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

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

Collaboration graph
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_-]+"

Detailed Description


Definition at line 20 of file

Constructor & Destructor Documentation

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

Definition at line 34 of file

References blocks, isCirc, numBlocks, and VALID_BLOCK_NAME.

org::gel::mauve::dcjx::Contig::Contig String  ch,
String  name

Definition at line 73 of file

Member Function Documentation

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

Definition at line 105 of file

References id.

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

Definition at line 83 of file

References blocks.

Referenced by org::gel::mauve::dcjx::Permutation::addAdjacencies().

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

Definition at line 87 of file

References blocks.

Referenced by org::gel::mauve::dcjx::Permutation::Permutation().

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

Definition at line 79 of file

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

Definition at line 91 of file

References blocks.

Member Data Documentation

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

Definition at line 28 of file

Referenced by Contig(), getBlocks(), hasBlocks(), and toString().

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

Definition at line 30 of file

Referenced by equals().

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

Definition at line 24 of file

Referenced by Contig(), and org::gel::mauve::dcjx::Permutation::Permutation().

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

Definition at line 32 of file

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

Definition at line 26 of file

Referenced by Contig().

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

Definition at line 22 of file

Referenced by Contig().

The documentation for this class was generated from the following file:
Generated on Mon Aug 19 06:03:57 2013 for Mauve by doxygen 1.3.6