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

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


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< Segment >	getGenPositionComparator (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().

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.