPanel _vp
_delta
double _delta
_base
double _base
_pLimL
double _pLimL
_pLimR
double _pLimR
_h
Point _h
_ml
Point _ml
_vp
VARNAPanel _vp
_prevMode
int _prevMode
_newMode
int _newMode
_prevFlat
boolean _prevFlat
_newFlat
boolean _newFlat
_backupCoords
ArrayList<E> _backupCoords
_backupCenters
ArrayList<E> _backupCenters
_vp
VARNAPanel _vp
_msbp
ModeleBP _msbp
_i
int _i
_j
int _j
_vp
VARNAPanel _vp
_angle
double _angle
_vp
VARNAPanel _vp
_index
int _index
_ox
double _ox
_oy
double _oy
_nx
double _nx
_ny
double _ny
_vp
VARNAPanel _vp
Package fr.orsay.lri.varna.models.annotations |
serialVersionUID: 5833315460145031242L
_mbfst
ModeleBase _mbfst
_mbsnd
ModeleBase _mbsnd
_color
Color _color
_intensity
double _intensity
_type
ChemProbAnnotation.ChemProbAnnotationType _type
_out
boolean _out
serialVersionUID: 7087014168028684775L
_bases
ArrayList<E> _bases
_outlineColor
Color _outlineColor
_fillColor
Color _fillColor
_radius
double _radius
serialVersionUID: 465236085501860747L
_texte
String _texte
_font
Font _font
_ancrage
Object _ancrage
_typeAncrage
int _typeAncrage
_color
Color _color
_angle
double _angle
Package fr.orsay.lri.varna.models.rna |
intervDroite
boolean intervDroite
intervGauche
boolean intervGauche
serialVersionUID: -3031358968555310380L
_mapping
Hashtable<K,V> _mapping
_invMapping
Hashtable<K,V> _invMapping
_BP
ModeleBP _BP
_checked
boolean _checked
intervDroite
boolean intervDroite
intervGauche
boolean intervGauche
_numStrand
int _numStrand
- Numero du brin auquel la base appartient.
_styleBase
ModeleStyleBase _styleBase
- The base style.
_colorie
Boolean _colorie
- TRUE if this InterfaceBase has to be colored, else FALSE.
_coords
VARNAPoint _coords
- The coordinate representation of this InterfaceBase on the final graphic.
_center
VARNAPoint _center
- The nearest loop center of this InterfaceBase.
_elementStructure
int _elementStructure
- The structure information associated with this InterfaceBase. It value
is:
-1 if the structure element associated is a point or a dash.
If the structure associated is an opening bracket, it'll be the index of
the closing bracket associated with this opening bracket.
If the structure associated is a closing bracket, it'll be the index of
the opening bracket associated with this closing bracket.
_value
double _value
_realIndex
int _realIndex
serialVersionUID: -5493938366569588113L
_c
String _c
_index
int _index
serialVersionUID: -2733063250714562463L
_base1
Character _base1
- The base of the first RNA associated with the base of the second RNA.
_base2
Character _base2
- The base of the second RNA associated with the base of the first RNA.
_appartenance
int _appartenance
- This ModeleBasesComparison owning statement. It's value will be 0 if this
base is common for both RNA that had been compared, 1 if this base is
related to the first RNA, 2 if related to the second. Default is -1.
_index
int _index
- This base's offset in the sequence
serialVersionUID: -1344722280822711931L
_partner5
ModeleBase _partner5
_edge5
ModeleBP.Edge _edge5
_partner3
ModeleBase _partner3
_edge3
ModeleBP.Edge _edge3
_stericity
ModeleBP.Stericity _stericity
_style
ModeleBPStyle _style
serialVersionUID: 3006493290669550139L
_isCustomColored
boolean _isCustomColored
_color
Color _color
_thickness
double _thickness
_bent
double _bent
serialVersionUID: 4055062096061553106L
_map
Vector<E> _map
_values
Vector<E> _values
serialVersionUID: -4331494086323517208L
_base_outline_color
Color _base_outline_color
_base_inner_color
Color _base_inner_color
_base_number_color
Color _base_number_color
_base_name_color
Color _base_name_color
_selected
boolean _selected
_listStrands
StructureTemp _listStrands
_spaceBetweenBases
Double _spaceBetweenBases
_listeBasesM
ArrayList<E> _listeBasesM
_ajustement
int _ajustement
_decalage
double _decalage
_rna
RNA _rna
serialVersionUID: 7541274455751497303L
_spaceBetweenBases
Double _spaceBetweenBases
_drawMode
int _drawMode
- The draw algorithm mode
BASE_RADIUS
int BASE_RADIUS
CHEM_PROB_DIST
double CHEM_PROB_DIST
CHEM_PROB_BASE_LENGTH
double CHEM_PROB_BASE_LENGTH
CHEM_PROB_ARROW_HEIGHT
double CHEM_PROB_ARROW_HEIGHT
CHEM_PROB_ARROW_WIDTH
double CHEM_PROB_ARROW_WIDTH
CHEM_PROB_TRIANGLE_WIDTH
double CHEM_PROB_TRIANGLE_WIDTH
CHEM_PROB_PIN_SEMIDIAG
double CHEM_PROB_PIN_SEMIDIAG
CHEM_PROB_DOT_RADIUS
double CHEM_PROB_DOT_RADIUS
_debugShape
GeneralPath _debugShape
_drawn
boolean _drawn
_bpHeightIncrement
double _bpHeightIncrement
_listeBases
ArrayList<E> _listeBases
- the base list
_listStrands
StructureTemp _listStrands
- the strand list
_structureAux
ArrayList<E> _structureAux
- Additional bonds and info can be specified here.
_listeAnnotations
ArrayList<E> _listeAnnotations
_listeRegionHighlights
ArrayList<E> _listeRegionHighlights
_name
String _name
_strandEndsAnnotated
boolean _strandEndsAnnotated
_ChemProbAnnotations
ArrayList<E> _ChemProbAnnotations
serialVersionUID: -436852923461989105L
_struct
ArrayList<E> _struct
serialVersionUID: 8815373295131046029L
x
double x
y
double y
Package fr.orsay.lri.varna.models.templates |
serialVersionUID: 1701307036024533400L
serialVersionUID: -201638492590138354L
Package fr.orsay.lri.varna.models.treealign |
serialVersionUID: -2709057098523675088L
serialVersionUID: 2034802149835891010L
serialVersionUID: 7782935062930780231L
Package fr.orsay.lri.varna.views |
serialVersionUID: 4525998278180950602L
_anim
VueAboutPanel.AboutAnimator _anim
_textPanel
JPanel _textPanel
_textArea
JTextArea _textArea
serialVersionUID: 1L
_mode
int _mode
_vp
VARNAPanel _vp
data
ArrayList<E> data
revdata
Hashtable<K,V> revdata
table
JTable table
specialTableModel
BaseTableModel specialTableModel
table
JTable table
_tm
VueBaseValues.ValueTableModel _tm
_vp
VARNAPanel _vp
data
ArrayList<E> data
_backup
ArrayList<E> _backup
columns
ArrayList<E> columns
table
JTable table
_tm
VueBPList.BPTableModel _tm
_vp
VARNAPanel _vp
data
ArrayList<E> data
_backup
ArrayList<E> _backup
columns
ArrayList<E> columns
_vp
VARNAPanel _vp
_gp
GradientEditorPanel _gp
_cb
JComboBox _cb
_code
JTextField _code
_backup
ModeleColorMap _backup
serialVersionUID: 1L
_vp
VARNAPanel _vp
data
ArrayList<E> data
table
JTable table
type
int type
specialTableModel
AnnotationTableModel specialTableModel
serialVersionUID: -1648400107478203724L
_vp
VARNAPanel _vp
urlCB
JRadioButton urlCB
fileCB
JRadioButton fileCB
urlAux
JPanel urlAux
fileAux
JPanel fileAux
l
CardLayout l
input
JPanel input
urlTxt
JTextField urlTxt
fileTxt
JTextField fileTxt
load
JButton load
serialVersionUID: 1L
_vp
VARNAPanel _vp
_controlerMenu
fr.orsay.lri.varna.controlers.ControleurMenu _controlerMenu
_itemOptionSpecialBaseColored
JCheckBoxMenuItem _itemOptionSpecialBaseColored
_itemShowWarnings
JCheckBoxMenuItem _itemShowWarnings
_itemOptionGapsBaseColored
JCheckBoxMenuItem _itemOptionGapsBaseColored
_itemOptionBondsColored
JCheckBoxMenuItem _itemOptionBondsColored
_itemShowNCBP
JCheckBoxMenuItem _itemShowNCBP
_itemShowOnlyPlanar
JCheckBoxMenuItem _itemShowOnlyPlanar
_itemFlatExteriorLoop
JCheckBoxMenuItem _itemFlatExteriorLoop
_itemShowColorMap
JCheckBoxMenuItem _itemShowColorMap
_dashBasesColor
JMenuItem _dashBasesColor
_disabled
ArrayList<E> _disabled
_rotation
JMenuItem _rotation
_bpHeightIncrement
JMenuItem _bpHeightIncrement
_spawnOrigin
Point _spawnOrigin
_subMenuBases
JMenu _subMenuBases
_selectionMenuIndex
Component _selectionMenuIndex