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org::gel::mauve::LCB Class Reference

The LCB class tracks locally collinear blocks: regions of homologous sequence that do not contain rearrangements. More...

List of all members.

Public Member Functions

int getLeftAdjacency (Genome g)
long getLeftEnd (Genome g)
long getLength (Genome g)
boolean getReverse (Genome g)
int getRightAdjacency (Genome g)
long getRightEnd (Genome g)
 LCB (LCB l)
 LCB (Match m, int id, int seq_count)
 LCB (int seq_count)
long midpoint (Genome g)
int multiplicity ()
void resetAdjacencies (int genomeCount)
void setLeftAdjacency (Genome g, int lcbID)
void setLeftEnd (Genome g, long leftEnd)
void setReference (Genome g)
void setReverse (Genome g, boolean r)
void setRightAdjacency (Genome g, int lcbID)
void setRightEnd (Genome g, long rightEnd)

Public Attributes

Color color
 The color of the LCB frame.

int id
 A numerical ID that can be assigned to this LCB.

Color match_color
 The color of matches within the LCB.

long weight
 The weight (or coverage) of this LCB.


Package Attributes

boolean keep
 set this to true to keep this LCB even when it's weight is too low


Private Attributes

int[] left_adjacency
 'Pointers' (actually IDs) to the LCBs on the left in each sequence

int[] right_adjacency
 'Pointers' (actually IDs) to the LCBs on the right in each sequence

Detailed Description

The LCB class tracks locally collinear blocks: regions of homologous sequence that do not contain rearrangements.

Definition at line 15 of file LCB.java.

Constructor & Destructor Documentation

org::gel::mauve::LCB::LCB (  int  seq_count  )  [inline]
 

Definition at line 52 of file LCB.java.

References left_adjacency, and right_adjacency.

org::gel::mauve::LCB::LCB (  Match  m,
int  id,
int  seq_count
)  [inline]
 

Definition at line 60 of file LCB.java.

References org::gel::mauve::Match::copyArrays(), keep, left_adjacency, and right_adjacency.

org::gel::mauve::LCB::LCB (  LCB  l  )  [inline]
 

Definition at line 79 of file LCB.java.

References color, id, keep, left_adjacency, match_color, right_adjacency, and weight.

Member Function Documentation

int org::gel::mauve::LCB::getLeftAdjacency (  Genome  g  )  [inline]
 

Definition at line 140 of file LCB.java.

References org::gel::mauve::Genome::getSourceIndex(), and left_adjacency.

Referenced by org::gel::mauve::contigs::ContigReorderer::getAdjacentLCB(), org::gel::mauve::LcbViewerModel::getLeftmostDeletedLCB(), org::gel::mauve::LcbViewerModel::getLeftmostVisibleLCB(), org::gel::mauve::LCBlist::greedyBreakpointElimination(), org::gel::mauve::LcbViewerModel::launchGrimmMGR(), and org::gel::mauve::LcbViewerModel::sanityCheck().

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

Definition at line 116 of file LCB.java.

References org::gel::mauve::Genome::getSourceIndex().

Referenced by org::gel::mauve::LCBLeftComparator::compare(), org::gel::mauve::LCBlist::computeLCBAdjacencies(), org::gel::mauve::contigs::ContigGrouper::ContigGroup::ContigGroup(), org::gel::mauve::gui::sequence::MatchPanel::drawLcbBounds(), org::gel::mauve::gui::sequence::MatchPanel::drawWhiteBackgrounds(), org::gel::mauve::gui::sequence::MatchPanel::drawXmfa(), org::gel::mauve::contigs::ContigReorderer::getClosestRelation(), org::gel::mauve::contigs::ContigGrouper::getEndChromosome(), org::gel::mauve::LcbViewerModel::getLCB(), org::gel::mauve::LcbViewerModel::getLCBRange(), org::gel::mauve::gui::sequence::MatchPanel::getLcbRectangle(), org::gel::mauve::contigs::ContigGrouper::ContigGroup::getNonEmpty(), org::gel::mauve::gui::LCBStatusBar::highlightChanged(), org::gel::mauve::contigs::ContigInverter::invertContigs(), org::gel::mauve::LCBlist::isNwayLcbList(), org::gel::mauve::contigs::ContigGrouper::isSolidlyOnContig(), org::gel::mauve::LcbViewerModel::launchGrimmMGR(), org::gel::mauve::contigs::ContigInverter::matchEdges(), org::gel::mauve::contigs::ContigGrouper::ContigGroup::matchedToEdge(), org::gel::mauve::gui::LcbLinePanel::nextVisibleGenome(), org::gel::mauve::contigs::ContigReorderer::removeBadLCBs(), org::gel::mauve::contigs::ContigInverter::reorderContigs(), org::gel::mauve::analysis::SnpExporter::SuppressWarnings(), and org::gel::mauve::contigs::ContigReorderer::trimLCBs().

long org::gel::mauve::LCB::getLength (  Genome  g  )  [inline]
 

Definition at line 112 of file LCB.java.

References org::gel::mauve::Genome::getSourceIndex().

Referenced by org::gel::mauve::gui::LCBStatusBar::highlightChanged(), and org::gel::mauve::contigs::ContigGrouper::isSolidlyOnContig().

boolean org::gel::mauve::LCB::getReverse (  Genome  g  )  [inline]
 

Definition at line 132 of file LCB.java.

References org::gel::mauve::Genome::getSourceIndex().

Referenced by org::gel::mauve::gui::sequence::MatchPanel::drawLcbBounds(), org::gel::mauve::gui::sequence::MatchPanel::drawWhiteBackgrounds(), org::gel::mauve::gui::sequence::MatchPanel::drawXmfa(), org::gel::mauve::gui::sequence::MatchPanel::getLcbRectangle(), org::gel::mauve::analysis::SnpExporter::getSNPs(), org::gel::mauve::LcbViewerModel::launchGrimmMGR(), org::gel::mauve::gui::LcbLinePanel::paint(), setReference(), and org::gel::mauve::analysis::SnpExporter::SuppressWarnings().

int org::gel::mauve::LCB::getRightAdjacency (  Genome  g  )  [inline]
 

Definition at line 148 of file LCB.java.

References org::gel::mauve::Genome::getSourceIndex(), and right_adjacency.

Referenced by org::gel::mauve::contigs::ContigReorderer::getAdjacentLCB(), org::gel::mauve::LcbViewerModel::getDeletedRightNeighbor(), org::gel::mauve::LcbViewerModel::getVisibleRightNeighbor(), org::gel::mauve::LcbViewerModel::launchGrimmMGR(), and org::gel::mauve::LcbViewerModel::sanityCheck().

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

Definition at line 124 of file LCB.java.

References org::gel::mauve::Genome::getSourceIndex().

Referenced by org::gel::mauve::contigs::ContigReorderer::adjustLCBs(), org::gel::mauve::gui::sequence::MatchPanel::drawLcbBounds(), org::gel::mauve::gui::sequence::MatchPanel::drawWhiteBackgrounds(), org::gel::mauve::gui::sequence::MatchPanel::drawXmfa(), org::gel::mauve::LcbViewerModel::getDeletedRightNeighbor(), org::gel::mauve::contigs::ContigGrouper::getEndChromosome(), org::gel::mauve::LcbViewerModel::getLCB(), org::gel::mauve::LcbViewerModel::getLCBRange(), org::gel::mauve::gui::sequence::MatchPanel::getLcbRectangle(), org::gel::mauve::contigs::ContigGrouper::ContigGroup::getNonEmpty(), org::gel::mauve::LcbViewerModel::getVisibleRightNeighbor(), org::gel::mauve::gui::LCBStatusBar::highlightChanged(), org::gel::mauve::contigs::ContigGrouper::isSolidlyOnContig(), org::gel::mauve::contigs::ContigInverter::matchEdges(), org::gel::mauve::contigs::ContigGrouper::ContigGroup::matchedToEdge(), and org::gel::mauve::analysis::SnpExporter::SuppressWarnings().

long org::gel::mauve::LCB::midpoint (  Genome  g  )  [inline]
 

Definition at line 99 of file LCB.java.

References org::gel::mauve::Genome::getSourceIndex().

Referenced by org::gel::mauve::gui::LcbLinePanel::paint().

int org::gel::mauve::LCB::multiplicity (   )  [inline]
 

Definition at line 161 of file LCB.java.

Referenced by org::gel::mauve::gui::sequence::MatchPanel::drawXmfa().

void org::gel::mauve::LCB::resetAdjacencies (  int  genomeCount  )  [inline]
 

Definition at line 156 of file LCB.java.

References left_adjacency, and right_adjacency.

Referenced by org::gel::mauve::LCBlist::computeLCBAdjacencies().

void org::gel::mauve::LCB::setLeftAdjacency (  Genome  g,
int  lcbID
)  [inline]
 

Definition at line 144 of file LCB.java.

References org::gel::mauve::Genome::getSourceIndex(), and left_adjacency.

Referenced by org::gel::mauve::LCBlist::computeLCBAdjacencies().

void org::gel::mauve::LCB::setLeftEnd (  Genome  g,
long  leftEnd
)  [inline]
 

Definition at line 120 of file LCB.java.

References org::gel::mauve::Genome::getSourceIndex().

Referenced by org::gel::mauve::LcbViewerModel::getLCB().

void org::gel::mauve::LCB::setReference (  Genome  g  )  [inline]
 

Definition at line 103 of file LCB.java.

References org::gel::mauve::BaseViewerModel::getGenomeBySourceIndex(), org::gel::mauve::Genome::getModel(), getReverse(), and setReverse().

Referenced by org::gel::mauve::LcbViewerModel::referenceUpdated(), and org::gel::mauve::XMFAAlignment::setReference().

void org::gel::mauve::LCB::setReverse (  Genome  g,
boolean  r
)  [inline]
 

Definition at line 136 of file LCB.java.

References org::gel::mauve::Genome::getSourceIndex().

Referenced by org::gel::mauve::LcbViewerModel::getLCB(), and setReference().

void org::gel::mauve::LCB::setRightAdjacency (  Genome  g,
int  lcbID
)  [inline]
 

Definition at line 152 of file LCB.java.

References org::gel::mauve::Genome::getSourceIndex(), and right_adjacency.

Referenced by org::gel::mauve::LCBlist::computeLCBAdjacencies().

void org::gel::mauve::LCB::setRightEnd (  Genome  g,
long  rightEnd
)  [inline]
 

Definition at line 128 of file LCB.java.

References org::gel::mauve::Genome::getSourceIndex().

Referenced by org::gel::mauve::LcbViewerModel::getLCB().

Member Data Documentation

Color org::gel::mauve::LCB::color
 

The color of the LCB frame.

Definition at line 40 of file LCB.java.

Referenced by org::gel::mauve::color::BackboneLcbColor::apply(), org::gel::mauve::color::LCBColorScheme::computeLCBColors(), org::gel::mauve::gui::sequence::MatchPanel::drawLcbBounds(), org::gel::mauve::gui::sequence::MatchPanel::drawXmfa(), LCB(), and org::gel::mauve::gui::LcbLinePanel::paint().

int org::gel::mauve::LCB::id
 

A numerical ID that can be assigned to this LCB.

Definition at line 30 of file LCB.java.

Referenced by org::gel::mauve::LcbIdComparator::compare(), org::gel::mauve::LCBlist::computeLCBAdjacencies(), org::gel::mauve::LCBlist::filterLCBs(), org::gel::mauve::contigs::ContigReorderer::getAdjacentLCB(), org::gel::mauve::analysis::SnpExporter::getSNPs(), org::gel::mauve::LCBlist::greedyBreakpointElimination(), LCB(), and org::gel::mauve::LcbViewerModel::sanityCheck().

boolean org::gel::mauve::LCB::keep [package]
 

set this to true to keep this LCB even when it's weight is too low

Definition at line 50 of file LCB.java.

Referenced by org::gel::mauve::LcbViewerModel::getLCB(), org::gel::mauve::LCBlist::greedyBreakpointElimination(), and LCB().

int [] org::gel::mauve::LCB::left_adjacency [private]
 

'Pointers' (actually IDs) to the LCBs on the left in each sequence

Definition at line 20 of file LCB.java.

Referenced by getLeftAdjacency(), LCB(), resetAdjacencies(), and setLeftAdjacency().

Color org::gel::mauve::LCB::match_color
 

The color of matches within the LCB.

Definition at line 45 of file LCB.java.

Referenced by org::gel::mauve::color::LCBColorScheme::apply(), org::gel::mauve::color::LCBColorScheme::computeLCBColors(), org::gel::mauve::LCBlist::filterLCBs(), and LCB().

int [] org::gel::mauve::LCB::right_adjacency [private]
 

'Pointers' (actually IDs) to the LCBs on the right in each sequence

Definition at line 25 of file LCB.java.

Referenced by getRightAdjacency(), LCB(), resetAdjacencies(), and setRightAdjacency().

long org::gel::mauve::LCB::weight
 

The weight (or coverage) of this LCB.

Definition at line 35 of file LCB.java.

Referenced by org::gel::mauve::LcbViewerModel::getLCB(), org::gel::mauve::LCBlist::greedyBreakpointElimination(), org::gel::mauve::gui::LCBStatusBar::highlightChanged(), org::gel::mauve::LcbViewerModel::initModelLCBs(), LCB(), org::gel::mauve::contigs::ContigGrouper::ContigGroup::mostWeightForward(), and org::gel::mauve::contigs::ContigInverter::placeConflicts().

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