Uses of Class
trans.roc.RocWindow

Packages that use RocWindow

trans.roc

For manipulating the BAC dmel spike in data and generating ROC curves.

Uses of RocWindow in trans.roc

Methods in trans.roc that return RocWindow

static RocWindow[]	ParsePatternedWindows.loadTxtRocFile(java.io.File file) reads a txt roc window (chrom, start, stop, middle(not used), score).
static RocWindow[]	ParsePatternedWindows.filterRocWindows(RocWindow[] windows, double cutOff, boolean greaterThan) Scans an array of RocWindow for those that are greater than (or less than if boolean is false) or equal to the cutOff.
static RocWindow[]	ParsePatternedWindows.loadRocWindows(java.io.File[] arrayLists) Loads all the RocWindows into one from serialized ArrayLists of RocWindows.
static RocWindow[]	ParsePatternedWindows.fetchProximalWindows(GeneGroup[] geneGrps, RocWindow[] windows, int sizeUpstream)
static RocWindow[]	ExtractNonOverlappingWindows.extractNonOverlappingWindows(RocWindow[] r) Assumes the windows are sorted

Methods in trans.roc with parameters of type RocWindow

boolean	RocWindow.intersects(RocWindow other)
static void	RocWindow.printSGRWindows(RocWindow[] w)
static void	ParsePatternedWindows.writeSGRFile(RocWindow[] r, java.io.File file) Writes an sgr file.
static void	ParsePatternedWindows.writeTxtRocFile(RocWindow[] r, java.io.File file) Writes a chrom, start, stop, score file.
static void	ParsePatternedWindows.printChroms(RocWindow[] r)
static RocWindow[]	ParsePatternedWindows.filterRocWindows(RocWindow[] windows, double cutOff, boolean greaterThan) Scans an array of RocWindow for those that are greater than (or less than if boolean is false) or equal to the cutOff.
static RocWindow[]	ParsePatternedWindows.fetchProximalWindows(GeneGroup[] geneGrps, RocWindow[] windows, int sizeUpstream)
static RocWindow[]	ExtractNonOverlappingWindows.extractNonOverlappingWindows(RocWindow[] r) Assumes the windows are sorted