Examples with Locus bacter.Locus used on opensource projects

Example 36 with Locus

use of bacter.Locus in project bacter by tgvaughan.

the class ConversionGraphStatsLogger method getMeanEdgeLength.

/**
 * Obtain mean length of converted edges in ACG.
 *
 * @param acg
 * @return mean length, or NaN if ACG has no converted edges
 */
public static double getMeanEdgeLength(ConversionGraph acg) {
    if (acg.getTotalConvCount() < 1)
        return Double.NaN;
    double mean = 0.0;
    for (Locus locus : acg.getLoci()) {
        for (Conversion conv : acg.getConversions(locus)) mean += conv.getHeight2() - conv.getHeight1();
    }
    mean /= acg.getTotalConvCount();
    return mean;
}

Example 37 with Locus

use of bacter.Locus in project bacter by tgvaughan.

the class ConvertedRegionLogger method init.

@Override
public void init(PrintStream out) {
    final ConversionGraph arg = acgInput.get();
    String mainID = (getID() == null || getID().matches(("\\s*"))) ? arg.getID() + ".converted" : getID();
    for (Locus locus : acgInput.get().getLoci()) out.print(mainID + "." + locus.getID() + "\t");
}