Reverse Symmetric Graph#

Graph#

class RevSymGraph#

Reverse symmetric graph class.

This graph is considering each orientation for all vertices and for all edges. It can contain several weakly connected components, which can contain only one strand or both merged.

Methods:

`attr`(attrname)	Return the value associated to attribute attrname.
`attrs`()	Return the dictionnary of all attributes.
`edges`()	Return the edge container.
`is_attr`(attrname)	Return True if there is an attribute called attrname.
`set_attr`(attrname, attrvalue)	Change the value of the attributes else create them.
`vertices`()	Return the vertices container.

attr(attrname)#

Return the value associated to attribute attrname.

Parameters:: attrname (str) – Attribute’s name
Returns:: Attribute value corresponding to the attribute name
Return type:: Any
Raises:: NoGraphAttribute – When there is no attribute key

attrs()#

Return the dictionnary of all attributes.

Returns:: Dictionnary of attribute name as key and their value
Return type:: dict

edges()#

Return the edge container.

Returns:: Edges container
Return type:: Edges

is_attr(attrname)#

Return True if there is an attribute called attrname.

Parameters:: attrname (str) – Attribute’s name answered
Returns:: If there is an attribute called attrname
Return type:: bool

set_attr(attrname, attrvalue)#

Change the value of the attributes else create them.

Parameters:

attrname (str) – Attribute’s name
attrvalue (Any) – Attribute’s value

vertices()#

Return the vertices container.

Returns:: Vertices container
Return type:: Vertices

Vertices Container#

class Vertices#

Vertices container class for both vertices’ orientations.

For each raw read \(r \in \mathcal{R_{aw}}\) there is one vertex for each orientation \(v \in V\) and \(\bar{v} \in V\).

Warning

You must not instantiate a Vertices object. Use it only for typing or get an already instanciated object.

Methods:

`__contains__`(vertex_index)	Return True if vertex index is in container, else False.
`__iter__`()	Iterate on oriented vertices.
`__len__`()	Return the number of oriented vertices.
`add`([number])	Add vertices to vertices container.
`attr`(vertex_index, attrname)	Return the value associated to vertex attribute attrname.
`attrs`(vertex_index)	Iterate over all vertex's attributes.
`card_index`()	Returns the number of distinct indices.
`delete`(vertex_index)	Remove vertex from vertices container.
`delete_several`(vertex_indices)	Remove vertices from vertices container.
`new_attr`(attrname, default)	Add an attribute entry.
`set_attr`(vertex_index, attrname, attrvalue)	Change the value of the attributes else create them.

__contains__(vertex_index)#

Return True if vertex index is in container, else False.

Parameters:: vertex_index (IndexT) – Vertex index
Returns:: True if oriented vertex is in container, else False
Return type:: bool

__iter__()#

Iterate on oriented vertices.

Yields:: IndOrT – Oriented vertices

__len__()#

Return the number of oriented vertices.

Returns:: Number of oriented vertices
Return type:: int

add(number=1)#

Add vertices to vertices container.

Parameters:: number (int, default 1) – Number of vertices to add
Returns:: Last vertex’s index (non-oriented)
Return type:: IndexT

attr(vertex_index, attrname)#

Return the value associated to vertex attribute attrname.

Parameters:

vertex_index (IndexT) – Vertex’s index
attrname (str) – Attribute name

Returns:

Attribute value corresponding to the attribute name

Return type:

Any

Raises:

NoVertexIndex – If vertex does not exist
NoVerticesAttribute – If there is no attribute nammed like this for vertices

attrs(vertex_index)#

Iterate over all vertex’s attributes.

Parameters:

vertex_index (IndexT) – Vertex’s index

Yields:

str – Attribute’s name
Any – Attribute’s value

Raises:

NoVertexIndex – If there is no vertex index

card_index()#

Returns the number of distinct indices.

Note

The cardinality of indices set \(V_{ind}\) is equal to \(|V_{ind}|\)

Returns:: Number of distinct indices
Return type:: int

delete(vertex_index)#

Remove vertex from vertices container.

Parameters:: vertex_index (IndexT) – Vertex to delete
Raises:: NoVertexIndex – If vertex does not exist

Warning

This operation may invalidate vertex indices. In fact, deleting one vertex implies shifting all next indices. Because of this, keys should always be removed in decreasing index order:

>>> for vertex in sorted(vertices_to_del, reverse=True):
>>>     graph.vertices().delete(vertex)

Note

All next vertex indices are decreased in edges they belong. But concerned edges’ indices are not.

delete_several(vertex_indices)#

Remove vertices from vertices container.

Parameters:: vertex_indices (iterable of IndexT) – Vertices to delete
Raises:: NoVertexIndex – If one vertex does not exist

Warning

This operation may invalidate vertex indices. In fact, deleting one vertex implies shifting all next indices.

Notes

At the oposite of delete() method, it is not necessary to sort vertex_indices. This is done internally.

All next vertex indices are decreased in edges they belong. But concerned edges’ indices are not.

new_attr(attrname, default)#

Add an attribute entry.

Parameters:

attrname (str) – Attribute’s name
default (Any) – Default attribute value

Note

Before setting attribute to one vertex, it is necessary to add an attribute entry using this method.

set_attr(vertex_index, attrname, attrvalue)#

Change the value of the attributes else create them.

Parameters:

vertex_index (IndexT) – Vertex’s index
attrname (str) – Attribute’s name
attrvalue (Any) – Attribute’s value

Raises:

NoVerticesAttribute – If there is no attribute nammed like this for vertices
WrongAttributeType – Given value does not correspond to attribute’s type
NoVertexIndex – If there is no vertex index

Note

Be sure having added an attribute entry using the method new_attr()

Edges Container#

class Edges#

Edges container class for both edges’ orientations.

For each overlap \(o \in \mathcal{O}\), there are two edges \(e \in E\) and \(\bar{e} \in E\) i.e. one for both orientations.

Warning

You must not call this class. Use it only for typing or get an already existing object.

Methods:

`__contains__`(edge)	Return True if the oriented edge is in edges container.
`__iter__`()	Iterate on oriented edges with edge index.
`__len__`()	Return the number of oriented edges.
`add`(first_vertex, second_vertex)	Add an edge to edges container.
`attr`(edge_index, attrname)	Return the edge attribute attrname.
`attrs`(edge_index)	Iterate over all edge's attributes.
`biggest_edge_index`()	Return the biggest edge index.
`delete`(first_vertex, second_vertex, edge_index)	Remove the edge.
`eindor_to_eind`(first_vertex, second_vertex)	Iterate over edge indices from oriented edge.
`neighbours`(vertex)	Return the generator of vertex's adjacencies vertices.
`new_attr`(attrname, default)	Add an attribute entry.
`preds`(vertex)	Iterate over vertex's predecessors.
`set_attr`(edge_index, attrname, attrvalue)	Change the value of one attribute.
`succs`(vertex)	Iterate over vertex's successors.

__contains__(edge)#

Return True if the oriented edge is in edges container.

Parameters:: edge (EIndOrT) – Oriented edge
Returns:: Oriented edges in edges container
Return type:: bool

__iter__()#

Iterate on oriented edges with edge index.

Yields:: EIndOrIndT – Oriented edges with their edge index

__len__()#

Return the number of oriented edges.

Returns:: Number of oriented edges
Return type:: int

Notes

\(\forall e \in E, \bar{e} \in E\)

add(first_vertex, second_vertex)#

Add an edge to edges container.

Parameters:

first_vertex (IndOrT) – First oriented vertex
second_vertex (IndOrT) – Second oriented vertex

Returns:

Edge index

Return type:

IndexT

Raises:

NoVertexIndex – If one vertex does not exist

Notes

Edges container contains the two orientations of each edge i.e. \(\forall e \in E, \bar{e} \in E\)

attr(edge_index, attrname)#

Return the edge attribute attrname.

Parameters:

edge_index (IndexT) – Edge’s index
attrname (str) – Attribute name

Returns:

Attribute value

Return type:

Any

Raises:

NoEdgeIndex – If edge does not exist
NoEdgesAttribute – If there is no attribute name like this for edges

Note

A removed edge still have a recorded attribute.

attrs(edge_index)#

Iterate over all edge’s attributes.

Parameters:

edge_index (IndexT) – Edge’s index

Yields:

str – Attribute’s name
Any – Attribute’s value

Raises:

NoEdgeIndex – If there is no edge index

Note

A removed edge still have a recorded attribute.

biggest_edge_index()#

Return the biggest edge index.

Returns:: The biggest edge index
Return type:: int

Notes

The number of distinct edges indices is equal to the biggest edge index plus one.

delete(first_vertex, second_vertex, edge_index)#

Remove the edge.

Parameters:

first_vertex (IndOrT) – First oriented vertex
second_vertex (IndOrT) – Second oriented vertex
edge_index (IndexT) – Edge’s index

Raises:

NoVertexIndex – If vertex does not exist
NoEdge – If there is no recorded edge with these vertices and this index

Note

When deleting, the edge is replacing by the last one in adjancy list, and the last element of the adjancy list is removed.

Warning

As :class::revsymg.graphs.Edges has the reverse symmetry property, removing one orientation of an edge has the consequence of removing the other orientation i.e. \(\forall e \in E, \bar{e} \notin E \setminus \{e\}\)

eindor_to_eind(first_vertex, second_vertex)#

Iterate over edge indices from oriented edge.

Parameters:

first_vertex (IndOrT) – First oriented vertex
second_vertex (IndOrT) – Second oriented vertex

Yields:

IndexT – Edge index

Raises:

NoVertexIndex – One of the vertex in edge does not exist

neighbours(vertex)#

Return the generator of vertex’s adjacencies vertices.

Parameters:: vertex (IndOrT) – Oriented vertex
Yields:: IndOrIndT – Oriented neighbouring vertices with edge index
Raises:: NoVertexIndex – If vertex does not exist

new_attr(attrname, default)#

Add an attribute entry.

Parameters:

attrname (str) – Attribute’s name
default (Any) – Default attribute value

Note

Before setting attribute to one edge, it is necessary to add an attribute entry using this method.

preds(vertex)#

Iterate over vertex’s predecessors.

Parameters:: vertex (IndOrT) – Oriented vertex
Yields:: IndOrIndT – Predecessor oriented vertex with edge index
Raises:: NoVertexIndex – If vertex does not exist

set_attr(edge_index, attrname, attrvalue)#

Change the value of one attribute.

Parameters:

edge_index (IndexT) – Edge’s index
attrname (str) – Attribute’s name
attrvalue (Any) – Attribute’s value

Raises:

NoEdgesAttribute – If there is no attribute nammed like this for edges
WrongAttributeType – Given value does not correspond to attribute’s type
NoEdgeIndex – If there is no vertex index

Note

Be sure having added an attribute entry using the method new_attr()

succs(vertex)#

Iterate over vertex’s successors.

Parameters:: vertex (IndOrT) – Oriented vertex
Yields:: IndOrIndT – Successor oriented vertex with edge index
Raises:: NoVertexIndex – If vertex does not exist