public final class Configuration
extends java.lang.Object
Modifier and Type | Class and Description |
---|---|
static class |
Configuration.EXT_NODE_DATA_RETURN_ON |
static class |
Configuration.UI |
Constructor and Description |
---|
Configuration() |
Configuration(java.lang.String cf,
boolean is_url,
boolean is_applet,
boolean verbose) |
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 NodeVisualData.NodeFill getDefaultNodeFill()
public NodeVisualData.NodeShape getDefaultNodeShape()
public short getDefaultNodeShapeSize()
public NodeDataField getExtDescNodeDataToReturn()
public Configuration.EXT_NODE_DATA_RETURN_ON getExtNodeDataReturnOn()
public int getFrameXSize()
public int getFrameYSize()
public java.lang.String getLabelForGetExtDescendentsData()
public java.io.File getPathToLocalFastme()
public java.io.File getPathToLocalMafft()
public java.io.File getPathToLocalRaxml()
public double getVectorDataHeight()
public java.awt.Color getVectorDataMaxColor()
public java.awt.Color getVectorDataMeanColor()
public java.awt.Color getVectorDataMinColor()
public int getVectorDataWidth()
public boolean isAbbreviateScientificTaxonNames()
public boolean isAllowThickStrokes()
public boolean isBackgroundColorGradient()
public boolean isColorByTaxonomicGroup()
public boolean isColorLabelsSameAsParentBranch()
public final boolean isLineUpRendarableNodeData()
public boolean isMidpointReroot()
public final boolean isRightLineUpDomains()
public boolean isShowAnnotationRefSource()
public boolean isShowDefaultNodeShapesExternal()
public boolean isShowDefaultNodeShapesForMarkedNodes()
public boolean isShowDefaultNodeShapesInternal()
public boolean isShowDomainLabels()
public void putDisplayColors(java.lang.String key, java.awt.Color color)
public void setAbbreviateScientificTaxonNames(boolean abbreviate_scientific_names)
public void setAddTaxonomyImagesCB(boolean b)
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(NodeVisualData.NodeFill default_node_fill)
public void setDefaultNodeShape(NodeVisualData.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 setDisplayGeneNames(boolean b)
public void setDisplayInternalData(boolean b)
public void setDisplayMultipleSequenceAlignment(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 setExtDescNodeDataToReturn(NodeDataField ext_desc_data_to_return)
public void setFrameXSize(int frame_x_size)
public void setFrameYSize(int frame_y_size)
public final void setLineUpRendarableNodeData(boolean line_up_renderable_node_data)
public void setMidpointReroot(boolean midpoint_root)
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 final void setRightLineUpDomains(boolean right_align_domains)
public void setShowDefaultNodeShapesExternal(boolean show_default_node_shapes_external)
public void setShowDefaultNodeShapesForMarkedNodes(boolean show_default_node_shapes_for_marked_nodes)
public void setShowDefaultNodeShapesInternal(boolean show_default_node_shapes_internal)
public void setShowDomainLabels(boolean show_domain_labels)
public void setShowScale(boolean show_scale)
public void setUseStyle(boolean b)