Uses of Class
trans.roc.Sgr

Packages that use Sgr

trans.graphics	For graphically representing '.cel' files and intervals.
trans.misc	Rough working scripts.
trans.roc	For manipulating the BAC dmel spike in data and generating ROC curves.

Uses of Sgr in trans.graphics

Methods in trans.graphics with parameters of type Sgr

static void

AggregatePlots.loadRegions(Sgr sgr, Positive[] pos) Checks to see if an sgr object is in the positives, if so, adds the sgr object to the positive.

Uses of Sgr in trans.misc

Methods in trans.misc that return Sgr

static Sgr[]	Util.loadSgrFile(java.io.File sgrFile) Reads in an sgr file.
static Sgr[]	Util.loadGrFile(java.io.File grFile, java.lang.String chromName) Reads in an sgr file.

Methods in trans.misc with parameters of type Sgr

java.util.HashMap	Sgr2Bar.saveChromSplitSgr(Sgr[][] s, java.io.File tempDirectory) Saves a chromosome split Sgr[][] into temp files.
void	Sgr2Bar.printBarFiles(Sgr[][] sgrs, java.lang.String name)

Uses of Sgr in trans.roc

Methods in trans.roc that return Sgr

static Sgr[][]	Sgr.splitByChromosome(Sgr[] sgrs) Splits a Sgr[] containing many chromosome lines to a Sgr[chrom][lines].
static Sgr[]	MethodTester.parseSgrFile(java.io.File sgrFile, boolean zeroNaNOrInfinityScores) Reads in an Sgr file.

Methods in trans.roc with parameters of type Sgr

static int	SgrBacCounter.positive(Positive[] pos, Sgr sgr) Checks to see if an sgr object is one of the positives, if not returns -1, otherwise returns index number.
Bin	SgrBacCounter.findBin(Sgr sgr) Finds an appropriate bin given an sgr object
static Sgr[][]	Sgr.splitByChromosome(Sgr[] sgrs) Splits a Sgr[] containing many chromosome lines to a Sgr[chrom][lines].
boolean	Positive.matches(Sgr sgr)
static int	ParseSgrsForParticularRegions.inRegion(Sgr sgr, Positive[] pos) Checks to see if an sgr object is in one of the positives, if not returns -1, otherwise returns index number.
static void	ParseSgrsForParticularRegions.loadRegions(Sgr sgr, Positive[] pos) Checks to see if an sgr object is in the positives, if so, adds the sgr object to the positive.
static int	ParseBarsForParticularRegions.inRegion(Sgr sgr, Positive[] pos) Checks to see if an sgr object is in one of the positives, if not returns -1, otherwise returns index number.
static int	MethodTester.positive(Positive[] pos, Sgr sgr) Checks to see if an sgr object is one of the positives, if not returns -1, otherwise returns index number.
Bin	MethodTester.findBin(Sgr sgr) Finds an appropriate bin given an sgr object