string temp = validParameter.validFile(parameters, "distance", false); if (temp == "not found") { temp = "false"; }
phylip = m->isTrue(temp);
- temp = validParameter.validFile(parameters, "random", false); if (temp == "not found") { temp = "true"; }
+ temp = validParameter.validFile(parameters, "random", false); if (temp == "not found") { temp = "f"; }
random = m->isTrue(temp);
if (!random) { iters = 0; } //turn off random calcs
m->mothurOut("The groups parameter allows you to specify which of the groups in your groupfile you would like analyzed. You must enter at least 1 valid group.\n");
m->mothurOut("The group names are separated by dashes. The iters parameter allows you to specify how many random trees you would like compared to your tree.\n");
m->mothurOut("The distance parameter allows you to create a distance file from the results. The default is false.\n");
- m->mothurOut("The random parameter allows you to shut off the comparison to random trees. The default is true, meaning compare your trees with randomly generated trees.\n");
+ m->mothurOut("The random parameter allows you to shut off the comparison to random trees. The default is false, meaning compare don't your trees with randomly generated trees.\n");
m->mothurOut("The unifrac.unweighted command should be in the following format: unifrac.unweighted(groups=yourGroups, iters=yourIters).\n");
m->mothurOut("Example unifrac.unweighted(groups=A-B-C, iters=500).\n");
m->mothurOut("The default value for groups is all the groups in your groupfile, and iters is 1000.\n");
validScores[randomData[k]] = randomData[k];
}
}
-
+
for(int a = 0; a < numComp; a++) {
float rcumul = 1.0000;
- //this loop fills the cumulative maps and put 0.0000 in the score freq map to make it easier to print.
- for (map<float,float>::iterator it = validScores.begin(); it != validScores.end(); it++) {
- //make rscoreFreq map and rCumul
- map<float,float>::iterator it2 = rscoreFreq[a].find(it->first);
- rCumul[a][it->first] = rcumul;
- //get percentage of random trees with that info
- if (it2 != rscoreFreq[a].end()) { rscoreFreq[a][it->first] /= iters; rcumul-= it2->second; }
- else { rscoreFreq[a][it->first] = 0.0000; } //no random trees with that score
- }
- if (random) { UWScoreSig[a].push_back(rCumul[a][userData[a]]); }
- else { UWScoreSig[a].push_back(0.0); }
+ if (random) {
+ //this loop fills the cumulative maps and put 0.0000 in the score freq map to make it easier to print.
+ for (map<float,float>::iterator it = validScores.begin(); it != validScores.end(); it++) {
+ //make rscoreFreq map and rCumul
+ map<float,float>::iterator it2 = rscoreFreq[a].find(it->first);
+ rCumul[a][it->first] = rcumul;
+ //get percentage of random trees with that info
+ if (it2 != rscoreFreq[a].end()) { rscoreFreq[a][it->first] /= iters; rcumul-= it2->second; }
+ else { rscoreFreq[a][it->first] = 0.0000; } //no random trees with that score
+ }
+ UWScoreSig[a].push_back(rCumul[a][userData[a]]);
+ }else { UWScoreSig[a].push_back(0.0); }
+
}