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

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

Collaboration graph
[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

Detailed Description

Author:
atritt

Definition at line 13 of file Permutation.java.


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.


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().


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().


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