org::gel::mauve::dcjx::Permutation Class Reference

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

[legend]List of all members.

Public Member Functions
Adjacency[]	getAdjacencies ()
FastAccessTable	getFAT ()
String	getName ()
	Permutation (String g, Map< String, Integer > blockIdMap)
	Permutation (String g, Map< String, Integer > blockIdMap, String name)
void	printDesc (PrintStream out)
String	toString ()
Static Public Member Functions
void	addAdjacencies (Contig[] chrom, Adjacency[] adj, int[][] loc, Map< String, Integer > blockIdMap)
void	addLocations (Block b1, Block b2, int idx, int[][] loc, Map< String, Integer > blockIdMap)
boolean	equalContents (String X, String Y)
	Returns true if the two permutations have equal content, false otherwise.
Private Attributes
Adjacency[]	adj
Contig[]	chrom
FastAccessTable	fat
int[][]	loc
	a BLOCK_COUNT x 2 array storing positions of heads and tails in the Adjacency array loc[][0] := tail loc[][1] := head
String	name = ""
int	numChrom
	A map for holding identifiers.
int	numLinear

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Detailed Description

Author:

atritt

Definition at line 13 of file Permutation.java.

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Constructor & Destructor Documentation

org::gel::mauve::dcjx::Permutation::Permutation (  String  g, Map< String, Integer >  blockIdMap, String  name )  [inline]

Definition at line 40 of file Permutation.java.

org::gel::mauve::dcjx::Permutation::Permutation (  String  g, Map< String, Integer >  blockIdMap )  [inline]

Definition at line 45 of file Permutation.java. References addAdjacencies(), adj, fat, org::gel::mauve::dcjx::Contig::hasBlocks(), org::gel::mauve::dcjx::Contig::isCirc, loc, numChrom, and numLinear.

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Member Function Documentation

void org::gel::mauve::dcjx::Permutation::addAdjacencies (  Contig[]  chrom, Adjacency[]  adj, int  loc[][], Map< String, Integer >  blockIdMap )  [inline, static]

Parameters: chrom  adj  loc  Definition at line 113 of file Permutation.java. References addLocations(), org::gel::mauve::dcjx::Contig::getBlocks(), org::gel::mauve::dcjx::Block::getLeftEnd(), org::gel::mauve::dcjx::Block::getName(), getName(), org::gel::mauve::dcjx::Block::getRightEnd(), and org::gel::mauve::dcjx::Block::isInverted(). Referenced by Permutation().

void org::gel::mauve::dcjx::Permutation::addLocations (  Block  b1, Block  b2, int  idx, int  loc[][], Map< String, Integer >  blockIdMap )  [inline, static]

Definition at line 90 of file Permutation.java. References org::gel::mauve::dcjx::Block::getName(), and org::gel::mauve::dcjx::Block::isInverted(). Referenced by addAdjacencies().

boolean org::gel::mauve::dcjx::Permutation::equalContents (  String  X, String  Y )  [inline, static]

Returns true if the two permutations have equal content, false otherwise. complexity ~ O(max(|X|,|Y|)) Parameters: X  Y  Returns: true if (X) U (Y) == empty set, false otherwise Definition at line 161 of file Permutation.java.

Adjacency [] org::gel::mauve::dcjx::Permutation::getAdjacencies (   )  [inline]

Definition at line 70 of file Permutation.java. References adj. Referenced by org::gel::mauve::dcjx::AdjacencyGraph::AdjacencyGraph().

FastAccessTable org::gel::mauve::dcjx::Permutation::getFAT (   )  [inline]

Definition at line 74 of file Permutation.java. References fat. Referenced by org::gel::mauve::dcjx::AdjacencyGraph::AdjacencyGraph().

String org::gel::mauve::dcjx::Permutation::getName (   )  [inline]

Definition at line 66 of file Permutation.java. Referenced by addAdjacencies().

void org::gel::mauve::dcjx::Permutation::printDesc (  PrintStream  out  )  [inline]

Definition at line 78 of file Permutation.java. References toString().

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

Definition at line 82 of file Permutation.java. Referenced by printDesc().

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Member Data Documentation

Adjacency [] org::gel::mauve::dcjx::Permutation::adj [private]

Definition at line 24 of file Permutation.java. Referenced by getAdjacencies(), and Permutation().

Contig [] org::gel::mauve::dcjx::Permutation::chrom [private]

Definition at line 34 of file Permutation.java.

FastAccessTable org::gel::mauve::dcjx::Permutation::fat [private]

Definition at line 32 of file Permutation.java. Referenced by getFAT(), and Permutation().

int [][] org::gel::mauve::dcjx::Permutation::loc [private]

a BLOCK_COUNT x 2 array storing positions of heads and tails in the Adjacency array loc[][0] := tail loc[][1] := head Definition at line 30 of file Permutation.java. Referenced by Permutation().

String org::gel::mauve::dcjx::Permutation::name = "" [private]

Definition at line 38 of file Permutation.java.

int org::gel::mauve::dcjx::Permutation::numChrom [private]

A map for holding identifiers. Definition at line 22 of file Permutation.java. Referenced by Permutation().

int org::gel::mauve::dcjx::Permutation::numLinear [private]

Definition at line 36 of file Permutation.java. Referenced by Permutation().

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

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

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