org::gel::mauve::dcjx::Adjacency Class Reference

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

[legend]List of all members.

Public Member Functions
	Adjacency (String first)
	Adjacency (String first, String second)
Adjacency	getE1 ()
Adjacency	getE2 ()
String	getFirstBlock ()
String	getFirstBlockEnd ()
String	getSecondBlock ()
String	getSecondBlockEnd ()
boolean	isTelo ()
void	resetVisited ()
void	setVisited ()
String	toString ()
boolean	wasVisited ()
Static Public Member Functions
void	addAdjacencyEdge (Adjacency a, Adjacency b)
Private Attributes
Adjacency	e1
Adjacency	e2
String	first
boolean	isTelo
String	second
boolean	visited

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Constructor & Destructor Documentation

org::gel::mauve::dcjx::Adjacency::Adjacency (  String  first, String  second )  [inline]

Definition at line 15 of file Adjacency.java. References isTelo.

org::gel::mauve::dcjx::Adjacency::Adjacency (  String  first  )  [inline]

Definition at line 21 of file Adjacency.java. References isTelo.

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Member Function Documentation

void org::gel::mauve::dcjx::Adjacency::addAdjacencyEdge (  Adjacency  a, Adjacency  b )  [inline, static]

Definition at line 60 of file Adjacency.java. References e1, and e2.

Adjacency org::gel::mauve::dcjx::Adjacency::getE1 (   )  [inline]

Definition at line 52 of file Adjacency.java. References e1. Referenced by org::gel::mauve::dcjx::AdjacencyGraph::countEdges(), org::gel::mauve::dcjx::AdjacencyGraph::isCycle(), and org::gel::mauve::dcjx::AdjacencyGraph::resetVisited().

Adjacency org::gel::mauve::dcjx::Adjacency::getE2 (   )  [inline]

Definition at line 56 of file Adjacency.java. References e2. Referenced by org::gel::mauve::dcjx::AdjacencyGraph::countEdges(), org::gel::mauve::dcjx::AdjacencyGraph::isCycle(), and org::gel::mauve::dcjx::AdjacencyGraph::resetVisited().

String org::gel::mauve::dcjx::Adjacency::getFirstBlock (   )  [inline]

Definition at line 86 of file Adjacency.java.

String org::gel::mauve::dcjx::Adjacency::getFirstBlockEnd (   )  [inline]

Definition at line 90 of file Adjacency.java. Referenced by org::gel::mauve::dcjx::AdjacencyGraph::AdjacencyGraph(), and org::gel::mauve::assembly::AssemblyScorer::computeAdjacencyErrors().

String org::gel::mauve::dcjx::Adjacency::getSecondBlock (   )  [inline]

Definition at line 98 of file Adjacency.java. References second.

String org::gel::mauve::dcjx::Adjacency::getSecondBlockEnd (   )  [inline]

Definition at line 94 of file Adjacency.java. References second. Referenced by org::gel::mauve::dcjx::AdjacencyGraph::AdjacencyGraph(), and org::gel::mauve::assembly::AssemblyScorer::computeAdjacencyErrors().

boolean org::gel::mauve::dcjx::Adjacency::isTelo (   )  [inline]

Definition at line 36 of file Adjacency.java.

void org::gel::mauve::dcjx::Adjacency::resetVisited (   )  [inline]

Definition at line 44 of file Adjacency.java. Referenced by org::gel::mauve::dcjx::AdjacencyGraph::resetVisited(), and org::gel::mauve::dcjx::AdjacencyGraph::resetVisitedAll().

void org::gel::mauve::dcjx::Adjacency::setVisited (   )  [inline]

Definition at line 48 of file Adjacency.java. Referenced by org::gel::mauve::dcjx::AdjacencyGraph::countEdges(), and org::gel::mauve::dcjx::AdjacencyGraph::isCycle().

String org::gel::mauve::dcjx::Adjacency::toString (   )  [inline]

Definition at line 28 of file Adjacency.java. References isTelo, and second.

boolean org::gel::mauve::dcjx::Adjacency::wasVisited (   )  [inline]

Definition at line 40 of file Adjacency.java. Referenced by org::gel::mauve::dcjx::AdjacencyGraph::countCycles(), org::gel::mauve::dcjx::AdjacencyGraph::countEdges(), org::gel::mauve::dcjx::AdjacencyGraph::countLen2Cycles(), org::gel::mauve::dcjx::AdjacencyGraph::countOddPaths(), org::gel::mauve::dcjx::AdjacencyGraph::countPathsGreaterThan2(), org::gel::mauve::dcjx::AdjacencyGraph::countSingleEdgePaths(), org::gel::mauve::dcjx::AdjacencyGraph::isCycle(), and org::gel::mauve::dcjx::AdjacencyGraph::resetVisited().

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Member Data Documentation

Adjacency org::gel::mauve::dcjx::Adjacency::e1 [private]

Definition at line 9 of file Adjacency.java. Referenced by addAdjacencyEdge(), and getE1().

Adjacency org::gel::mauve::dcjx::Adjacency::e2 [private]

Definition at line 11 of file Adjacency.java. Referenced by addAdjacencyEdge(), and getE2().

String org::gel::mauve::dcjx::Adjacency::first [private]

Definition at line 5 of file Adjacency.java.

boolean org::gel::mauve::dcjx::Adjacency::isTelo [private]

Definition at line 7 of file Adjacency.java. Referenced by Adjacency(), org::gel::mauve::dcjx::AdjacencyGraph::AdjacencyGraph(), org::gel::mauve::dcjx::AdjacencyGraph::countEdges(), org::gel::mauve::dcjx::AdjacencyGraph::isCycle(), org::gel::mauve::dcjx::AdjacencyGraph::resetVisited(), and toString().

String org::gel::mauve::dcjx::Adjacency::second [private]

Definition at line 6 of file Adjacency.java. Referenced by getSecondBlock(), getSecondBlockEnd(), and toString().

boolean org::gel::mauve::dcjx::Adjacency::visited [private]

Definition at line 13 of file Adjacency.java.

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

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

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