org::gel::mauve::backbone::Backbone Class Reference

List of all members.

Public Member Functions
boolean	exists (Genome g)
Color	getColor ()
int	getLcbIndex ()
long	getLeftColumn ()
long	getLeftEnd (Genome g)
long	getLength ()
long	getRightEnd (Genome g)
boolean[]	getSeqs ()
void	setColor (Color color)
void	setLcbIndex (int lcb_index)
void	setLeftColumn (long left_col)
void	setLeftEnd (long[] left_end)
void	setLength (long length)
void	setRightEnd (long[] right_end)
void	setSeqs (boolean[] seqs)
Protected Attributes
Color	color
int	lcb_index
long	left_col
long	length
boolean	seqs []

---

Member Function Documentation

boolean org::gel::mauve::backbone::Backbone::exists (  Genome  g  )  [inline]

Definition at line 70 of file Backbone.java. References org::gel::mauve::Genome::getSourceIndex(), and seqs.

Color org::gel::mauve::backbone::Backbone::getColor (   )  [inline]

Definition at line 75 of file Backbone.java. References color. Referenced by org::gel::mauve::gui::sequence::MatchPanel::drawXmfa().

int org::gel::mauve::backbone::Backbone::getLcbIndex (   )  [inline]

Definition at line 20 of file Backbone.java. References lcb_index. Referenced by org::gel::mauve::color::BackboneLcbColor::apply(), org::gel::mauve::backbone::BackboneList::BbComparator::compare(), and org::gel::mauve::analysis::OneToOneOrthologExporter::getBackboneSegs().

long org::gel::mauve::backbone::Backbone::getLeftColumn (   )  [inline]

Definition at line 28 of file Backbone.java. References left_col. Referenced by org::gel::mauve::backbone::BackboneList::BbComparator::compare().

long org::gel::mauve::backbone::Backbone::getLeftEnd (  Genome  g  )  [inline]

Definition at line 52 of file Backbone.java. References org::gel::mauve::Genome::getSourceIndex(). Referenced by org::gel::mauve::SimilarityIndex::calculateIndex(), org::gel::mauve::backbone::BackboneList::BbLeftEndComparator::compare(), org::gel::mauve::gui::sequence::MatchPanel::drawXmfa(), org::gel::mauve::backbone::BackboneList::getBackbone(), org::gel::mauve::analysis::OneToOneOrthologExporter::getBackboneSegs(), org::gel::mauve::backbone::BackboneList::getNextBackbone(), and org::gel::mauve::contigs::ContigGrouper::ContigGroup::getNonEmpty().

long org::gel::mauve::backbone::Backbone::getLength (   )  [inline]

Definition at line 36 of file Backbone.java. Referenced by org::gel::mauve::color::BackboneMultiplicityColor::apply().

long org::gel::mauve::backbone::Backbone::getRightEnd (  Genome  g  )  [inline]

Definition at line 61 of file Backbone.java. References org::gel::mauve::Genome::getSourceIndex(). Referenced by org::gel::mauve::SimilarityIndex::calculateIndex(), org::gel::mauve::backbone::BackboneList::BbLeftEndComparator::compare(), org::gel::mauve::gui::sequence::MatchPanel::drawXmfa(), org::gel::mauve::backbone::BackboneList::getBackbone(), and org::gel::mauve::contigs::ContigGrouper::ContigGroup::getNonEmpty().

boolean [] org::gel::mauve::backbone::Backbone::getSeqs (   )  [inline]

Definition at line 44 of file Backbone.java. References seqs. Referenced by org::gel::mauve::color::BackboneMultiplicityColor::apply(), org::gel::mauve::backbone::BackboneListBuilder::build(), org::gel::mauve::SimilarityIndex::calculateIndex(), org::gel::mauve::backbone::BackboneList::BbComparator::compare(), and org::gel::mauve::backbone::BackboneList::BbLeftEndComparator::compare().

void org::gel::mauve::backbone::Backbone::setColor (  Color  color  )  [inline]

Definition at line 79 of file Backbone.java.

void org::gel::mauve::backbone::Backbone::setLcbIndex (  int  lcb_index  )  [inline]

Definition at line 24 of file Backbone.java. Referenced by org::gel::mauve::backbone::BackboneListBuilder::build(), and org::gel::mauve::backbone::BackboneList::getNextBackbone().

void org::gel::mauve::backbone::Backbone::setLeftColumn (  long  left_col  )  [inline]

Definition at line 32 of file Backbone.java. Referenced by org::gel::mauve::backbone::BackboneListBuilder::build(), and org::gel::mauve::backbone::BackboneList::getNextBackbone().

void org::gel::mauve::backbone::Backbone::setLeftEnd (  long[]  left_end  )  [inline]

Definition at line 57 of file Backbone.java. Referenced by org::gel::mauve::backbone::BackboneListBuilder::build(), and org::gel::mauve::backbone::BackboneList::getNextBackbone().

void org::gel::mauve::backbone::Backbone::setLength (  long  length  )  [inline]

Definition at line 40 of file Backbone.java. Referenced by org::gel::mauve::backbone::BackboneListBuilder::build(), and org::gel::mauve::backbone::BackboneList::getNextBackbone().

void org::gel::mauve::backbone::Backbone::setRightEnd (  long[]  right_end  )  [inline]

Definition at line 66 of file Backbone.java. Referenced by org::gel::mauve::backbone::BackboneListBuilder::build(), and org::gel::mauve::backbone::BackboneList::getNextBackbone().

void org::gel::mauve::backbone::Backbone::setSeqs (  boolean[]  seqs  )  [inline]

Definition at line 48 of file Backbone.java. Referenced by org::gel::mauve::backbone::BackboneListBuilder::build(), and org::gel::mauve::backbone::BackboneList::getNextBackbone().

---

Member Data Documentation

Color org::gel::mauve::backbone::Backbone::color [protected]

Definition at line 18 of file Backbone.java. Referenced by getColor().

int org::gel::mauve::backbone::Backbone::lcb_index [protected]

Definition at line 10 of file Backbone.java. Referenced by getLcbIndex().

long org::gel::mauve::backbone::Backbone::left_col [protected]

Definition at line 12 of file Backbone.java. Referenced by getLeftColumn().

long org::gel::mauve::backbone::Backbone::length [protected]

Definition at line 14 of file Backbone.java. Referenced by org::gel::mauve::color::BackboneMultiplicityColor::apply(), org::gel::mauve::color::BackboneLcbColor::apply(), org::gel::mauve::backbone::BackboneListBuilder::build(), and org::gel::mauve::backbone::BackboneList::getNextBackbone().

boolean org::gel::mauve::backbone::Backbone::seqs[] [protected]

Definition at line 16 of file Backbone.java. Referenced by exists(), and getSeqs().

---

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

• src/org/gel/mauve/backbone/Backbone.java

---