public final class Configuration
extends java.lang.Object
Modifier and Type | Class and Description |
---|---|
static class |
Configuration.UI |
Constructor and Description |
---|
Configuration() |
Configuration(java.lang.String cf,
boolean is_url,
boolean is_applet,
boolean verbose) |
Modifier and Type | Method and Description |
---|---|
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) |
public Configuration()
public Configuration(java.lang.String cf, boolean is_url, boolean is_applet, boolean verbose)
public java.lang.String getBaseFontFamilyName()
public int getDefaultBootstrapSamples()
public NodeVisualization.NodeFill getDefaultNodeFill()
public NodeVisualization.NodeShape getDefaultNodeShape()
public short getDefaultNodeShapeSize()
public java.awt.Color getDomainStructureBaseColor()
public java.awt.Color getDomainStructureFontColor()
public boolean isAbbreviateScientificTaxonNames()
public boolean isBackgroundColorGradient()
public boolean isColorLabelsSameAsParentBranch()
public boolean isShowDefaultNodeShapes()
public boolean isShowDomainLabels()
public boolean isTaxonomyColorizeNodeShapes()
public void putDisplayColors(java.lang.String key, java.awt.Color color)
public void setAbbreviateScientificTaxonNames(boolean abbreviate_scientific_names)
public void setBackgroundColorGradient(boolean background_color_gradient)
public void setBaseFontFamilyName(java.lang.String base_font_family_name)
public void setBaseFontSize(int base_font_size)
public void setColorizeBranches(boolean b)
public void setColorLabelsSameAsParentBranch(boolean color_labels_same_as_parent_branch)
public void setDefaultNodeFill(NodeVisualization.NodeFill default_node_fill)
public void setDefaultNodeShape(NodeVisualization.NodeShape default_node_shape)
public void setDefaultNodeShapeSize(short default_node_shape_size)
public void setDisplayAsPhylogram(boolean b)
public void setDisplayColors(java.util.SortedMap<java.lang.String,java.awt.Color> display_colors)
public void setDisplayConfidenceValues(boolean b)
public void setDisplayInternalData(boolean b)
public void setDisplayNodeNames(boolean b)
public void setDisplaySequenceAcc(boolean b)
public void setDisplaySequenceNames(boolean b)
public void setDisplaySequenceRelations(boolean display_sequence_relations)
public void setDisplaySequenceSymbols(boolean b)
public void setDisplayTaxonomyCode(boolean b)
public void setDisplayTaxonomyCommonNames(boolean b)
public void setDisplayTaxonomyImages(boolean b)
public void setDisplayTaxonomyScientificNames(boolean b)
public void setDynamicallyHideData(boolean b)
public void setExtractPfamTaxonomyCodesInNhParsing(boolean nh_parsing_extract_pfam_taxonomy_codes)
public void setMinConfidenceValue(double min_confidence_value)
public void setNodeLabelDirection(Options.NODE_LABEL_DIRECTION node_label_direction)
public void setNumberOfDigitsAfterCommaForBranchLengthValue(short _number_of_digits_after_comma_for_branch_length_values)
public void setNumberOfDigitsAfterCommaForConfidenceValues(short _number_of_digits_after_comma_for_confidence_values)
public void setPhylogenyGraphicsType(Options.PHYLOGENY_GRAPHICS_TYPE phylogeny_graphics_type)
public void setPrintLineWidth(float print_line_width)
public void setReplaceUnderscoresInNhParsing(boolean nh_parsing_replace_underscores)
public void setShowBranchLengthValues(boolean show_branch_length_values)
public void setShowDefaultNodeShapes(boolean show_default_node_shapes)
public void setShowDomainLabels(boolean show_domain_labels)
public void setShowScale(boolean show_scale)
public void setTaxonomyColorize(boolean b)
public void setTaxonomyColorizeNodeShapes(boolean taxonomy_colorize_node_shapes)
public void setUseBranchesWidths(boolean b)
public java.io.File getPathToMafft()
public java.io.File getPathToClustalOmega()
public java.io.File getPathToFastME()
public void setPathToMafft(java.io.File mafft)
public void setPathToClustalOmega(java.io.File clustalo)
public void setPathToFastME(java.io.File fastme)