org::gel::mauve::analysis::OneToOneOrthologExporter Class Reference

List of all members.

Static Public Member Functions
void	export (XmfaViewerModel model, BufferedWriter output, OrthologExportParameters oep) throws IOException
LiteWeightFeature[]	getFeaturesByType (int genSrcIdx, Iterator i, String featureType)
	Takes an Iterator over features and trims it down to an array of LiteWeightFeatures that contains only those features specified by featureType.
void	main (String[] args)
Static Private Member Functions
void	addOverlappingCDS (XmfaViewerModel model, LiteWeightFeature[] cds, Quad bb, HashMap hm, int gI, int gJ)
String	format80 (String sequence)
Quad[]	getBackboneSegs (XmfaViewerModel model, Genome g_i, LiteWeightFeature cds)

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Member Function Documentation

void org::gel::mauve::analysis::OneToOneOrthologExporter::addOverlappingCDS (  XmfaViewerModel  model, LiteWeightFeature[]  cds, Quad  bb, HashMap  hm, int  gI, int  gJ )  [inline, static, private]

Definition at line 265 of file OneToOneOrthologExporter.java. References org::gel::mauve::XMFAAlignment::getColumnCoordinates(), org::gel::mauve::BaseViewerModel::getGenomeBySourceIndex(), org::gel::mauve::XMFAAlignment::getLCBAndColumn(), org::gel::mauve::analysis::LiteWeightFeature::getLeft(), org::gel::mauve::analysis::LiteWeightFeature::getRight(), org::gel::mauve::BaseViewerModel::getSequenceCount(), org::gel::mauve::XmfaViewerModel::getXmfa(), org::gel::mauve::analysis::OneToOneOrthologExporter::Quad::left, org::gel::mauve::analysis::OneToOneOrthologExporter::CdsOverlap::left_i, org::gel::mauve::analysis::OneToOneOrthologExporter::CdsOverlap::length_i, org::gel::mauve::analysis::OneToOneOrthologExporter::CdsOverlap::length_j, org::gel::mauve::analysis::OneToOneOrthologExporter::Quad::right, and org::gel::mauve::analysis::OneToOneOrthologExporter::CdsOverlap::right_i. Referenced by export().

void org::gel::mauve::analysis::OneToOneOrthologExporter::export (  XmfaViewerModel  model, BufferedWriter  output, OrthologExportParameters  oep )  throws IOException [inline, static]

Definition at line 327 of file OneToOneOrthologExporter.java. References addOverlappingCDS(), format80(), org::gel::mauve::Genome::getAnnotationSequence(), getBackboneSegs(), getFeaturesByType(), org::gel::mauve::analysis::LiteWeightFeature::getLeft(), org::gel::mauve::Genome::getLength(), org::gel::mauve::analysis::LiteWeightFeature::getRight(), org::gel::mauve::analysis::OneToOneOrthologExporter::CdsOverlap::left_i, org::gel::mauve::analysis::OneToOneOrthologExporter::CdsOverlap::length_i, org::gel::mauve::analysis::OneToOneOrthologExporter::CdsOverlap::length_j, and org::gel::mauve::analysis::OneToOneOrthologExporter::CdsOverlap::right_i. Referenced by main().

String org::gel::mauve::analysis::OneToOneOrthologExporter::format80 (  String  sequence  )  [inline, static, private]

Definition at line 670 of file OneToOneOrthologExporter.java. Referenced by export().

Quad [] org::gel::mauve::analysis::OneToOneOrthologExporter::getBackboneSegs (  XmfaViewerModel  model, Genome  g_i, LiteWeightFeature  cds )  [inline, static, private]

Definition at line 186 of file OneToOneOrthologExporter.java. References org::gel::mauve::backbone::BackboneList::getBackbone(), org::gel::mauve::XmfaViewerModel::getBackboneList(), org::gel::mauve::XMFAAlignment::getColumnCoordinates(), org::gel::mauve::LcbViewerModel::getFullLcbList(), org::gel::mauve::XMFAAlignment::getLCBAndColumn(), org::gel::mauve::backbone::Backbone::getLcbIndex(), org::gel::mauve::analysis::LiteWeightFeature::getLeft(), org::gel::mauve::backbone::Backbone::getLeftEnd(), org::gel::mauve::backbone::BackboneList::getNextBackbone(), org::gel::mauve::analysis::LiteWeightFeature::getRight(), org::gel::mauve::BaseViewerModel::getSequenceCount(), org::gel::mauve::Genome::getSourceIndex(), org::gel::mauve::XmfaViewerModel::getXmfa(), org::gel::mauve::analysis::OneToOneOrthologExporter::Quad::left, and org::gel::mauve::analysis::OneToOneOrthologExporter::Quad::right. Referenced by export().

LiteWeightFeature [] org::gel::mauve::analysis::OneToOneOrthologExporter::getFeaturesByType (  int  genSrcIdx, Iterator  i, String  featureType )  [inline, static]

Takes an Iterator over features and trims it down to an array of LiteWeightFeatures that contains only those features specified by featureType. Parameters: genSrcIdx  i  featureType  Returns: Definition at line 114 of file OneToOneOrthologExporter.java. References org::gel::mauve::analysis::LiteWeightFeature::compareTo(), and org::gel::mauve::analysis::LiteWeightFeature::getLocus(). Referenced by export().

void org::gel::mauve::analysis::OneToOneOrthologExporter::main (  String[]  args  )  [inline, static]

Definition at line 683 of file OneToOneOrthologExporter.java. References org::gel::mauve::analysis::OneToOneOrthologExporter::OrthologExportParameters::alignmentOutputFile, export(), org::gel::mauve::analysis::OneToOneOrthologExporter::OrthologExportParameters::featureType, org::gel::mauve::analysis::OneToOneOrthologExporter::OrthologExportParameters::max_conserved_length, org::gel::mauve::analysis::OneToOneOrthologExporter::OrthologExportParameters::max_nucleotide_id, org::gel::mauve::analysis::OneToOneOrthologExporter::OrthologExportParameters::min_conserved_length, org::gel::mauve::analysis::OneToOneOrthologExporter::OrthologExportParameters::min_nucleotide_id, and org::gel::mauve::analysis::OneToOneOrthologExporter::OrthologExportParameters::predictUnannotated.

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

• src/org/gel/mauve/analysis/OneToOneOrthologExporter.java

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