org.forester.archaeopteryx
Class Configuration

java.lang.Object
  org.forester.archaeopteryx.Configuration

public final class Configuration
extends java.lang.Object

Nested Class Summary

static class

Configuration.UI

Constructor Summary

Configuration()

Configuration(java.lang.String cf, boolean is_url, boolean is_applet, boolean verbose)

Method Summary

java.lang.String	getBaseFontFamilyName()
int	getDefaultBootstrapSamples()
NodeVisualization.NodeFill	getDefaultNodeFill()
NodeVisualization.NodeShape	getDefaultNodeShape()
short	getDefaultNodeShapeSize()
java.awt.Color	getDomainStructureBaseColor()
java.awt.Color	getDomainStructureFontColor()
java.io.File	getPathToClustalOmega()
java.io.File	getPathToFastME()
java.io.File	getPathToMafft()
boolean	isAbbreviateScientificTaxonNames()
boolean	isBackgroundColorGradient()
boolean	isColorLabelsSameAsParentBranch()
boolean	isShowDefaultNodeShapes()
boolean	isShowDomainLabels()
boolean	isTaxonomyColorizeNodeShapes()
void	putDisplayColors(java.lang.String key, java.awt.Color color)
void	setAbbreviateScientificTaxonNames(boolean abbreviate_scientific_names)
void	setBackgroundColorGradient(boolean background_color_gradient)
void	setBaseFontFamilyName(java.lang.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(NodeVisualization.NodeFill default_node_fill)
void	setDefaultNodeShape(NodeVisualization.NodeShape default_node_shape)
void	setDefaultNodeShapeSize(short default_node_shape_size)
void	setDisplayAsPhylogram(boolean b)
void	setDisplayColors(java.util.SortedMap<java.lang.String,java.awt.Color> display_colors)
void	setDisplayConfidenceValues(boolean b)
void	setDisplayInternalData(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	setExtractPfamTaxonomyCodesInNhParsing(boolean nh_parsing_extract_pfam_taxonomy_codes)
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	setPathToClustalOmega(java.io.File clustalo)
void	setPathToFastME(java.io.File fastme)
void	setPathToMafft(java.io.File mafft)
void	setPhylogenyGraphicsType(Options.PHYLOGENY_GRAPHICS_TYPE phylogeny_graphics_type)
void	setPrintLineWidth(float print_line_width)
void	setReplaceUnderscoresInNhParsing(boolean nh_parsing_replace_underscores)
void	setShowBranchLengthValues(boolean show_branch_length_values)
void	setShowDefaultNodeShapes(boolean show_default_node_shapes)
void	setShowDomainLabels(boolean show_domain_labels)
void	setShowScale(boolean show_scale)
void	setTaxonomyColorize(boolean b)
void	setTaxonomyColorizeNodeShapes(boolean taxonomy_colorize_node_shapes)
void	setUseBranchesWidths(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(java.lang.String cf,
                     boolean is_url,
                     boolean is_applet,
                     boolean verbose)

Method Detail

getBaseFontFamilyName

public java.lang.String getBaseFontFamilyName()

getDefaultBootstrapSamples

public int getDefaultBootstrapSamples()

getDefaultNodeFill

public NodeVisualization.NodeFill getDefaultNodeFill()

getDefaultNodeShape

public NodeVisualization.NodeShape getDefaultNodeShape()

getDefaultNodeShapeSize

public short getDefaultNodeShapeSize()

getDomainStructureBaseColor

public java.awt.Color getDomainStructureBaseColor()

getDomainStructureFontColor

public java.awt.Color getDomainStructureFontColor()

isAbbreviateScientificTaxonNames

public boolean isAbbreviateScientificTaxonNames()

isBackgroundColorGradient

public boolean isBackgroundColorGradient()

isColorLabelsSameAsParentBranch

public boolean isColorLabelsSameAsParentBranch()

isShowDefaultNodeShapes

public boolean isShowDefaultNodeShapes()

isShowDomainLabels

public boolean isShowDomainLabels()

isTaxonomyColorizeNodeShapes

public boolean isTaxonomyColorizeNodeShapes()

putDisplayColors

public void putDisplayColors(java.lang.String key,
                             java.awt.Color color)

setAbbreviateScientificTaxonNames

public void setAbbreviateScientificTaxonNames(boolean abbreviate_scientific_names)

setBackgroundColorGradient

public void setBackgroundColorGradient(boolean background_color_gradient)

setBaseFontFamilyName

public void setBaseFontFamilyName(java.lang.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(NodeVisualization.NodeFill default_node_fill)

setDefaultNodeShape

public void setDefaultNodeShape(NodeVisualization.NodeShape default_node_shape)

setDefaultNodeShapeSize

public void setDefaultNodeShapeSize(short default_node_shape_size)

setDisplayAsPhylogram

public void setDisplayAsPhylogram(boolean b)

setDisplayColors

public void setDisplayColors(java.util.SortedMap<java.lang.String,java.awt.Color> display_colors)

setDisplayConfidenceValues

public void setDisplayConfidenceValues(boolean b)

setDisplayInternalData

public void setDisplayInternalData(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)

setExtractPfamTaxonomyCodesInNhParsing

public void setExtractPfamTaxonomyCodesInNhParsing(boolean nh_parsing_extract_pfam_taxonomy_codes)

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)

setShowBranchLengthValues

public void setShowBranchLengthValues(boolean show_branch_length_values)

setShowDefaultNodeShapes

public void setShowDefaultNodeShapes(boolean show_default_node_shapes)

setShowDomainLabels

public void setShowDomainLabels(boolean show_domain_labels)

setShowScale

public void setShowScale(boolean show_scale)

setTaxonomyColorize

public void setTaxonomyColorize(boolean b)

setTaxonomyColorizeNodeShapes

public void setTaxonomyColorizeNodeShapes(boolean taxonomy_colorize_node_shapes)

setUseBranchesWidths

public void setUseBranchesWidths(boolean b)

getPathToMafft

public java.io.File getPathToMafft()

getPathToClustalOmega

public java.io.File getPathToClustalOmega()

getPathToFastME

public java.io.File getPathToFastME()

setPathToMafft

public void setPathToMafft(java.io.File mafft)

setPathToClustalOmega

public void setPathToClustalOmega(java.io.File clustalo)

setPathToFastME

public void setPathToFastME(java.io.File fastme)