Unit test for DENOPTIMGraph. More...

Collaboration diagram for denoptim.graph.DGraphTest:

Public Member Functions
void	testRemoveUnusedRCVs () throws Exception

void	testGetEmbeddingPath () throws Exception

void	testGetEmbeddedGraphInClone () throws Exception

void	testGetSourceVertex () throws Exception

void	testGetLevel () throws Exception

void	testReplaceVertex () throws Exception

void	testReplaceVertex_inRing () throws Exception

void	testReplaceSubGraph () throws Exception

void	testReplaceSubGraph_inTemplate () throws Exception

void	testRemoveVertex () throws Exception

void	testSameAs_Equal () throws DENOPTIMException

void	testSameAs_DiffVertex () throws DENOPTIMException

void	testSameAs_SameSymmSet () throws Exception

void	testSameAs_DiffSymmSet () throws Exception

void	testSameAs_SameRings () throws DENOPTIMException

void	testSameAs_DisorderRings () throws Exception

void	testSameAs_DiffRings () throws DENOPTIMException

void	testGetAvailableAPs_returnsListOfAvailableAPs () throws DENOPTIMException

void	testClone () throws DENOPTIMException

void	testGetMutationSites () throws DENOPTIMException

void	testRemoveCapping () throws Exception

void	testFromToJSON () throws Exception

void	testGraphIsomorphism () throws Exception

void	testExtractSubgraph () throws Exception

void	testExtractSubgraphFromCollection () throws Exception

void	testFindVertex () throws Exception

void	testSymmetricSetLabels () throws Exception

void	testConvertSymmetricLabelsToSymmetricSets () throws Exception

void	testGetSymmetricSubGraphs () throws Exception

void	testGetChildrenTree () throws Exception

void	testGetChildrenTreeWithBranchIdentifier () throws Exception

void	testGetInterfaceAPs () throws Exception

void	testGetSubgraphAPs () throws Exception

DGraph[]	makeIsostructuralGraphs () throws Exception

void	testIsIsostructuralTo () throws Exception

void	testGetEdgesWithSrcOrTrg () throws Exception

void	testEmbedPatternsInTemplates () throws Exception

void	testFindSymmetrySetsOfChildVertexes () throws Exception

void	testDetectSymVertexSets () throws Exception

Static Public Member Functions
static FragmentSpace	prepare () throws DENOPTIMException

static DGraph	makeDeeplyEmbeddedGraph () throws DENOPTIMException
	Returns a graph that contains a 10-layered recursive structure. More...

static DGraph	makeTestGraphA ()
	Build a graph meant to be used in unit tests. More...

static DGraph	makeTestGraphA2 ()
	Build a graph meant to be used in unit tests. More...

static DGraph	makeTestGraphM () throws DENOPTIMException
	Returns a graph with definition of symmetric vertexes and symmetric APs meant for testing purposes. More...

static DGraph	makeTestGraphN () throws DENOPTIMException
	Returns a graph with peculiar definition of symmetric vertexes and symmetric APs meant for testing purposes. More...

Private Member Functions
DGraph	makeTestGraphB (FragmentSpace fs) throws DENOPTIMException
	Creates a test graph that looks like this: More...

DGraph	makeTestGraphC (FragmentSpace fs) throws DENOPTIMException
	Creates a test graph that looks like this: More...

DGraph	makeTestGraphD (FragmentSpace fs) throws DENOPTIMException
	Creates a test graph that looks like this: More...

DGraph	makeTestGraphDSub1 (FragmentSpace fs) throws DENOPTIMException
	Creates a test graph that looks like this: More...

DGraph	makeTestGraphDSub2 (FragmentSpace fs) throws DENOPTIMException
	Creates a test graph that looks like this: More...

DGraph	makeTestGraphE (FragmentSpace fs) throws DENOPTIMException
	Creates a test graph that looks like this: More...

DGraph	makeTestGraphF (FragmentSpace fs) throws DENOPTIMException
	Creates a test graph that looks like this: More...

DGraph	makeTestGraphG (FragmentSpace fs) throws DENOPTIMException
	Creates a test graph that looks like this: More...

DGraph	makeTestGraphH (FragmentSpace fs) throws DENOPTIMException
	Creates a test graph that looks like this: More...

DGraph	makeTestGraphI (FragmentSpace fs) throws Exception
	Creates a test graph that looks like this: More...

DGraph	makeTestGraphJ (FragmentSpace fs) throws DENOPTIMException
	Creates a test graph that looks like this: More...

DGraph	makeTestGraphK (FragmentSpace fs) throws DENOPTIMException
	Creates a test graph that looks like this: More...

DGraph	makeTestGraphL (FragmentSpace fs) throws DENOPTIMException
	Creates a test graph that looks like this: More...

DGraph	makeDisorderedGraph (FragmentSpace fs) throws DENOPTIMException
	Makes a graph with disordered list of vertexes, i.e., the first vertex is not the source. More...

void	buildVertexAndConnectToGraph (EmptyVertex v, int apCount, DGraph graph) throws DENOPTIMException

Static Private Member Functions
static DGraph	makeTestGraph0 (FragmentSpace fs) throws Exception
	Build a graph meant to be used in unit tests. More...

static DGraph	makeTestGraph1 (FragmentSpace fs) throws Exception
	Build a graph meant to be used in unit tests. More...

Static Private Attributes
static APClass	APCA

static APClass	APCB

static APClass	APCC

static APClass	APCD

static APClass	CAPP

static String	a ="A"

static String	b ="B"

static String	c ="C"

static String	d ="D"

static String	cap ="cap"

Detailed Description

Unit test for DENOPTIMGraph.

Author: Marco Foscato

Definition at line 71 of file DGraphTest.java.

Member Function Documentation

◆ buildVertexAndConnectToGraph()

void denoptim.graph.DGraphTest.buildVertexAndConnectToGraph	(	EmptyVertex	v,
		int	apCount,
		DGraph	graph
	)		throws DENOPTIMException

private

Definition at line 2859 of file DGraphTest.java.

Here is the caller graph for this function:

◆ makeDeeplyEmbeddedGraph()

static DGraph denoptim.graph.DGraphTest.makeDeeplyEmbeddedGraph ( ) throws DENOPTIMException

static

Returns a graph that contains a 10-layered recursive structure.

Before running this you must run DGraphTest#prepare()

Definition at line 1281 of file DGraphTest.java.

References denoptim.graph.EmptyVertex.addAP(), denoptim.graph.DGraph.addVertex(), denoptim.graph.DGraphTest.APCA, denoptim.graph.DGraphTest.APCB, denoptim.graph.DGraphTest.APCC, denoptim.graph.DGraphTest.APCD, denoptim.graph.DGraph.appendVertexOnAP(), denoptim.graph.Vertex.getAP(), denoptim.graph.Template.setInnerGraph(), and denoptim.graph.Vertex.BBType.UNDEFINED.

Referenced by denoptim.graph.DGraphTest.testGetEmbeddedGraphInClone(), denoptim.graph.DGraphTest.testGetEmbeddingPath(), and denoptim.ga.XoverSiteTest.testProjectToClonedGraphs().

Here is the call graph for this function:

Here is the caller graph for this function:

◆ makeDisorderedGraph()

DGraph denoptim.graph.DGraphTest.makeDisorderedGraph ( FragmentSpace fs ) throws DENOPTIMException

private

Makes a graph with disordered list of vertexes, i.e., the first vertex is not the source.


v5-0-->0-v3-1-->1-v4-0-->0-v1-1-->0-v2

Returns: a disordered graph

Exceptions

DENOPTIMException

Definition at line 1247 of file DGraphTest.java.

References denoptim.graph.DGraph.addEdge(), denoptim.graph.DGraph.addVertex(), denoptim.graph.Vertex.BBType.FRAGMENT, denoptim.graph.Vertex.getAP(), and denoptim.graph.Vertex.newVertexFromLibrary().

Referenced by denoptim.graph.DGraphTest.testGetLevel(), and denoptim.graph.DGraphTest.testGetSourceVertex().

Here is the call graph for this function:

Here is the caller graph for this function:

◆ makeIsostructuralGraphs()

DGraph[] denoptim.graph.DGraphTest.makeIsostructuralGraphs ( ) throws Exception

Definition at line 3643 of file DGraphTest.java.

References denoptim.graph.EmptyVertex.addAP(), denoptim.graph.DGraph.addRing(), denoptim.graph.DGraph.addVertex(), denoptim.graph.DGraphTest.APCA, denoptim.graph.DGraphTest.APCB, denoptim.graph.DGraph.appendVertexOnAP(), denoptim.graph.Vertex.getAP(), denoptim.graph.Vertex.setAsRCV(), denoptim.graph.Vertex.setProperty(), and denoptim.graph.Vertex.setUniquefyingProperty().

Referenced by denoptim.graph.DGraphTest.testIsIsostructuralTo().

Here is the call graph for this function:

Here is the caller graph for this function:

◆ makeTestGraph0()

static DGraph denoptim.graph.DGraphTest.makeTestGraph0 ( FragmentSpace fs ) throws Exception

staticprivate

Build a graph meant to be used in unit tests.

The returned graph has only the scaffold.

Returns: a new instance of the test graph.

Definition at line 2527 of file DGraphTest.java.

References denoptim.graph.DGraph.addVertex(), denoptim.graph.Vertex.newVertexFromLibrary(), and denoptim.graph.Vertex.BBType.SCAFFOLD.

Referenced by denoptim.graph.DGraphTest.testGraphIsomorphism(), and denoptim.graph.DGraphTest.testIsIsostructuralTo().

Here is the call graph for this function:

Here is the caller graph for this function:

◆ makeTestGraph1()

static DGraph denoptim.graph.DGraphTest.makeTestGraph1 ( FragmentSpace fs ) throws Exception

staticprivate

Build a graph meant to be used in unit tests.

The returned graph has only the scaffold and one vertex, plus the edge

Returns: a new instance of the test graph.

Definition at line 2544 of file DGraphTest.java.

References denoptim.graph.DGraph.addEdge(), denoptim.graph.DGraph.addVertex(), denoptim.graph.Vertex.BBType.FRAGMENT, denoptim.graph.Vertex.getAP(), denoptim.graph.Vertex.newVertexFromLibrary(), and denoptim.graph.Vertex.BBType.SCAFFOLD.

Referenced by denoptim.graph.DGraphTest.testGraphIsomorphism(), and denoptim.graph.DGraphTest.testIsIsostructuralTo().

Here is the call graph for this function:

Here is the caller graph for this function:

◆ makeTestGraphA()

static DGraph denoptim.graph.DGraphTest.makeTestGraphA ( )

static

Build a graph meant to be used in unit tests.

The returned graph has the following structure:

       (free)
       ap2
      /
[C1-C0-ap0]-[ap0-O-ap1]-[ap0-H]
 |    \
 ap3   ap1
 |       \
(free)    [ap0-H]

Returns: a new instance of the test graph.

Definition at line 2577 of file DGraphTest.java.

References denoptim.graph.Fragment.addAP(), denoptim.graph.DGraph.addEdge(), denoptim.graph.DGraph.addVertex(), denoptim.graph.Vertex.BBType.CAP, denoptim.graph.Vertex.BBType.FRAGMENT, denoptim.graph.Vertex.getAP(), and denoptim.graph.Vertex.BBType.SCAFFOLD.

Referenced by denoptim.ga.EAUtilsTest.testCrowdingProbability().

Here is the call graph for this function:

Here is the caller graph for this function:

◆ makeTestGraphA2()

static DGraph denoptim.graph.DGraphTest.makeTestGraphA2 ( )

static

Build a graph meant to be used in unit tests.

The structure of the graph is the following:

         [ap1-EV1-ap0]-[ap0-EV2]
        /
       ap2
      /
[C1-C0-ap0]-[ap0-O-ap1]-[ap0-H]
 |    \
 ap3   ap1
 |       \
 |        [ap0-H]
 [ap0-EV3]

Contrary to test graph A, this graph contains:

mixture of vertex types
APClasses

Returns: a new instance of the test graph.

Definition at line 2666 of file DGraphTest.java.

References denoptim.graph.DGraphTest.a, denoptim.graph.EmptyVertex.addAP(), denoptim.graph.Fragment.addAP(), denoptim.graph.DGraph.addEdge(), denoptim.graph.DGraph.addVertex(), denoptim.graph.DGraphTest.b, denoptim.graph.DGraphTest.c, denoptim.graph.Vertex.BBType.CAP, denoptim.graph.DGraphTest.d, denoptim.graph.Vertex.BBType.FRAGMENT, denoptim.graph.Vertex.getAP(), denoptim.graph.APClass.make(), denoptim.graph.Edge.BondType.NONE, denoptim.graph.Vertex.BBType.SCAFFOLD, denoptim.graph.Vertex.setBuildingBlockId(), denoptim.graph.Edge.BondType.SINGLE, and denoptim.graph.Edge.BondType.TRIPLE.

Referenced by denoptim.graph.DGraphTest.testFindVertex().

Here is the call graph for this function:

Here is the caller graph for this function:

◆ makeTestGraphB()

DGraph denoptim.graph.DGraphTest.makeTestGraphB ( FragmentSpace fs ) throws DENOPTIMException

private

Creates a test graph that looks like this:

       (C)-(C)-v3
      /
     | (B)-(B)-v2
     |/
 (A)-v1-(B)-(B)-v2
      |
     (A)
      |
     (A)
   scaffold
     (A)
      |
     0(A)
      |
2(A)-v1-1(B)-(B)-v2
     |\
     | 3(B)-(B)-v2
     \
      4(C)-(C)-v3

Definition at line 232 of file DGraphTest.java.

References denoptim.graph.DGraph.addEdge(), denoptim.graph.DGraph.addSymmetricSetOfVertices(), denoptim.graph.DGraph.addVertex(), denoptim.graph.Vertex.BBType.FRAGMENT, denoptim.graph.Vertex.getAP(), denoptim.graph.Vertex.newVertexFromLibrary(), denoptim.graph.DGraph.renumberGraphVertices(), and denoptim.graph.Vertex.BBType.SCAFFOLD.

Referenced by denoptim.graph.DGraphTest.testGraphIsomorphism(), denoptim.graph.DGraphTest.testIsIsostructuralTo(), denoptim.graph.DGraphTest.testReplaceVertex(), and denoptim.graph.DGraphTest.testSymmetricSetLabels().

Here is the call graph for this function:

Here is the caller graph for this function:

◆ makeTestGraphC()

DGraph denoptim.graph.DGraphTest.makeTestGraphC ( FragmentSpace fs ) throws DENOPTIMException

private

Creates a test graph that looks like this:

    v1-(B)-(B)-v1-(B)-(B)-v1-(B)-(B)-v1
     |           \
    (A)           (A)-(A)-v0
     |
    (A)
  scaffold
    (A)
     |
    0(A)
     |
     v1-1(B)-(B)-v1-(B)-(B)-v1-(B)-(B)-v1

Definition at line 308 of file DGraphTest.java.

References denoptim.graph.DGraph.addSymmetricSetOfVertices(), denoptim.graph.DGraph.addVertex(), denoptim.graph.DGraph.appendVertexOnAP(), denoptim.graph.Vertex.BBType.FRAGMENT, denoptim.graph.Vertex.getAP(), denoptim.graph.Vertex.newVertexFromLibrary(), denoptim.graph.DGraph.renumberGraphVertices(), and denoptim.graph.Vertex.BBType.SCAFFOLD.

Referenced by denoptim.graph.DGraphTest.testGetLevel(), and denoptim.graph.DGraphTest.testGetSourceVertex().

Here is the call graph for this function:

Here is the caller graph for this function:

◆ makeTestGraphD()

DGraph denoptim.graph.DGraphTest.makeTestGraphD ( FragmentSpace fs ) throws DENOPTIMException

private

Creates a test graph that looks like this:

       (C)-(C)-v6-(D)--(B)-v7
       /                    |
      /                   chord
     |                      |
     | (B)-(C)-v6-(D)--(B)-v7
     |/
 (A)-v1-(B)-(C)-v6-(D)--(B)-v7
      |                     |
     (A)                    |
      |                   chord
     (A)                    |
   scaffold(D)----------(B)-v7
     (A)
      |
     0(A)
      |
     v1
      |
     2(A)
      |
     0(A)
      |
2(A)-v1-1(B)-(B)-v2
     |\
     | 3(B)-(B)-v2
     \
      4(C)-(C)-v3

Definition at line 404 of file DGraphTest.java.

References denoptim.graph.DGraph.addEdge(), denoptim.graph.DGraph.addRing(), denoptim.graph.DGraph.addSymmetricSetOfVertices(), denoptim.graph.DGraph.addVertex(), denoptim.graph.Vertex.BBType.FRAGMENT, denoptim.graph.Vertex.getAP(), denoptim.graph.Vertex.newVertexFromLibrary(), denoptim.graph.DGraph.renumberGraphVertices(), and denoptim.graph.Vertex.BBType.SCAFFOLD.

Referenced by denoptim.graph.DGraphTest.testExtractSubgraph(), denoptim.graph.DGraphTest.testExtractSubgraphFromCollection(), denoptim.graph.DGraphTest.testGetChildrenTree(), denoptim.graph.DGraphTest.testGetChildrenTreeWithBranchIdentifier(), denoptim.graph.DGraphTest.testGraphIsomorphism(), denoptim.graph.DGraphTest.testIsIsostructuralTo(), denoptim.graph.DGraphTest.testReplaceSubGraph(), and denoptim.graph.DGraphTest.testReplaceVertex_inRing().

Here is the call graph for this function:

Here is the caller graph for this function:

◆ makeTestGraphDSub1()

DGraph denoptim.graph.DGraphTest.makeTestGraphDSub1 ( FragmentSpace fs ) throws DENOPTIMException

private

Creates a test graph that looks like this:

      (C)-(C)-v6-(D)--(B)-v7
      /                    |
     /                   chord
    |                      |
    | (B)-(C)-v6-(D)--(B)-v7
    |/
(A)-v1-(B)-(C)-v6-(D)--(B)-v7

Definition at line 500 of file DGraphTest.java.

References denoptim.graph.DGraph.addEdge(), denoptim.graph.DGraph.addRing(), denoptim.graph.DGraph.addVertex(), denoptim.graph.Vertex.BBType.FRAGMENT, denoptim.graph.Vertex.getAP(), denoptim.graph.Vertex.newVertexFromLibrary(), and denoptim.graph.DGraph.renumberGraphVertices().

Referenced by denoptim.graph.DGraphTest.testExtractSubgraph(), and denoptim.graph.DGraphTest.testIsIsostructuralTo().

Here is the call graph for this function:

Here is the caller graph for this function:

◆ makeTestGraphDSub2()

DGraph denoptim.graph.DGraphTest.makeTestGraphDSub2 ( FragmentSpace fs ) throws DENOPTIMException

private

Creates a test graph that looks like this:

       0(A)
      /
2(A)-v1-1(B)-(B)-v2
     |\
     | 3(B)-(B)-v2
     \
      4(C)-(C)-v3

Definition at line 555 of file DGraphTest.java.

References denoptim.graph.DGraph.addEdge(), denoptim.graph.DGraph.addSymmetricSetOfVertices(), denoptim.graph.DGraph.addVertex(), denoptim.graph.Vertex.BBType.FRAGMENT, denoptim.graph.Vertex.getAP(), denoptim.graph.Vertex.newVertexFromLibrary(), and denoptim.graph.DGraph.renumberGraphVertices().

Referenced by denoptim.graph.DGraphTest.testExtractSubgraph().

Here is the call graph for this function:

Here is the caller graph for this function:

◆ makeTestGraphE()

DGraph denoptim.graph.DGraphTest.makeTestGraphE ( FragmentSpace fs ) throws DENOPTIMException

private

Creates a test graph that looks like this:


2(A)-v1-1(B)-2(A)-v1(*)-1(B)-2(A)-v1(**)
     | \           |\
     |  |          | 3(B)-2(A)-v1(**)
     |  |
     |  3(B)-2(A)-v1(*)-1(B)-2(A)-v1
     |             |\
     |             | 3(B)-2(A)-v1
     \
      4(C)-2(A)-v1

where only those marked with a star are included in the symmetric sets.

Definition at line 604 of file DGraphTest.java.

References denoptim.graph.DGraph.addEdge(), denoptim.graph.DGraph.addSymmetricSetOfVertices(), denoptim.graph.DGraph.addVertex(), denoptim.graph.Vertex.BBType.FRAGMENT, denoptim.graph.Vertex.getAP(), denoptim.graph.Vertex.newVertexFromLibrary(), and denoptim.graph.DGraph.renumberGraphVertices().

Referenced by denoptim.graph.DGraphTest.testConvertSymmetricLabelsToSymmetricSets().

Here is the call graph for this function:

Here is the caller graph for this function:

◆ makeTestGraphF()

DGraph denoptim.graph.DGraphTest.makeTestGraphF ( FragmentSpace fs ) throws DENOPTIMException

private

Creates a test graph that looks like this:

      (C)-(C)-v6-(D)--(D)-v7
      /                    |
     /                   chord
    |                      |
    | (B)-(C)-v6-(D)--(D)-v7  
    |  |
    | /     (B)  (A)           (B) 
    |/         \/              /
(A)-v1-(B)-(B)-v1-(A)--(A)-v1--(B)
     |          |          |\
    (A)         |          | (C)
                |         (A)  
                |
                (C)--(C)-v6-(D)

Definition at line 682 of file DGraphTest.java.

References denoptim.graph.DGraph.addEdge(), denoptim.graph.DGraph.addRing(), denoptim.graph.DGraph.addSymmetricSetOfVertices(), denoptim.graph.DGraph.addVertex(), denoptim.graph.Vertex.BBType.FRAGMENT, denoptim.graph.Vertex.getAP(), denoptim.graph.Vertex.newVertexFromLibrary(), and denoptim.graph.DGraph.renumberGraphVertices().

Referenced by denoptim.graph.DGraphTest.testGetEdgesWithSrcOrTrg(), denoptim.graph.DGraphTest.testGetSymmetricSubGraphs(), and denoptim.graph.DGraphTest.testReplaceSubGraph().

Here is the call graph for this function:

Here is the caller graph for this function:

◆ makeTestGraphG()

DGraph denoptim.graph.DGraphTest.makeTestGraphG ( FragmentSpace fs ) throws DENOPTIMException

private

Creates a test graph that looks like this:


       (C)-(C)-v6-(D)--(B)-v7
       /                    |
      /                   chord
     |                      |
     | (B)-(C)-v6-(D)--(B)-v7  
     |  |            --------------(C)-v6-(D)--(B)-v7  
     |  /           /                              |
     | /     (A)  (B)           (B)                |
     |/         \/              /                chord
 (A)-v1-(B)-(B)-v1-(A)--(A)-v1--(B)                | 
      |          |          |\                     |
     (A)         |          | (C)--(C)-v6-(D)--(B)-v7 
      |          |          |
      |          |         (A)--(C)-v6-(D)--(B)-v7  
      |          |                              |
      |          |                            chord
      |          |                              |
      |          ---------(C)--(C)-v6-(D)--(B)--v7                
      |                    
     0(A)
      |
     v1
      |
     2(A)
      |
     0(A)
      |
2(A)-v1-1(B)-(B)-v2
     |\
     | 3(B)-(B)-v2
     \
      4(C)-(C)-v3

This is the result of replacing two vertexes in graph D with Graph F and welding connections.

Definition at line 779 of file DGraphTest.java.

References denoptim.graph.DGraph.addEdge(), denoptim.graph.DGraph.addRing(), denoptim.graph.DGraph.addSymmetricSetOfVertices(), denoptim.graph.DGraph.addVertex(), denoptim.graph.Vertex.BBType.FRAGMENT, denoptim.graph.Vertex.getAP(), and denoptim.graph.Vertex.newVertexFromLibrary().

Referenced by denoptim.graph.DGraphTest.testReplaceSubGraph().

Here is the call graph for this function:

Here is the caller graph for this function:

◆ makeTestGraphH()

DGraph denoptim.graph.DGraphTest.makeTestGraphH ( FragmentSpace fs ) throws DENOPTIMException

private

Creates a test graph that looks like this:

      (C)-(C)-v6-(D)--(B)-v7
      /                    |
     /                   chord
    |                      |
    | (B)-(C)-v6-(D)--(B)-v7
    |/
(A)-v1-(B)
     \
      (A)

Definition at line 912 of file DGraphTest.java.

References denoptim.graph.DGraph.addEdge(), denoptim.graph.DGraph.addRing(), denoptim.graph.DGraph.addVertex(), denoptim.graph.Vertex.BBType.FRAGMENT, denoptim.graph.Vertex.getAP(), denoptim.graph.Vertex.newVertexFromLibrary(), and denoptim.graph.DGraph.renumberGraphVertices().

Referenced by denoptim.graph.DGraphTest.makeTestGraphI().

Here is the call graph for this function:

Here is the caller graph for this function:

◆ makeTestGraphI()

DGraph denoptim.graph.DGraphTest.makeTestGraphI ( FragmentSpace fs ) throws Exception

private

Creates a test graph that looks like this:

      (A)-(C)-v6-(D)--(B)-v7
      /                    |
     /                   chord
    |                      |
    | (B)-(C)-v6-(D)--(B)-v7
    |/
template-(A)

Definition at line 959 of file DGraphTest.java.

References denoptim.graph.DGraph.addEdge(), denoptim.graph.DGraph.addRing(), denoptim.graph.DGraph.addVertex(), denoptim.graph.Vertex.BBType.FRAGMENT, denoptim.graph.Vertex.getAP(), denoptim.graph.DGraphTest.makeTestGraphH(), denoptim.graph.Vertex.newVertexFromLibrary(), denoptim.graph.DGraph.renumberGraphVertices(), and denoptim.graph.Template.setInnerGraph().

Referenced by denoptim.graph.DGraphTest.testGetInterfaceAPs(), denoptim.graph.DGraphTest.testGetSubgraphAPs(), and denoptim.graph.DGraphTest.testReplaceSubGraph_inTemplate().

Here is the call graph for this function:

Here is the caller graph for this function:

◆ makeTestGraphJ()

DGraph denoptim.graph.DGraphTest.makeTestGraphJ ( FragmentSpace fs ) throws DENOPTIMException

private

Creates a test graph that looks like this:

              
                    0(A)
                   /
       0(A)--2(A)-v1-1(B)
      /           | \
2(A)-v1-1(B)       \  3(B)
     |\             4(C)
     | 3(B)
     \
      4(C)

Definition at line 1010 of file DGraphTest.java.

References denoptim.graph.DGraph.addEdge(), denoptim.graph.DGraph.addVertex(), denoptim.graph.Vertex.BBType.FRAGMENT, denoptim.graph.Vertex.getAP(), denoptim.graph.Vertex.newVertexFromLibrary(), and denoptim.graph.DGraph.renumberGraphVertices().

Referenced by denoptim.graph.DGraphTest.testReplaceSubGraph_inTemplate().

Here is the call graph for this function:

Here is the caller graph for this function:

◆ makeTestGraphK()

DGraph denoptim.graph.DGraphTest.makeTestGraphK ( FragmentSpace fs ) throws DENOPTIMException

private

Creates a test graph that looks like this:

      (C)-(C)-v6-(D)--(C)-v1-(capped)
     /
    | (B)-(C)-v6*-(D)--(C)-v1**-(capped)
    |/
(A)-v1-(B)-(C)-v6*-(D)--(C)-v1**-(capped)

where vertexes marked with either * or ** are in symmetric sets, and "capped" means all APs have been used by capping groups.

Definition at line 1041 of file DGraphTest.java.

References denoptim.graph.DGraph.addEdge(), denoptim.graph.DGraph.addSymmetricSetOfVertices(), denoptim.graph.DGraph.addVertex(), denoptim.graph.DGraph.appendVertexOnAP(), denoptim.graph.Vertex.BBType.CAP, denoptim.graph.DGraphTest.cap, denoptim.graph.Vertex.BBType.FRAGMENT, denoptim.graph.Vertex.getAP(), denoptim.graph.Vertex.newVertexFromLibrary(), and denoptim.graph.DGraph.renumberGraphVertices().

Referenced by denoptim.graph.DGraphTest.testGetSymmetricSubGraphs().

Here is the call graph for this function:

Here is the caller graph for this function:

◆ makeTestGraphL()

DGraph denoptim.graph.DGraphTest.makeTestGraphL ( FragmentSpace fs ) throws DENOPTIMException

private

Creates a test graph that looks like this:

       (C)-(C)-v6-(D)--(B)-v7
       /                    |
      /                   chord
     |                      |
     | (B)-(C)-v6-(D)--(B)-v7
     |/
 (A)-v1-(B)
      |
     0(A)
      |
     2(A)
      |
  (B)-v1-(C)-v6-(D)--(B)-v7
      |                  |
     0(A)                 |
      |                chord
     (A)                 |
   v1_scaffold(D)-------(B)-v7
     (A)
      |
     0(A)
      |
     v1
      |
     2(A)
      |
     0(A)
      |
2(A)-v1-1(B)-(B)-v2
     |\
     | 3(B)-(B)-v2
     \
      4(C)-(C)-v3

Definition at line 1149 of file DGraphTest.java.

References denoptim.graph.DGraph.addEdge(), denoptim.graph.DGraph.addRing(), denoptim.graph.DGraph.addSymmetricSetOfVertices(), denoptim.graph.DGraph.addVertex(), denoptim.graph.Vertex.BBType.FRAGMENT, denoptim.graph.Vertex.getAP(), denoptim.graph.Vertex.newVertexFromLibrary(), denoptim.graph.DGraph.renumberGraphVertices(), and denoptim.graph.Vertex.BBType.SCAFFOLD.

Referenced by denoptim.graph.DGraphTest.testEmbedPatternsInTemplates().

Here is the call graph for this function:

Here is the caller graph for this function:

◆ makeTestGraphM()

static DGraph denoptim.graph.DGraphTest.makeTestGraphM ( ) throws DENOPTIMException

static

Returns a graph with definition of symmetric vertexes and symmetric APs meant for testing purposes.

Before running this you must run DGraphTest#prepare()

This is the graph we return (symmetric APs are marked by s and s'):

              s(B)-(B)-v3
             / 
       (A)-v1-s(B)-(B)-v4
       /     \
      /       s(B)-(B)-v5
     /
  s(A)  s'(B)-v9  
 /     /
v0==== 
 \     \
  s(A)   s'(B)-v10
    |
     \        s(B)-(B)-v6
      \      / 
       (A)-v2-s(B)-(B)-v7
             \
              s(B)-(B)-v8

Definition at line 3889 of file DGraphTest.java.

References denoptim.graph.EmptyVertex.addAP(), denoptim.graph.EmptyVertex.addSymmetricAPSet(), denoptim.graph.DGraph.addVertex(), denoptim.graph.DGraphTest.APCA, denoptim.graph.DGraphTest.APCB, denoptim.graph.DGraph.appendVertexOnAP(), denoptim.graph.EmptyVertex.clone(), denoptim.graph.Vertex.getAP(), and denoptim.graph.Vertex.setVertexId().

Referenced by denoptim.graph.DGraphTest.testDetectSymVertexSets(), and denoptim.graph.DGraphTest.testFindSymmetrySetsOfChildVertexes().

Here is the call graph for this function:

Here is the caller graph for this function:

◆ makeTestGraphN()

static DGraph denoptim.graph.DGraphTest.makeTestGraphN ( ) throws DENOPTIMException

static

Returns a graph with peculiar definition of symmetric vertexes and symmetric APs meant for testing purposes.

Before running this you must run DGraphTest#prepare()

This is the graph we return (symmetric APs are marked by s and s'):

              s(B)-(B)-v3
             / 
       (B)s-v1-s(B)-(B)-v4
       /     \
      /       s(B)-(B)-v5                     s(B)     
     /                                       /
  s(B)  s(B)---------------------------(B)s-v9-s(B)  
 /     /                                     \
v0====        (v0 is SCAFFOLD!)               s(B)  
 \     \
  s(B)  s(B)
    |
     \        s(B)-(B)-v6
      \      / 
       (B)s-v2-s(B)-(B)-v7
             \
              s(B)

Definition at line 4055 of file DGraphTest.java.

References denoptim.graph.EmptyVertex.addAP(), denoptim.graph.EmptyVertex.addSymmetricAPSet(), denoptim.graph.DGraph.addVertex(), denoptim.graph.DGraphTest.APCB, denoptim.graph.DGraph.appendVertexOnAP(), denoptim.graph.EmptyVertex.clone(), denoptim.graph.Vertex.BBType.FRAGMENT, denoptim.graph.Vertex.getAP(), denoptim.graph.Vertex.BBType.SCAFFOLD, denoptim.graph.Vertex.setBuildingBlockType(), and denoptim.graph.Vertex.setVertexId().

Here is the call graph for this function:

◆ prepare()

static FragmentSpace denoptim.graph.DGraphTest.prepare ( ) throws DENOPTIMException

static

Definition at line 80 of file DGraphTest.java.

Here is the call graph for this function:

Here is the caller graph for this function:

◆ testClone()

void denoptim.graph.DGraphTest.testClone ( ) throws DENOPTIMException

Definition at line 2407 of file DGraphTest.java.

Here is the call graph for this function:

◆ testConvertSymmetricLabelsToSymmetricSets()

void denoptim.graph.DGraphTest.testConvertSymmetricLabelsToSymmetricSets ( ) throws Exception

Definition at line 3389 of file DGraphTest.java.

References denoptim.graph.DGraph.convertSymmetricLabelsToSymmetricSets(), denoptim.graph.DGraph.getSymmetricSetCount(), denoptim.graph.DGraph.getSymSetsIterator(), denoptim.graph.DGraph.getVertexAtPosition(), denoptim.graph.DGraphTest.makeTestGraphE(), denoptim.graph.DGraphTest.prepare(), denoptim.graph.Vertex.setProperty(), and denoptim.constants.DENOPTIMConstants.VRTSYMMSETID.

Here is the call graph for this function:

◆ testDetectSymVertexSets()

void denoptim.graph.DGraphTest.testDetectSymVertexSets ( ) throws Exception

Definition at line 4172 of file DGraphTest.java.

References denoptim.graph.DGraph.detectSymVertexSets(), denoptim.graph.DGraph.getSymmetricSetCount(), denoptim.graph.DGraph.getSymSetForVertex(), denoptim.graph.DGraph.getVertexAtPosition(), denoptim.graph.DGraphTest.makeTestGraphM(), and denoptim.graph.DGraphTest.prepare().

Here is the call graph for this function:

◆ testEmbedPatternsInTemplates()

void denoptim.graph.DGraphTest.testEmbedPatternsInTemplates ( ) throws Exception

Definition at line 3835 of file DGraphTest.java.

References denoptim.graph.DGraph.embedPatternsInTemplates(), denoptim.graph.Vertex.BBType.FRAGMENT, denoptim.graph.DGraph.getEdgeCount(), denoptim.graph.DGraph.getRingCount(), denoptim.graph.DGraph.getVertexCount(), denoptim.graph.DGraph.getVertexList(), denoptim.graph.DGraphTest.makeTestGraphL(), denoptim.graph.DGraphTest.prepare(), denoptim.graph.GraphPattern.RING, and denoptim.graph.Vertex.BBType.SCAFFOLD.

Here is the call graph for this function:

◆ testExtractSubgraph()

void denoptim.graph.DGraphTest.testExtractSubgraph ( ) throws Exception

Definition at line 2996 of file DGraphTest.java.

References denoptim.graph.DGraph.extractSubgraph(), denoptim.graph.DGraph.getRingCount(), denoptim.graph.DGraph.getSymmetricSetCount(), denoptim.graph.DGraph.getVertexAtPosition(), denoptim.graph.DGraph.isIsomorphicTo(), denoptim.graph.DGraphTest.makeTestGraphD(), denoptim.graph.DGraphTest.makeTestGraphDSub1(), denoptim.graph.DGraphTest.makeTestGraphDSub2(), and denoptim.graph.DGraphTest.prepare().

Here is the call graph for this function:

◆ testExtractSubgraphFromCollection()

void denoptim.graph.DGraphTest.testExtractSubgraphFromCollection ( ) throws Exception

Definition at line 3037 of file DGraphTest.java.

References denoptim.graph.DGraph.extractSubgraph(), denoptim.graph.DGraph.getVertexAtPosition(), denoptim.graph.DGraph.getVertexCount(), denoptim.graph.DGraph.getVertexWithId(), denoptim.graph.DGraphTest.makeTestGraphD(), and denoptim.graph.DGraphTest.prepare().

Here is the call graph for this function:

◆ testFindSymmetrySetsOfChildVertexes()

void denoptim.graph.DGraphTest.testFindSymmetrySetsOfChildVertexes ( ) throws Exception

Definition at line 3949 of file DGraphTest.java.

References denoptim.graph.DGraph.findSymmetrySetsOfChildVertexes(), denoptim.graph.Vertex.getSymmetricAPSets(), denoptim.graph.DGraph.getVertexAtPosition(), denoptim.graph.DGraphTest.makeTestGraphM(), and denoptim.graph.DGraphTest.prepare().

Here is the call graph for this function:

◆ testFindVertex()

void denoptim.graph.DGraphTest.testFindVertex ( ) throws Exception

Definition at line 3095 of file DGraphTest.java.

References denoptim.graph.DGraphTest.b, denoptim.graph.DGraphTest.c, denoptim.graph.Vertex.BBType.CAP, denoptim.graph.DGraphTest.d, denoptim.graph.Vertex.VertexType.EmptyVertex, denoptim.graph.DGraph.findVertices(), denoptim.graph.DGraph.getVertexAtPosition(), denoptim.graph.Vertex.getVertexId(), denoptim.graph.DGraph.getVertexList(), denoptim.graph.APClass.make(), denoptim.graph.DGraphTest.makeTestGraphA2(), denoptim.graph.Vertex.VertexType.MolecularFragment, and denoptim.graph.Edge.BondType.TRIPLE.

Here is the call graph for this function:

◆ testFromToJSON()

void denoptim.graph.DGraphTest.testFromToJSON ( ) throws Exception

Definition at line 2871 of file DGraphTest.java.

References denoptim.graph.SymmetricSet< T >.add(), denoptim.graph.DGraph.addEdge(), denoptim.graph.DGraph.addRing(), denoptim.graph.DGraph.addSymmetricSetOfVertices(), denoptim.graph.DGraphTest.buildVertexAndConnectToGraph(), denoptim.graph.DGraph.fromJson(), denoptim.graph.Vertex.getAP(), and denoptim.graph.DGraph.toJson().

Here is the call graph for this function:

◆ testGetAvailableAPs_returnsListOfAvailableAPs()

void denoptim.graph.DGraphTest.testGetAvailableAPs_returnsListOfAvailableAPs ( ) throws DENOPTIMException

Definition at line 2380 of file DGraphTest.java.

References denoptim.graph.EmptyVertex.addAP(), denoptim.graph.DGraph.addEdge(), denoptim.graph.DGraph.addVertex(), denoptim.graph.Vertex.getAP(), denoptim.graph.DGraph.getAvailableAPs(), and denoptim.graph.Vertex.getVertexId().

Here is the call graph for this function:

◆ testGetChildrenTree()

void denoptim.graph.DGraphTest.testGetChildrenTree ( ) throws Exception

Definition at line 3493 of file DGraphTest.java.

References denoptim.graph.DGraph.getChildrenTree(), denoptim.graph.DGraph.getVertexAtPosition(), denoptim.graph.DGraphTest.makeTestGraphD(), and denoptim.graph.DGraphTest.prepare().

Here is the call graph for this function:

◆ testGetChildrenTreeWithBranchIdentifier()

void denoptim.graph.DGraphTest.testGetChildrenTreeWithBranchIdentifier ( ) throws Exception

Definition at line 3533 of file DGraphTest.java.

References denoptim.graph.DGraph.directedPathExists(), denoptim.graph.DGraph.getBranchIdOfVertexAtPosition(), denoptim.graph.DGraph.getChildrenTree(), denoptim.graph.DGraph.getVertexAtPosition(), denoptim.graph.DGraphTest.makeTestGraphD(), and denoptim.graph.DGraphTest.prepare().

Here is the call graph for this function:

◆ testGetEdgesWithSrcOrTrg()

void denoptim.graph.DGraphTest.testGetEdgesWithSrcOrTrg ( ) throws Exception

Definition at line 3813 of file DGraphTest.java.

References denoptim.graph.DGraph.getEdgesWithSrc(), denoptim.graph.DGraph.getEdgesWithTrg(), denoptim.graph.DGraph.getVertexAtPosition(), denoptim.graph.DGraphTest.makeTestGraphF(), and denoptim.graph.DGraphTest.prepare().

Here is the call graph for this function:

◆ testGetEmbeddedGraphInClone()

void denoptim.graph.DGraphTest.testGetEmbeddedGraphInClone ( ) throws Exception

Definition at line 1472 of file DGraphTest.java.

References denoptim.graph.DGraph.clone(), denoptim.graph.DGraph.getEmbeddedGraphInClone(), denoptim.graph.DGraph.getEmbeddingPath(), denoptim.graph.Template.getInnerGraph(), denoptim.graph.DGraphTest.makeDeeplyEmbeddedGraph(), and denoptim.graph.DGraphTest.prepare().

Here is the call graph for this function:

◆ testGetEmbeddingPath()

void denoptim.graph.DGraphTest.testGetEmbeddingPath ( ) throws Exception

Definition at line 1444 of file DGraphTest.java.

References denoptim.graph.DGraph.getEmbeddingPath(), denoptim.graph.Template.getInnerGraph(), denoptim.graph.DGraphTest.makeDeeplyEmbeddedGraph(), and denoptim.graph.DGraphTest.prepare().

Here is the call graph for this function:

◆ testGetInterfaceAPs()

void denoptim.graph.DGraphTest.testGetInterfaceAPs ( ) throws Exception

Definition at line 3578 of file DGraphTest.java.

References denoptim.graph.Vertex.getAP(), denoptim.graph.DGraph.getInterfaceAPs(), denoptim.graph.DGraph.getVertexAtPosition(), denoptim.graph.DGraphTest.makeTestGraphI(), and denoptim.graph.DGraphTest.prepare().

Here is the call graph for this function:

◆ testGetLevel()

void denoptim.graph.DGraphTest.testGetLevel ( ) throws Exception

Definition at line 1544 of file DGraphTest.java.

References denoptim.graph.DGraph.getLevel(), denoptim.graph.DGraph.getVertexAtPosition(), denoptim.graph.DGraph.getVertexCount(), denoptim.graph.DGraphTest.makeDisorderedGraph(), denoptim.graph.DGraphTest.makeTestGraphC(), and denoptim.graph.DGraphTest.prepare().

Here is the call graph for this function:

◆ testGetMutationSites()

void denoptim.graph.DGraphTest.testGetMutationSites ( ) throws DENOPTIMException

Definition at line 2498 of file DGraphTest.java.

References denoptim.graph.DGraph.addVertex(), denoptim.graph.Template.ContractLevel.FIXED, denoptim.graph.Template.ContractLevel.FREE, denoptim.graph.DGraph.getMutableSites(), and denoptim.graph.Template.getTestTemplate().

Here is the call graph for this function:

◆ testGetSourceVertex()

void denoptim.graph.DGraphTest.testGetSourceVertex ( ) throws Exception

Definition at line 1527 of file DGraphTest.java.

References denoptim.graph.DGraph.getSourceVertex(), denoptim.graph.DGraph.getVertexAtPosition(), denoptim.graph.DGraphTest.makeDisorderedGraph(), denoptim.graph.DGraphTest.makeTestGraphC(), and denoptim.graph.DGraphTest.prepare().

Here is the call graph for this function:

◆ testGetSubgraphAPs()

void denoptim.graph.DGraphTest.testGetSubgraphAPs ( ) throws Exception

Definition at line 3616 of file DGraphTest.java.

References denoptim.graph.Vertex.getAP(), denoptim.graph.DGraph.getSubgraphAPs(), denoptim.graph.DGraph.getVertexAtPosition(), denoptim.graph.DGraphTest.makeTestGraphI(), and denoptim.graph.DGraphTest.prepare().

Here is the call graph for this function:

◆ testGetSymmetricSubGraphs()

void denoptim.graph.DGraphTest.testGetSymmetricSubGraphs ( ) throws Exception

Definition at line 3437 of file DGraphTest.java.

References denoptim.graph.DGraph.getSymmetricSubGraphs(), denoptim.graph.DGraph.getVertexAtPosition(), denoptim.graph.Vertex.getVertexId(), denoptim.graph.DGraphTest.makeTestGraphF(), denoptim.graph.DGraphTest.makeTestGraphK(), and denoptim.graph.DGraphTest.prepare().

Here is the call graph for this function:

◆ testGraphIsomorphism()

void denoptim.graph.DGraphTest.testGraphIsomorphism ( ) throws Exception

Definition at line 2933 of file DGraphTest.java.

Here is the call graph for this function:

◆ testIsIsostructuralTo()

void denoptim.graph.DGraphTest.testIsIsostructuralTo ( ) throws Exception

Definition at line 3722 of file DGraphTest.java.

Here is the call graph for this function:

◆ testRemoveCapping()

void denoptim.graph.DGraphTest.testRemoveCapping ( ) throws Exception

Definition at line 2758 of file DGraphTest.java.

References denoptim.graph.Fragment.addAP(), denoptim.graph.DGraph.addEdge(), denoptim.graph.DGraph.addVertex(), denoptim.graph.Vertex.BBType.CAP, denoptim.graph.DGraph.containsVertex(), denoptim.graph.Vertex.BBType.FRAGMENT, denoptim.graph.Vertex.getAP(), denoptim.graph.Vertex.getGraphOwner(), denoptim.graph.DGraph.getVertexCount(), denoptim.graph.DGraph.removeCappingGroups(), denoptim.graph.DGraph.removeCappingGroupsOn(), and denoptim.graph.Vertex.BBType.SCAFFOLD.

Here is the call graph for this function:

◆ testRemoveUnusedRCVs()

void denoptim.graph.DGraphTest.testRemoveUnusedRCVs ( ) throws Exception

Definition at line 1321 of file DGraphTest.java.

Here is the call graph for this function:

◆ testRemoveVertex()

void denoptim.graph.DGraphTest.testRemoveVertex ( ) throws Exception

Definition at line 1831 of file DGraphTest.java.

References denoptim.graph.SymmetricSet< T >.add(), denoptim.graph.DGraph.addEdge(), denoptim.graph.DGraph.addRing(), denoptim.graph.DGraph.addSymmetricSetOfVertices(), denoptim.graph.DGraphTest.buildVertexAndConnectToGraph(), denoptim.graph.Vertex.getAP(), denoptim.graph.DGraph.getEdgeCount(), denoptim.graph.DGraph.getRingCount(), denoptim.graph.DGraph.getSymmetricSetCount(), denoptim.graph.DGraph.getVertexCount(), and denoptim.graph.DGraph.removeVertex().

Here is the call graph for this function:

◆ testReplaceSubGraph()

void denoptim.graph.DGraphTest.testReplaceSubGraph ( ) throws Exception

Definition at line 1726 of file DGraphTest.java.

Here is the call graph for this function:

◆ testReplaceSubGraph_inTemplate()

void denoptim.graph.DGraphTest.testReplaceSubGraph_inTemplate ( ) throws Exception

Definition at line 1778 of file DGraphTest.java.

Here is the call graph for this function:

◆ testReplaceVertex()

void denoptim.graph.DGraphTest.testReplaceVertex ( ) throws Exception

Definition at line 1567 of file DGraphTest.java.

Here is the call graph for this function:

◆ testReplaceVertex_inRing()

void denoptim.graph.DGraphTest.testReplaceVertex_inRing ( ) throws Exception

Definition at line 1701 of file DGraphTest.java.

References denoptim.graph.Vertex.BBType.FRAGMENT, denoptim.graph.DGraph.getVertexAtPosition(), denoptim.graph.DGraph.isIsomorphicTo(), denoptim.graph.DGraphTest.makeTestGraphD(), denoptim.graph.DGraphTest.prepare(), and denoptim.graph.DGraph.replaceVertex().

Here is the call graph for this function:

◆ testSameAs_DiffRings()

void denoptim.graph.DGraphTest.testSameAs_DiffRings ( ) throws DENOPTIMException

Definition at line 2304 of file DGraphTest.java.

References denoptim.graph.DGraph.addEdge(), denoptim.graph.DGraph.addRing(), denoptim.graph.DGraphTest.buildVertexAndConnectToGraph(), denoptim.graph.Vertex.getAP(), and denoptim.graph.DGraph.sameAs().

Here is the call graph for this function:

◆ testSameAs_DiffSymmSet()

void denoptim.graph.DGraphTest.testSameAs_DiffSymmSet ( ) throws Exception

Definition at line 2080 of file DGraphTest.java.

References denoptim.graph.SymmetricSet< T >.add(), denoptim.graph.DGraph.addEdge(), denoptim.graph.DGraph.addSymmetricSetOfVertices(), denoptim.graph.DGraphTest.buildVertexAndConnectToGraph(), denoptim.graph.Vertex.getAP(), and denoptim.graph.DGraph.sameAs().

Here is the call graph for this function:

◆ testSameAs_DiffVertex()

void denoptim.graph.DGraphTest.testSameAs_DiffVertex ( ) throws DENOPTIMException

Definition at line 1971 of file DGraphTest.java.

References denoptim.graph.DGraph.addEdge(), denoptim.graph.DGraphTest.buildVertexAndConnectToGraph(), denoptim.graph.Vertex.getAP(), and denoptim.graph.DGraph.sameAs().

Here is the call graph for this function:

◆ testSameAs_DisorderRings()

void denoptim.graph.DGraphTest.testSameAs_DisorderRings ( ) throws Exception

Definition at line 2226 of file DGraphTest.java.

References denoptim.graph.DGraph.addEdge(), denoptim.graph.DGraph.addRing(), denoptim.graph.DGraphTest.buildVertexAndConnectToGraph(), denoptim.graph.Vertex.getAP(), and denoptim.graph.DGraph.sameAs().

Here is the call graph for this function:

◆ testSameAs_Equal()

void denoptim.graph.DGraphTest.testSameAs_Equal ( ) throws DENOPTIMException

Definition at line 1936 of file DGraphTest.java.

References denoptim.graph.DGraph.addEdge(), denoptim.graph.DGraphTest.buildVertexAndConnectToGraph(), denoptim.graph.Vertex.getAP(), and denoptim.graph.DGraph.sameAs().

Here is the call graph for this function:

◆ testSameAs_SameRings()

void denoptim.graph.DGraphTest.testSameAs_SameRings ( ) throws DENOPTIMException

Definition at line 2148 of file DGraphTest.java.

References denoptim.graph.DGraph.addEdge(), denoptim.graph.DGraph.addRing(), denoptim.graph.DGraphTest.buildVertexAndConnectToGraph(), denoptim.graph.Vertex.getAP(), and denoptim.graph.DGraph.sameAs().

Here is the call graph for this function:

◆ testSameAs_SameSymmSet()

void denoptim.graph.DGraphTest.testSameAs_SameSymmSet ( ) throws Exception

Definition at line 2006 of file DGraphTest.java.

References denoptim.graph.SymmetricSet< T >.add(), denoptim.graph.DGraph.addEdge(), denoptim.graph.DGraph.addSymmetricSetOfVertices(), denoptim.graph.DGraphTest.buildVertexAndConnectToGraph(), denoptim.graph.Vertex.getAP(), and denoptim.graph.DGraph.sameAs().

Here is the call graph for this function:

◆ testSymmetricSetLabels()

void denoptim.graph.DGraphTest.testSymmetricSetLabels ( ) throws Exception

Definition at line 3355 of file DGraphTest.java.

References denoptim.graph.Vertex.getProperty(), denoptim.graph.DGraph.getVertexAtPosition(), denoptim.graph.DGraph.getVertexList(), denoptim.graph.DGraphTest.makeTestGraphB(), denoptim.graph.DGraphTest.prepare(), denoptim.graph.DGraph.reassignSymmetricLabels(), and denoptim.constants.DENOPTIMConstants.VRTSYMMSETID.

Here is the call graph for this function:

Member Data Documentation

◆ a

String denoptim.graph.DGraphTest.a ="A"

staticprivate

Definition at line 75 of file DGraphTest.java.

Referenced by denoptim.graph.DGraphTest.makeTestGraphA2(), and denoptim.graph.DGraphTest.prepare().

◆ APCA

APClass denoptim.graph.DGraphTest.APCA

staticprivate

Definition at line 74 of file DGraphTest.java.

Referenced by denoptim.graph.DGraphTest.makeDeeplyEmbeddedGraph(), denoptim.graph.DGraphTest.makeIsostructuralGraphs(), denoptim.graph.DGraphTest.makeTestGraphM(), and denoptim.graph.DGraphTest.prepare().

◆ APCB

APClass denoptim.graph.DGraphTest.APCB

staticprivate

Definition at line 74 of file DGraphTest.java.

Referenced by denoptim.graph.DGraphTest.makeDeeplyEmbeddedGraph(), denoptim.graph.DGraphTest.makeIsostructuralGraphs(), denoptim.graph.DGraphTest.makeTestGraphM(), denoptim.graph.DGraphTest.makeTestGraphN(), and denoptim.graph.DGraphTest.prepare().

◆ APCC

APClass denoptim.graph.DGraphTest.APCC

staticprivate

Definition at line 74 of file DGraphTest.java.

Referenced by denoptim.graph.DGraphTest.makeDeeplyEmbeddedGraph(), denoptim.graph.DGraphTest.prepare(), and denoptim.graph.DGraphTest.testIsIsostructuralTo().

◆ APCD

APClass denoptim.graph.DGraphTest.APCD

staticprivate

Definition at line 74 of file DGraphTest.java.

Referenced by denoptim.graph.DGraphTest.makeDeeplyEmbeddedGraph(), denoptim.graph.DGraphTest.prepare(), and denoptim.graph.DGraphTest.testIsIsostructuralTo().

◆ b

String denoptim.graph.DGraphTest.b ="B"

staticprivate

Definition at line 75 of file DGraphTest.java.

Referenced by denoptim.graph.DGraphTest.makeTestGraphA2(), denoptim.graph.DGraphTest.prepare(), and denoptim.graph.DGraphTest.testFindVertex().

◆ c

String denoptim.graph.DGraphTest.c ="C"

staticprivate

Definition at line 75 of file DGraphTest.java.

Referenced by denoptim.graph.DGraphTest.makeTestGraphA2(), denoptim.graph.DGraphTest.prepare(), and denoptim.graph.DGraphTest.testFindVertex().

◆ cap

String denoptim.graph.DGraphTest.cap ="cap"

staticprivate

Definition at line 75 of file DGraphTest.java.

Referenced by denoptim.graph.DGraphTest.makeTestGraphK(), denoptim.graph.DGraphTest.prepare(), and denoptim.graph.DGraphTest.testRemoveUnusedRCVs().

◆ CAPP

APClass denoptim.graph.DGraphTest.CAPP

staticprivate

Definition at line 74 of file DGraphTest.java.

Referenced by denoptim.graph.DGraphTest.prepare().

◆ d

String denoptim.graph.DGraphTest.d ="D"

staticprivate

Definition at line 75 of file DGraphTest.java.

Referenced by denoptim.graph.DGraphTest.makeTestGraphA2(), denoptim.graph.DGraphTest.prepare(), and denoptim.graph.DGraphTest.testFindVertex().

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

/github/workspace/src/test/java/denoptim/graph/DGraphTest.java

Public Member Functions

Static Public Member Functions

Private Member Functions

Static Private Member Functions

Static Private Attributes

Detailed Description

Member Function Documentation

◆ buildVertexAndConnectToGraph()

◆ makeDeeplyEmbeddedGraph()

◆ makeDisorderedGraph()

◆ makeIsostructuralGraphs()

◆ makeTestGraph0()

◆ makeTestGraph1()

◆ makeTestGraphA()

◆ makeTestGraphA2()

◆ makeTestGraphB()

◆ makeTestGraphC()

◆ makeTestGraphD()

◆ makeTestGraphDSub1()

◆ makeTestGraphDSub2()

◆ makeTestGraphE()

◆ makeTestGraphF()

◆ makeTestGraphG()

◆ makeTestGraphH()

◆ makeTestGraphI()

◆ makeTestGraphJ()

◆ makeTestGraphK()

◆ makeTestGraphL()

◆ makeTestGraphM()

◆ makeTestGraphN()

◆ prepare()

◆ testClone()

◆ testConvertSymmetricLabelsToSymmetricSets()

◆ testDetectSymVertexSets()

◆ testEmbedPatternsInTemplates()

◆ testExtractSubgraph()

◆ testExtractSubgraphFromCollection()

◆ testFindSymmetrySetsOfChildVertexes()

◆ testFindVertex()

◆ testFromToJSON()

◆ testGetAvailableAPs_returnsListOfAvailableAPs()

◆ testGetChildrenTree()

◆ testGetChildrenTreeWithBranchIdentifier()

◆ testGetEdgesWithSrcOrTrg()

◆ testGetEmbeddedGraphInClone()

◆ testGetEmbeddingPath()

◆ testGetInterfaceAPs()

◆ testGetLevel()

◆ testGetMutationSites()

◆ testGetSourceVertex()

◆ testGetSubgraphAPs()

◆ testGetSymmetricSubGraphs()

◆ testGraphIsomorphism()

◆ testIsIsostructuralTo()

◆ testRemoveCapping()

◆ testRemoveUnusedRCVs()

◆ testRemoveVertex()

◆ testReplaceSubGraph()

◆ testReplaceSubGraph_inTemplate()

◆ testReplaceVertex()

◆ testReplaceVertex_inRing()

◆ testSameAs_DiffRings()

◆ testSameAs_DiffSymmSet()

◆ testSameAs_DiffVertex()

◆ testSameAs_DisorderRings()

◆ testSameAs_Equal()

◆ testSameAs_SameRings()

◆ testSameAs_SameSymmSet()

◆ testSymmetricSetLabels()

Member Data Documentation

◆ a

◆ APCA

◆ APCB

◆ APCC

◆ APCD

◆ b

◆ c

◆ cap

◆ CAPP

◆ d