org.forester.archaeopteryx

Class Configuration

java.lang.Object

org.forester.archaeopteryx.Configuration

public final class Configuration
extends Object

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	Configuration.EXT_NODE_DATA_RETURN_ON
static class	Configuration.UI

Constructor Summary

Constructors

Constructor and Description
Configuration()
Configuration(String cf, boolean is_url, boolean is_applet, boolean verbose)

Method Summary

Modifier and Type	Method and Description
String	getBaseFontFamilyName()
int	getDefaultBootstrapSamples()
NodeVisualData.NodeFill	getDefaultNodeFill()
NodeVisualData.NodeShape	getDefaultNodeShape()
short	getDefaultNodeShapeSize()
NodeDataField	getExtDescNodeDataToReturn()
Configuration.EXT_NODE_DATA_RETURN_ON	getExtNodeDataReturnOn()
int	getFrameXSize()
int	getFrameYSize()
String	getLabelForGetExtDescendentsData()
File	getPathToLocalFastme()
File	getPathToLocalMafft()
File	getPathToLocalRaxml()
double	getVectorDataHeight()
Color	getVectorDataMaxColor()
Color	getVectorDataMeanColor()
Color	getVectorDataMinColor()
int	getVectorDataWidth()
boolean	isAbbreviateScientificTaxonNames()
boolean	isAllowThickStrokes()
boolean	isBackgroundColorGradient()
boolean	isColorByTaxonomicGroup()
boolean	isColorLabelsSameAsParentBranch()
boolean	isLineUpRendarableNodeData()
boolean	isMidpointReroot()
boolean	isRightLineUpDomains()
boolean	isShowAnnotationRefSource()
boolean	isShowDefaultNodeShapesExternal()
boolean	isShowDefaultNodeShapesForMarkedNodes()
boolean	isShowDefaultNodeShapesInternal()
boolean	isShowDomainLabels()
void	putDisplayColors(String key, Color color)
void	setAbbreviateScientificTaxonNames(boolean abbreviate_scientific_names)
void	setAddTaxonomyImagesCB(boolean b)
void	setBackgroundColorGradient(boolean background_color_gradient)
void	setBaseFontFamilyName(String base_font_family_name)
void	setBaseFontSize(int base_font_size)
void	setColorizeBranches(boolean b)
void	setColorLabelsSameAsParentBranch(boolean color_labels_same_as_parent_branch)
void	setDefaultNodeFill(NodeVisualData.NodeFill default_node_fill)
void	setDefaultNodeShape(NodeVisualData.NodeShape default_node_shape)
void	setDefaultNodeShapeSize(short default_node_shape_size)
void	setDisplayAsPhylogram(boolean b)
void	setDisplayColors(SortedMap<String,Color> display_colors)
void	setDisplayConfidenceValues(boolean b)
void	setDisplayGeneNames(boolean b)
void	setDisplayInternalData(boolean b)
void	setDisplayMultipleSequenceAlignment(boolean b)
void	setDisplayNodeNames(boolean b)
void	setDisplaySequenceAcc(boolean b)
void	setDisplaySequenceNames(boolean b)
void	setDisplaySequenceRelations(boolean display_sequence_relations)
void	setDisplaySequenceSymbols(boolean b)
void	setDisplayTaxonomyCode(boolean b)
void	setDisplayTaxonomyCommonNames(boolean b)
void	setDisplayTaxonomyImages(boolean b)
void	setDisplayTaxonomyScientificNames(boolean b)
void	setDynamicallyHideData(boolean b)
void	setExtDescNodeDataToReturn(NodeDataField ext_desc_data_to_return)
void	setFrameXSize(int frame_x_size)
void	setFrameYSize(int frame_y_size)
void	setLineUpRendarableNodeData(boolean line_up_renderable_node_data)
void	setMidpointReroot(boolean midpoint_root)
void	setMinConfidenceValue(double min_confidence_value)
void	setNodeLabelDirection(Options.NODE_LABEL_DIRECTION node_label_direction)
void	setNumberOfDigitsAfterCommaForBranchLengthValue(short number_of_digits_after_comma_for_branch_length_values)
void	setNumberOfDigitsAfterCommaForConfidenceValues(short number_of_digits_after_comma_for_confidence_values)
void	setPhylogenyGraphicsType(Options.PHYLOGENY_GRAPHICS_TYPE phylogeny_graphics_type)
void	setPrintLineWidth(float print_line_width)
void	setReplaceUnderscoresInNhParsing(boolean nh_parsing_replace_underscores)
void	setRightLineUpDomains(boolean right_align_domains)
void	setShowDefaultNodeShapesExternal(boolean show_default_node_shapes_external)
void	setShowDefaultNodeShapesForMarkedNodes(boolean show_default_node_shapes_for_marked_nodes)
void	setShowDefaultNodeShapesInternal(boolean show_default_node_shapes_internal)
void	setShowDomainLabels(boolean show_domain_labels)
void	setShowScale(boolean show_scale)
void	setUseStyle(boolean b)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

Configuration

public Configuration()

Configuration

public Configuration(String cf,
                     boolean is_url,
                     boolean is_applet,
                     boolean verbose)

Method Detail

getBaseFontFamilyName

public String getBaseFontFamilyName()

getDefaultBootstrapSamples

public int getDefaultBootstrapSamples()

getDefaultNodeFill

public NodeVisualData.NodeFill getDefaultNodeFill()

getDefaultNodeShape

public NodeVisualData.NodeShape getDefaultNodeShape()

getDefaultNodeShapeSize

public short getDefaultNodeShapeSize()

getExtDescNodeDataToReturn

public NodeDataField getExtDescNodeDataToReturn()

getExtNodeDataReturnOn

public Configuration.EXT_NODE_DATA_RETURN_ON getExtNodeDataReturnOn()

getFrameXSize

public int getFrameXSize()

getFrameYSize

public int getFrameYSize()

getLabelForGetExtDescendentsData

public String getLabelForGetExtDescendentsData()

getPathToLocalFastme

public File getPathToLocalFastme()

getPathToLocalMafft

public File getPathToLocalMafft()

getPathToLocalRaxml

public File getPathToLocalRaxml()

getVectorDataHeight

public double getVectorDataHeight()

getVectorDataMaxColor

public Color getVectorDataMaxColor()

getVectorDataMeanColor

public Color getVectorDataMeanColor()

getVectorDataMinColor

public Color getVectorDataMinColor()

getVectorDataWidth

public int getVectorDataWidth()

isAbbreviateScientificTaxonNames

public boolean isAbbreviateScientificTaxonNames()

isAllowThickStrokes

public boolean isAllowThickStrokes()

isBackgroundColorGradient

public boolean isBackgroundColorGradient()

isColorByTaxonomicGroup

public boolean isColorByTaxonomicGroup()

isColorLabelsSameAsParentBranch

public boolean isColorLabelsSameAsParentBranch()

isLineUpRendarableNodeData

public final boolean isLineUpRendarableNodeData()

isMidpointReroot

public boolean isMidpointReroot()

isRightLineUpDomains

public final boolean isRightLineUpDomains()

isShowAnnotationRefSource

public boolean isShowAnnotationRefSource()

isShowDefaultNodeShapesExternal

public boolean isShowDefaultNodeShapesExternal()

isShowDefaultNodeShapesForMarkedNodes

public boolean isShowDefaultNodeShapesForMarkedNodes()

isShowDefaultNodeShapesInternal

public boolean isShowDefaultNodeShapesInternal()

isShowDomainLabels

public boolean isShowDomainLabels()

putDisplayColors

public void putDisplayColors(String key,
                             Color color)

setAbbreviateScientificTaxonNames

public void setAbbreviateScientificTaxonNames(boolean abbreviate_scientific_names)

setAddTaxonomyImagesCB

public void setAddTaxonomyImagesCB(boolean b)

setBackgroundColorGradient

public void setBackgroundColorGradient(boolean background_color_gradient)

setBaseFontFamilyName

public void setBaseFontFamilyName(String base_font_family_name)

setBaseFontSize

public void setBaseFontSize(int base_font_size)

setColorizeBranches

public void setColorizeBranches(boolean b)

setColorLabelsSameAsParentBranch

public void setColorLabelsSameAsParentBranch(boolean color_labels_same_as_parent_branch)

setDefaultNodeFill

public void setDefaultNodeFill(NodeVisualData.NodeFill default_node_fill)

setDefaultNodeShape

public void setDefaultNodeShape(NodeVisualData.NodeShape default_node_shape)

setDefaultNodeShapeSize

public void setDefaultNodeShapeSize(short default_node_shape_size)

setDisplayAsPhylogram

public void setDisplayAsPhylogram(boolean b)

setDisplayColors

public void setDisplayColors(SortedMap<String,Color> display_colors)

setDisplayConfidenceValues

public void setDisplayConfidenceValues(boolean b)

setDisplayGeneNames

public void setDisplayGeneNames(boolean b)

setDisplayInternalData

public void setDisplayInternalData(boolean b)

setDisplayMultipleSequenceAlignment

public void setDisplayMultipleSequenceAlignment(boolean b)

setDisplayNodeNames

public void setDisplayNodeNames(boolean b)

setDisplaySequenceAcc

public void setDisplaySequenceAcc(boolean b)

setDisplaySequenceNames

public void setDisplaySequenceNames(boolean b)

setDisplaySequenceRelations

public void setDisplaySequenceRelations(boolean display_sequence_relations)

setDisplaySequenceSymbols

public void setDisplaySequenceSymbols(boolean b)

setDisplayTaxonomyCode

public void setDisplayTaxonomyCode(boolean b)

setDisplayTaxonomyCommonNames

public void setDisplayTaxonomyCommonNames(boolean b)

setDisplayTaxonomyImages

public void setDisplayTaxonomyImages(boolean b)

setDisplayTaxonomyScientificNames

public void setDisplayTaxonomyScientificNames(boolean b)

setDynamicallyHideData

public void setDynamicallyHideData(boolean b)

setExtDescNodeDataToReturn

public void setExtDescNodeDataToReturn(NodeDataField ext_desc_data_to_return)

setFrameXSize

public void setFrameXSize(int frame_x_size)

setFrameYSize

public void setFrameYSize(int frame_y_size)

setLineUpRendarableNodeData

public final void setLineUpRendarableNodeData(boolean line_up_renderable_node_data)

setMidpointReroot

public void setMidpointReroot(boolean midpoint_root)

setMinConfidenceValue

public void setMinConfidenceValue(double min_confidence_value)

setNodeLabelDirection

public void setNodeLabelDirection(Options.NODE_LABEL_DIRECTION node_label_direction)

setNumberOfDigitsAfterCommaForBranchLengthValue

public void setNumberOfDigitsAfterCommaForBranchLengthValue(short number_of_digits_after_comma_for_branch_length_values)

setNumberOfDigitsAfterCommaForConfidenceValues

public void setNumberOfDigitsAfterCommaForConfidenceValues(short number_of_digits_after_comma_for_confidence_values)

setPhylogenyGraphicsType

public void setPhylogenyGraphicsType(Options.PHYLOGENY_GRAPHICS_TYPE phylogeny_graphics_type)

setPrintLineWidth

public void setPrintLineWidth(float print_line_width)

setReplaceUnderscoresInNhParsing

public void setReplaceUnderscoresInNhParsing(boolean nh_parsing_replace_underscores)

setRightLineUpDomains

public final void setRightLineUpDomains(boolean right_align_domains)

setShowDefaultNodeShapesExternal

public void setShowDefaultNodeShapesExternal(boolean show_default_node_shapes_external)

setShowDefaultNodeShapesForMarkedNodes

public void setShowDefaultNodeShapesForMarkedNodes(boolean show_default_node_shapes_for_marked_nodes)

setShowDefaultNodeShapesInternal

public void setShowDefaultNodeShapesInternal(boolean show_default_node_shapes_internal)

setShowDomainLabels

public void setShowDomainLabels(boolean show_domain_labels)

setShowScale

public void setShowScale(boolean show_scale)

setUseStyle

public void setUseStyle(boolean b)