Uses of Class
trans.main.Oligo

Packages that use Oligo

trans.graphics	For graphically representing '.cel' files and intervals.
trans.main	Principle classes and scripts used in TiMAT2 analysis.

Uses of Oligo in trans.graphics

Methods in trans.graphics with parameters of type Oligo

static double	IntervalDrawPanel.fetchClosestOligoScore(Oligo[] oligos, int position) Finds the closes Oligo to a bp point and returns the indexed score.
static double	IntervalDrawPanel.fetchMaxOligoScore(Oligo[] oligos, int startBp, int stopBp) Scans oligos for a max score when given a bp range.

Uses of Oligo in trans.main

Methods in trans.main that return Oligo

Oligo[]	SubWindow.getOligos()
Oligo[]	PeakPicker.getOligos()
Oligo[]	Interval.extractSubRegionOligos(int start, int end) Given a bp start and bp end as well as a larger Oligo[] returns a sub array of the oligos flanking and including the start and end.
Oligo[]	Interval.getOligos()

Methods in trans.main with parameters of type Oligo

void	SubWindow.setOligos(Oligo[] oligos)
void	PeakPicker.setOligos(Oligo[] oligos)
static double	IntervalReportPrinter.calculateMeanNumberOligoMatches(Oligo[] oligos) Calculates the average number of oligo matches to the genome.
static void	IntervalGFFPrinter.gff(Oligo o, Interval i, java.lang.String name, int oligoNumber, java.lang.StringBuffer s) Appends a GFF3 line for an Oligo.
void	Interval.setOligos(Oligo[] oligos)
java.lang.String	BindingPeak.toString(Oligo[] oligos, int oligoLength) Score, Left, Peak, Right