org::gel::mauve::contigs::ContigGrouper::ContigGroup Class Reference

Collaboration diagram for org::gel::mauve::contigs::ContigGrouper::ContigGroup:

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List of all members.

Public Member Functions

void calculateWeight ()
 ContigGroup (LCB lcb)
HashSet getLCBs ()
long getLength ()
LinkedList getNonEmpty ()
boolean isReversed ()
boolean matchedToEdge (boolean left)
boolean mostWeightForward ()
void setReversed (boolean reverse)
String toString ()

Protected Attributes

Chromosome end
LCB first
LCB last
Boolean reversed
Chromosome start
long weight

Constructor & Destructor Documentation

org::gel::mauve::contigs::ContigGrouper::ContigGroup::ContigGroup LCB  lcb  )  [inline]
 

Definition at line 181 of file ContigGrouper.java.

References calculateWeight(), org::gel::mauve::contigs::ContigGrouper::getFirstOfLinkedContigs(), org::gel::mauve::LCB::getLeftEnd(), and getNonEmpty().


Member Function Documentation

void org::gel::mauve::contigs::ContigGrouper::ContigGroup::calculateWeight  )  [inline]
 

Definition at line 250 of file ContigGrouper.java.

References getLCBs(), and weight.

Referenced by ContigGroup().

HashSet org::gel::mauve::contigs::ContigGrouper::ContigGroup::getLCBs  )  [inline]
 

Definition at line 239 of file ContigGrouper.java.

References first, and last.

Referenced by calculateWeight(), and mostWeightForward().

long org::gel::mauve::contigs::ContigGrouper::ContigGroup::getLength  )  [inline]
 

Definition at line 192 of file ContigGrouper.java.

References getNonEmpty().

LinkedList org::gel::mauve::contigs::ContigGrouper::ContigGroup::getNonEmpty  )  [inline]
 

Definition at line 270 of file ContigGrouper.java.

References first, org::gel::mauve::Chromosome::getEnd(), org::gel::mauve::backbone::Backbone::getLeftEnd(), org::gel::mauve::LCB::getLeftEnd(), org::gel::mauve::Chromosome::getLength(), org::gel::mauve::backbone::Backbone::getRightEnd(), org::gel::mauve::LCB::getRightEnd(), org::gel::mauve::Chromosome::getStart(), org::gel::mauve::contigs::ContigGrouper::isSolidlyOnContig(), and last.

Referenced by ContigGroup(), and getLength().

boolean org::gel::mauve::contigs::ContigGrouper::ContigGroup::isReversed  )  [inline]
 

Definition at line 226 of file ContigGrouper.java.

References reversed.

boolean org::gel::mauve::contigs::ContigGrouper::ContigGroup::matchedToEdge boolean  left  )  [inline]
 

Definition at line 208 of file ContigGrouper.java.

References first, org::gel::mauve::Chromosome::getEnd(), org::gel::mauve::LCB::getLeftEnd(), org::gel::mauve::LCB::getRightEnd(), org::gel::mauve::Chromosome::getStart(), and last.

boolean org::gel::mauve::contigs::ContigGrouper::ContigGroup::mostWeightForward  )  [inline]
 

Definition at line 256 of file ContigGrouper.java.

References getLCBs(), and org::gel::mauve::LCB::weight.

void org::gel::mauve::contigs::ContigGrouper::ContigGroup::setReversed boolean  reverse  )  [inline]
 

Definition at line 234 of file ContigGrouper.java.

References reversed.

String org::gel::mauve::contigs::ContigGrouper::ContigGroup::toString  )  [inline]
 

Definition at line 221 of file ContigGrouper.java.

References first, and last.


Member Data Documentation

Chromosome org::gel::mauve::contigs::ContigGrouper::ContigGroup::end [protected]
 

Definition at line 173 of file ContigGrouper.java.

Referenced by org::gel::mauve::contigs::ContigGrouper::getFirstOfLinkedContigs(), and org::gel::mauve::contigs::ContigInverter::placeUntouched().

LCB org::gel::mauve::contigs::ContigGrouper::ContigGroup::first [protected]
 

Definition at line 174 of file ContigGrouper.java.

Referenced by org::gel::mauve::contigs::ContigGrouper::getFirstOfLinkedContigs(), getLCBs(), getNonEmpty(), matchedToEdge(), and toString().

LCB org::gel::mauve::contigs::ContigGrouper::ContigGroup::last [protected]
 

Definition at line 175 of file ContigGrouper.java.

Referenced by org::gel::mauve::contigs::ContigGrouper::getFirstOfLinkedContigs(), getLCBs(), getNonEmpty(), matchedToEdge(), and toString().

Boolean org::gel::mauve::contigs::ContigGrouper::ContigGroup::reversed [protected]
 

Definition at line 177 of file ContigGrouper.java.

Referenced by isReversed(), and setReversed().

Chromosome org::gel::mauve::contigs::ContigGrouper::ContigGroup::start [protected]
 

Definition at line 172 of file ContigGrouper.java.

Referenced by org::gel::mauve::contigs::ContigGrouper::getFirstOfLinkedContigs(), and org::gel::mauve::contigs::ContigInverter::placeUntouched().

long org::gel::mauve::contigs::ContigGrouper::ContigGroup::weight [protected]
 

Definition at line 176 of file ContigGrouper.java.

Referenced by calculateWeight().


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