Serialized Form


Package fr.orsay.lri.varna

Class fr.orsay.lri.varna.VARNAPanel extends JPanel implements Serializable

serialVersionUID: 8194421570308956001L

Serialized Fields

_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

Class fr.orsay.lri.varna.components.ActionEditor extends AbstractCellEditor implements Serializable

Serialized Fields

_btn

JButton _btn

Class fr.orsay.lri.varna.components.ActionRenderer extends JButton implements Serializable

serialVersionUID: 1L

Class fr.orsay.lri.varna.components.AnnotationTableModel extends AbstractTableModel implements Serializable

serialVersionUID: 1L

Serialized Fields

columnNames

String[] columnNames

data

ArrayList<E> data

Class fr.orsay.lri.varna.components.BaseSpecialColorEditor extends AbstractCellEditor implements Serializable

serialVersionUID: 1L

Serialized Fields

currentColor

Color currentColor

button

JButton button

colorChooser

JColorChooser colorChooser

dialog

JDialog dialog

_vueBases

VueBases _vueBases

_controleurSpecialColorEditor

fr.orsay.lri.varna.controlers.ControleurBaseSpecialColorEditor _controleurSpecialColorEditor

Class fr.orsay.lri.varna.components.BaseTableModel extends AbstractTableModel implements Serializable

serialVersionUID: 1L

Serialized Fields

columnNames

String[] columnNames

data

ArrayList<E> data

outlineColor

Color outlineColor

innerColor

Color innerColor

baseColor

Color baseColor

numberColor

Color numberColor

Class fr.orsay.lri.varna.components.ColorRenderer extends JLabel implements Serializable

serialVersionUID: 1L

Serialized Fields

unselectedBorder

Border unselectedBorder

selectedBorder

Border selectedBorder

isBordered

boolean isBordered

Class fr.orsay.lri.varna.components.GradientEditorPanel extends JPanel implements Serializable

Serialized Fields

_mcm

ModeleColorMap _mcm

EDGES

Color EDGES

BUTTONS

Color BUTTONS

_selectedIndex

int _selectedIndex

Class fr.orsay.lri.varna.components.ReorderableJList extends JList implements Serializable

Serialized Fields

dragSource

DragSource dragSource

dropTarget

DropTarget dropTarget

dropTargetIndex

int dropTargetIndex

draggedIndex

int draggedIndex

Class fr.orsay.lri.varna.components.VARNAConsole extends JFrame implements Serializable

Serialized Fields

_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

Class fr.orsay.lri.varna.models.FullBackup extends Object implements Serializable

serialVersionUID: -5468893731117925140L

Serialized Fields

config

VARNAConfig config

rna

RNA rna

name

String name

Class fr.orsay.lri.varna.models.VARNAConfig extends Object implements Serializable

serialVersionUID: 2853916694420964233L

Serialized Fields

_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

Class fr.orsay.lri.varna.models.VARNAEdits.AddBPEdit extends AbstractUndoableEdit implements Serializable

Serialized Fields

_msbp

ModeleBP _msbp

_i

int _i

_j

int _j

_vp

VARNAPanel _vp

Class fr.orsay.lri.varna.models.VARNAEdits.BasesShiftEdit extends AbstractUndoableEdit implements Serializable

Serialized Fields

_indices

ArrayList<E> _indices

_dx

double _dx

_dy

double _dy

_vp

VARNAPanel _vp

Class fr.orsay.lri.varna.models.VARNAEdits.HelixFlipEdit extends AbstractUndoableEdit implements Serializable

Serialized Fields

_h

Point _h

_vp

VARNAPanel _vp

Class fr.orsay.lri.varna.models.VARNAEdits.HelixRotateEdit extends AbstractUndoableEdit implements Serializable

Serialized Fields

_delta

double _delta

_base

double _base

_pLimL

double _pLimL

_pLimR

double _pLimR

_h

Point _h

_ml

Point _ml

_vp

VARNAPanel _vp

Class fr.orsay.lri.varna.models.VARNAEdits.RedrawEdit extends AbstractUndoableEdit implements Serializable

Serialized Fields

_prevMode

int _prevMode

_newMode

int _newMode

_prevFlat

boolean _prevFlat

_newFlat

boolean _newFlat

_backupCoords

ArrayList<E> _backupCoords

_backupCenters

ArrayList<E> _backupCenters

_vp

VARNAPanel _vp

Class fr.orsay.lri.varna.models.VARNAEdits.RemoveBPEdit extends AbstractUndoableEdit implements Serializable

Serialized Fields

_msbp

ModeleBP _msbp

_i

int _i

_j

int _j

_vp

VARNAPanel _vp

Class fr.orsay.lri.varna.models.VARNAEdits.RotateRNAEdit extends AbstractUndoableEdit implements Serializable

Serialized Fields

_angle

double _angle

_vp

VARNAPanel _vp

Class fr.orsay.lri.varna.models.VARNAEdits.SingleBaseMoveEdit extends AbstractUndoableEdit implements Serializable

Serialized Fields

_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

Class fr.orsay.lri.varna.models.annotations.ChemProbAnnotation extends Object implements Serializable

serialVersionUID: 5833315460145031242L

Serialized Fields

_mbfst

ModeleBase _mbfst

_mbsnd

ModeleBase _mbsnd

_color

Color _color

_intensity

double _intensity

_type

ChemProbAnnotation.ChemProbAnnotationType _type

_out

boolean _out

Class fr.orsay.lri.varna.models.annotations.HighlightRegionAnnotation extends Object implements Serializable

serialVersionUID: 7087014168028684775L

Serialized Fields

_bases

ArrayList<E> _bases

_outlineColor

Color _outlineColor

_fillColor

Color _fillColor

_radius

double _radius

Class fr.orsay.lri.varna.models.annotations.TextAnnotation extends Object implements Serializable

serialVersionUID: 465236085501860747L

Serialized Fields

_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

Class fr.orsay.lri.varna.models.rna.ExtendedMB extends ModeleBase implements Serializable

Serialized Fields

intervDroite

boolean intervDroite

intervGauche

boolean intervGauche

Class fr.orsay.lri.varna.models.rna.Mapping extends Object implements Serializable

serialVersionUID: -3031358968555310380L

Serialized Fields

_mapping

Hashtable<K,V> _mapping

_invMapping

Hashtable<K,V> _invMapping

Class fr.orsay.lri.varna.models.rna.ModeleBase extends Object implements Serializable

Serialized Fields

_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

Class fr.orsay.lri.varna.models.rna.ModeleBaseNucleotide extends ModeleBase implements Serializable

serialVersionUID: -5493938366569588113L

Serialized Fields

_c

String _c

_index

int _index

Class fr.orsay.lri.varna.models.rna.ModeleBasesComparison extends ModeleBase implements Serializable

serialVersionUID: -2733063250714562463L

Serialized Fields

_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

Class fr.orsay.lri.varna.models.rna.ModeleBP extends Object implements Serializable

serialVersionUID: -1344722280822711931L

Serialized Fields

_partner5

ModeleBase _partner5

_edge5

ModeleBP.Edge _edge5

_partner3

ModeleBase _partner3

_edge3

ModeleBP.Edge _edge3

_stericity

ModeleBP.Stericity _stericity

_style

ModeleBPStyle _style

Class fr.orsay.lri.varna.models.rna.ModeleBPStyle extends Object implements Serializable

serialVersionUID: 3006493290669550139L

Serialized Fields

_isCustomColored

boolean _isCustomColored

_color

Color _color

_thickness

double _thickness

_bent

double _bent

Class fr.orsay.lri.varna.models.rna.ModeleColorMap extends Object implements Serializable

serialVersionUID: 4055062096061553106L

Serialized Fields

_map

Vector<E> _map

_values

Vector<E> _values

Class fr.orsay.lri.varna.models.rna.ModeleStyleBase extends Object implements Serializable

serialVersionUID: -4331494086323517208L

Serialized Fields

_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

Class fr.orsay.lri.varna.models.rna.Motif extends Object implements Serializable

Serialized Fields

_listStrands

StructureTemp _listStrands

_spaceBetweenBases

Double _spaceBetweenBases

_listeBasesM

ArrayList<E> _listeBasesM

_ajustement

int _ajustement

_decalage

double _decalage

_rna

RNA _rna

Class fr.orsay.lri.varna.models.rna.RNA extends InterfaceVARNAObservable implements Serializable

serialVersionUID: 7541274455751497303L

Serialized Fields

_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

Class fr.orsay.lri.varna.models.rna.StructureTemp extends Object implements Serializable

serialVersionUID: -436852923461989105L

Serialized Fields

_struct

ArrayList<E> _struct

Class fr.orsay.lri.varna.models.rna.VARNAPoint extends Object implements Serializable

serialVersionUID: 8815373295131046029L

Serialized Fields

x

double x

y

double y

Package fr.orsay.lri.varna.models.templates

Class fr.orsay.lri.varna.models.templates.RNATemplateDrawingAlgorithmException extends fr.orsay.lri.varna.exceptions.ExceptionDrawingAlgorithm implements Serializable

serialVersionUID: 1701307036024533400L

Class fr.orsay.lri.varna.models.templates.RNATemplateMappingException extends Exception implements Serializable

serialVersionUID: -201638492590138354L


Package fr.orsay.lri.varna.models.treealign

Class fr.orsay.lri.varna.models.treealign.RNANodeValue2WrongTypeException extends NullPointerException implements Serializable

serialVersionUID: -2709057098523675088L

Class fr.orsay.lri.varna.models.treealign.RNATree2Exception extends Exception implements Serializable

serialVersionUID: 2034802149835891010L

Class fr.orsay.lri.varna.models.treealign.TreeAlignException extends Exception implements Serializable

serialVersionUID: 7782935062930780231L


Package fr.orsay.lri.varna.views

Class fr.orsay.lri.varna.views.VueAboutPanel extends JPanel implements Serializable

serialVersionUID: 4525998278180950602L

Serialized Fields

_anim

VueAboutPanel.AboutAnimator _anim

_textPanel

JPanel _textPanel

_textArea

JTextArea _textArea

Class fr.orsay.lri.varna.views.VueBases extends JPanel implements Serializable

serialVersionUID: 1L

Serialized Fields

_mode

int _mode

_vp

VARNAPanel _vp

data

ArrayList<E> data

revdata

Hashtable<K,V> revdata

table

JTable table

specialTableModel

BaseTableModel specialTableModel

Class fr.orsay.lri.varna.views.VueBaseValues extends JPanel implements Serializable

Serialized Fields

table

JTable table

_tm

VueBaseValues.ValueTableModel _tm

_vp

VARNAPanel _vp

data

ArrayList<E> data

_backup

ArrayList<E> _backup

columns

ArrayList<E> columns

Class fr.orsay.lri.varna.views.VueBPList extends JPanel implements Serializable

Serialized Fields

table

JTable table

_tm

VueBPList.BPTableModel _tm

_vp

VARNAPanel _vp

data

ArrayList<E> data

_backup

ArrayList<E> _backup

columns

ArrayList<E> columns

Class fr.orsay.lri.varna.views.VueColorMapStyle extends JPanel implements Serializable

Serialized Fields

_vp

VARNAPanel _vp

_gp

GradientEditorPanel _gp

_cb

JComboBox _cb

_code

JTextField _code

_backup

ModeleColorMap _backup

Class fr.orsay.lri.varna.views.VueListeAnnotations extends JPanel implements Serializable

serialVersionUID: 1L

Serialized Fields

_vp

VARNAPanel _vp

data

ArrayList<E> data

table

JTable table

type

int type

specialTableModel

AnnotationTableModel specialTableModel

Class fr.orsay.lri.varna.views.VueLoadColorMapValues extends JPanel implements Serializable

serialVersionUID: -1648400107478203724L

Serialized Fields

_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

Class fr.orsay.lri.varna.views.VueMenu extends JPopupMenu implements Serializable

serialVersionUID: 1L

Serialized Fields

_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