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org::gel::mauve::Genome Class Reference

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List of all members.

Public Member Functions

 Genome (long length, BaseViewerModel model, int sourceIndex)
SupportedFormat getAnnotationFormat ()
FeatureHolder getAnnotationsAt (long left, long right, boolean rev)
 Returns annotations overlapping the given position of this genome.

Sequence getAnnotationSequence ()
Chromosome getChromosomeAt (long loc)
List< Chromosome > getChromosomes ()
 Returns an unmodifiable sorted list of the chromosomes comprising this genome.

String getDisplayName ()
String getID ()
long getLength ()
BaseViewerModel getModel ()
Vector getSortedMatches ()
int getSourceIndex ()
int getViewIndex ()
long getViewLength ()
long getViewStart ()
boolean getVisible ()
boolean isCircular (int chrI)
 Returns true if the specified chromosome is circular.

void setAnnotationSequence (Sequence annotationSequence, SupportedFormat format)
void setChromosomes (List list)
void setDisplayName (String displayName)
void setID (String id)
void setViewIndex (int viewIndex)
void setViewLength (long viewLength)
void setViewStart (long viewStart)
void setVisible (boolean v)
String toString ()

Private Attributes

Sequence annotationSequence
List< Chromosome > chromosomes = new ArrayList<Chromosome> ()
String displayName
SupportedFormat format
String id
long length
BaseViewerModel model
Vector sortedMatches
int sourceIndex
int viewIndex
long viewLength
long viewStart
boolean visible = true

Constructor & Destructor Documentation

org::gel::mauve::Genome::Genome (  long  length,
BaseViewerModel  model,
int  sourceIndex
)  [inline]
 

Definition at line 45 of file Genome.java.

Member Function Documentation

SupportedFormat org::gel::mauve::Genome::getAnnotationFormat (   )  [inline]
 

Definition at line 78 of file Genome.java.

Referenced by org::gel::mauve::gui::sequence::FeaturePanel::init().

FeatureHolder org::gel::mauve::Genome::getAnnotationsAt (  long  left,
long  right,
boolean  rev
)  [inline]
 

Returns annotations overlapping the given position of this genome.

Parameters:
left left position
right right position
rev true of the query position lies on complementary strand, false otherwise
Returns:
a FeatureHolder containing the features in this genome that overlap the given position.

Definition at line 92 of file Genome.java.

References annotationSequence.

Referenced by org::gel::mauve::analysis::Gap::getFeatures().

Sequence org::gel::mauve::Genome::getAnnotationSequence (   )  [inline]
 

Definition at line 74 of file Genome.java.

References annotationSequence.

Referenced by org::gel::mauve::assembly::AssemblyScorer::computeBrokenCDS(), org::gel::mauve::gui::sequence::SeqPanel::configureLayout(), org::gel::mauve::analysis::OneToOneOrthologExporter::export(), org::gel::mauve::SeqFeatureData::findFeatures(), org::gel::mauve::MauveHelperFunctions::getContigFeatures(), org::gel::mauve::contigs::FastAContigChangeWriter::getContigFeatures(), org::gel::mauve::MauveHelperFunctions::getFeatures(), org::gel::mauve::gui::sequence::MultiGenomeRectangularBeadRenderer::getOffset(), org::gel::mauve::XmfaViewerModel::getSequence(), org::gel::mauve::gui::sequence::FlatFileFeatureImporter::importAnnotationFile(), org::gel::mauve::gui::sequence::FeaturePanel::init(), org::gel::mauve::gui::sequence::SeqPanel::SeqPanel(), org::gel::mauve::gui::sequence::MultiGenomeRectangularBeadRenderer::setOffset(), org::gel::mauve::summary::output::PartialFastaWriter::startModule(), and org::gel::mauve::SeqFeatureData::userSelectableGenomes().

Chromosome org::gel::mauve::Genome::getChromosomeAt (  long  loc  )  [inline]
 

Definition at line 118 of file Genome.java.

References org::gel::mauve::Chromosome::getEnd(), and org::gel::mauve::Chromosome::getStart().

Referenced by org::gel::mauve::analysis::SNP::addTaxa(), org::gel::mauve::contigs::FastAContigChangeWriter::FastAContigChangeWriter(), org::gel::mauve::summary::AnalysisModuleFrame::fixSegmentByContigs(), org::gel::mauve::analysis::Gap::Gap(), org::gel::mauve::contigs::DefaultContigHandler::getContigCoord(), org::gel::mauve::contigs::DefaultContigHandler::getContigName(), org::gel::mauve::contigs::ContigGrouper::getEndChromosome(), org::gel::mauve::gui::LCBStatusBar::highlightChanged(), and org::gel::mauve::contigs::ChangedFeatureWriter::shouldPrintRow().

List<Chromosome> org::gel::mauve::Genome::getChromosomes (   )  [inline]
 

Returns an unmodifiable sorted list of the chromosomes comprising this genome.

Returns:
an unmodifiable sorted list of chromosomes.

Definition at line 114 of file Genome.java.

Referenced by org::gel::mauve::assembly::AssemblyScorer::computeContigSizeStats(), org::gel::mauve::contigs::DefaultContigHandler::getChromosomeFromName(), org::gel::mauve::contigs::DefaultContigHandler::getContigCoord(), org::gel::mauve::assembly::AssemblyScorer::getReferenceChromosomes(), org::gel::mauve::analysis::SnpExporter::getUniqueChromosomes(), org::gel::mauve::gui::sequence::FlatFileFeatureImporter::importAnnotationFile(), org::gel::mauve::contigs::ContigReorderer::initMauveData(), org::gel::mauve::LcbViewerModel::launchGrimmMGR(), org::gel::mauve::assembly::AssemblyScorer::numContigs(), org::gel::mauve::assembly::AssemblyScorer::numReplicons(), org::gel::mauve::contigs::ContigInverter::placeConflicts(), org::gel::mauve::contigs::FeatureFixer::process(), org::gel::mauve::contigs::ContigRenamer::process(), org::gel::mauve::contigs::ContigReorderer::readKeepers(), org::gel::mauve::contigs::FeatureFixer::readOrdered(), org::gel::mauve::contigs::ContigReorderer::readOrdered(), and org::gel::mauve::contigs::ContigReorderer::trimLCBs().

String org::gel::mauve::Genome::getDisplayName (   )  [inline]
 

Definition at line 101 of file Genome.java.

References displayName.

Referenced by org::gel::mauve::summary::output::AlignedSequenceWriter::AlignedSequenceWriter(), org::gel::mauve::MauveHelperFunctions::genomeNameToFasta(), org::gel::mauve::assembly::ScoreAssembly::getSumText(), org::gel::mauve::analysis::SnpExporter::getUniqueChromosomes(), org::gel::mauve::contigs::ContigReorderer::initMauveData(), org::gel::mauve::gui::sequence::SeqPanel::SeqPanel(), toString(), org::gel::mauve::summary::output::AlignedSequenceWriter::writeFasta(), and org::gel::mauve::MauveHelperFunctions::writeGenomesWithIndices().

String org::gel::mauve::Genome::getID (   )  [inline]
 

Definition at line 139 of file Genome.java.

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

Definition at line 55 of file Genome.java.

Referenced by org::gel::mauve::histogram::HistogramBuilder::build(), org::gel::mauve::assembly::AssemblyScorer::calculateMissingGC(), org::gel::mauve::analysis::OneToOneOrthologExporter::export(), org::gel::mauve::XMFAAlignment::getColumnCoordinates(), org::gel::mauve::backbone::BackboneList::getNextBackbone(), org::gel::mauve::gui::sequence::HighlightPanel::mouseMoved(), org::gel::mauve::assembly::AssemblyScorer::numBasesAssembly(), org::gel::mauve::assembly::AssemblyScorer::numBasesReference(), org::gel::mauve::gui::sequence::HistogramPanel::paintComponent(), org::gel::mauve::assembly::AssemblyScorer::percentExtraBases(), org::gel::mauve::assembly::AssemblyScorer::percentMissedBases(), org::gel::mauve::recombination::WeakArgModelBuilder::WeakArgXmlHandler::recordRecEdge(), org::gel::mauve::gui::sequence::RulerPanel::RulerPanel(), org::gel::mauve::summary::AnalysisModuleFrame::setModel(), org::gel::mauve::SimilarityIndex::setSequence(), org::gel::mauve::contigs::ContigReorderer::trimLCBs(), org::gel::mauve::BaseViewerModel::zoomAndMove(), and org::gel::mauve::histogram::ZoomHistogram::ZoomHistogram().

BaseViewerModel org::gel::mauve::Genome::getModel (   )  [inline]
 

Definition at line 65 of file Genome.java.

Referenced by org::gel::mauve::LCB::setReference().

Vector org::gel::mauve::Genome::getSortedMatches (   )  [inline]
 

Definition at line 171 of file Genome.java.

References org::gel::mauve::BaseViewerModel::sortedMatches(), and sortedMatches.

Referenced by org::gel::mauve::LcbViewerModel::alignView(), org::gel::mauve::LcbViewerModel::getHighlightArray(), org::gel::mauve::BaseViewerModel::getMatchRange(), and org::gel::mauve::gui::sequence::MatchPanel::mouseClicked().

int org::gel::mauve::Genome::getSourceIndex (   )  [inline]
 

Definition at line 51 of file Genome.java.

References sourceIndex.

Referenced by org::gel::mauve::gui::sequence::FlatFileFeatureImporter::addedMoreOfTypes(), org::gel::mauve::gui::sequence::FlatFileFeatureImporter::addFeatureType(), org::gel::mauve::BaseViewerModel::alignView(), org::gel::mauve::analysis::SNP::areEqual(), org::gel::mauve::SimilarityIndex::calculateIndex(), org::gel::mauve::backbone::BackboneList::BbLeftEndComparator::compare(), org::gel::mauve::contigs::ContigGrouper::ContigGrouper(), org::gel::mauve::backbone::Backbone::exists(), org::gel::mauve::analysis::OneToOneOrthologExporter::getBackboneSegs(), org::gel::mauve::XMFAAlignment::getColumnCoordinates(), org::gel::mauve::XMFAAlignment::getCoordinate(), org::gel::mauve::XmfaViewerModel::getHighlight(), org::gel::mauve::LCB::getLeftAdjacency(), org::gel::mauve::LCB::getLeftEnd(), org::gel::mauve::backbone::Backbone::getLeftEnd(), org::gel::mauve::Match::getLength(), org::gel::mauve::LCB::getLength(), org::gel::mauve::backbone::BackboneList::getNextBackbone(), org::gel::mauve::XMFAAlignment::getRange(), org::gel::mauve::Match::getReverse(), org::gel::mauve::LCB::getReverse(), org::gel::mauve::LCB::getRightAdjacency(), org::gel::mauve::LCB::getRightEnd(), org::gel::mauve::backbone::Backbone::getRightEnd(), org::gel::mauve::XmfaViewerModel::getSim(), org::gel::mauve::analysis::SnpExporter::getSNPs(), org::gel::mauve::Match::getStart(), org::gel::mauve::analysis::SnpExporter::getUniqueChromosomes(), org::gel::mauve::analysis::SnpExporter::isUnique(), org::gel::mauve::MatchStartComparator::MatchStartComparator(), org::gel::mauve::LCB::midpoint(), org::gel::mauve::contigs::ContigInverter::placeUntouched(), org::gel::mauve::XmfaViewerModel::setFocus(), org::gel::mauve::BaseViewerModel::setFocus(), org::gel::mauve::LCB::setLeftAdjacency(), org::gel::mauve::LCB::setLeftEnd(), org::gel::mauve::Match::setLength(), org::gel::mauve::Match::setReverse(), org::gel::mauve::LCB::setReverse(), org::gel::mauve::LCB::setRightAdjacency(), org::gel::mauve::LCB::setRightEnd(), org::gel::mauve::Match::setStart(), and org::gel::mauve::SimilarityIndex::skipGapColumns().

int org::gel::mauve::Genome::getViewIndex (   )  [inline]
 

Definition at line 159 of file Genome.java.

References viewIndex.

Referenced by org::gel::mauve::gui::sequence::FlatFileFeatureImporter::addedMoreOfTypes(), org::gel::mauve::gui::sequence::FlatFileFeatureImporter::addFeatureType(), org::gel::mauve::gui::sequence::ControlPanel::ControlPanel(), and org::gel::mauve::gui::sequence::SeqPanel::SeqPanel().

long org::gel::mauve::Genome::getViewLength (   )  [inline]
 

Definition at line 143 of file Genome.java.

References viewLength.

Referenced by org::gel::mauve::gui::sequence::FeaturePanel::adjustScaleAndTranslation(), org::gel::mauve::BaseViewerModel::alignView(), org::gel::mauve::gui::sequence::MatchPanel::MatchPanel(), org::gel::mauve::gui::sequence::HighlightPanel::paintComponent(), org::gel::mauve::gui::sequence::AbstractSequencePanel::pixelToCenterSequenceCoordinate(), org::gel::mauve::gui::sequence::AbstractSequencePanel::pixelToLeftSequenceCoordinate(), org::gel::mauve::gui::sequence::AbstractSequencePanel::pixelToRightSequenceCoordinate(), org::gel::mauve::gui::sequence::AbstractSequencePanel::sequenceCoordinateToCenterPixel(), org::gel::mauve::gui::sequence::AbstractSequencePanel::sequenceCoordinateToLeftPixel(), org::gel::mauve::gui::sequence::AbstractSequencePanel::sequenceCoordinateToRightPixel(), org::gel::mauve::remote::MauveInterfaceImpl::setDisplayBlockAndColumn(), org::gel::mauve::remote::MauveInterfaceImpl::setDisplayRange(), org::gel::mauve::BaseViewerModel::setFocus(), org::gel::mauve::BaseViewerModel::zoomAndCenter(), and org::gel::mauve::BaseViewerModel::zoomAndMove().

long org::gel::mauve::Genome::getViewStart (   )  [inline]
 

Definition at line 151 of file Genome.java.

References viewStart.

Referenced by org::gel::mauve::gui::sequence::FeaturePanel::adjustScaleAndTranslation(), org::gel::mauve::BaseViewerModel::alignView(), org::gel::mauve::gui::sequence::MatchPanel::MatchPanel(), org::gel::mauve::gui::sequence::HighlightPanel::paintComponent(), org::gel::mauve::gui::sequence::AbstractSequencePanel::pixelToCenterSequenceCoordinate(), org::gel::mauve::gui::sequence::AbstractSequencePanel::pixelToLeftSequenceCoordinate(), org::gel::mauve::gui::sequence::AbstractSequencePanel::pixelToRightSequenceCoordinate(), org::gel::mauve::gui::sequence::AbstractSequencePanel::sequenceCoordinateToCenterPixel(), org::gel::mauve::gui::sequence::AbstractSequencePanel::sequenceCoordinateToLeftPixel(), org::gel::mauve::gui::sequence::AbstractSequencePanel::sequenceCoordinateToRightPixel(), org::gel::mauve::BaseViewerModel::zoomAndCenter(), and org::gel::mauve::BaseViewerModel::zoomAndMove().

boolean org::gel::mauve::Genome::getVisible (   )  [inline]
 

Definition at line 184 of file Genome.java.

References visible.

Referenced by org::gel::mauve::gui::sequence::SeqPanel::configureLayout(), org::gel::mauve::gui::sequence::ControlPanel::ControlPanel(), org::gel::mauve::gui::RearrangementPanel::genomeVisibilityChanged(), org::gel::mauve::gui::LcbLinePanel::nextVisibleGenome(), org::gel::mauve::gui::RearrangementPanel::reorderSequences(), and org::gel::mauve::BaseViewerModel::setVisible().

boolean org::gel::mauve::Genome::isCircular (  int  chrI  )  [inline]
 

Returns true if the specified chromosome is circular.

Parameters:
chrI the chromosome of interest
Returns:
true if chromosome chrI is circular, false otherwise.

Definition at line 200 of file Genome.java.

void org::gel::mauve::Genome::setAnnotationSequence (  Sequence  annotationSequence,
SupportedFormat  format
)  [inline]
 

Definition at line 59 of file Genome.java.

Referenced by org::gel::mauve::GenomeBuilder::buildGenome().

void org::gel::mauve::Genome::setChromosomes (  List  list  )  [inline]
 

Definition at line 70 of file Genome.java.

Referenced by org::gel::mauve::GenomeBuilder::buildGenome().

void org::gel::mauve::Genome::setDisplayName (  String  displayName  )  [inline]
 

Definition at line 105 of file Genome.java.

Referenced by org::gel::mauve::GenomeBuilder::buildGenome().

void org::gel::mauve::Genome::setID (  String  id  )  [inline]
 

Definition at line 135 of file Genome.java.

Referenced by org::gel::mauve::ModelBuilder::buildModel().

void org::gel::mauve::Genome::setViewIndex (  int  viewIndex  )  [inline]
 

Definition at line 164 of file Genome.java.

References sortedMatches.

Referenced by org::gel::mauve::BaseViewerModel::reorderSequences(), and org::gel::mauve::BaseViewerModel::setGenome().

void org::gel::mauve::Genome::setViewLength (  long  viewLength  )  [inline]
 

Definition at line 147 of file Genome.java.

Referenced by org::gel::mauve::BaseViewerModel::alignView(), org::gel::mauve::BaseViewerModel::setGenome(), and org::gel::mauve::BaseViewerModel::zoomAndMove().

void org::gel::mauve::Genome::setViewStart (  long  viewStart  )  [inline]
 

Definition at line 155 of file Genome.java.

Referenced by org::gel::mauve::BaseViewerModel::alignView(), and org::gel::mauve::BaseViewerModel::zoomAndMove().

void org::gel::mauve::Genome::setVisible (  boolean  v  )  [inline]
 

Definition at line 187 of file Genome.java.

References visible.

Referenced by org::gel::mauve::BaseViewerModel::setVisible().

String org::gel::mauve::Genome::toString (   )  [inline]
 

Definition at line 191 of file Genome.java.

References getDisplayName().

Member Data Documentation

Sequence org::gel::mauve::Genome::annotationSequence [private]
 

Definition at line 25 of file Genome.java.

Referenced by getAnnotationsAt(), and getAnnotationSequence().

List<Chromosome> org::gel::mauve::Genome::chromosomes = new ArrayList<Chromosome> () [private]
 

Definition at line 27 of file Genome.java.

String org::gel::mauve::Genome::displayName [private]
 

Definition at line 29 of file Genome.java.

Referenced by getDisplayName().

SupportedFormat org::gel::mauve::Genome::format [private]
 

Definition at line 31 of file Genome.java.

String org::gel::mauve::Genome::id [private]
 

Definition at line 33 of file Genome.java.

long org::gel::mauve::Genome::length [private]
 

Definition at line 21 of file Genome.java.

Referenced by org::gel::mauve::LcbViewerModel::alignView(), org::gel::mauve::BaseViewerModel::correctMatchReversals(), org::gel::mauve::dcjx::DCJDistance::DCJDistance(), org::gel::mauve::SeqFeatureData::findFeatures(), org::gel::mauve::analysis::Gap::Gap(), org::gel::mauve::BaseViewerModel::getGenomes(), org::gel::mauve::XmfaViewerModel::getHomologousCoordinate(), org::gel::mauve::BaseViewerModel::getSequenceCount(), org::gel::mauve::gui::SequenceNavigator::goToFeatureByName(), org::gel::mauve::analysis::SnpExporter::isUnique(), org::gel::mauve::dcjx::DCJDistance::loadMatrices(), org::gel::mauve::contigs::ContigInverter::matchEdges(), org::gel::mauve::BaseViewerModel::numGenomes(), org::gel::mauve::dcjx::DCJDistance::printHeader(), org::gel::mauve::BaseViewerModel::reorderSequences(), org::gel::mauve::XmfaViewerModel::setFocus(), org::gel::mauve::BaseViewerModel::setFocus(), org::gel::mauve::BaseViewerModel::setGenome(), org::gel::mauve::analysis::SnpExporter::SuppressWarnings(), and org::gel::mauve::BaseViewerModel::zoomAndMove().

BaseViewerModel org::gel::mauve::Genome::model [private]
 

Definition at line 23 of file Genome.java.

Vector org::gel::mauve::Genome::sortedMatches [private]
 

Definition at line 41 of file Genome.java.

Referenced by getSortedMatches(), and setViewIndex().

int org::gel::mauve::Genome::sourceIndex [private]
 

Definition at line 43 of file Genome.java.

Referenced by getSourceIndex().

int org::gel::mauve::Genome::viewIndex [private]
 

Definition at line 39 of file Genome.java.

Referenced by getViewIndex().

long org::gel::mauve::Genome::viewLength [private]
 

Definition at line 37 of file Genome.java.

Referenced by getViewLength().

long org::gel::mauve::Genome::viewStart [private]
 

Definition at line 35 of file Genome.java.

Referenced by getViewStart().

boolean org::gel::mauve::Genome::visible = true [private]
 

Definition at line 44 of file Genome.java.

Referenced by getVisible(), and setVisible().

The documentation for this class was generated from the following file:
Generated on Sat May 25 06:03:38 2013 for Mauve by doxygen 1.3.6