org::gel::mauve::analysis::Segment Class Reference

Collaboration diagram for org::gel::mauve::analysis::Segment:

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List of all members.

Public Member Functions

void append (Segment add, boolean remove)
double getAvgSegmentLength ()
long getSegmentLength (int sequence)
long[] getSegmentLengths ()
long multiplicityType ()
 compute a number indicating which genomes the local alignment is defined in.

void remove (int seq_index)
 Segment ()
 Segment (int count)
 Segment (int count, boolean links)
 Segment (long[] l, long[] r, boolean[] c)
String toString ()
 format the ungapped local alignment coordinates into a string


Static Public Member Functions

Comparator< SegmentgetGenPositionComparator (int genSrcIdx)

Public Attributes

long[] left
 The start coordinate of this match in each sequence.

Segment[] nexts
Segment[] prevs
boolean[] reverse
 The direction of each match.

long[] right
 The ends of this match in each sequence.

String typed_id

Static Public Attributes

final Segment END = new Segment (0, false)
final String MULTIPLICITY_STRING = "multiplicity"

Protected Attributes

long mult_type

Static Package Attributes

final long serialVersionUID = 1

Constructor & Destructor Documentation

org::gel::mauve::analysis::Segment::Segment long[]  l,
long[]  r,
boolean[]  c
[inline]
 

Definition at line 40 of file Segment.java.

References reverse.

org::gel::mauve::analysis::Segment::Segment int  count,
boolean  links
[inline]
 

Definition at line 46 of file Segment.java.

References nexts, prevs, and reverse.

org::gel::mauve::analysis::Segment::Segment int  count  )  [inline]
 

Definition at line 56 of file Segment.java.

org::gel::mauve::analysis::Segment::Segment  )  [inline]
 

Definition at line 60 of file Segment.java.


Member Function Documentation

void org::gel::mauve::analysis::Segment::append Segment  add,
boolean  remove
[inline]
 

Definition at line 82 of file Segment.java.

References left, nexts, prevs, remove(), and right.

Referenced by org::gel::mauve::summary::output::SegmentDataProcessor::compressBackboneSegments().

double org::gel::mauve::analysis::Segment::getAvgSegmentLength  )  [inline]
 

Definition at line 134 of file Segment.java.

References getSegmentLengths().

Referenced by org::gel::mauve::summary::output::TroubleMatchWriter::shouldPrintRow(), and org::gel::mauve::summary::output::IslandCoordinateWriter::shouldPrintRow().

Comparator<Segment> org::gel::mauve::analysis::Segment::getGenPositionComparator int  genSrcIdx  )  [inline, static]
 

Definition at line 147 of file Segment.java.

long org::gel::mauve::analysis::Segment::getSegmentLength int  sequence  )  [inline]
 

Definition at line 127 of file Segment.java.

Referenced by getSegmentLengths(), org::gel::mauve::summary::output::OverviewFileWriter::performCalculations(), and org::gel::mauve::summary::output::IslandFeatureWriter::shouldPrintRow().

long [] org::gel::mauve::analysis::Segment::getSegmentLengths  )  [inline]
 

Definition at line 120 of file Segment.java.

References getSegmentLength().

Referenced by getAvgSegmentLength(), and org::gel::mauve::summary::output::TroubleMatchWriter::shouldPrintRow().

long org::gel::mauve::analysis::Segment::multiplicityType  )  [inline]
 

compute a number indicating which genomes the local alignment is defined in.

This is a binary number where a 1 indicates that the match is defined and a 0 indicates it is undefined. For example, a local alignment shared by the first and the fourth (out of five) genomes would be represented as 10010.

Definition at line 70 of file Segment.java.

References mult_type.

Referenced by org::gel::mauve::summary::output::SegmentDataProcessor::assignIDs(), org::gel::mauve::summary::output::SegmentDataProcessor::compressBackboneSegments(), org::gel::mauve::summary::output::SegmentDataProcessor::findContigsInUniques(), org::gel::mauve::summary::AnalysisModuleFrame::fixSegmentByContigs(), org::gel::mauve::summary::output::IslandGeneFeatureWriter::getData(), org::gel::mauve::MauveHelperFunctions::getReadableMultiplicity(), org::gel::mauve::summary::output::OverviewFileWriter::performCalculations(), org::gel::mauve::summary::output::IslandGeneFeatureWriter::shouldPrintRow(), org::gel::mauve::summary::output::IslandFeatureWriter::shouldPrintRow(), org::gel::mauve::summary::output::IslandCoordinateWriter::shouldPrintRow(), and org::gel::mauve::summary::output::IslandGeneFeatureWriter::shouldPrintSegment().

void org::gel::mauve::analysis::Segment::remove int  seq_index  )  [inline]
 

Definition at line 97 of file Segment.java.

References nexts, and prevs.

Referenced by append(), and org::gel::mauve::summary::output::SegmentDataProcessor::compressBackboneSegments().

String org::gel::mauve::analysis::Segment::toString  )  [inline]
 

format the ungapped local alignment coordinates into a string

Definition at line 104 of file Segment.java.

References reverse.


Member Data Documentation

final Segment org::gel::mauve::analysis::Segment::END = new Segment (0, false) [static]
 

Definition at line 33 of file Segment.java.

Referenced by org::gel::mauve::summary::output::SegmentDataProcessor::addDataLinks(), org::gel::mauve::summary::output::SegmentDataProcessor::addUniques(), org::gel::mauve::summary::output::SegmentDataProcessor::assignIDs(), org::gel::mauve::summary::output::SegmentDataProcessor::compressBackboneSegments(), org::gel::mauve::summary::output::SegmentDataProcessor::findContigsInUniques(), org::gel::mauve::summary::output::SegmentDataProcessor::init(), org::gel::mauve::summary::output::AbstractMatchDataWriter::initSubClassParticulars(), org::gel::mauve::summary::output::AbstractMatchDataWriter::moreRowsToPrint(), org::gel::mauve::summary::output::OverviewFileWriter::performCalculations(), org::gel::mauve::summary::output::IslandGeneFeatureWriter::performComplexIteration(), and org::gel::mauve::summary::output::IslandGeneFeatureWriter::shouldPrintRow().

long [] org::gel::mauve::analysis::Segment::left
 

The start coordinate of this match in each sequence.

Definition at line 15 of file Segment.java.

Referenced by org::gel::mauve::summary::output::SegmentDataProcessor::addDataLinks(), org::gel::mauve::summary::output::SegmentDataProcessor::addUniques(), append(), org::gel::mauve::analysis::SegmentComparator::compare(), org::gel::mauve::analysis::Segment::GenomePositionComparator::compare(), org::gel::mauve::summary::output::SegmentDataProcessor::compressBackboneSegments(), org::gel::mauve::summary::AnalysisModuleFrame::fixSegmentByContigs(), org::gel::mauve::summary::output::IslandFeatureWriter::getData(), org::gel::mauve::summary::output::AbstractMatchDataWriter::getData(), org::gel::mauve::MauveHelperFunctions::getReadableMultiplicity(), org::gel::mauve::summary::output::IslandGeneFeatureWriter::performComplexIteration(), org::gel::mauve::summary::output::IslandGeneFeatureWriter::shouldPrintRow(), org::gel::mauve::summary::ProcessBackboneFile::storeRow(), and org::gel::mauve::summary::output::AlignedSequenceWriter::useSegment().

long org::gel::mauve::analysis::Segment::mult_type [protected]
 

Definition at line 38 of file Segment.java.

Referenced by multiplicityType().

final String org::gel::mauve::analysis::Segment::MULTIPLICITY_STRING = "multiplicity" [static]
 

Definition at line 35 of file Segment.java.

Segment [] org::gel::mauve::analysis::Segment::nexts
 

Definition at line 29 of file Segment.java.

Referenced by org::gel::mauve::summary::output::SegmentDataProcessor::addDataLinks(), org::gel::mauve::summary::output::SegmentDataProcessor::addUniques(), append(), org::gel::mauve::summary::output::SegmentDataProcessor::assignIDs(), org::gel::mauve::summary::output::SegmentDataProcessor::compressBackboneSegments(), org::gel::mauve::summary::output::SegmentDataProcessor::findContigsInUniques(), org::gel::mauve::summary::AnalysisModuleFrame::fixSegmentByContigs(), org::gel::mauve::summary::output::AbstractMatchDataWriter::moreRowsToPrint(), org::gel::mauve::summary::output::OverviewFileWriter::performCalculations(), remove(), Segment(), and org::gel::mauve::summary::output::IslandGeneFeatureWriter::shouldPrintRow().

Segment [] org::gel::mauve::analysis::Segment::prevs
 

Definition at line 27 of file Segment.java.

Referenced by org::gel::mauve::summary::output::SegmentDataProcessor::addDataLinks(), org::gel::mauve::summary::output::SegmentDataProcessor::addUniques(), append(), org::gel::mauve::summary::output::SegmentDataProcessor::compressBackboneSegments(), org::gel::mauve::summary::AnalysisModuleFrame::fixSegmentByContigs(), org::gel::mauve::summary::output::IslandGeneFeatureWriter::performComplexIteration(), remove(), and Segment().

boolean [] org::gel::mauve::analysis::Segment::reverse
 

The direction of each match.

false is forward, true is reverse

Definition at line 25 of file Segment.java.

Referenced by org::gel::mauve::analysis::Segment::GenomePositionComparator::compare(), org::gel::mauve::summary::output::SegmentDataProcessor::compressBackboneSegments(), org::gel::mauve::summary::AnalysisModuleFrame::fixSegmentByContigs(), org::gel::mauve::summary::output::IslandFeatureWriter::getData(), org::gel::mauve::summary::output::AbstractMatchDataWriter::getData(), org::gel::mauve::summary::output::SegmentDataProcessor::getReferenceSequence(), Segment(), org::gel::mauve::summary::ProcessBackboneFile::storeRow(), and toString().

long [] org::gel::mauve::analysis::Segment::right
 

The ends of this match in each sequence.

Definition at line 20 of file Segment.java.

Referenced by org::gel::mauve::summary::output::SegmentDataProcessor::addUniques(), append(), org::gel::mauve::analysis::Segment::GenomePositionComparator::compare(), org::gel::mauve::summary::output::SegmentDataProcessor::compressBackboneSegments(), org::gel::mauve::summary::AnalysisModuleFrame::fixSegmentByContigs(), org::gel::mauve::summary::output::IslandFeatureWriter::getData(), org::gel::mauve::summary::output::AbstractMatchDataWriter::getData(), org::gel::mauve::summary::output::IslandGeneFeatureWriter::moreRowsToPrint(), org::gel::mauve::summary::output::IslandGeneFeatureWriter::shouldPrintRow(), and org::gel::mauve::summary::ProcessBackboneFile::storeRow().

final long org::gel::mauve::analysis::Segment::serialVersionUID = 1 [static, package]
 

Definition at line 10 of file Segment.java.

String org::gel::mauve::analysis::Segment::typed_id
 

Definition at line 31 of file Segment.java.

Referenced by org::gel::mauve::summary::output::SegmentDataProcessor::assignIDs(), org::gel::mauve::summary::output::IslandGeneFeatureWriter::getData(), org::gel::mauve::summary::output::IslandFeatureWriter::getData(), and org::gel::mauve::summary::output::IslandCoordinateWriter::getData().


The documentation for this class was generated from the following file:
Generated on Mon Aug 19 06:03:49 2013 for Mauve by doxygen 1.3.6