X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=rarefactcommand.cpp;h=dabcef486ee7541c183fc594f10da9a9f6624561;hb=91a27e0483827c06c21c4fe89558923bbfe86573;hp=8d1cfc864d35d12d2127672f68af60802cd8b02d;hpb=1b0bddfbf4ac5df7e2dad03c8a5350e71b052f78;p=mothur.git diff --git a/rarefactcommand.cpp b/rarefactcommand.cpp index 8d1cfc8..dabcef4 100644 --- a/rarefactcommand.cpp +++ b/rarefactcommand.cpp @@ -253,17 +253,17 @@ RareFactCommand::RareFactCommand(string option) { string temp; temp = validParameter.validFile(parameters, "freq", false); if (temp == "not found") { temp = "100"; } - convert(temp, freq); + m->mothurConvert(temp, freq); temp = validParameter.validFile(parameters, "abund", false); if (temp == "not found") { temp = "10"; } - convert(temp, abund); + m->mothurConvert(temp, abund); temp = validParameter.validFile(parameters, "iters", false); if (temp == "not found") { temp = "1000"; } - convert(temp, nIters); + m->mothurConvert(temp, nIters); temp = validParameter.validFile(parameters, "processors", false); if (temp == "not found"){ temp = m->getProcessors(); } m->setProcessors(temp); - convert(temp, processors); + m->mothurConvert(temp, processors); temp = validParameter.validFile(parameters, "groupmode", false); if (temp == "not found") { temp = "T"; } groupMode = m->isTrue(temp); @@ -287,7 +287,7 @@ int RareFactCommand::execute(){ if (m->control_pressed) { return 0; } - map nameMap; + map file2Group; //index in outputNames[i] -> group for (int p = 0; p < inputFileNames.size(); p++) { string fileNameRoot = outputDir + m->getRootName(m->getSimpleName(inputFileNames[p])); @@ -296,7 +296,6 @@ int RareFactCommand::execute(){ if (inputFileNames.size() > 1) { m->mothurOutEndLine(); m->mothurOut("Processing group " + groups[p]); m->mothurOutEndLine(); m->mothurOutEndLine(); - nameMap[fileNameRoot] = groups[p]; } int i; ValidCalculators validCalculator; @@ -352,6 +351,7 @@ int RareFactCommand::execute(){ rDisplays.push_back(new RareDisplay(new NSeqs(), new ThreeColumnFile(fileNameRoot+"r_nseqs"))); outputNames.push_back(fileNameRoot+"r_nseqs"); outputTypes["r_nseqs"].push_back(fileNameRoot+"r_nseqs"); } + if (inputFileNames.size() > 1) { file2Group[outputNames.size()-1] = groups[p]; } } } @@ -450,7 +450,7 @@ int RareFactCommand::execute(){ if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; } //create summary file containing all the groups data for each label - this function just combines the info from the files already created. - if ((sharedfile != "") && (groupMode)) { outputNames = createGroupFile(outputNames, nameMap); } + if ((sharedfile != "") && (groupMode)) { outputNames = createGroupFile(outputNames, file2Group); } if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; } @@ -467,13 +467,14 @@ int RareFactCommand::execute(){ } } //********************************************************************************************************************** -vector RareFactCommand::createGroupFile(vector& outputNames, map nameMap) { +vector RareFactCommand::createGroupFile(vector& outputNames, map file2Group) { try { vector newFileNames; //find different types of files - map > typesFiles; + map > typesFiles; + map temp; for (int i = 0; i < outputNames.size(); i++) { string extension = m->getExtension(outputNames[i]); @@ -485,7 +486,8 @@ vector RareFactCommand::createGroupFile(vector& outputNames, map newLine += "\tGroup" + labels.substr(labels.find_first_of('\t')); - typesFiles[extension].push_back(outputNames[i]); + temp[outputNames[i]] = file2Group[i]; + typesFiles[extension] = temp; string combineFileName = outputDir + m->getRootName(m->getSimpleName(sharedfile)) + "groups" + extension; @@ -499,37 +501,31 @@ vector RareFactCommand::createGroupFile(vector& outputNames, map //for each type create a combo file map lineToNumber; - for (map >::iterator it = typesFiles.begin(); it != typesFiles.end(); it++) { + for (map >::iterator it = typesFiles.begin(); it != typesFiles.end(); it++) { ofstream out; string combineFileName = outputDir + m->getRootName(m->getSimpleName(sharedfile)) + "groups" + it->first; m->openOutputFileAppend(combineFileName, out); newFileNames.push_back(combineFileName); - vector thisTypesFiles = it->second; + map thisTypesFiles = it->second; //open each type summary file map > files; //maps file name to lines in file int maxLines = 0; int numColumns = 0; - for (int i=0; i::iterator itFileNameGroup = thisTypesFiles.begin(); itFileNameGroup != thisTypesFiles.end(); itFileNameGroup++) { + + string thisfilename = itFileNameGroup->first; + string group = itFileNameGroup->second; + ifstream temp; - m->openInputFile(thisTypesFiles[i], temp); + m->openInputFile(thisfilename, temp); //read through first line - labels m->getline(temp); m->gobble(temp); vector thisFilesLines; - string fileNameRoot = m->getRootName(thisTypesFiles[i]); - map::iterator itName = nameMap.find(fileNameRoot); - string group = ""; - if (itName != nameMap.end()) { - group = itName->second; - }else { - group = "not found" + i; - m->mothurOut("[ERROR]: can't parse filename."); m->mothurOutEndLine(); - } thisFilesLines.push_back(group); int count = 1; @@ -549,13 +545,13 @@ vector RareFactCommand::createGroupFile(vector& outputNames, map m->gobble(temp); } - files[thisTypesFiles[i]] = thisFilesLines; + files[thisfilename] = thisFilesLines; //save longest file for below if (maxLines < thisFilesLines.size()) { maxLines = thisFilesLines.size(); } temp.close(); - m->mothurRemove(thisTypesFiles[i]); + m->mothurRemove(thisfilename); } @@ -563,17 +559,19 @@ vector RareFactCommand::createGroupFile(vector& outputNames, map for (int k = 1; k < maxLines; k++) { //grab data for each group - for (int i=0; i::iterator itFileNameGroup = thisTypesFiles.begin(); itFileNameGroup != thisTypesFiles.end(); itFileNameGroup++) { + + string thisfilename = itFileNameGroup->first; + map::iterator itLine = lineToNumber.find(k); if (itLine != lineToNumber.end()) { string output = toString(itLine->second); - if (k < files[thisTypesFiles[i]].size()) { - string line = files[thisTypesFiles[i]][k]; + if (k < files[thisfilename].size()) { + string line = files[thisfilename][k]; output = line.substr(0, line.find_first_of('\t')); - output += '\t' + files[thisTypesFiles[i]][0] + '\t' + line.substr(line.find_first_of('\t')); + output += '\t' + files[thisfilename][0] + '\t' + line.substr(line.find_first_of('\t')); }else{ - output += '\t' + files[thisTypesFiles[i]][0] + '\t'; + output += '\t' + files[thisfilename][0] + '\t'; for (int h = 0; h < numColumns; h++) { output += "NA\t"; }