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

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

Collaboration graph
[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

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.


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().


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().


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