Split Strands Graph#

Graph#

class SplitStrandsGraph#

Graph containing only one DNA strand.

For this graph \(G = (V, E)\) we have:

\(\forall v \in V, \bar{v} \notin V\)
\(\forall e \in E, \bar{e} \notin E\)

Methods:

`attr`(attrname)	Return the value associated to attribute attrname.
`attrs`()	Return the dictionnary of all attributes.
`edges`()	Return the edge container.
`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:: SplitStrandsEdges

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:: SplitStrandsVertices

Vertices Container#

class SplitStrandsVertices#

Unique oriented vertices container.

This vertices container is containing only one orientation for each of its vertex i.e. \(\forall v \in V, \bar{v} \notin V\)

Warning

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

Methods:

`__contains__`(vertex)	Answer if vertex is in vertices container.
`__iter__`()	Iterate on oriented vertices.
`__len__`()	Return the number of oriented vertices.
`add`(orientation)	Add the vertex to the connected component record.
`attr`(vertex_index, attrname)	Return the value associated to vertex attribute attrname.
`attrs`(vertex_index)	Iterate over all vertex's attributes.
`contains_indor`(vertex)	Answer if oriented vertex in vertices container.
`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.
`orientation`(vertex_index)	Return the orientation of vertex's index.
`set_attr`(vertex_index, attrname, attrvalue)	Change the value of the attributes else create them.

__contains__(vertex)#

Answer if vertex is in vertices container.

Returns:: Vertex is in vertices container
Return type:: bool

__iter__()#

Iterate on oriented vertices.

Yields:: IndexT – Vertices

__len__()#

Return the number of oriented vertices.

Returns:: Number of orient
Return type:: int

add(orientation)#

Add the vertex to the connected component record.

Parameters:: orientation (OrT) – New orientation to add to vertices container
Returns:: Last vertex’s index
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

contains_indor(vertex)#

Answer if oriented vertex in vertices container.

Parameters:: vertex (IndOrT) – Oriented vertex
Returns:: Oriented vertex in vertices container
Return type:: bool

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 concerning edge 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 concerning edge 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.

orientation(vertex_index)#

Return the orientation of vertex’s index.

Parameters:: vertex_index (IndexT) – Vertex’s index
Returns:: Vertex’s index orientation
Return type:: OrT
Raises:: NoVertexIndex – If there is no vertex index

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 SplitStrandsEdges#

Unique oriented edges container.

This edges container is containing only one orientation for each of its edge i.e. \(\forall e \in E, \bar{e} \notin E\)

Warning

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

Methods:

`__contains__`(edge)	Return True if the indices edge is in edges container.
`__iter__`()	Iterate over indices edges with edge index.
`__len__`()	Return the number of edges.
`add`(first_vertex, second_vertex)	Add edge to edges.
`attr`(edge_index, attrname)	Return the edge attribute attrname.
`attrs`(edge_index)	Iterate over all edge's attributes.
`delete`(first_vertex, second_vertex, edge_index)	Remove the edge.
`eindor_to_eind`(first_vertex, second_vertex)	Iterate over edge index from indices edge.
`neighbours`(vertex)	Iterate over 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 indices edge is in edges container.

Parameters:: edge (EIndT) – Indices edge
Returns:: Indices edge in edges container
Return type:: bool

__iter__()#

Iterate over indices edges with edge index.

Yields:: EIndIndT – Indices edges with their edge index

__len__()#

Return the number of edges.

Returns:: Number of edges
Return type:: int

Notes

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

add(first_vertex, second_vertex)#

Add edge to edges.

Parameters:

first_vertex (IndexT) – First vertex
second_vertex (IndexT) – Second vertex

Returns:

Edge index

Return type:

IndexT

Raises:

NoVertexIndex – If one vertex does not exist

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.

delete(first_vertex, second_vertex, edge_index)#

Remove the edge.

Parameters:

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

Raises:

NoVertexIndex – If vertex does not exist
NoIndicesEdge – 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.

eindor_to_eind(first_vertex, second_vertex)#

Iterate over edge index from indices edge.

Parameters:

first_vertex (IndexT) – First vertex
second_vertex (IndexT) – Second vertex

Yields:

IndexT – Edge index

Raises:

NoVertexIndex – One of the vertex in edge does not exist

neighbours(vertex)#

Iterate over vertex’s adjacencies vertices.

Parameters:: vertex (IndexT) – Vertex’s index
Yields:: IndIndT – Adjacent vertices’s index 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 (IndexT) – Vertex’s index
Yields:: IndIndT – Predecessor vertex’s index 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 (IndexT) – Vertex’s index
Yields:: IndIndT – Successors vertex’s index with edge index
Raises:: NoVertexIndex – If vertex does not exist