org::gel::mauve::dcjx::AdjacencyGraph Class Reference

Collaboration diagram for org::gel::mauve::dcjx::AdjacencyGraph:

[legend]List of all members.

Public Member Functions
	AdjacencyGraph (Permutation A, Permutation B)
Adjacency[]	getGenomeA ()
Adjacency[]	getGenomeB ()
int	numCycles ()
	Returns the number of cycles in the adjacency graph.
int	numLen1Paths ()
	Returns the number of paths in the adjacency graph of length 1.
int	numLen2Cycles ()
	Returns the number of cycles in the adjacency graph of length 2.
int	numOddPaths ()
	Returns the number of paths in the adjacency graph with an odd length.
int	numPaths2 ()
	Returns the number of paths in the adjacency graph of length 2 or more.
Private Member Functions
int	countCycles ()
int	countEdges (Adjacency a)
int	countLen2Cycles ()
int	countOddPaths ()
int	countPathsGreaterThan2 ()
int	countSingleEdgePaths ()
boolean	isCycle (Adjacency a)
void	resetVisited (Adjacency a)
void	resetVisitedAll ()
Private Attributes
Adjacency[]	adjA
Adjacency[]	adjB
int	numCycles
int	numLen1Paths
int	numLen2Cycles
int	numOddPaths
int	numPathsGreaterThan2

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Constructor & Destructor Documentation

org::gel::mauve::dcjx::AdjacencyGraph::AdjacencyGraph (  Permutation  A, Permutation  B )  [inline]

Definition at line 23 of file AdjacencyGraph.java. References adjA, adjB, countCycles(), countLen2Cycles(), countOddPaths(), countPathsGreaterThan2(), countSingleEdgePaths(), org::gel::mauve::dcjx::Permutation::getAdjacencies(), org::gel::mauve::dcjx::FastAccessTable::getAdjacency(), org::gel::mauve::dcjx::Permutation::getFAT(), org::gel::mauve::dcjx::Adjacency::getFirstBlockEnd(), org::gel::mauve::dcjx::Adjacency::getSecondBlockEnd(), org::gel::mauve::dcjx::Adjacency::isTelo, numCycles, numLen1Paths, numLen2Cycles, numOddPaths, and numPathsGreaterThan2.

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Member Function Documentation

int org::gel::mauve::dcjx::AdjacencyGraph::countCycles (   )  [inline, private]

Definition at line 130 of file AdjacencyGraph.java. References adjA, isCycle(), resetVisitedAll(), and org::gel::mauve::dcjx::Adjacency::wasVisited(). Referenced by AdjacencyGraph().

int org::gel::mauve::dcjx::AdjacencyGraph::countEdges (  Adjacency  a  )  [inline, private]

Definition at line 190 of file AdjacencyGraph.java. References org::gel::mauve::dcjx::Adjacency::getE1(), org::gel::mauve::dcjx::Adjacency::getE2(), org::gel::mauve::dcjx::Adjacency::isTelo, org::gel::mauve::dcjx::Adjacency::setVisited(), and org::gel::mauve::dcjx::Adjacency::wasVisited(). Referenced by countLen2Cycles(), countOddPaths(), countPathsGreaterThan2(), and countSingleEdgePaths().

int org::gel::mauve::dcjx::AdjacencyGraph::countLen2Cycles (   )  [inline, private]

Definition at line 113 of file AdjacencyGraph.java. References adjA, countEdges(), isCycle(), resetVisited(), resetVisitedAll(), and org::gel::mauve::dcjx::Adjacency::wasVisited(). Referenced by AdjacencyGraph().

int org::gel::mauve::dcjx::AdjacencyGraph::countOddPaths (   )  [inline, private]

Definition at line 145 of file AdjacencyGraph.java. References adjA, countEdges(), resetVisitedAll(), and org::gel::mauve::dcjx::Adjacency::wasVisited(). Referenced by AdjacencyGraph().

int org::gel::mauve::dcjx::AdjacencyGraph::countPathsGreaterThan2 (   )  [inline, private]

Definition at line 173 of file AdjacencyGraph.java. References adjA, countEdges(), isCycle(), resetVisited(), resetVisitedAll(), and org::gel::mauve::dcjx::Adjacency::wasVisited(). Referenced by AdjacencyGraph().

int org::gel::mauve::dcjx::AdjacencyGraph::countSingleEdgePaths (   )  [inline, private]

Definition at line 159 of file AdjacencyGraph.java. References adjA, countEdges(), resetVisitedAll(), and org::gel::mauve::dcjx::Adjacency::wasVisited(). Referenced by AdjacencyGraph().

Adjacency [] org::gel::mauve::dcjx::AdjacencyGraph::getGenomeA (   )  [inline]

Definition at line 56 of file AdjacencyGraph.java. References adjA.

Adjacency [] org::gel::mauve::dcjx::AdjacencyGraph::getGenomeB (   )  [inline]

Definition at line 60 of file AdjacencyGraph.java. References adjB.

boolean org::gel::mauve::dcjx::AdjacencyGraph::isCycle (  Adjacency  a  )  [inline, private]

Definition at line 217 of file AdjacencyGraph.java. References org::gel::mauve::dcjx::Adjacency::getE1(), org::gel::mauve::dcjx::Adjacency::getE2(), org::gel::mauve::dcjx::Adjacency::isTelo, org::gel::mauve::dcjx::Adjacency::setVisited(), and org::gel::mauve::dcjx::Adjacency::wasVisited(). Referenced by countCycles(), countLen2Cycles(), and countPathsGreaterThan2().

int org::gel::mauve::dcjx::AdjacencyGraph::numCycles (   )  [inline]

Returns the number of cycles in the adjacency graph. Returns: the number of cycles in the adjacency graph Definition at line 79 of file AdjacencyGraph.java.

int org::gel::mauve::dcjx::AdjacencyGraph::numLen1Paths (   )  [inline]

Returns the number of paths in the adjacency graph of length 1. Returns: the number of paths of length 1 Definition at line 99 of file AdjacencyGraph.java.

int org::gel::mauve::dcjx::AdjacencyGraph::numLen2Cycles (   )  [inline]

Returns the number of cycles in the adjacency graph of length 2. Returns: the number of cycles of length 2 Definition at line 89 of file AdjacencyGraph.java.

int org::gel::mauve::dcjx::AdjacencyGraph::numOddPaths (   )  [inline]

Returns the number of paths in the adjacency graph with an odd length. Returns: the number of paths with an odd length Definition at line 70 of file AdjacencyGraph.java.

int org::gel::mauve::dcjx::AdjacencyGraph::numPaths2 (   )  [inline]

Returns the number of paths in the adjacency graph of length 2 or more. Returns: the number of paths of length 2 or more Definition at line 109 of file AdjacencyGraph.java. References numPathsGreaterThan2. Referenced by org::gel::mauve::dcjx::DCJ::calculateDistances().

void org::gel::mauve::dcjx::AdjacencyGraph::resetVisited (  Adjacency  a  )  [inline, private]

Definition at line 241 of file AdjacencyGraph.java. References org::gel::mauve::dcjx::Adjacency::getE1(), org::gel::mauve::dcjx::Adjacency::getE2(), org::gel::mauve::dcjx::Adjacency::isTelo, org::gel::mauve::dcjx::Adjacency::resetVisited(), and org::gel::mauve::dcjx::Adjacency::wasVisited(). Referenced by countLen2Cycles(), and countPathsGreaterThan2().

void org::gel::mauve::dcjx::AdjacencyGraph::resetVisitedAll (   )  [inline, private]

Definition at line 232 of file AdjacencyGraph.java. References adjA, adjB, and org::gel::mauve::dcjx::Adjacency::resetVisited(). Referenced by countCycles(), countLen2Cycles(), countOddPaths(), countPathsGreaterThan2(), and countSingleEdgePaths().

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Member Data Documentation

Adjacency [] org::gel::mauve::dcjx::AdjacencyGraph::adjA [private]

Definition at line 5 of file AdjacencyGraph.java. Referenced by AdjacencyGraph(), countCycles(), countLen2Cycles(), countOddPaths(), countPathsGreaterThan2(), countSingleEdgePaths(), getGenomeA(), and resetVisitedAll().

Adjacency [] org::gel::mauve::dcjx::AdjacencyGraph::adjB [private]

Definition at line 9 of file AdjacencyGraph.java. Referenced by AdjacencyGraph(), getGenomeB(), and resetVisitedAll().

int org::gel::mauve::dcjx::AdjacencyGraph::numCycles [private]

Definition at line 11 of file AdjacencyGraph.java. Referenced by AdjacencyGraph(), org::gel::mauve::dcjx::DCJ::calculateDistances(), org::gel::mauve::dcjx::DCJ::computeDCJ(), and org::gel::mauve::dcjx::VestigialDCJ::main().

int org::gel::mauve::dcjx::AdjacencyGraph::numLen1Paths [private]

Definition at line 17 of file AdjacencyGraph.java. Referenced by AdjacencyGraph(), and org::gel::mauve::dcjx::DCJ::calculateDistances().

int org::gel::mauve::dcjx::AdjacencyGraph::numLen2Cycles [private]

Definition at line 15 of file AdjacencyGraph.java. Referenced by AdjacencyGraph(), and org::gel::mauve::dcjx::DCJ::calculateDistances().

int org::gel::mauve::dcjx::AdjacencyGraph::numOddPaths [private]

Definition at line 13 of file AdjacencyGraph.java. Referenced by AdjacencyGraph(), org::gel::mauve::dcjx::DCJ::calculateDistances(), org::gel::mauve::dcjx::DCJ::computeDCJ(), and org::gel::mauve::dcjx::VestigialDCJ::main().

int org::gel::mauve::dcjx::AdjacencyGraph::numPathsGreaterThan2 [private]

Definition at line 19 of file AdjacencyGraph.java. Referenced by AdjacencyGraph(), and numPaths2().

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

• src/org/gel/mauve/dcjx/AdjacencyGraph.java

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