public static void run(
String infile,
String outfile,
String statsOutFile,
String distanceMeasureString,
String gapScalingFactorMultipliersString) {
// testing
// System.out.println ("zallstring that I heard in Driver.java: |" +
// gapScalingFactorMultipliersString + "|");
double[] gapScalingFactorMultipliers =
parseGapScalingFactorMultipliersString(gapScalingFactorMultipliersString);
Sequence[] seqs = Parser.parseMSA(infile);
// arg - to satisfy compiler
double[][] distances = new double[0][0];
DistanceWithGapMethod distance = getDistanceWithGapMethod(distanceMeasureString);
// unfortunately, for cache get/set - no easy way of outputting
// to stats file if logdet distance error occurred??
// so just output to STDOUT
if (distance instanceof GappedDistance) {
GappedDistance gappedDistance = (GappedDistance) distance;
// do this cache set only once per all GSFM settings
gappedDistance.cacheSetSimpleDistanceMatrices(seqs);
// rerun for all gsfm settings as necessary
for (int i = 0; i < gapScalingFactorMultipliers.length; i++) {
double gsfm = gapScalingFactorMultipliers[i];
// testing
// System.out.println (gsfm);
String gsfmOutfile = outfile + GSFM_FILENAME_DELIMITER + (new Double(gsfm)).toString();
String gsfmStatsOutfile =
statsOutFile + GSFM_FILENAME_DELIMITER + (new Double(gsfm)).toString();
// change printwriter to new filename
changePrintWriter(gsfmStatsOutfile);
distances = gappedDistance.cacheGetDistanceMatrix(gsfm);
Writer.writePhylipDistanceMatrix(seqs, distances, gsfmOutfile);
flushAndClosePrintWriter();
}
}
// LATER ADD IN PARAMETERIZING PASS IN MULTIPLE GAP OPEN/EXTEND
// PARAMETER COSTS FOR AFFINE DISTANCES
else if (distance instanceof AffineDistance) {
// parse out rest of parameters from distanceMeasureString
GapPenalties gapPenalties = parseAffineDistanceMeasureStringParameters(distanceMeasureString);
AffineDistance affineDistance = (AffineDistance) distance;
// do this cache set only once per all GSFM settings
affineDistance.cacheSetSimpleDistanceMatrices(seqs);
// rerun for all gsfm settings as necessary
// affine distance params
// concatenated onto affine distance name
for (int i = 0; i < gapScalingFactorMultipliers.length; i++) {
double gsfm = gapScalingFactorMultipliers[i];
String gsfmOutfile = outfile + GSFM_FILENAME_DELIMITER + (new Double(gsfm)).toString();
String gsfmStatsOutfile =
statsOutFile + GSFM_FILENAME_DELIMITER + (new Double(gsfm)).toString();
// WARNING - MUST MUST MUST have this set
// appropriately for both gsfm AND affine penalties!!!
// change printwriter to new filename
changePrintWriter(gsfmStatsOutfile);
distances =
affineDistance.cacheGetDistanceMatrix(
gsfm, gapPenalties.gapOpenPenalty, gapPenalties.gapExtendPenalty);
Writer.writePhylipDistanceMatrix(seqs, distances, gsfmOutfile);
flushAndClosePrintWriter();
}
} else { // no caching of simple distances for non-gapped distance methods
if ((gapScalingFactorMultipliers.length != 1) || (gapScalingFactorMultipliers[0] != 0.0)) {
printUsage();
System.exit(1);
}
String gsfmFilenameSuffix = GSFM_FILENAME_DELIMITER + gapScalingFactorMultipliers[0];
// change printwriter to filename
changePrintWriter(statsOutFile + gsfmFilenameSuffix);
distances = distance.getDistanceMatrix(seqs);
Writer.writePhylipDistanceMatrix(seqs, distances, outfile + gsfmFilenameSuffix);
flushAndClosePrintWriter();
}
}
