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

List of all members.

Public Member Functions
void	cycleDCJ ()
boolean	DCJ (Vert v)
	DCJ (StringTokenizer A, StringTokenizer B, String species1, String species2)
	DCJ (StringTokenizer A, StringTokenizer B)
	DCJ ()
int	getCount ()
String	getLog ()
String	getOpBuf ()
void	loadGenome (StringTokenizer tokenA, StringTokenizer tokenB)
void	parseAndLoadBlack (String s)
void	parseAndLoadGrey (String s, SB[] sbArray)
void	printSBBlack ()
void	printSBV ()
void	resetSbVisit ()
int[]	toIntArray (String s)
SB[]	toSBArray ()
void	traverseAndClose ()
Vert	traverseBlack (Vert last, SB current)
Public Attributes
StringBuffer	buf
int	bufsize = 256
int	counta = 0
int	countb = 0
int	countDCJ = 0
StringBuffer	opBuf
boolean	suppress = false
Package Attributes
Vector	capVector
Vector	greyVector
Vector	sbVector
String	speciesA = ""
String	speciesB = ""

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Detailed Description

Deprecated:

Author:

Mike Tsai

Definition at line 10 of file DCJ.java.

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Constructor & Destructor Documentation

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

Definition at line 435 of file DCJ.java. References buf, bufsize, and greyVector.

org::gel::mauve::dcj::DCJ::DCJ (  StringTokenizer  A, StringTokenizer  B )  [inline]

Definition at line 442 of file DCJ.java. References buf, bufsize, greyVector, loadGenome(), and opBuf.

org::gel::mauve::dcj::DCJ::DCJ (  StringTokenizer  A, StringTokenizer  B, String  species1, String  species2 )  [inline]

Definition at line 454 of file DCJ.java. References buf, bufsize, greyVector, loadGenome(), opBuf, speciesA, and speciesB.

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

Definition at line 507 of file DCJ.java. References buf, countDCJ, org::gel::mauve::dcj::DCJ::Vert::getBlack(), org::gel::mauve::dcj::DCJ::Vert::getGene(), org::gel::mauve::dcj::DCJ::Vert::getGrey(), org::gel::mauve::dcj::DCJ::Vert::isOneCycle(), org::gel::mauve::dcj::DCJ::Vert::joinBlack(), opBuf, and suppress.

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Member Function Documentation

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

Definition at line 469 of file DCJ.java. References buf, countDCJ, greyVector, and suppress.

int org::gel::mauve::dcj::DCJ::getCount (   )  [inline]

Definition at line 502 of file DCJ.java. References countDCJ. Referenced by org::gel::mauve::dcj::DCJWindow::SubmitData::actionPerformed(), and org::gel::mauve::dcj::DCJWindow::performDCJ().

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

Definition at line 486 of file DCJ.java.

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

Definition at line 490 of file DCJ.java. Referenced by org::gel::mauve::dcj::DCJWindow::SubmitData::actionPerformed(), and org::gel::mauve::dcj::DCJWindow::performDCJ().

void org::gel::mauve::dcj::DCJ::loadGenome (  StringTokenizer  tokenA, StringTokenizer  tokenB )  [inline]

Definition at line 668 of file DCJ.java. Referenced by DCJ().

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

Definition at line 572 of file DCJ.java. References capVector, org::gel::mauve::dcj::DCJ::SB::setVertPointers(), and org::gel::mauve::dcj::DCJ::SB::turnValue().

void org::gel::mauve::dcj::DCJ::parseAndLoadGrey (  String  s, SB[]  sbArray )  [inline]

Definition at line 549 of file DCJ.java. References capVector, org::gel::mauve::dcj::DCJ::SB::getHeadB(), org::gel::mauve::dcj::DCJ::Vert::joinGrey(), and org::gel::mauve::dcj::DCJ::SB::setValueB().

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

Definition at line 735 of file DCJ.java. References buf, org::gel::mauve::dcj::DCJ::Vert::getBlack(), org::gel::mauve::dcj::DCJ::Vert::getGene(), org::gel::mauve::dcj::DCJ::SB::getLeft(), org::gel::mauve::dcj::DCJ::Vert::getSB(), org::gel::mauve::dcj::DCJ::Vert::isCap, traverseBlack(), and org::gel::mauve::dcj::DCJ::SB::wasVisited().

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

Definition at line 718 of file DCJ.java. References org::gel::mauve::dcj::DCJ::SB::getLeft(), org::gel::mauve::dcj::DCJ::SB::getRight(), and org::gel::mauve::dcj::DCJ::Vert::printMe().

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

Definition at line 709 of file DCJ.java. References org::gel::mauve::dcj::DCJ::SB::setVisited().

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

Definition at line 658 of file DCJ.java.

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

Definition at line 640 of file DCJ.java. References org::gel::mauve::dcj::DCJ::SB::getValueA().

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

Definition at line 607 of file DCJ.java. References org::gel::mauve::dcj::DCJ::Vert::closePath(), org::gel::mauve::dcj::DCJ::Vert::getBlack(), org::gel::mauve::dcj::DCJ::Vert::getCap(), org::gel::mauve::dcj::DCJ::Vert::getGrey(), org::gel::mauve::dcj::DCJ::SB::getLeft(), org::gel::mauve::dcj::DCJ::SB::getRight(), greyVector, sbVector, org::gel::mauve::dcj::DCJ::Vert::seen(), org::gel::mauve::dcj::DCJ::Vert::setSeen(), and org::gel::mauve::dcj::DCJ::Vert::traversePath().

Vert org::gel::mauve::dcj::DCJ::traverseBlack (  Vert  last, SB  current )  [inline]

Definition at line 690 of file DCJ.java. References buf, org::gel::mauve::dcj::DCJ::Vert::getBlack(), org::gel::mauve::dcj::DCJ::SB::getLeft(), org::gel::mauve::dcj::DCJ::SB::getRight(), org::gel::mauve::dcj::DCJ::Vert::getSB(), org::gel::mauve::dcj::DCJ::SB::getValueA(), org::gel::mauve::dcj::DCJ::Vert::isCap, org::gel::mauve::dcj::DCJ::SB::setVisited(), and org::gel::mauve::dcj::DCJ::SB::wasVisited(). Referenced by printSBBlack().

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Member Data Documentation

StringBuffer org::gel::mauve::dcj::DCJ::buf

Definition at line 419 of file DCJ.java. Referenced by cycleDCJ(), DCJ(), printSBBlack(), and traverseBlack().

int org::gel::mauve::dcj::DCJ::bufsize = 256

Definition at line 417 of file DCJ.java. Referenced by DCJ().

Vector org::gel::mauve::dcj::DCJ::capVector [package]

Definition at line 429 of file DCJ.java. Referenced by parseAndLoadBlack(), and parseAndLoadGrey().

int org::gel::mauve::dcj::DCJ::counta = 0

Definition at line 411 of file DCJ.java.

int org::gel::mauve::dcj::DCJ::countb = 0

Definition at line 413 of file DCJ.java.

int org::gel::mauve::dcj::DCJ::countDCJ = 0

Definition at line 415 of file DCJ.java. Referenced by cycleDCJ(), DCJ(), and getCount().

Vector org::gel::mauve::dcj::DCJ::greyVector [package]

Definition at line 433 of file DCJ.java. Referenced by cycleDCJ(), DCJ(), and traverseAndClose().

StringBuffer org::gel::mauve::dcj::DCJ::opBuf

Definition at line 421 of file DCJ.java. Referenced by DCJ().

Vector org::gel::mauve::dcj::DCJ::sbVector [package]

Definition at line 431 of file DCJ.java. Referenced by traverseAndClose().

String org::gel::mauve::dcj::DCJ::speciesA = "" [package]

Definition at line 425 of file DCJ.java. Referenced by DCJ().

String org::gel::mauve::dcj::DCJ::speciesB = "" [package]

Definition at line 427 of file DCJ.java. Referenced by DCJ().

boolean org::gel::mauve::dcj::DCJ::suppress = false

Definition at line 423 of file DCJ.java. Referenced by cycleDCJ(), and DCJ().

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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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