Package org.forester.archaeopteryx

Class Configuration

java.lang.Object
org.forester.archaeopteryx.Configuration
public final class Configuration extends Object

  • Constructor Details

    • Configuration

      public Configuration()

    • Configuration

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

  • Method Details

    • 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)