seqan.io package

Submodules

seqan.io.graphtool module

Create a graphtool graph of a suffix tree.

class seqan.io.graphtool.Builder(index, predicate=None)

Bases: object

Build a graphtool graph.

get_vertex(index_it)

map_vertices(function, property_map=None, proptype='string')

Fills in the property map with the values returned from function(iterator).

visitvertex(it)

Descend the index adding edges.

seqan.io.graphtool.color_edges_by_first_symbol(builder, color_map=None, defaultcolor='black')

seqan.io.graphtool.dash_non_suffix_edges(builder, suffix)

seqan.io.graphtool.edge_labels_for_output(builder, maxlabellen=3)

seqan.io.graphtool.edges_in_suffix(builder, suffix)

Iterate over the edges in the graph and yield (edge, insuffix).

seqan.io.graphtool.root_vertex_property(builder, proptype='float', rootvalue=2.0)

Create a property of type proptype which is only set on the root node of the suffix tree.

seqan.io.pgf module

Write a suffix tree as PGF.

We’re looking for something like:

\tikz [
    font=\footnotesize,
    grow=right, level 1/.style={sibling distance=6em},
    level 2/.style={sibling distance=1em}, level distance=5cm
]
\node {Computational Complexity} % root
child { node {Computational Problems} }
child { node {Problem Measures} }
child { node {Problem Aspects} }

seqan.io.pgf.write_pgf(tikz, index, highlightsuffix=None, maxdepth=None, only_highlight=False)

Test writing a PGF representing a suffix tree.

Module contents

I/O for seqan.