X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=indicatorcommand.cpp;h=fd818acb44c4c5280c6a54971d3d39413307861d;hp=dc9f121a0e83758d4ecf4977294e8221b3da0712;hb=050a3ff02473a3d4c0980964e1a9ebe52e55d6b8;hpb=6c2b1e530a5c0bb87040e58a3e410097acdfcc3d diff --git a/indicatorcommand.cpp b/indicatorcommand.cpp index dc9f121..fd818ac 100644 --- a/indicatorcommand.cpp +++ b/indicatorcommand.cpp @@ -14,16 +14,16 @@ //********************************************************************************************************************** vector IndicatorCommand::setParameters(){ try { - CommandParameter piters("iters", "Number", "", "1000", "", "", "",false,false); parameters.push_back(piters); - CommandParameter pdesign("design", "InputTypes", "", "", "TreeDesign", "TreeDesign", "none",false,false); parameters.push_back(pdesign); - CommandParameter pshared("shared", "InputTypes", "", "", "SharedRel", "SharedRel", "none",false,false); parameters.push_back(pshared); - CommandParameter prelabund("relabund", "InputTypes", "", "", "SharedRel", "SharedRel", "none",false,false); parameters.push_back(prelabund); - CommandParameter pgroups("groups", "String", "", "", "", "", "",false,false); parameters.push_back(pgroups); - CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel); - CommandParameter ptree("tree", "InputTypes", "", "", "TreeDesign", "TreeDesign", "none",false,false); parameters.push_back(ptree); - CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir); - CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir); - CommandParameter pprocessors("processors", "Number", "", "1", "", "", "",false,false); parameters.push_back(pprocessors); + CommandParameter piters("iters", "Number", "", "1000", "", "", "","",false,false); parameters.push_back(piters); + CommandParameter pdesign("design", "InputTypes", "", "", "TreeDesign", "TreeDesign", "none","summary",false,false,true); parameters.push_back(pdesign); + CommandParameter pshared("shared", "InputTypes", "", "", "SharedRel", "SharedRel", "none","summary",false,false,true); parameters.push_back(pshared); + CommandParameter prelabund("relabund", "InputTypes", "", "", "SharedRel", "SharedRel", "none","summary",false,false); parameters.push_back(prelabund); + CommandParameter pgroups("groups", "String", "", "", "", "", "","",false,false); parameters.push_back(pgroups); + CommandParameter plabel("label", "String", "", "", "", "", "","",false,false); parameters.push_back(plabel); + CommandParameter ptree("tree", "InputTypes", "", "", "TreeDesign", "TreeDesign", "none","tree-summary",false,false,true); parameters.push_back(ptree); + CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir); + CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir); + CommandParameter pprocessors("processors", "Number", "", "1", "", "", "","",false,false); parameters.push_back(pprocessors); vector myArray; for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); } @@ -58,25 +58,20 @@ string IndicatorCommand::getHelpString(){ } } //********************************************************************************************************************** -string IndicatorCommand::getOutputFileNameTag(string type, string inputName=""){ - try { - string outputFileName = ""; - map >::iterator it; +string IndicatorCommand::getOutputPattern(string type) { + try { + string pattern = ""; - //is this a type this command creates - it = outputTypes.find(type); - if (it == outputTypes.end()) { m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); } - else { - if (type == "tree") { outputFileName = "indicator.tre"; } - else if (type == "summary") { outputFileName = "indicator.summary"; } - else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true; } - } - return outputFileName; - } - catch(exception& e) { - m->errorOut(e, "IndicatorCommand", "getOutputFileNameTag"); - exit(1); - } + if (type == "tree") { pattern = "[filename],indicator.tre"; } + else if (type == "summary") { pattern = "[filename],indicator.summary"; } + else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; } + + return pattern; + } + catch(exception& e) { + m->errorOut(e, "IndicatorCommand", "getOutputPattern"); + exit(1); + } } //********************************************************************************************************************** IndicatorCommand::IndicatorCommand(){ @@ -296,8 +291,8 @@ int IndicatorCommand::execute(){ for (int i = 0; i < m->Treenames.size(); i++) { nameMap.insert(m->Treenames[i]); //sanity check - is this a group that is not in the sharedfile? + if (i == 0) { gps.insert("Group1"); } if (designfile == "") { - if (i == 0) { gps.insert("Group1"); } if (!(m->inUsersGroups(m->Treenames[i], m->getAllGroups()))) { m->mothurOut("[ERROR]: " + m->Treenames[i] + " is not a group in your shared or relabund file."); m->mothurOutEndLine(); mismatch = true; @@ -410,13 +405,15 @@ int IndicatorCommand::GetIndicatorSpecies(){ try { string thisOutputDir = outputDir; if (outputDir == "") { thisOutputDir += m->hasPath(inputFileName); } - string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(inputFileName)) + getOutputFileNameTag("summary"); + map variables; + variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(inputFileName)); + string outputFileName = getOutputFileName("summary", variables); outputNames.push_back(outputFileName); outputTypes["summary"].push_back(outputFileName); ofstream out; m->openOutputFile(outputFileName, out); out.setf(ios::fixed, ios::floatfield); out.setf(ios::showpoint); - m->mothurOutEndLine(); m->mothurOut("Species\tIndicatorValue\tpValue\n"); + m->mothurOutEndLine(); m->mothurOut("Species\tIndicator_Groups\tIndicatorValue\tpValue\n"); int numBins = 0; if (sharedfile != "") { numBins = lookup[0]->getNumBins(); } @@ -430,6 +427,7 @@ int IndicatorCommand::GetIndicatorSpecies(){ vector indicatorValues; //size of numBins vector pValues; + vector indicatorGroups; map< vector, vector > randomGroupingsMap; //maps location in groupings to location in groupings, ie, [0][0] -> [1][2]. This is so we don't have to actually move the sharedRabundVectors. if (sharedfile != "") { @@ -453,9 +451,9 @@ int IndicatorCommand::GetIndicatorSpecies(){ if (groupsAlreadyAdded.size() != lookup.size()) { m->mothurOut("[ERROR]: could not make proper groupings."); m->mothurOutEndLine(); } - indicatorValues = getValues(groupings, randomGroupingsMap); + indicatorValues = getValues(groupings, indicatorGroups, randomGroupingsMap); - pValues = getPValues(groupings, randomGroupingsMap, lookup.size(), indicatorValues); + pValues = getPValues(groupings, lookup.size(), indicatorValues); }else { vector< vector > groupings; set groupsAlreadyAdded; @@ -476,9 +474,9 @@ int IndicatorCommand::GetIndicatorSpecies(){ if (groupsAlreadyAdded.size() != lookupFloat.size()) { m->mothurOut("[ERROR]: could not make proper groupings."); m->mothurOutEndLine(); } - indicatorValues = getValues(groupings, randomGroupingsMap); + indicatorValues = getValues(groupings, indicatorGroups, randomGroupingsMap); - pValues = getPValues(groupings, randomGroupingsMap, lookupFloat.size(), indicatorValues); + pValues = getPValues(groupings, lookupFloat.size(), indicatorValues); } if (m->control_pressed) { out.close(); return 0; } @@ -487,22 +485,22 @@ int IndicatorCommand::GetIndicatorSpecies(){ /******************************************************/ //output indicator values to table form // /*****************************************************/ - out << "OTU\tIndicator_Value\tpValue" << endl; + out << "OTU\tIndicator_Groups\tIndicator_Value\tpValue" << endl; for (int j = 0; j < indicatorValues.size(); j++) { if (m->control_pressed) { out.close(); return 0; } - out << m->currentBinLabels[j] << '\t' << indicatorValues[j] << '\t'; + out << m->currentBinLabels[j] << '\t' << indicatorGroups[j] << '\t' << indicatorValues[j] << '\t'; if (pValues[j] > (1/(float)iters)) { out << pValues[j] << endl; } else { out << "<" << (1/(float)iters) << endl; } if (pValues[j] <= 0.05) { - cout << m->currentBinLabels[j] << '\t' << indicatorValues[j] << '\t'; + cout << m->currentBinLabels[j] << '\t' << indicatorGroups[j] << '\t' << indicatorValues[j] << '\t'; string pValueString = "<" + toString((1/(float)iters)); if (pValues[j] > (1/(float)iters)) { pValueString = toString(pValues[j]); cout << pValues[j];} else { cout << "<" << (1/(float)iters); } - m->mothurOutJustToLog(m->currentBinLabels[j] + "\t" + toString(indicatorValues[j]) + "\t" + pValueString); + m->mothurOutJustToLog(m->currentBinLabels[j] + "\t" + indicatorGroups[j] + "\t" + toString(indicatorValues[j]) + "\t" + pValueString); m->mothurOutEndLine(); } } @@ -525,7 +523,9 @@ int IndicatorCommand::GetIndicatorSpecies(Tree*& T){ string thisOutputDir = outputDir; if (outputDir == "") { thisOutputDir += m->hasPath(inputFileName); } - string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(inputFileName)) + getOutputFileNameTag("summary"); + map variables; + variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(inputFileName)); + string outputFileName = getOutputFileName("summary",variables); outputNames.push_back(outputFileName); outputTypes["summary"].push_back(outputFileName); ofstream out; @@ -538,14 +538,15 @@ int IndicatorCommand::GetIndicatorSpecies(Tree*& T){ //print headings out << "TreeNode\t"; - for (int i = 0; i < numBins; i++) { out << m->currentBinLabels[i] << "_IndValue" << '\t' << "pValue" << '\t'; } + for (int i = 0; i < numBins; i++) { out << m->currentBinLabels[i] << "_IndGroups" << '\t' << m->currentBinLabels[i] << "_IndValue" << '\t' << "pValue" << '\t'; } out << endl; - m->mothurOutEndLine(); m->mothurOut("Node\tSpecies\tIndicatorValue\tpValue\n"); + m->mothurOutEndLine(); m->mothurOut("Node\tSpecies\tIndicator_Groups\tIndicatorValue\tpValue\n"); string treeOutputDir = outputDir; if (outputDir == "") { treeOutputDir += m->hasPath(treefile); } - string outputTreeFileName = treeOutputDir + m->getRootName(m->getSimpleName(treefile)) + getOutputFileNameTag("tree"); + variables["[filename]"] = treeOutputDir + m->getRootName(m->getSimpleName(treefile)); + string outputTreeFileName = getOutputFileName("tree", variables); //create a map from tree node index to names of descendants, save time later to know which sharedRabund you need @@ -572,6 +573,7 @@ int IndicatorCommand::GetIndicatorSpecies(Tree*& T){ vector indicatorValues; //size of numBins vector pValues; + vector indicatorGroups; map< vector, vector > randomGroupingsMap; //maps location in groupings to location in groupings, ie, [0][0] -> [1][2]. This is so we don't have to actually move the sharedRabundVectors. if (sharedfile != "") { @@ -623,9 +625,9 @@ int IndicatorCommand::GetIndicatorSpecies(Tree*& T){ if (groupsAlreadyAdded.size() != lookup.size()) { m->mothurOut("[ERROR]: could not make proper groupings."); m->mothurOutEndLine(); } - indicatorValues = getValues(groupings, randomGroupingsMap); + indicatorValues = getValues(groupings, indicatorGroups, randomGroupingsMap); - pValues = getPValues(groupings, randomGroupingsMap, lookup.size(), indicatorValues); + pValues = getPValues(groupings, lookup.size(), indicatorValues); }else { vector< vector > groupings; @@ -672,9 +674,9 @@ int IndicatorCommand::GetIndicatorSpecies(Tree*& T){ if (groupsAlreadyAdded.size() != lookupFloat.size()) { m->mothurOut("[ERROR]: could not make proper groupings."); m->mothurOutEndLine(); } - indicatorValues = getValues(groupings, randomGroupingsMap); + indicatorValues = getValues(groupings, indicatorGroups, randomGroupingsMap); - pValues = getPValues(groupings, randomGroupingsMap, lookupFloat.size(), indicatorValues); + pValues = getPValues(groupings, lookupFloat.size(), indicatorValues); } if (m->control_pressed) { out.close(); return 0; } @@ -689,17 +691,17 @@ int IndicatorCommand::GetIndicatorSpecies(Tree*& T){ if (m->control_pressed) { out.close(); return 0; } if (pValues[j] < (1/(float)iters)) { - out << indicatorValues[j] << '\t' << '<' << (1/(float)iters) << '\t'; + out << indicatorGroups[j] << '\t' << indicatorValues[j] << '\t' << '<' << (1/(float)iters) << '\t'; }else { - out << indicatorValues[j] << '\t' << pValues[j] << '\t'; + out << indicatorGroups[j] << '\t' << indicatorValues[j] << '\t' << pValues[j] << '\t'; } if (pValues[j] <= 0.05) { - cout << i+1 << '\t' << m->currentBinLabels[j] << '\t' << indicatorValues[j] << '\t'; + cout << i+1 << '\t' << m->currentBinLabels[j] << '\t' << indicatorGroups[j] << '\t' << indicatorValues[j] << '\t'; string pValueString = "<" + toString((1/(float)iters)); if (pValues[j] > (1/(float)iters)) { pValueString = toString(pValues[j]); cout << pValues[j];} else { cout << "<" << (1/(float)iters); } - m->mothurOutJustToLog(toString(i) + "\t" + m->currentBinLabels[j] + "\t" + toString(indicatorValues[j]) + "\t" + pValueString); + m->mothurOutJustToLog(toString(i) + "\t" + m->currentBinLabels[j] + "\t" + indicatorGroups[j] + "\t" + toString(indicatorValues[j]) + "\t" + pValueString); m->mothurOutEndLine(); } } @@ -724,11 +726,25 @@ int IndicatorCommand::GetIndicatorSpecies(Tree*& T){ } } //********************************************************************************************************************** -vector IndicatorCommand::getValues(vector< vector >& groupings, map< vector, vector > groupingsMap){ +vector IndicatorCommand::getValues(vector< vector >& groupings, vector& indicatorGroupings, map< vector, vector > groupingsMap){ try { vector values; map< vector, vector >::iterator it; - + + indicatorGroupings.clear(); + + //create grouping strings + vector groupingsGroups; + for (int j = 0; j < groupings.size(); j++) { + string tempGrouping = ""; + for (int k = 0; k < groupings[j].size()-1; k++) { + tempGrouping += groupings[j][k]->getGroup() + "-"; + } + tempGrouping += groupings[j][groupings[j].size()-1]->getGroup(); + groupingsGroups.push_back(tempGrouping); + } + + //for each otu for (int i = 0; i < groupings[0][0]->getNumBins(); i++) { @@ -768,15 +784,17 @@ vector IndicatorCommand::getValues(vector< vector maxIndVal) { maxIndVal = thisValue; } + if (thisValue > maxIndVal) { maxIndVal = thisValue; maxGrouping = groupingsGroups[j]; } } values.push_back(maxIndVal); + indicatorGroupings.push_back(maxGrouping); } return values; @@ -788,17 +806,24 @@ vector IndicatorCommand::getValues(vector< vector IndicatorCommand::getValues(vector< vector >& groupings, map< vector, vector > groupingsMap){ +vector IndicatorCommand::getValues(vector< vector >& groupings, vector& indicatorGroupings, map< vector, vector > groupingsMap){ try { vector values; - - /*for (int j = 0; j < groupings.size(); j++) { - cout << "grouping " << j << endl; - for (int k = 0; k < groupings[j].size(); k++) { - cout << groupings[j][k]->getGroup() << endl; - } - }*/ map< vector, vector >::iterator it; + + indicatorGroupings.clear(); + + //create grouping strings + vector groupingsGroups; + for (int j = 0; j < groupings.size(); j++) { + string tempGrouping = ""; + for (int k = 0; k < groupings[j].size()-1; k++) { + tempGrouping += groupings[j][k]->getGroup() + "-"; + } + tempGrouping += groupings[j][groupings[j].size()-1]->getGroup(); + groupingsGroups.push_back(tempGrouping); + } + //for each otu for (int i = 0; i < groupings[0][0]->getNumBins(); i++) { @@ -835,15 +860,17 @@ vector IndicatorCommand::getValues(vector< vector >& } float maxIndVal = 0.0; + string maxGrouping = ""; for (int j = 0; j < terms.size(); j++) { float thisAij = (terms[j] / AijDenominator); //relative abundance float thisValue = thisAij * Bij[j] * 100.0; //save largest - if (thisValue > maxIndVal) { maxIndVal = thisValue; } + if (thisValue > maxIndVal) { maxIndVal = thisValue; maxGrouping = groupingsGroups[j]; } } values.push_back(maxIndVal); + indicatorGroupings.push_back(maxGrouping); } return values; @@ -1115,15 +1142,16 @@ int IndicatorCommand::getSharedFloat(){ } } //********************************************************************************************************************** -vector IndicatorCommand::driver(vector< vector >& groupings, map< vector, vector > groupingsMap, int num, vector indicatorValues, int numIters){ +vector IndicatorCommand::driver(vector< vector >& groupings, int num, vector indicatorValues, int numIters){ try { vector pvalues; pvalues.resize(indicatorValues.size(), 0); + vector notUsedGroupings; //we dont care about the grouping for the pvalues since they are randomized, but we need to pass the function something to make it work. for(int i=0;icontrol_pressed) { break; } - groupingsMap = randomizeGroupings(groupings, num); - vector randomIndicatorValues = getValues(groupings, groupingsMap); + map< vector, vector > groupingsMap = randomizeGroupings(groupings, num); + vector randomIndicatorValues = getValues(groupings, notUsedGroupings, groupingsMap); for (int j = 0; j < indicatorValues.size(); j++) { if (randomIndicatorValues[j] >= indicatorValues[j]) { pvalues[j]++; } @@ -1138,23 +1166,29 @@ vector IndicatorCommand::driver(vector< vector } } //********************************************************************************************************************** -vector IndicatorCommand::getPValues(vector< vector >& groupings, map< vector, vector > groupingsMap, int num, vector indicatorValues){ +vector IndicatorCommand::getPValues(vector< vector >& groupings, int num, vector indicatorValues){ try { vector pvalues; - -#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix) + if(processors == 1){ - pvalues = driver(groupings, groupingsMap, num, indicatorValues, iters); - for (int i = 0; i < pvalues.size(); i++) { pvalues[i] /= (double)iters; } + pvalues = driver(groupings, num, indicatorValues, iters); + for (int i = 0; i < pvalues.size(); i++) { pvalues[i] /= (double)iters; } }else{ + //divide iters between processors + vector procIters; + int numItersPerProcessor = iters / processors; + + //divide iters between processes + for (int h = 0; h < processors; h++) { + if(h == processors - 1){ numItersPerProcessor = iters - h * numItersPerProcessor; } + procIters.push_back(numItersPerProcessor); + } + + vector processIDS; + int process = 1; - //divide iters between processors - int numItersPerProcessor = iters / processors; - - vector processIDS; - int process = 1; - int num = 0; - +#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix) + //loop through and create all the processes you want while (process != processors) { int pid = fork(); @@ -1163,7 +1197,7 @@ vector IndicatorCommand::getPValues(vector< vector IndicatorCommand::getPValues(vector< vector IndicatorCommand::getPValues(vector< vectormothurRemove(tempFile); } - for (int i = 0; i < pvalues.size(); i++) { pvalues[i] /= (double)iters; } - } + for (int i = 0; i < pvalues.size(); i++) { pvalues[i] /= (double)iters; } #else - pvalues = driver(groupings, groupingsMap, num, indicatorValues, iters); - for (int i = 0; i < pvalues.size(); i++) { pvalues[i] /= (double)iters; } + + //fill in functions + vector pDataArray; + DWORD dwThreadIdArray[processors-1]; + HANDLE hThreadArray[processors-1]; + + //Create processor worker threads. + for( int i=1; i > newGroupings; + + for (int k = 0; k < groupings.size(); k++) { + vector newLookup; + for (int l = 0; l < groupings[k].size(); l++) { + SharedRAbundFloatVector* temp = new SharedRAbundFloatVector(); + temp->setLabel(groupings[k][l]->getLabel()); + temp->setGroup(groupings[k][l]->getGroup()); + newLookup.push_back(temp); + } + newGroupings.push_back(newLookup); + } + + //for each bin + for (int l = 0; l < groupings.size(); l++) { + for (int k = 0; k < groupings[l][0]->getNumBins(); k++) { + if (m->control_pressed) { for (int j = 0; j < newGroupings.size(); j++) { for (int u = 0; u < newGroupings[j].size(); u++) { delete newGroupings[j][u]; } } return pvalues; } + + for (int j = 0; j < groupings[l].size(); j++) { newGroupings[l][j]->push_back(groupings[l][j]->getAbundance(k), groupings[l][j]->getGroup()); } + } + } + + vector copyIValues = indicatorValues; + + indicatorData* temp = new indicatorData(m, procIters[i], newGroupings, num, copyIValues); + pDataArray.push_back(temp); + processIDS.push_back(i); + + hThreadArray[i-1] = CreateThread(NULL, 0, MyIndicatorThreadFunction, pDataArray[i-1], 0, &dwThreadIdArray[i-1]); + } + + //do my part + pvalues = driver(groupings, num, indicatorValues, procIters[0]); + + //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]->pvalues.size(); j++) { pvalues[j] += pDataArray[i]->pvalues[j]; } + + for (int l = 0; l < pDataArray[i]->groupings.size(); l++) { + for (int j = 0; j < pDataArray[i]->groupings[l].size(); j++) { delete pDataArray[i]->groupings[l][j]; } + } + + CloseHandle(hThreadArray[i]); + delete pDataArray[i]; + } + + for (int i = 0; i < pvalues.size(); i++) { pvalues[i] /= (double)iters; } #endif + } + return pvalues; } @@ -1228,15 +1319,16 @@ vector IndicatorCommand::getPValues(vector< vector IndicatorCommand::driver(vector< vector >& groupings, map< vector, vector > groupingsMap, int num, vector indicatorValues, int numIters){ +vector IndicatorCommand::driver(vector< vector >& groupings, int num, vector indicatorValues, int numIters){ try { vector pvalues; pvalues.resize(indicatorValues.size(), 0); + vector notUsedGroupings; //we dont care about the grouping for the pvalues since they are randomized, but we need to pass the function something to make it work. for(int i=0;icontrol_pressed) { break; } - groupingsMap = randomizeGroupings(groupings, num); - vector randomIndicatorValues = getValues(groupings, groupingsMap); + map< vector, vector > groupingsMap = randomizeGroupings(groupings, num); + vector randomIndicatorValues = getValues(groupings, notUsedGroupings, groupingsMap); for (int j = 0; j < indicatorValues.size(); j++) { if (randomIndicatorValues[j] >= indicatorValues[j]) { pvalues[j]++; } @@ -1252,22 +1344,29 @@ vector IndicatorCommand::driver(vector< vector >& gr } //********************************************************************************************************************** //same as above, just data type difference -vector IndicatorCommand::getPValues(vector< vector >& groupings, map< vector, vector > groupingsMap, int num, vector indicatorValues){ +vector IndicatorCommand::getPValues(vector< vector >& groupings, int num, vector indicatorValues){ try { vector pvalues; - -#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix) + if(processors == 1){ - pvalues = driver(groupings, groupingsMap, num, indicatorValues, iters); - for (int i = 0; i < pvalues.size(); i++) { pvalues[i] /= (double)iters; } + pvalues = driver(groupings, num, indicatorValues, iters); + for (int i = 0; i < pvalues.size(); i++) { pvalues[i] /= (double)iters; } }else{ + //divide iters between processors + vector procIters; + int numItersPerProcessor = iters / processors; + + //divide iters between processes + for (int h = 0; h < processors; h++) { + if(h == processors - 1){ numItersPerProcessor = iters - h * numItersPerProcessor; } + procIters.push_back(numItersPerProcessor); + } + + vector processIDS; + int process = 1; - //divide iters between processors - int numItersPerProcessor = iters / processors; - - vector processIDS; - int process = 1; - +#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix) + //loop through and create all the processes you want while (process != processors) { int pid = fork(); @@ -1276,7 +1375,7 @@ vector IndicatorCommand::getPValues(vector< vector > processIDS.push_back(pid); //create map from line number to pid so you can append files in correct order later process++; }else if (pid == 0){ - pvalues = driver(groupings, groupingsMap, num, indicatorValues, numItersPerProcessor); + pvalues = driver(groupings, num, indicatorValues, procIters[process]); //pass pvalues to parent ofstream out; @@ -1292,49 +1391,106 @@ vector IndicatorCommand::getPValues(vector< vector > out.close(); exit(0); - }else { - m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine(); + }else { + m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine(); for (int i = 0; i < processIDS.size(); i++) { kill (processIDS[i], SIGINT); } exit(0); } } //do my part - //special case for last processor in case it doesn't divide evenly - numItersPerProcessor = iters - ((processors-1) * numItersPerProcessor); - pvalues = driver(groupings, groupingsMap, num, indicatorValues, numItersPerProcessor); + pvalues = driver(groupings, num, indicatorValues, procIters[0]); //force parent to wait until all the processes are done - for (int i=0;iopenInputFile(tempFile, in); ////// to do /////////// - int numTemp; numTemp = 0; + int numTemp; numTemp = 0; for (int j = 0; j < pvalues.size(); j++) { in >> numTemp; m->gobble(in); pvalues[j] += numTemp; } in.close(); m->mothurRemove(tempFile); } - for (int i = 0; i < pvalues.size(); i++) { pvalues[i] /= (double)iters; } - } + for (int i = 0; i < pvalues.size(); i++) { pvalues[i] /= (double)iters; } #else - pvalues = driver(groupings, groupingsMap, num, indicatorValues, iters); - for (int i = 0; i < pvalues.size(); i++) { pvalues[i] /= (double)iters; } + + //fill in functions + vector pDataArray; + DWORD dwThreadIdArray[processors-1]; + HANDLE hThreadArray[processors-1]; + + //Create processor worker threads. + for( int i=1; i > newGroupings; + + for (int k = 0; k < groupings.size(); k++) { + vector newLookup; + for (int l = 0; l < groupings[k].size(); l++) { + SharedRAbundFloatVector* temp = new SharedRAbundFloatVector(); + temp->setLabel(groupings[k][l]->getLabel()); + temp->setGroup(groupings[k][l]->getGroup()); + newLookup.push_back(temp); + } + newGroupings.push_back(newLookup); + } + + //for each bin + for (int l = 0; l < groupings.size(); l++) { + for (int k = 0; k < groupings[l][0]->getNumBins(); k++) { + if (m->control_pressed) { for (int j = 0; j < newGroupings.size(); j++) { for (int u = 0; u < newGroupings[j].size(); u++) { delete newGroupings[j][u]; } } return pvalues; } + + for (int j = 0; j < groupings[l].size(); j++) { newGroupings[l][j]->push_back((float)(groupings[l][j]->getAbundance(k)), groupings[l][j]->getGroup()); } + } + } + + vector copyIValues = indicatorValues; + + indicatorData* temp = new indicatorData(m, procIters[i], newGroupings, num, copyIValues); + pDataArray.push_back(temp); + processIDS.push_back(i); + + hThreadArray[i-1] = CreateThread(NULL, 0, MyIndicatorThreadFunction, pDataArray[i-1], 0, &dwThreadIdArray[i-1]); + } + + //do my part + pvalues = driver(groupings, num, indicatorValues, procIters[0]); + + //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]->pvalues.size(); j++) { pvalues[j] += pDataArray[i]->pvalues[j]; } + + for (int l = 0; l < pDataArray[i]->groupings.size(); l++) { + for (int j = 0; j < pDataArray[i]->groupings[l].size(); j++) { delete pDataArray[i]->groupings[l][j]; } + } + + CloseHandle(hThreadArray[i]); + delete pDataArray[i]; + } + + for (int i = 0; i < pvalues.size(); i++) { pvalues[i] /= (double)iters; } #endif + } + return pvalues; } catch(exception& e) { - m->errorOut(e, "IndicatorCommand", "getPValues"); + m->errorOut(e, "IndicatorCommand", "getPValues"); exit(1); } }