CommandParameter plabel("label", "String", "", "", "", "", "","",false,false); parameters.push_back(plabel);
CommandParameter psubsample("subsample", "String", "", "", "", "", "","phylip",false,false); parameters.push_back(psubsample);
CommandParameter pdistance("distance", "Boolean", "", "F", "", "", "","phylip",false,false); parameters.push_back(pdistance);
- CommandParameter pcalc("calc", "Multiple", "sharedchao-sharedsobs-sharedace-jabund-sorabund-jclass-sorclass-jest-sorest-thetayc-thetan-kstest-whittaker-sharednseqs-ochiai-anderberg-kulczynski-kulczynskicody-lennon-morisitahorn-braycurtis-odum-canberra-structeuclidean-structchord-hellinger-manhattan-structpearson-soergel-spearman-structkulczynski-speciesprofile-structchi2-hamming-gower-memchi2-memchord-memeuclidean-mempearson", "sharedsobs-sharedchao-sharedace-jabund-sorabund-jclass-sorclass-jest-sorest-thetayc-thetan", "", "", "","",true,false,true); parameters.push_back(pcalc);
+ CommandParameter pcalc("calc", "Multiple", "sharedchao-sharedsobs-sharedace-jabund-sorabund-jclass-sorclass-jest-sorest-thetayc-thetan-kstest-whittaker-sharednseqs-ochiai-anderberg-kulczynski-kulczynskicody-lennon-morisitahorn-braycurtis-odum-canberra-structeuclidean-structchord-hellinger-manhattan-structpearson-soergel-spearman-structkulczynski-speciesprofile-structchi2-hamming-gower-memchi2-memchord-memeuclidean-mempearson-jsd", "sharedsobs-sharedchao-sharedace-jabund-sorabund-jclass-sorclass-jest-sorest-thetayc-thetan", "", "", "","",true,false,true); parameters.push_back(pcalc);
CommandParameter poutput("output", "Multiple", "lt-square", "lt", "", "", "","",false,false); parameters.push_back(poutput);
CommandParameter pall("all", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(pall);
CommandParameter piters("iters", "Number", "", "1000", "", "", "","",false,false); parameters.push_back(piters);
string temp = validParameter.validFile(parameters, "all", false); if (temp == "not found") { temp = "false"; }
all = m->isTrue(temp);
- temp = validParameter.validFile(parameters, "distance", false); if (temp == "not found") { temp = "false"; }
- createPhylip = m->isTrue(temp);
-
temp = validParameter.validFile(parameters, "iters", false); if (temp == "not found") { temp = "1000"; }
m->mothurConvert(temp, iters);
if (subsample == false) { iters = 0; }
+ temp = validParameter.validFile(parameters, "distance", false); if (temp == "not found") { temp = "false"; }
+ createPhylip = m->isTrue(temp);
+ if (subsample) { createPhylip = true; }
+
temp = validParameter.validFile(parameters, "processors", false); if (temp == "not found"){ temp = m->getProcessors(); }
m->setProcessors(temp);
m->mothurConvert(temp, processors);
sumCalculators.push_back(new MemEuclidean());
}else if (Estimators[i] == "mempearson") {
sumCalculators.push_back(new MemPearson());
+ }else if (Estimators[i] == "jsd") {
+ sumCalculators.push_back(new JSD());
}
}
}
vector<summarySharedData*> pDataArray;
DWORD dwThreadIdArray[processors-1];
- HANDLE hThreadArray[processors-1];
+ HANDLE hThreadArray[processors-1];
//Create processor worker threads.
for( int i=1; i<processors; i++ ){
temp->setGroup(thisLookup[k]->getGroup());
newLookup.push_back(temp);
}
+
//for each bin
for (int k = 0; k < thisLookup[0]->getNumBins(); k++) {
//Close all thread handles and free memory allocations.
for(int i=0; i < pDataArray.size(); i++){
+ if (pDataArray[i]->count != (pDataArray[i]->end-pDataArray[i]->start)) {
+ m->mothurOut("[ERROR]: process " + toString(i) + " only processed " + toString(pDataArray[i]->count) + " of " + toString(pDataArray[i]->end-pDataArray[i]->start) + " groups assigned to it, quitting. \n"); m->control_pressed = true;
+ }
m->appendFiles((sumFileName + toString(processIDS[i]) + ".temp"), sumFileName);
m->mothurRemove((sumFileName + toString(processIDS[i]) + ".temp"));