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