eg

Class Graphing

java.lang.Object

eg.Graphing

public class Graphing
extends java.lang.Object

Using various MML Models of Graphs, analyse a given Graph defined in a file. Also see [the book] and the [home page].

Field Summary

Fields

Modifier and Type	Field and Description
static Graph	C3 Some possible motifs (subgraphs).
static Graph	C4 Some possible motifs (subgraphs).
static Graph	CD4 Some possible motifs (subgraphs).
static Graph	CD5 Some possible motifs (subgraphs).
static Graph	CD6 Some possible motifs (subgraphs).
static Type.Tuple	Chars2 'CHARS × CHARS' Type, i.e., a pair of CHARS (Strings).
static Graph	FFL Some possible motifs (subgraphs).
static Graph	FFL4 Some possible motifs (subgraphs).
static Type	Gtype The Type is Directed.unlabelled in this case.
static Graph	K22 Some possible motifs (subgraphs).
static Graph	K23 Some possible motifs (subgraphs).
static Graph	K33 Some possible motifs (subgraphs).
static Graph	K5 Some possible motifs (subgraphs).
static Graph	KD23 Some possible motifs (subgraphs).
static Graph	KD33 Some possible motifs (subgraphs).
static Graph	M5 Some possible motifs (subgraphs).
static Discretes	Poisson1 Poisson1 = Poisson0.shifted(1).
static Graph	STAR3 Some possible motifs (subgraphs).
static Graph	STAR4 Some possible motifs (subgraphs).
static Graph	STAR5 Some possible motifs (subgraphs).
static Graph	STAR6 Some possible motifs (subgraphs).
static Graph	W5 Some possible motifs (subgraphs).

Constructor Summary

Constructors

Constructor and Description
Graphing()

Method Summary

Modifier and Type	Method and Description
static Vector	getData(java.lang.String filename) Get the raw String data (two columns: v0 v1) defining a Graph from the named file using Vector.csv(boolean, boolean, char, la.la.Type.Tuple, int, java.io.InputStream).
static Graph	getGraph(java.lang.String filename) Get the graph from 'filename'.
static void	greedy(Graphs.Motifs[] UMMs, Graph[] motifs, Value.Cts V_cts, Graph G) For each of several UnParameterised Motifs Models of Graphs UMMs[0], UMMs[1], ..., and one Graph 'G' do greedy(,,,[G]).
static void	greedy(Graphs.Motifs[] UMMs, Graph[] motifs, Value.Cts V_cts, Graph[] Gs) For each of several UnParameterised Motifs Models of Graphs UMMs[0], UMMs[1], ..., and data-set of Graphs 'Gs' do greedy(,,,Gs).
static void	greedy(Graphs.Motifs UMM, Graph[] motifs, Value.Cts V_cts, Graph G) For UnParameterised Motifs Model of Graphs 'UMM' and one Graph 'G' do greedy(,,,[G]).
static void	greedy(Graphs.Motifs UMM, Graph[] motifs, Value.Cts V_cts, Graph[] Gs) For UnParameterised Motifs Model of Graphs 'UMM', perform a greedy(,,) search to select zero or more of several given candidate 'motifs' (subGraphs) to form a fully-parameterised Model.
static void	main(java.lang.String[] argv) Analyse the Graph defined in the nominated file.
static void	tests(int V) Perform some elementary tests of Graph Models on random Graphs of 'V' vertices.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

Chars2

public static Type.Tuple Chars2

'CHARS × CHARS' Type, i.e., a pair of CHARS (Strings).

Gtype

public static Type Gtype

The Type is Directed.unlabelled in this case.

Poisson1

public static Discretes Poisson1

Poisson1 = Poisson0.shifted(1).

K5

public static final Graph K5

Some possible motifs (subgraphs). 'C' cyclic, 'K'_|V| complete, 'K_mn' complete bipartite, 'D' bidirectional, FFL feed-forward loop, STAR_|V| ~hub, M-shaped and W-shaped.

K22

public static final Graph K22

Some possible motifs (subgraphs). 'C' cyclic, 'K'_|V| complete, 'K_mn' complete bipartite, 'D' bidirectional, FFL feed-forward loop, STAR_|V| ~hub, M-shaped and W-shaped.

K23

public static final Graph K23

Some possible motifs (subgraphs). 'C' cyclic, 'K'_|V| complete, 'K_mn' complete bipartite, 'D' bidirectional, FFL feed-forward loop, STAR_|V| ~hub, M-shaped and W-shaped.

K33

public static final Graph K33

Some possible motifs (subgraphs). 'C' cyclic, 'K'_|V| complete, 'K_mn' complete bipartite, 'D' bidirectional, FFL feed-forward loop, STAR_|V| ~hub, M-shaped and W-shaped.

KD23

public static final Graph KD23

Some possible motifs (subgraphs). 'C' cyclic, 'K'_|V| complete, 'K_mn' complete bipartite, 'D' bidirectional, FFL feed-forward loop, STAR_|V| ~hub, M-shaped and W-shaped.

KD33

public static final Graph KD33

Some possible motifs (subgraphs). 'C' cyclic, 'K'_|V| complete, 'K_mn' complete bipartite, 'D' bidirectional, FFL feed-forward loop, STAR_|V| ~hub, M-shaped and W-shaped.

C3

public static final Graph C3

Some possible motifs (subgraphs). 'C' cyclic, 'K'_|V| complete, 'K_mn' complete bipartite, 'D' bidirectional, FFL feed-forward loop, STAR_|V| ~hub, M-shaped and W-shaped.

C4

public static final Graph C4

Some possible motifs (subgraphs). 'C' cyclic, 'K'_|V| complete, 'K_mn' complete bipartite, 'D' bidirectional, FFL feed-forward loop, STAR_|V| ~hub, M-shaped and W-shaped.

CD4

public static final Graph CD4

Some possible motifs (subgraphs). 'C' cyclic, 'K'_|V| complete, 'K_mn' complete bipartite, 'D' bidirectional, FFL feed-forward loop, STAR_|V| ~hub, M-shaped and W-shaped.

CD5

public static final Graph CD5

Some possible motifs (subgraphs). 'C' cyclic, 'K'_|V| complete, 'K_mn' complete bipartite, 'D' bidirectional, FFL feed-forward loop, STAR_|V| ~hub, M-shaped and W-shaped.

CD6

public static final Graph CD6

Some possible motifs (subgraphs). 'C' cyclic, 'K'_|V| complete, 'K_mn' complete bipartite, 'D' bidirectional, FFL feed-forward loop, STAR_|V| ~hub, M-shaped and W-shaped.

STAR3

public static final Graph STAR3

Some possible motifs (subgraphs). 'C' cyclic, 'K'_|V| complete, 'K_mn' complete bipartite, 'D' bidirectional, FFL feed-forward loop, STAR_|V| ~hub, M-shaped and W-shaped.

STAR4

public static final Graph STAR4

Some possible motifs (subgraphs). 'C' cyclic, 'K'_|V| complete, 'K_mn' complete bipartite, 'D' bidirectional, FFL feed-forward loop, STAR_|V| ~hub, M-shaped and W-shaped.

STAR5

public static final Graph STAR5

Some possible motifs (subgraphs). 'C' cyclic, 'K'_|V| complete, 'K_mn' complete bipartite, 'D' bidirectional, FFL feed-forward loop, STAR_|V| ~hub, M-shaped and W-shaped.

STAR6

public static final Graph STAR6

Some possible motifs (subgraphs). 'C' cyclic, 'K'_|V| complete, 'K_mn' complete bipartite, 'D' bidirectional, FFL feed-forward loop, STAR_|V| ~hub, M-shaped and W-shaped.

W5

public static final Graph W5

Some possible motifs (subgraphs). 'C' cyclic, 'K'_|V| complete, 'K_mn' complete bipartite, 'D' bidirectional, FFL feed-forward loop, STAR_|V| ~hub, M-shaped and W-shaped.

M5

public static final Graph M5

Some possible motifs (subgraphs). 'C' cyclic, 'K'_|V| complete, 'K_mn' complete bipartite, 'D' bidirectional, FFL feed-forward loop, STAR_|V| ~hub, M-shaped and W-shaped.

FFL

public static final Graph FFL

Some possible motifs (subgraphs). 'C' cyclic, 'K'_|V| complete, 'K_mn' complete bipartite, 'D' bidirectional, FFL feed-forward loop, STAR_|V| ~hub, M-shaped and W-shaped.

FFL4

public static final Graph FFL4

Some possible motifs (subgraphs). 'C' cyclic, 'K'_|V| complete, 'K_mn' complete bipartite, 'D' bidirectional, FFL feed-forward loop, STAR_|V| ~hub, M-shaped and W-shaped.

Constructor Detail

Graphing

public Graphing()

Method Detail

tests

public static void tests(int V)

Perform some elementary tests of Graph Models on random Graphs of 'V' vertices.

getData

public static Vector getData(java.lang.String filename)

Get the raw String data (two columns: v₀ v₁) defining a Graph from the named file using Vector.csv(boolean, boolean, char, la.la.Type.Tuple, int, java.io.InputStream). Used in getGraph(fn).

getGraph

public static Graph getGraph(java.lang.String filename)

Get the graph from 'filename'. Uses getData(...).

greedy

public static void greedy(Graphs.Motifs UMM,
                          Graph[] motifs,
                          Value.Cts V_cts,
                          Graph[] Gs)

For UnParameterised Motifs Model of Graphs 'UMM', perform a greedy(,,) search to select zero or more of several given candidate 'motifs' (subGraphs) to form a fully-parameterised Model. 'Gs' is the data-set of Graphs being modelled.

greedy

public static void greedy(Graphs.Motifs[] UMMs,
                          Graph[] motifs,
                          Value.Cts V_cts,
                          Graph[] Gs)

For each of several UnParameterised Motifs Models of Graphs UMMs[0], UMMs[1], ..., and data-set of Graphs 'Gs' do greedy(,,,Gs).

greedy

public static void greedy(Graphs.Motifs[] UMMs,
                          Graph[] motifs,
                          Value.Cts V_cts,
                          Graph G)

For each of several UnParameterised Motifs Models of Graphs UMMs[0], UMMs[1], ..., and one Graph 'G' do greedy(,,,[G]).

greedy

public static void greedy(Graphs.Motifs UMM,
                          Graph[] motifs,
                          Value.Cts V_cts,
                          Graph G)

For UnParameterised Motifs Model of Graphs 'UMM' and one Graph 'G' do greedy(,,,[G]).

main

public static void main(java.lang.String[] argv)

Analyse the Graph defined in the nominated file. 'Graphing [-r] [filename]' '-r': randomise the Graph.