Class Configuration


  • public final class Configuration
    extends java.lang.Object
    • 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()
      • getDefaultNodeShapeSize

        public short getDefaultNodeShapeSize()
      • getExtDescNodeDataToReturn

        public NodeDataField getExtDescNodeDataToReturn()
      • getFrameXSize

        public int getFrameXSize()
      • getFrameYSize

        public int getFrameYSize()
      • getLabelForGetExtDescendentsData

        public java.lang.String getLabelForGetExtDescendentsData()
      • getPathToLocalFastme

        public java.io.File getPathToLocalFastme()
      • getPathToLocalMafft

        public java.io.File getPathToLocalMafft()
      • getPathToLocalRaxml

        public java.io.File getPathToLocalRaxml()
      • getVectorDataHeight

        public double getVectorDataHeight()
      • getVectorDataMaxColor

        public java.awt.Color getVectorDataMaxColor()
      • getVectorDataMeanColor

        public java.awt.Color getVectorDataMeanColor()
      • getVectorDataMinColor

        public java.awt.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​(java.lang.String key,
                                     java.awt.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​(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)
      • 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)
      • 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)
      • 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)
      • 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)