org::gel::mauve::summary::output::SegmentDataProcessor Class Reference

Inheritance diagram for org::gel::mauve::summary::output::SegmentDataProcessor:

[legend]Collaboration diagram for org::gel::mauve::summary::output::SegmentDataProcessor:


Public Member Functions
long	multiplicityForGenome (int index)
	SegmentDataProcessor (Hashtable map)
Static Public Member Functions
long	multiplicityForGenome (int index, int count)
Protected Member Functions
void	addDataLinks ()
void	addUniques ()
void	assignIDs ()
void	compressBackboneSegments ()
void	findContigsInUniques ()
int	getReferenceSequence ()
List	getSegmentsSortedBySeq (int sequence)
void	init ()
Vector	makeDefaultStartEndColumnHeaders ()
Protected Attributes
long	all_seq_multiplicity
Vector	backbone
int	backbone_min
int	count
Segment	current
Segment[]	firsts
int	reference = -1

Constructor & Destructor Documentation

org::gel::mauve::summary::output::SegmentDataProcessor::SegmentDataProcessor ( Hashtable map ) [inline]

Definition at line 32 of file SegmentDataProcessor.java.
References init().

Member Function Documentation

void org::gel::mauve::summary::output::SegmentDataProcessor::addDataLinks ( ) [inline, protected]

Definition at line 132 of file SegmentDataProcessor.java.
References org::gel::mauve::analysis::Segment::END, org::gel::mauve::analysis::Segment::left, org::gel::mauve::analysis::Segment::nexts, and org::gel::mauve::analysis::Segment::prevs.
Referenced by init().

void org::gel::mauve::summary::output::SegmentDataProcessor::addUniques ( ) [inline, protected]

Definition at line 155 of file SegmentDataProcessor.java.
References org::gel::mauve::analysis::Segment::END, org::gel::mauve::analysis::Segment::left, org::gel::mauve::analysis::Segment::nexts, org::gel::mauve::analysis::Segment::prevs, and org::gel::mauve::analysis::Segment::right.
Referenced by init().

void org::gel::mauve::summary::output::SegmentDataProcessor::assignIDs ( ) [inline, protected]

Definition at line 81 of file SegmentDataProcessor.java.
References org::gel::mauve::analysis::Segment::END, multiplicityForGenome(), org::gel::mauve::analysis::Segment::multiplicityType(), org::gel::mauve::analysis::Segment::nexts, and org::gel::mauve::analysis::Segment::typed_id.
Referenced by init().

void org::gel::mauve::summary::output::SegmentDataProcessor::findContigsInUniques ( ) [inline, protected]

Definition at line 65 of file SegmentDataProcessor.java.
References org::gel::mauve::analysis::Segment::END, org::gel::mauve::contigs::ContigHandler::fixSegmentByContigs(), multiplicityForGenome(), org::gel::mauve::analysis::Segment::multiplicityType(), and org::gel::mauve::analysis::Segment::nexts.

int org::gel::mauve::summary::output::SegmentDataProcessor::getReferenceSequence ( ) [inline, protected]

Definition at line 110 of file SegmentDataProcessor.java.
References org::gel::mauve::analysis::Segment::reverse.

List org::gel::mauve::summary::output::SegmentDataProcessor::getSegmentsSortedBySeq ( int sequence ) [inline, protected]

Definition at line 280 of file SegmentDataProcessor.java.

void org::gel::mauve::summary::output::SegmentDataProcessor::init ( ) [inline, protected]

Definition at line 42 of file SegmentDataProcessor.java.
References addDataLinks(), addUniques(), assignIDs(), and org::gel::mauve::analysis::Segment::END.
Referenced by SegmentDataProcessor().

Vector org::gel::mauve::summary::output::SegmentDataProcessor::makeDefaultStartEndColumnHeaders ( ) [inline, protected]

Definition at line 260 of file SegmentDataProcessor.java.
Referenced by org::gel::mauve::summary::output::AbstractMatchDataWriter::setColumnHeaders().

long org::gel::mauve::summary::output::SegmentDataProcessor::multiplicityForGenome ( int index,

int count

) [inline, static]

Definition at line 104 of file SegmentDataProcessor.java.