org::gel::mauve::Chromosome Class Reference

List of all members.

Public Member Functions
	Chromosome (long start, long end, String name, boolean circular)
boolean	equals (Object comp)
boolean	getCircular ()
long	getEnd ()
long	getLength ()
String	getName ()
long	getStart ()
long	relativeLocation (long location)
void	setName (String n)
String	toString ()
Package Attributes
boolean	circular
Private Attributes
long	end
String	name
long	start

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Constructor & Destructor Documentation

org::gel::mauve::Chromosome::Chromosome (  long  start, long  end, String  name, boolean  circular )  [inline]

Definition at line 12 of file Chromosome.java.

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Member Function Documentation

boolean org::gel::mauve::Chromosome::equals (  Object  comp  )  [inline]

Definition at line 51 of file Chromosome.java. References getName().

boolean org::gel::mauve::Chromosome::getCircular (   )  [inline]

Definition at line 43 of file Chromosome.java. References circular. Referenced by org::gel::mauve::contigs::ContigFeatureWriter::correctPseudoCoords().

long org::gel::mauve::Chromosome::getEnd (   )  [inline]

Definition at line 23 of file Chromosome.java. References end. Referenced by org::gel::mauve::contigs::ContigFeatureWriter::correctPseudoCoords(), org::gel::mauve::gui::sequence::MatchPanel::drawChromosomeBoundaries(), org::gel::mauve::summary::AnalysisModuleFrame::fixSegmentByContigs(), org::gel::mauve::Genome::getChromosomeAt(), org::gel::mauve::contigs::ContigFeatureWriter::getData(), org::gel::mauve::contigs::ContigGrouper::getEndChromosome(), org::gel::mauve::contigs::ContigGrouper::ContigGroup::getNonEmpty(), org::gel::mauve::analysis::SnpExporter::getUniqueChromosomes(), org::gel::mauve::contigs::ContigGrouper::isSolidlyOnContig(), org::gel::mauve::contigs::ContigGrouper::ContigGroup::matchedToEdge(), toString(), and org::gel::mauve::contigs::ContigReorderer::trimLCBs().

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

Definition at line 27 of file Chromosome.java. References end, and start. Referenced by org::gel::mauve::contigs::ContigFeatureWriter::correctPseudoCoords(), org::gel::mauve::contigs::ChangedFeatureWriter::getData(), org::gel::mauve::contigs::ContigGrouper::ContigGroup::getNonEmpty(), and org::gel::mauve::contigs::ContigGrouper::isSolidlyOnContig().

String org::gel::mauve::Chromosome::getName (   )  [inline]

Definition at line 31 of file Chromosome.java. References name. Referenced by org::gel::mauve::contigs::ContigFeatureWriter::correctPseudoCoords(), equals(), org::gel::mauve::contigs::DefaultContigHandler::getChromosomeFromName(), org::gel::mauve::contigs::DefaultContigHandler::getContigName(), org::gel::mauve::contigs::ContigRenamer::getContigName(), org::gel::mauve::contigs::ContigFeatureWriter::getData(), org::gel::mauve::contigs::ChangedFeatureWriter::getData(), org::gel::mauve::assembly::AssemblyScorer::getReferenceChromosomes(), org::gel::mauve::gui::LCBStatusBar::highlightChanged(), 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(), toString(), org::gel::mauve::analysis::Gap::toString(), and org::gel::mauve::contigs::ContigReorderer::trimLCBs().

long org::gel::mauve::Chromosome::getStart (   )  [inline]

Definition at line 19 of file Chromosome.java. References start. Referenced by org::gel::mauve::MauveHelperFunctions::addChromByStart(), org::gel::mauve::analysis::SNP::addTaxa(), org::gel::mauve::gui::sequence::MatchPanel::drawChromosomeBoundaries(), org::gel::mauve::MauveHelperFunctions::getChromByStart(), org::gel::mauve::Genome::getChromosomeAt(), org::gel::mauve::contigs::ContigFeatureWriter::getData(), org::gel::mauve::contigs::ChangedFeatureWriter::getData(), org::gel::mauve::contigs::ContigGrouper::getEndChromosome(), org::gel::mauve::MauveHelperFunctions::getFeatByStart(), org::gel::mauve::contigs::ContigGrouper::ContigGroup::getNonEmpty(), org::gel::mauve::analysis::SNP::getPositionInContig(), org::gel::mauve::contigs::DefaultContigHandler::getPseudoCoord(), org::gel::mauve::assembly::AssemblyScorer::getReferenceChromosomes(), org::gel::mauve::analysis::SnpExporter::getUniqueChromosomes(), org::gel::mauve::contigs::ContigGrouper::isSolidlyOnContig(), org::gel::mauve::contigs::ContigGrouper::ContigGroup::matchedToEdge(), org::gel::mauve::MauveHelperFunctions::removeChromByStart(), toString(), and org::gel::mauve::analysis::Gap::toString().

long org::gel::mauve::Chromosome::relativeLocation (  long  location  )  [inline]

Definition at line 39 of file Chromosome.java. References start. Referenced by org::gel::mauve::contigs::DefaultContigHandler::getContigCoord(), and org::gel::mauve::gui::LCBStatusBar::highlightChanged().

void org::gel::mauve::Chromosome::setName (  String  n  )  [inline]

Definition at line 35 of file Chromosome.java. References name. Referenced by org::gel::mauve::contigs::ContigRenamer::process(), and org::gel::mauve::contigs::FeatureFixer::readOrdered().

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

Definition at line 47 of file Chromosome.java. References getEnd(), getName(), and getStart().

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Member Data Documentation

boolean org::gel::mauve::Chromosome::circular [package]

Definition at line 10 of file Chromosome.java. Referenced by getCircular().

long org::gel::mauve::Chromosome::end [private]

Definition at line 6 of file Chromosome.java. Referenced by getEnd(), and getLength().

String org::gel::mauve::Chromosome::name [private]

Definition at line 8 of file Chromosome.java. Referenced by getName(), and setName().

long org::gel::mauve::Chromosome::start [private]

Definition at line 4 of file Chromosome.java. Referenced by getLength(), getStart(), and relativeLocation().

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

• src/org/gel/mauve/Chromosome.java

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