fr.orsay.lri.varna.models
Class VARNAConfigLoader
java.lang.Object
fr.orsay.lri.varna.models.VARNAConfigLoader
public class VARNAConfigLoader
- extends Object
An RNA 2d Panel demo applet
- Author:
- Yann Ponty
Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
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
VARNAConfigLoader
public VARNAConfigLoader(InterfaceParameterLoader il)
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
-