fr.orsay.lri.varna.models
Class VARNAConfigLoader

java.lang.Object
  extended by fr.orsay.lri.varna.models.VARNAConfigLoader

public class VARNAConfigLoader
extends Object

An RNA 2d Panel demo applet

Author:
Yann Ponty

Field Summary
private  String _algo
           
 String _annotations
           
private  boolean _autoHelices
           
private  boolean _autoInteriorLoops
           
private  boolean _autoTerminalLoops
           
private  String _auxBPs
           
private  Color _backboneColor
           
private  Color _backgroundColor
           
private  Color _baseInnerColor
           
private  Color _baseNameColor
           
private  Color _baseNumColor
           
private  Color _baseOutlineColor
           
private  ArrayList<ModeleStyleBase> _basesStyleList
           
private  Color _bondColor
           
private  Dimension _border
           
private  double _bpIncrement
           
private  VARNAConfig.BP_STYLE _bpStyle
           
 String _chemProbs
           
private  String _colorMapCaption
           
private  String _colorMapStyle
           
private  String _colorMapValues
           
private  boolean _comparisonMode
           
private  String _customBases
           
private  String _customBPs
           
private  RNA _defaultRNA
           
private  boolean _drawBackbone
           
private  boolean _drawColorMap
           
private  boolean _drawNC
           
private  boolean _drawTertiary
           
private  boolean _error
           
private  String _firstSequence
           
private  String _firstStructure
           
private  boolean _flatExteriorLoop
           
private  Color _gapsColor
           
private  String _highlightRegion
           
private  VARNAPanel _mainSurface
           
private  boolean _modifiable
           
private  Color _nonStandardColor
           
private  int _numColumns
           
private  int _numRows
           
(package private)  InterfaceParameterLoader _optionProducer
           
private  String _orientation
           
private  int _periodResNum
           
private  double _rotation
           
private  String _secondSequence
           
private  String _secondStructure
           
private  String _sseq
           
private  String _sstruct
           
private  String _title
           
private  Color _titleColor
           
private  int _titleSize
           
private  String _URL
           
private  boolean _useBaseNameColor
           
private  boolean _useBaseNumbersColor
           
private  boolean _useBaseOutlineColor
           
private  boolean _useGapsColor
           
private  boolean _useInnerBaseColor
           
private  boolean _useNonStandardColor
           
protected  ArrayList<VARNAPanel> _VARNAPanelList
           
private  boolean _warning
           
private  double _zoom
           
private  double _zoomAmount
           
static String algoOpt
           
static String ALGORITHM_CIRCULAR
           
static String ALGORITHM_LINE
           
static String ALGORITHM_MOTIF_VIEW
           
static String ALGORITHM_NAVIEW
           
static String ALGORITHM_RADIATE
           
static String ALGORITHM_VARNA_VIEW
           
static String annotationsOpt
           
static String applyBasesStyleOpt
           
static String autoHelicesOpt
           
static String autoInteriorLoopsOpt
           
static String autoTerminalLoopsOpt
           
static String auxBPsOpt
           
static String backboneColorOpt
           
static String backgroundColorOpt
           
static String baseInnerColorOpt
           
static String baseNameColorOpt
           
static String baseNumbersColorOpt
           
static String baseOutlineColorOpt
           
static String basesStyleOpt
           
static String bondColorOpt
           
static String borderOpt
           
static String bpIncrementOpt
           
static String bpStyleOpt
           
static String chemProbOpt
           
static String colorMapCaptionOpt
           
static String colorMapDefOpt
           
static String colorMapOpt
           
static String comparisonModeOpt
           
static String customBasesOpt
           
static String customBPsOpt
           
static String drawBackboneOpt
           
static String drawColorMapOpt
           
static String drawNCOpt
           
static String drawTertiaryOpt
           
static String errorOpt
           
static String firstSequenceForComparisonOpt
           
static String firstStructureForComparisonOpt
           
static String flatExteriorLoopOpt
           
static String gapsBaseColorOpt
           
static String highlightRegionOpt
           
static String LEONTIS_WESTHOF_BP_STYLE
           
private static int MAXSTYLE
           
static String modifiableOpt
           
static String NONE_BP_STYLE
           
static String nonStandardColorOpt
           
static String numColumnsOpt
           
static String numRowsOpt
           
static String orientationOpt
           
static String periodNumOpt
           
static String RNAVIZ_BP_STYLE
           
static String rotationOpt
           
static String secondSequenceForComparisonOpt
           
static String secondStructureForComparisonOpt
           
static String sequenceOpt
           
static String SIMPLE_BP_STYLE
           
static String structureOpt
           
static String titleColorOpt
           
static String titleOpt
           
static String titleSizeOpt
           
static String URLOpt
           
static String warningOpt
           
static String zoomAmountOpt
           
static String zoomOpt
           
 
Constructor Summary
VARNAConfigLoader(InterfaceParameterLoader il)
           
 
Method Summary
private  void applyAnnotations(VARNAPanel vp)
          Format: string:[type=[H|B|L|P]|x=double|y=double|anchor=int|size=int|color=Color];
private  void applyAuxBPs(VARNAPanel vp)
           
private  void applyBasesCustomStyles(VARNAPanel vp)
           
private  void applyBasesStyle(String n)
           
private  void applyBPsCustomStyles(VARNAPanel vp)
           
private  void applyChemProbs(VARNAPanel vp)
           
private  void applyColorMapStyle(VARNAPanel vp)
           
private  void applyColorMapValues(VARNAPanel vp)
           
private  void applyHighlightRegion(VARNAPanel vp)
           
private  void applyValues(String n)
           
 ArrayList<VARNAPanel> createVARNAPanels()
           
 int getNbColumns()
           
 int getNbRows()
           
static String[][] getParameterInfo()
           
private  VARNAConfig.BP_STYLE getSafeBPStyle(String opt, VARNAConfig.BP_STYLE def)
           
static Color getSafeColor(String col, Color def)
           
private  void initValues()
           
private  Dimension parseDimension(String s)
           
private  void retrieveParametersValues()
           
 void setRNA(RNA r)
           
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

MAXSTYLE

private static final int MAXSTYLE
See Also:
Constant Field Values

numColumnsOpt

public static String numColumnsOpt

numRowsOpt

public static String numRowsOpt

algoOpt

public static String algoOpt

annotationsOpt

public static String annotationsOpt

applyBasesStyleOpt

public static String applyBasesStyleOpt

auxBPsOpt

public static String auxBPsOpt

autoHelicesOpt

public static String autoHelicesOpt

autoInteriorLoopsOpt

public static String autoInteriorLoopsOpt

autoTerminalLoopsOpt

public static String autoTerminalLoopsOpt

backboneColorOpt

public static String backboneColorOpt

backgroundColorOpt

public static String backgroundColorOpt

baseInnerColorOpt

public static String baseInnerColorOpt

baseNameColorOpt

public static String baseNameColorOpt

baseNumbersColorOpt

public static String baseNumbersColorOpt

baseOutlineColorOpt

public static String baseOutlineColorOpt

basesStyleOpt

public static String basesStyleOpt

borderOpt

public static String borderOpt

bondColorOpt

public static String bondColorOpt

bpIncrementOpt

public static String bpIncrementOpt

bpStyleOpt

public static String bpStyleOpt

colorMapOpt

public static String colorMapOpt

colorMapCaptionOpt

public static String colorMapCaptionOpt

colorMapDefOpt

public static String colorMapDefOpt

chemProbOpt

public static String chemProbOpt

customBasesOpt

public static String customBasesOpt

customBPsOpt

public static String customBPsOpt

drawNCOpt

public static String drawNCOpt

drawTertiaryOpt

public static String drawTertiaryOpt

drawColorMapOpt

public static String drawColorMapOpt

drawBackboneOpt

public static String drawBackboneOpt

errorOpt

public static String errorOpt

flatExteriorLoopOpt

public static String flatExteriorLoopOpt

highlightRegionOpt

public static String highlightRegionOpt

nonStandardColorOpt

public static String nonStandardColorOpt

orientationOpt

public static String orientationOpt

modifiableOpt

public static String modifiableOpt

periodNumOpt

public static String periodNumOpt

rotationOpt

public static String rotationOpt

sequenceOpt

public static String sequenceOpt

structureOpt

public static String structureOpt

titleOpt

public static String titleOpt

titleColorOpt

public static String titleColorOpt

titleSizeOpt

public static String titleSizeOpt

URLOpt

public static String URLOpt

zoomOpt

public static String zoomOpt

zoomAmountOpt

public static String zoomAmountOpt

warningOpt

public static String warningOpt

comparisonModeOpt

public static String comparisonModeOpt

gapsBaseColorOpt

public static String gapsBaseColorOpt

firstSequenceForComparisonOpt

public static String firstSequenceForComparisonOpt

secondSequenceForComparisonOpt

public static String secondSequenceForComparisonOpt

firstStructureForComparisonOpt

public static String firstStructureForComparisonOpt

secondStructureForComparisonOpt

public static String secondStructureForComparisonOpt

_algo

private String _algo

_annotations

public String _annotations

_chemProbs

public String _chemProbs

_rotation

private double _rotation

_sseq

private String _sseq

_sstruct

private String _sstruct

_numRows

private int _numRows

_numColumns

private int _numColumns

_title

private String _title

_titleSize

private int _titleSize

_titleColor

private Color _titleColor

_auxBPs

private String _auxBPs

_highlightRegion

private String _highlightRegion

_autoHelices

private boolean _autoHelices

_autoInteriorLoops

private boolean _autoInteriorLoops

_autoTerminalLoops

private boolean _autoTerminalLoops

_drawBackbone

private boolean _drawBackbone

_backboneColor

private Color _backboneColor

_bondColor

private Color _bondColor

_bpStyle

private VARNAConfig.BP_STYLE _bpStyle

_baseOutlineColor

private Color _baseOutlineColor

_baseInnerColor

private Color _baseInnerColor

_baseNumColor

private Color _baseNumColor

_baseNameColor

private Color _baseNameColor

_gapsColor

private Color _gapsColor

_nonStandardColor

private Color _nonStandardColor

_flatExteriorLoop

private boolean _flatExteriorLoop

_customBases

private String _customBases

_customBPs

private String _customBPs

_colorMapStyle

private String _colorMapStyle

_colorMapCaption

private String _colorMapCaption

_colorMapValues

private String _colorMapValues

_drawNC

private boolean _drawNC

_drawTertiary

private boolean _drawTertiary

_drawColorMap

private boolean _drawColorMap

_periodResNum

private int _periodResNum

_border

private Dimension _border

_backgroundColor

private Color _backgroundColor

_orientation

private String _orientation

_warning

private boolean _warning

_error

private boolean _error

_modifiable

private boolean _modifiable

_zoom

private double _zoom

_zoomAmount

private double _zoomAmount

_basesStyleList

private ArrayList<ModeleStyleBase> _basesStyleList

_comparisonMode

private boolean _comparisonMode

_firstSequence

private String _firstSequence

_secondSequence

private String _secondSequence

_firstStructure

private String _firstStructure

_secondStructure

private String _secondStructure

_mainSurface

private VARNAPanel _mainSurface

_useNonStandardColor

private boolean _useNonStandardColor

_useGapsColor

private boolean _useGapsColor

_bpIncrement

private double _bpIncrement

_useInnerBaseColor

private boolean _useInnerBaseColor

_useBaseNameColor

private boolean _useBaseNameColor

_useBaseNumbersColor

private boolean _useBaseNumbersColor

_useBaseOutlineColor

private boolean _useBaseOutlineColor

_URL

private String _URL

_VARNAPanelList

protected ArrayList<VARNAPanel> _VARNAPanelList

_optionProducer

InterfaceParameterLoader _optionProducer

LEONTIS_WESTHOF_BP_STYLE

public static final String LEONTIS_WESTHOF_BP_STYLE
See Also:
Constant Field Values

SIMPLE_BP_STYLE

public static final String SIMPLE_BP_STYLE
See Also:
Constant Field Values

RNAVIZ_BP_STYLE

public static final String RNAVIZ_BP_STYLE
See Also:
Constant Field Values

NONE_BP_STYLE

public static final String NONE_BP_STYLE
See Also:
Constant Field Values

_defaultRNA

private RNA _defaultRNA

ALGORITHM_CIRCULAR

public static final String ALGORITHM_CIRCULAR
See Also:
Constant Field Values

ALGORITHM_NAVIEW

public static final String ALGORITHM_NAVIEW
See Also:
Constant Field Values

ALGORITHM_LINE

public static final String ALGORITHM_LINE
See Also:
Constant Field Values

ALGORITHM_RADIATE

public static final String ALGORITHM_RADIATE
See Also:
Constant Field Values

ALGORITHM_VARNA_VIEW

public static final String ALGORITHM_VARNA_VIEW
See Also:
Constant Field Values

ALGORITHM_MOTIF_VIEW

public static final String ALGORITHM_MOTIF_VIEW
See Also:
Constant Field Values
Constructor Detail

VARNAConfigLoader

public VARNAConfigLoader(InterfaceParameterLoader il)
Method Detail

createVARNAPanels

public ArrayList<VARNAPanel> createVARNAPanels()
                                        throws fr.orsay.lri.varna.exceptions.ExceptionParameterError,
                                               fr.orsay.lri.varna.exceptions.ExceptionModeleStyleBaseSyntaxError,
                                               fr.orsay.lri.varna.exceptions.ExceptionNonEqualLength,
                                               IOException,
                                               fr.orsay.lri.varna.exceptions.ExceptionFileFormatOrSyntax,
                                               fr.orsay.lri.varna.exceptions.ExceptionLoadingFailed
Throws:
fr.orsay.lri.varna.exceptions.ExceptionParameterError
fr.orsay.lri.varna.exceptions.ExceptionModeleStyleBaseSyntaxError
fr.orsay.lri.varna.exceptions.ExceptionNonEqualLength
IOException
fr.orsay.lri.varna.exceptions.ExceptionFileFormatOrSyntax
fr.orsay.lri.varna.exceptions.ExceptionLoadingFailed

getNbRows

public int getNbRows()

getNbColumns

public int getNbColumns()

initValues

private void initValues()

getSafeColor

public static Color getSafeColor(String col,
                                 Color def)

getSafeBPStyle

private VARNAConfig.BP_STYLE getSafeBPStyle(String opt,
                                            VARNAConfig.BP_STYLE def)

getParameterInfo

public static String[][] getParameterInfo()

retrieveParametersValues

private void retrieveParametersValues()
                               throws fr.orsay.lri.varna.exceptions.ExceptionParameterError,
                                      fr.orsay.lri.varna.exceptions.ExceptionModeleStyleBaseSyntaxError,
                                      fr.orsay.lri.varna.exceptions.ExceptionNonEqualLength,
                                      IOException,
                                      fr.orsay.lri.varna.exceptions.ExceptionFileFormatOrSyntax,
                                      fr.orsay.lri.varna.exceptions.ExceptionLoadingFailed
Throws:
fr.orsay.lri.varna.exceptions.ExceptionParameterError
fr.orsay.lri.varna.exceptions.ExceptionModeleStyleBaseSyntaxError
fr.orsay.lri.varna.exceptions.ExceptionNonEqualLength
IOException
fr.orsay.lri.varna.exceptions.ExceptionFileFormatOrSyntax
fr.orsay.lri.varna.exceptions.ExceptionLoadingFailed

setRNA

public void setRNA(RNA r)

applyValues

private void applyValues(String n)
                  throws fr.orsay.lri.varna.exceptions.ExceptionParameterError,
                         fr.orsay.lri.varna.exceptions.ExceptionNonEqualLength,
                         IOException,
                         fr.orsay.lri.varna.exceptions.ExceptionFileFormatOrSyntax,
                         fr.orsay.lri.varna.exceptions.ExceptionLoadingFailed
Throws:
fr.orsay.lri.varna.exceptions.ExceptionParameterError
fr.orsay.lri.varna.exceptions.ExceptionNonEqualLength
IOException
fr.orsay.lri.varna.exceptions.ExceptionFileFormatOrSyntax
fr.orsay.lri.varna.exceptions.ExceptionLoadingFailed

applyBasesStyle

private void applyBasesStyle(String n)
                      throws fr.orsay.lri.varna.exceptions.ExceptionParameterError
Throws:
fr.orsay.lri.varna.exceptions.ExceptionParameterError

applyColorMapStyle

private void applyColorMapStyle(VARNAPanel vp)

applyColorMapValues

private void applyColorMapValues(VARNAPanel vp)

applyBasesCustomStyles

private void applyBasesCustomStyles(VARNAPanel vp)

applyHighlightRegion

private void applyHighlightRegion(VARNAPanel vp)

parseDimension

private Dimension parseDimension(String s)

applyBPsCustomStyles

private void applyBPsCustomStyles(VARNAPanel vp)

applyChemProbs

private void applyChemProbs(VARNAPanel vp)

applyAuxBPs

private void applyAuxBPs(VARNAPanel vp)

applyAnnotations

private void applyAnnotations(VARNAPanel vp)
Format: string:[type=[H|B|L|P]|x=double|y=double|anchor=int|size=int|color=Color];

Parameters:
vp -