org::gel::mauve::dcjx::Contig Class Reference

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

[legend]List of all members.

Public Member Functions
	Contig (String ch, String name)
	Contig (String ch)
boolean	equals (Contig o)
Block[]	getBlocks ()
boolean	hasBlocks ()
boolean	isCirc ()
String	toString ()
Private Attributes
Block[]	blocks
String	id
boolean	isCirc
String	name = ""
int	numBlocks
Static Private Attributes
String	VALID_BLOCK_NAME = "[A-Za-z0-9_-]+"

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Detailed Description

Author:

atritt

Definition at line 20 of file Contig.java.

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Constructor & Destructor Documentation

org::gel::mauve::dcjx::Contig::Contig (  String  ch  )  [inline]

Definition at line 34 of file Contig.java. References blocks, isCirc, numBlocks, and VALID_BLOCK_NAME.

org::gel::mauve::dcjx::Contig::Contig (  String  ch, String  name )  [inline]

Definition at line 73 of file Contig.java.

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Member Function Documentation

boolean org::gel::mauve::dcjx::Contig::equals (  Contig  o  )  [inline]

Definition at line 105 of file Contig.java. References id.

Block [] org::gel::mauve::dcjx::Contig::getBlocks (   )  [inline]

Definition at line 83 of file Contig.java. References blocks. Referenced by org::gel::mauve::dcjx::Permutation::addAdjacencies().

boolean org::gel::mauve::dcjx::Contig::hasBlocks (   )  [inline]

Definition at line 87 of file Contig.java. References blocks. Referenced by org::gel::mauve::dcjx::Permutation::Permutation().

boolean org::gel::mauve::dcjx::Contig::isCirc (   )  [inline]

Definition at line 79 of file Contig.java.

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

Definition at line 91 of file Contig.java. References blocks.

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Member Data Documentation

Block [] org::gel::mauve::dcjx::Contig::blocks [private]

Definition at line 28 of file Contig.java. Referenced by Contig(), getBlocks(), hasBlocks(), and toString().

String org::gel::mauve::dcjx::Contig::id [private]

Definition at line 30 of file Contig.java. Referenced by equals().

boolean org::gel::mauve::dcjx::Contig::isCirc [private]

Definition at line 24 of file Contig.java. Referenced by Contig(), and org::gel::mauve::dcjx::Permutation::Permutation().

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

Definition at line 32 of file Contig.java.

int org::gel::mauve::dcjx::Contig::numBlocks [private]

Definition at line 26 of file Contig.java. Referenced by Contig().

String org::gel::mauve::dcjx::Contig::VALID_BLOCK_NAME = "[A-Za-z0-9_-]+" [static, private]

Definition at line 22 of file Contig.java. Referenced by Contig().

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

• src/org/gel/mauve/dcjx/Contig.java

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