| addListener(ScaledWindowParserListener listener) | broad.core.siphy.TreeScalerIO | |
| addWindow(ScaledWindow sw) | broad.core.siphy.TreeScalerIO | |
| clear() | broad.core.siphy.TreeScalerIO | |
| getEstimationWindow() | broad.core.siphy.TreeScalerIO | |
| getScaledWindows() | broad.core.siphy.TreeScalerIO | |
| getTotalInSources() | broad.core.siphy.TreeScalerIO | |
| load(InputStream is, int shift, String chr) | broad.core.siphy.TreeScalerIO | |
| load(File source, int shift, String chr) | broad.core.siphy.TreeScalerIO | |
| load(InputStream is) | broad.core.siphy.TreeScalerIO | |
| loadAtMostRandom(File source, String chr, int maxNeutralOmegas) | broad.core.siphy.TreeScalerIO | |
| loadIntegrated(File source, double minPVal) | broad.core.siphy.TreeScalerIO | |
| loadIntoDistribution(File source, EmpiricalDistribution ed, boolean shortFormat) | broad.core.siphy.TreeScalerIO | |
| loadOldIntegrated(File source, int shift, String chr, double minPVal) | broad.core.siphy.TreeScalerIO | |
| parse(File source, int shift, String chr) | broad.core.siphy.TreeScalerIO | |
| permute() | broad.core.siphy.TreeScalerIO | |
| setEstimationWindow(int estimationWindow) | broad.core.siphy.TreeScalerIO | |
| setNumberFormatter(DecimalFormat formatter) | broad.core.siphy.TreeScalerIO | |
| stitch(int window, int skip) | broad.core.siphy.TreeScalerIO | |
| TreeScalerIO(int windowSize) | broad.core.siphy.TreeScalerIO | |
| TreeScalerIO() | broad.core.siphy.TreeScalerIO | |
| writeFull(BufferedWriter bw, List< ScaledWindow > windows) | broad.core.siphy.TreeScalerIO | |
| writeFull(BufferedWriter bw) | broad.core.siphy.TreeScalerIO | |
| writeFullAsGenomeGraphUsingLogPval(BufferedWriter bw) | broad.core.siphy.TreeScalerIO | |
1.8.7
