A toolkit for working with phylogenetic data.
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PhyloxmlColorWriterPlugin Class Reference

#include <genesis/tree/formats/phyloxml/color_writer_plugin.hpp>

Inherits ColorWriterPlugin.

Detailed Description

Plugin class for PhyloXML output that allows coloring of edges.

The effect of this class on the PhyloXML output is that (if enabled) a color tag will be added to each clade like this:

<clade>
    [other tags, like name or branch_length]
    <color>
        <red>0</red>
        <green>128</green>
        <blue>255</blue>
    </color>
</clade>

For more information, see ColorWriterPlugin class.

Definition at line 66 of file phyloxml/color_writer_plugin.hpp.

Public Member Functions

 PhyloxmlColorWriterPlugin ()=default
 
 PhyloxmlColorWriterPlugin (PhyloxmlColorWriterPlugin const &)=default
 
 PhyloxmlColorWriterPlugin (PhyloxmlColorWriterPlugin &&)=default
 
virtual ~PhyloxmlColorWriterPlugin ()=default
 
void edge_to_element (TreeEdge const &edge, utils::XmlElement &element) const
 
PhyloxmlColorWriterPluginoperator= (PhyloxmlColorWriterPlugin const &)=default
 
PhyloxmlColorWriterPluginoperator= (PhyloxmlColorWriterPlugin &&)=default
 
void prepare_writing (Tree const &tree, utils::XmlDocument &xml) const
 
void register_with (PhyloxmlWriter &writer) const
 
- Public Member Functions inherited from ColorWriterPlugin
virtual ~ColorWriterPlugin ()
 
void edge_colors (std::vector< utils::Color > const &color_vector)
 Set the edge colors that shall be written to the output. More...
 
std::vector< utils::Color > const & edge_colors () const
 Return the edge colors that are currently set. More...
 
void enable_color (bool value)
 Set whether colors tags are written to the output. More...
 
bool enable_color () const
 Returns whether colors tags are written to the output. More...
 
void ignored_color (utils::Color value)
 Set a color that is used as marker for partially disabling the output of color tags. More...
 
utils::Color ignored_color () const
 Return the currently set ignored color. See the setter for more information. More...
 
void use_ignored_color (bool value)
 Set whether to use the ignored_color(). More...
 
bool use_ignored_color () const
 Return whether currently an ignored color is used. More...
 

Constructor & Destructor Documentation

virtual ~PhyloxmlColorWriterPlugin ( )
virtualdefault

Member Function Documentation

void edge_to_element ( TreeEdge const &  edge,
utils::XmlElement element 
) const
inline

Definition at line 106 of file phyloxml/color_writer_plugin.hpp.

PhyloxmlColorWriterPlugin& operator= ( PhyloxmlColorWriterPlugin const &  )
default
void prepare_writing ( Tree const &  tree,
utils::XmlDocument xml 
) const
inline

Definition at line 87 of file phyloxml/color_writer_plugin.hpp.

void register_with ( PhyloxmlWriter writer) const
inline

Definition at line 119 of file phyloxml/color_writer_plugin.hpp.


The documentation for this class was generated from the following file: