#include "metastatscommand.h"
#include "metastats.h"
#include "sharedutilities.h"
-#include "mothurmetastats.h"
+
//**********************************************************************************************************************
vector<string> MetaStatsCommand::setParameters(){
if (numGroups == 2) { processors = 1; }
else if (numGroups < 2) { m->mothurOut("Not enough sets, I need at least 2 valid sets. Unable to complete command."); m->mothurOutEndLine(); m->control_pressed = true; }
- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+// #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
if(processors != 1){
int numPairs = namesOfGroupCombos.size();
int numPairsPerProcessor = numPairs / processors;
lines.push_back(linePair(startPos, numPairsPerProcessor));
}
}
- #endif
+// #endif
//as long as you are not at the end of the file or done wih the lines you want
while((lookup[0] != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
int MetaStatsCommand::process(vector<SharedRAbundVector*>& thisLookUp){
try {
- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+
if(processors == 1){
driver(0, namesOfGroupCombos.size(), thisLookUp);
}else{
int process = 1;
vector<int> processIDS;
-
+ #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
//loop through and create all the processes you want
while (process != processors) {
int pid = fork();
int temp = processIDS[i];
wait(&temp);
}
- }
- #else
- driver(0, namesOfGroupCombos.size(), thisLookUp);
- #endif
+ #else
+
+ //////////////////////////////////////////////////////////////////////////////////////////////////////
+ //Windows version shared memory, so be careful when passing variables through the summarySharedData struct.
+ //Above fork() will clone, so memory is separate, but that's not the case with windows,
+ //Taking advantage of shared memory to pass results vectors.
+ //////////////////////////////////////////////////////////////////////////////////////////////////////
+
+ vector<metastatsData*> pDataArray;
+ DWORD dwThreadIdArray[processors-1];
+ HANDLE hThreadArray[processors-1];
+
+ //Create processor worker threads.
+ for( int i=1; i<processors; i++ ){
+
+ //make copy of lookup so we don't get access violations
+ vector<SharedRAbundVector*> newLookup;
+ vector<string> designMapGroups;
+ for (int k = 0; k < thisLookUp.size(); k++) {
+ SharedRAbundVector* temp = new SharedRAbundVector();
+ temp->setLabel(thisLookUp[k]->getLabel());
+ temp->setGroup(thisLookUp[k]->getGroup());
+ newLookup.push_back(temp);
+ designMapGroups.push_back(designMap->getGroup(thisLookUp[k]->getGroup()));
+ }
+
+ //for each bin
+ for (int k = 0; k < thisLookUp[0]->getNumBins(); k++) {
+ if (m->control_pressed) { for (int j = 0; j < newLookup.size(); j++) { delete newLookup[j]; } return 0; }
+ for (int j = 0; j < thisLookUp.size(); j++) { newLookup[j]->push_back(thisLookUp[j]->getAbundance(k), thisLookUp[j]->getGroup()); }
+ }
+
+ // Allocate memory for thread data.
+ metastatsData* tempSum = new metastatsData(sharedfile, outputDir, m, lines[i].start, lines[i].num, namesOfGroupCombos, newLookup, designMapGroups, iters, threshold);
+ pDataArray.push_back(tempSum);
+ processIDS.push_back(i);
+
+ hThreadArray[i-1] = CreateThread(NULL, 0, MyMetastatsThreadFunction, pDataArray[i-1], 0, &dwThreadIdArray[i-1]);
+ }
+
+ //do my part
+ driver(lines[0].start, lines[0].num, thisLookUp);
+
+ //Wait until all threads have terminated.
+ WaitForMultipleObjects(processors-1, hThreadArray, TRUE, INFINITE);
+
+ //Close all thread handles and free memory allocations.
+ for(int i=0; i < pDataArray.size(); i++){
+ for (int j = 0; j < pDataArray[i]->thisLookUp.size(); j++) { delete pDataArray[i]->thisLookUp[j]; }
+ for (int j = 0; j < pDataArray[i]->outputNames.size(); j++) {
+ outputNames.push_back(pDataArray[i]->outputNames[j]);
+ outputTypes["metastats"].push_back(pDataArray[i]->outputNames[j]);
+ }
+
+ CloseHandle(hThreadArray[i]);
+ delete pDataArray[i];
+ }
+ #endif
+ }
+
return 0;
}
//get set names
string setA = namesOfGroupCombos[c][0];
string setB = namesOfGroupCombos[c][1];
- //cout << setA << '\t' << setB << endl;
+
//get filename
string outputFileName = outputDir + m->getRootName(m->getSimpleName(sharedfile)) + thisLookUp[0]->getLabel() + "." + setA + "-" + setB + ".metastats";
outputNames.push_back(outputFileName); outputTypes["metastats"].push_back(outputFileName);
setACount++;
}
}
-
- //for (int i = 0; i < subset.size(); i++) { cout << designMap->getGroup(subset[i]->getGroup()) << endl; }
- //cout << setACount << endl;
-
+
if ((setACount == 0) || (setBCount == 0)) {
m->mothurOut("Missing shared info for " + setA + " or " + setB + ". Skipping comparison."); m->mothurOutEndLine();
outputNames.pop_back();
#include "command.hpp"
#include "inputdata.h"
#include "sharedrabundvector.h"
+#include "mothurmetastats.h"
class MetaStatsCommand : public Command {
int driver(int, int, vector<SharedRAbundVector*>&);
};
+/**************************************************************************************************/
+//custom data structure for threads to use.
+// This is passed by void pointer so it can be any data type
+// that can be passed using a single void pointer (LPVOID).
+struct metastatsData {
+ vector<SharedRAbundVector*> thisLookUp;
+ vector< vector<string> > namesOfGroupCombos;
+ vector<string> designMapGroups;
+ vector<string> outputNames;
+ int start;
+ int num, iters;
+ float threshold;
+ MothurOut* m;
+ string sharedfile;
+ string outputDir;
+
+ metastatsData(){}
+ metastatsData(string sf, string oDir, MothurOut* mout, int st, int en, vector< vector<string> > ns, vector<SharedRAbundVector*> lu, vector<string> dg, int i, float thr) {
+ sharedfile = sf;
+ outputDir = oDir;
+ m = mout;
+ start = st;
+ num = en;
+ namesOfGroupCombos = ns;
+ thisLookUp = lu;
+ designMapGroups = dg;
+ iters = i;
+ threshold = thr;
+ }
+};
+/**************************************************************************************************/
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+#else
+static DWORD WINAPI MyMetastatsThreadFunction(LPVOID lpParam){
+ metastatsData* pDataArray;
+ pDataArray = (metastatsData*)lpParam;
+
+ try {
+
+ //for each combo
+ for (int c = pDataArray->start; c < (pDataArray->start+pDataArray->num); c++) {
+
+ //get set names
+ string setA = pDataArray->namesOfGroupCombos[c][0];
+ string setB = pDataArray->namesOfGroupCombos[c][1];
+
+ //get filename
+ string outputFileName = pDataArray->outputDir + pDataArray->m->getRootName(pDataArray->m->getSimpleName(pDataArray->sharedfile)) + pDataArray->thisLookUp[0]->getLabel() + "." + setA + "-" + setB + ".metastats";
+ pDataArray->outputNames.push_back(outputFileName);
+
+ vector< vector<double> > data2; data2.resize(pDataArray->thisLookUp[0]->getNumBins());
+
+ vector<SharedRAbundVector*> subset;
+ int setACount = 0;
+ int setBCount = 0;
+ for (int i = 0; i < pDataArray->thisLookUp.size(); i++) {
+ //is this group for a set we want to compare??
+ //sorting the sets by putting setB at the back and setA in the front
+ if (pDataArray->designMapGroups[i] == setB) {
+ subset.push_back(pDataArray->thisLookUp[i]);
+ setBCount++;
+ }else if (pDataArray->designMapGroups[i] == setA) {
+ subset.insert(subset.begin()+setACount, pDataArray->thisLookUp[i]);
+ setACount++;
+ }
+ }
+
+ if ((setACount == 0) || (setBCount == 0)) {
+ pDataArray->m->mothurOut("Missing shared info for " + setA + " or " + setB + ". Skipping comparison."); pDataArray->m->mothurOutEndLine();
+ pDataArray->outputNames.pop_back();
+ }else {
+ //fill data
+ for (int j = 0; j < pDataArray->thisLookUp[0]->getNumBins(); j++) {
+ data2[j].resize(subset.size(), 0.0);
+ for (int i = 0; i < subset.size(); i++) {
+ data2[j][i] = (subset[i]->getAbundance(j));
+ }
+ }
+
+ pDataArray->m->mothurOut("Comparing " + setA + " and " + setB + "..."); pDataArray->m->mothurOutEndLine();
+
+ pDataArray->m->mothurOutEndLine();
+ MothurMetastats mothurMeta(pDataArray->threshold, pDataArray->iters);
+ mothurMeta.runMetastats(outputFileName, data2, setACount);
+ pDataArray->m->mothurOutEndLine();
+ pDataArray->m->mothurOutEndLine();
+ }
+ }
+
+ return 0;
+
+ }
+ catch(exception& e) {
+ pDataArray->m->errorOut(e, "MetaStatsCommand", "MyMetastatsThreadFunction");
+ exit(1);
+ }
+}
+#endif
+
+
+
#endif
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