X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=metastatscommand.cpp;h=b7aa7e5fcb3bcc809c89ac3cc82c1ecae9d6272a;hb=8dd3c225255d7084e3aff8740aa4f1f1cabb367a;hp=f637eec8b5821e45bbeae41a5282481a809a272b;hpb=1d898dc6edaf9e9f287fab53bf1f21fb29757a17;p=mothur.git diff --git a/metastatscommand.cpp b/metastatscommand.cpp index f637eec..b7aa7e5 100644 --- a/metastatscommand.cpp +++ b/metastatscommand.cpp @@ -10,6 +10,7 @@ #include "metastatscommand.h" #include "metastats.h" #include "sharedutilities.h" +#include "mothurmetastats.h" //********************************************************************************************************************** vector MetaStatsCommand::setParameters(){ @@ -83,6 +84,7 @@ MetaStatsCommand::MetaStatsCommand(string option) { //allow user to run help if(option == "help") { help(); abort = true; calledHelp = true; } + else if(option == "citation") { citation(); abort = true; calledHelp = true;} else { vector myArray = setParameters(); @@ -133,7 +135,7 @@ MetaStatsCommand::MetaStatsCommand(string option) { sharedfile = m->getSharedFile(); if (sharedfile != "") { m->mothurOut("Using " + sharedfile + " as input file for the shared parameter."); m->mothurOutEndLine(); } else { m->mothurOut("You have no current sharedfile and the shared parameter is required."); m->mothurOutEndLine(); abort = true; } - } + }else { m->setSharedFile(sharedfile); } //check for required parameters designfile = validParameter.validFile(parameters, "design", true); @@ -143,7 +145,7 @@ MetaStatsCommand::MetaStatsCommand(string option) { designfile = m->getDesignFile(); if (designfile != "") { m->mothurOut("Using " + designfile + " as input file for the design parameter."); m->mothurOutEndLine(); } else { m->mothurOut("You have no current designfile and the design parameter is required."); m->mothurOutEndLine(); abort = true; } - } + }else { m->setDesignFile(designfile); } //if the user changes the output directory command factory will send this info to us in the output parameter outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){ @@ -165,7 +167,7 @@ MetaStatsCommand::MetaStatsCommand(string option) { else { pickedGroups = true; m->splitAtDash(groups, Groups); - m->Groups = Groups; + m->setGroups(Groups); } sets = validParameter.validFile(parameters, "sets", false); @@ -176,14 +178,14 @@ MetaStatsCommand::MetaStatsCommand(string option) { string temp = validParameter.validFile(parameters, "iters", false); if (temp == "not found") { temp = "1000"; } - convert(temp, iters); + m->mothurConvert(temp, iters); temp = validParameter.validFile(parameters, "threshold", false); if (temp == "not found") { temp = "0.05"; } - convert(temp, threshold); + m->mothurConvert(temp, threshold); temp = validParameter.validFile(parameters, "processors", false); if (temp == "not found"){ temp = m->getProcessors(); } m->setProcessors(temp); - convert(temp, processors); + m->mothurConvert(temp, processors); } } @@ -213,8 +215,9 @@ int MetaStatsCommand::execute(){ //setup the pairwise comparions of sets for metastats //calculate number of comparisons i.e. with groups A,B,C = AB, AC, BC = 3; //make sure sets are all in designMap - SharedUtil* util = new SharedUtil(); - util->setGroups(Sets, designMap->namesOfGroups); + SharedUtil* util = new SharedUtil(); + vector dGroups = designMap->getNamesOfGroups(); + util->setGroups(Sets, dGroups); delete util; int numGroups = Sets.size(); @@ -248,7 +251,7 @@ int MetaStatsCommand::execute(){ //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))) { - if (m->control_pressed) { outputTypes.clear(); for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } m->Groups.clear(); delete input; delete designMap; for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; } + if (m->control_pressed) { outputTypes.clear(); for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } m->clearGroups(); delete input; delete designMap; for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; } if(allLines == 1 || labels.count(lookup[0]->getLabel()) == 1){ @@ -279,13 +282,13 @@ int MetaStatsCommand::execute(){ //prevent memory leak for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; lookup[i] = NULL; } - if (m->control_pressed) { outputTypes.clear(); m->Groups.clear(); delete input; delete designMap; for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; } + if (m->control_pressed) { outputTypes.clear(); m->clearGroups(); delete input; delete designMap; for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; } //get next line to process lookup = input->getSharedRAbundVectors(); } - if (m->control_pressed) { outputTypes.clear(); m->Groups.clear(); delete input; delete designMap; for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; } + if (m->control_pressed) { outputTypes.clear(); m->clearGroups(); delete input; delete designMap; for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; } //output error messages about any remaining user labels set::iterator it; @@ -313,11 +316,11 @@ int MetaStatsCommand::execute(){ } //reset groups parameter - m->Groups.clear(); + m->clearGroups(); delete input; delete designMap; - if (m->control_pressed) { outputTypes.clear(); for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0;} + if (m->control_pressed) { outputTypes.clear(); for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0;} m->mothurOutEndLine(); m->mothurOut("Output File Names: "); m->mothurOutEndLine(); @@ -391,17 +394,19 @@ int MetaStatsCommand::driver(int start, int num, vector& th //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); - int nameLength = outputFileName.length(); - char * output = new char[nameLength]; - strcpy(output, outputFileName.c_str()); + //int nameLength = outputFileName.length(); + //char * output = new char[nameLength]; + //strcpy(output, outputFileName.c_str()); //build matrix from shared rabunds - double** data; - data = new double*[thisLookUp[0]->getNumBins()]; + //double** data; + //data = new double*[thisLookUp[0]->getNumBins()]; + + vector< vector > data2; data2.resize(thisLookUp[0]->getNumBins()); vector subset; int setACount = 0; @@ -419,29 +424,39 @@ int MetaStatsCommand::driver(int start, int num, vector& th 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(); }else { //fill data for (int j = 0; j < thisLookUp[0]->getNumBins(); j++) { - data[j] = new double[subset.size()]; + //data[j] = new double[subset.size()]; + data2[j].resize(subset.size(), 0.0); for (int i = 0; i < subset.size(); i++) { - data[j][i] = (subset[i]->getAbundance(j)); + //data[j][i] = (subset[i]->getAbundance(j)); + data2[j][i] = (subset[i]->getAbundance(j)); } } m->mothurOut("Comparing " + setA + " and " + setB + "..."); m->mothurOutEndLine(); - metastat_main(output, thisLookUp[0]->getNumBins(), subset.size(), threshold, iters, data, setACount); + //metastat_main(output, thisLookUp[0]->getNumBins(), subset.size(), threshold, iters, data, setACount); + + m->mothurOutEndLine(); + MothurMetastats mothurMeta(threshold, iters); + mothurMeta.runMetastats(outputFileName , data2, setACount); + m->mothurOutEndLine(); m->mothurOutEndLine(); } //free memory - delete output; - for(int i = 0; i < thisLookUp[0]->getNumBins(); i++) { delete[] data[i]; } - delete[] data; + //delete output; + //for(int i = 0; i < thisLookUp[0]->getNumBins(); i++) { delete[] data[i]; } + //delete[] data; } return 0;