org::gel::mauve::dcj::DCJ::Vert Class Reference

Collaboration diagram for org::gel::mauve::dcj::DCJ::Vert:

[legend]List of all members.

Public Member Functions
Vert	cap (boolean b)
void	closePath (Vert b)
Vert	getBlack ()
String	getCap ()
String	getChromosome ()
String	getGene ()
Vert	getGrey ()
SB	getSB ()
boolean	isCap ()
boolean	isOneCycle ()
void	joinBlack (Vert b)
void	joinGrey (Vert b)
void	printMe ()
boolean	seen ()
void	setBlack (Vert v)
void	setChromosome (String s)
void	setGene (String s)
void	setGrey (Vert v)
void	setIsCap (String b)
void	setSB (SB s)
void	setSeen (boolean b)
Vert	traversePath (boolean b, Vector v)
Vert	traversePath (boolean b)
	Vert (String s)
	Vert (Vert b, Vert g, String s)
	Vert ()
Private Attributes
Vert	black
String	chromosome
String	gene
Vert	grey
String	isCap
SB	sb
boolean	seenCap

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Constructor & Destructor Documentation

org::gel::mauve::dcj::DCJ::Vert::Vert (   )  [inline]

Definition at line 181 of file DCJ.java. References black, chromosome, gene, grey, isCap, sb, and seenCap. Referenced by cap().

org::gel::mauve::dcj::DCJ::Vert::Vert (  Vert  b, Vert  g, String  s )  [inline]

Definition at line 192 of file DCJ.java. References chromosome, gene, grey, isCap, sb, and seenCap.

org::gel::mauve::dcj::DCJ::Vert::Vert (  String  s  )  [inline]

Definition at line 202 of file DCJ.java. References chromosome, isCap, sb, and seenCap.

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Member Function Documentation

Vert org::gel::mauve::dcj::DCJ::Vert::cap (  boolean  b  )  [inline]

Definition at line 245 of file DCJ.java. References getGene(), setBlack(), setGene(), setGrey(), setIsCap(), setSB(), and Vert().

void org::gel::mauve::dcj::DCJ::Vert::closePath (  Vert  b  )  [inline]

Definition at line 359 of file DCJ.java. References getCap(), getGrey(), and setGrey(). Referenced by org::gel::mauve::dcj::DCJ::traverseAndClose().

Vert org::gel::mauve::dcj::DCJ::Vert::getBlack (   )  [inline]

Definition at line 272 of file DCJ.java. References black. Referenced by org::gel::mauve::dcj::DCJ::DCJ(), org::gel::mauve::dcj::DCJ::printSBBlack(), org::gel::mauve::dcj::DCJ::traverseAndClose(), org::gel::mauve::dcj::DCJ::traverseBlack(), and traversePath().

String org::gel::mauve::dcj::DCJ::Vert::getCap (   )  [inline]

Definition at line 284 of file DCJ.java. Referenced by closePath(), and org::gel::mauve::dcj::DCJ::traverseAndClose().

String org::gel::mauve::dcj::DCJ::Vert::getChromosome (   )  [inline]

Definition at line 292 of file DCJ.java.

String org::gel::mauve::dcj::DCJ::Vert::getGene (   )  [inline]

Definition at line 268 of file DCJ.java. Referenced by cap(), org::gel::mauve::dcj::DCJ::DCJ(), and org::gel::mauve::dcj::DCJ::printSBBlack().

Vert org::gel::mauve::dcj::DCJ::Vert::getGrey (   )  [inline]

Definition at line 276 of file DCJ.java. References grey. Referenced by closePath(), org::gel::mauve::dcj::DCJ::DCJ(), and org::gel::mauve::dcj::DCJ::traverseAndClose().

SB org::gel::mauve::dcj::DCJ::Vert::getSB (   )  [inline]

Definition at line 280 of file DCJ.java. Referenced by org::gel::mauve::dcj::DCJ::printSBBlack(), and org::gel::mauve::dcj::DCJ::traverseBlack().

boolean org::gel::mauve::dcj::DCJ::Vert::isCap (   )  [inline]

Definition at line 288 of file DCJ.java.

boolean org::gel::mauve::dcj::DCJ::Vert::isOneCycle (   )  [inline]

Definition at line 398 of file DCJ.java. Referenced by org::gel::mauve::dcj::DCJ::DCJ().

void org::gel::mauve::dcj::DCJ::Vert::joinBlack (  Vert  b  )  [inline]

Definition at line 385 of file DCJ.java. References setBlack(). Referenced by org::gel::mauve::dcj::DCJ::DCJ().

void org::gel::mauve::dcj::DCJ::Vert::joinGrey (  Vert  b  )  [inline]

Definition at line 391 of file DCJ.java. References setGrey(). Referenced by org::gel::mauve::dcj::DCJ::parseAndLoadGrey().

void org::gel::mauve::dcj::DCJ::Vert::printMe (   )  [inline]

Definition at line 303 of file DCJ.java. Referenced by org::gel::mauve::dcj::DCJ::printSBV().

boolean org::gel::mauve::dcj::DCJ::Vert::seen (   )  [inline]

Definition at line 296 of file DCJ.java. Referenced by org::gel::mauve::dcj::DCJ::traverseAndClose().

void org::gel::mauve::dcj::DCJ::Vert::setBlack (  Vert  v  )  [inline]

Definition at line 213 of file DCJ.java. Referenced by cap(), and joinBlack().

void org::gel::mauve::dcj::DCJ::Vert::setChromosome (  String  s  )  [inline]

Definition at line 230 of file DCJ.java.

void org::gel::mauve::dcj::DCJ::Vert::setGene (  String  s  )  [inline]

Definition at line 225 of file DCJ.java. Referenced by cap().

void org::gel::mauve::dcj::DCJ::Vert::setGrey (  Vert  v  )  [inline]

Definition at line 217 of file DCJ.java. Referenced by cap(), closePath(), and joinGrey().

void org::gel::mauve::dcj::DCJ::Vert::setIsCap (  String  b  )  [inline]

Definition at line 235 of file DCJ.java. Referenced by cap().

void org::gel::mauve::dcj::DCJ::Vert::setSB (  SB  s  )  [inline]

Definition at line 221 of file DCJ.java. Referenced by cap().

void org::gel::mauve::dcj::DCJ::Vert::setSeen (  boolean  b  )  [inline]

Definition at line 240 of file DCJ.java. Referenced by org::gel::mauve::dcj::DCJ::traverseAndClose().

Vert org::gel::mauve::dcj::DCJ::Vert::traversePath (  boolean  b, Vector  v )  [inline]

Definition at line 344 of file DCJ.java.

Vert org::gel::mauve::dcj::DCJ::Vert::traversePath (  boolean  b  )  [inline]

Definition at line 335 of file DCJ.java. References getBlack(). Referenced by org::gel::mauve::dcj::DCJ::traverseAndClose().

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Member Data Documentation

Vert org::gel::mauve::dcj::DCJ::Vert::black [private]

Definition at line 165 of file DCJ.java. Referenced by getBlack(), and Vert().

String org::gel::mauve::dcj::DCJ::Vert::chromosome [private]

Definition at line 175 of file DCJ.java. Referenced by Vert().

String org::gel::mauve::dcj::DCJ::Vert::gene [private]

Definition at line 171 of file DCJ.java. Referenced by Vert().

Vert org::gel::mauve::dcj::DCJ::Vert::grey [private]

Definition at line 167 of file DCJ.java. Referenced by getGrey(), and Vert().

String org::gel::mauve::dcj::DCJ::Vert::isCap [private]

Definition at line 173 of file DCJ.java. Referenced by org::gel::mauve::dcj::DCJ::printSBBlack(), org::gel::mauve::dcj::DCJ::traverseBlack(), and Vert().

SB org::gel::mauve::dcj::DCJ::Vert::sb [private]

Definition at line 169 of file DCJ.java. Referenced by Vert().

boolean org::gel::mauve::dcj::DCJ::Vert::seenCap [private]

Definition at line 177 of file DCJ.java. Referenced by Vert().

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

• src/org/gel/mauve/dcj/DCJ.java

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