X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=preclustercommand.cpp;fp=preclustercommand.cpp;h=0000000000000000000000000000000000000000;hb=4a877efa127e56e81a21f53cfdbbfd3bfbe8c4ff;hp=bcff0fcd820a497da04405bef0ddb42d7d60ded9;hpb=a6cf29fa4dac0909c7582cb1094151d34093ee76;p=mothur.git diff --git a/preclustercommand.cpp b/preclustercommand.cpp deleted file mode 100644 index bcff0fc..0000000 --- a/preclustercommand.cpp +++ /dev/null @@ -1,725 +0,0 @@ -/* - * preclustercommand.cpp - * Mothur - * - * Created by westcott on 12/21/09. - * Copyright 2009 Schloss Lab. All rights reserved. - * - */ - -#include "preclustercommand.h" -#include "deconvolutecommand.h" - -//********************************************************************************************************************** -vector PreClusterCommand::setParameters(){ - try { - CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pfasta); - CommandParameter pname("name", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pname); - CommandParameter pgroup("group", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pgroup); - CommandParameter pdiffs("diffs", "Number", "", "0", "", "", "",false,false); parameters.push_back(pdiffs); - CommandParameter pprocessors("processors", "Number", "", "1", "", "", "",false,false); parameters.push_back(pprocessors); - CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir); - CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir); - - vector myArray; - for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); } - return myArray; - } - catch(exception& e) { - m->errorOut(e, "PreClusterCommand", "setParameters"); - exit(1); - } -} -//********************************************************************************************************************** -string PreClusterCommand::getHelpString(){ - try { - string helpString = ""; - helpString += "The pre.cluster command groups sequences that are within a given number of base mismatches.\n"; - helpString += "The pre.cluster command outputs a new fasta and name file.\n"; - helpString += "The pre.cluster command parameters are fasta, names and diffs. The fasta parameter is required. \n"; - helpString += "The names parameter allows you to give a list of seqs that are identical. This file is 2 columns, first column is name or representative sequence, second column is a list of its identical sequences separated by commas.\n"; - helpString += "The group parameter allows you to provide a group file so you can cluster by group. \n"; - helpString += "The diffs parameter allows you to specify maximum number of mismatched bases allowed between sequences in a grouping. The default is 1.\n"; - helpString += "The pre.cluster command should be in the following format: \n"; - helpString += "pre.cluster(fasta=yourFastaFile, names=yourNamesFile, diffs=yourMaxDiffs) \n"; - helpString += "Example pre.cluster(fasta=amazon.fasta, diffs=2).\n"; - helpString += "Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n"; - return helpString; - } - catch(exception& e) { - m->errorOut(e, "PreClusterCommand", "getHelpString"); - exit(1); - } -} - -//********************************************************************************************************************** -PreClusterCommand::PreClusterCommand(){ - try { - abort = true; calledHelp = true; - setParameters(); - vector tempOutNames; - outputTypes["fasta"] = tempOutNames; - outputTypes["name"] = tempOutNames; - outputTypes["map"] = tempOutNames; - } - catch(exception& e) { - m->errorOut(e, "PreClusterCommand", "PreClusterCommand"); - exit(1); - } -} -//********************************************************************************************************************** - -PreClusterCommand::PreClusterCommand(string option) { - try { - abort = false; calledHelp = false; - - //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(); - - OptionParser parser(option); - map parameters = parser.getParameters(); - - ValidParameters validParameter; - map::iterator it; - - //check to make sure all parameters are valid for command - for (map::iterator it2 = parameters.begin(); it2 != parameters.end(); it2++) { - if (validParameter.isValidParameter(it2->first, myArray, it2->second) != true) { abort = true; } - } - - //initialize outputTypes - vector tempOutNames; - outputTypes["fasta"] = tempOutNames; - outputTypes["name"] = tempOutNames; - outputTypes["map"] = tempOutNames; - - //if the user changes the input directory command factory will send this info to us in the output parameter - string inputDir = validParameter.validFile(parameters, "inputdir", false); - if (inputDir == "not found"){ inputDir = ""; } - else { - string path; - it = parameters.find("fasta"); - //user has given a template file - if(it != parameters.end()){ - path = m->hasPath(it->second); - //if the user has not given a path then, add inputdir. else leave path alone. - if (path == "") { parameters["fasta"] = inputDir + it->second; } - } - - it = parameters.find("name"); - //user has given a template file - if(it != parameters.end()){ - path = m->hasPath(it->second); - //if the user has not given a path then, add inputdir. else leave path alone. - if (path == "") { parameters["name"] = inputDir + it->second; } - } - - it = parameters.find("group"); - //user has given a template file - if(it != parameters.end()){ - path = m->hasPath(it->second); - //if the user has not given a path then, add inputdir. else leave path alone. - if (path == "") { parameters["group"] = inputDir + it->second; } - } - } - - //check for required parameters - fastafile = validParameter.validFile(parameters, "fasta", true); - if (fastafile == "not found") { - fastafile = m->getFastaFile(); - if (fastafile != "") { m->mothurOut("Using " + fastafile + " as input file for the fasta parameter."); m->mothurOutEndLine(); } - else { m->mothurOut("You have no current fastafile and the fasta parameter is required."); m->mothurOutEndLine(); abort = true; } - } - else if (fastafile == "not open") { abort = true; } - else { m->setFastaFile(fastafile); } - - //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"){ - outputDir = ""; - outputDir += m->hasPath(fastafile); //if user entered a file with a path then preserve it - } - - //check for optional parameter and set defaults - // ...at some point should added some additional type checking... - namefile = validParameter.validFile(parameters, "name", true); - if (namefile == "not found") { namefile = ""; } - else if (namefile == "not open") { namefile = ""; abort = true; } - else { m->setNameFile(namefile); } - - groupfile = validParameter.validFile(parameters, "group", true); - if (groupfile == "not found") { groupfile = ""; bygroup = false; } - else if (groupfile == "not open") { abort = true; groupfile = ""; } - else { m->setGroupFile(groupfile); bygroup = true; } - - string temp = validParameter.validFile(parameters, "diffs", false); if(temp == "not found"){ temp = "1"; } - m->mothurConvert(temp, diffs); - - temp = validParameter.validFile(parameters, "processors", false); if (temp == "not found"){ temp = m->getProcessors(); } - m->setProcessors(temp); - m->mothurConvert(temp, processors); - - if (namefile == "") { - vector files; files.push_back(fastafile); - parser.getNameFile(files); - } - } - - } - catch(exception& e) { - m->errorOut(e, "PreClusterCommand", "PreClusterCommand"); - exit(1); - } -} -//********************************************************************************************************************** - -int PreClusterCommand::execute(){ - try { - - if (abort == true) { if (calledHelp) { return 0; } return 2; } - - int start = time(NULL); - - string fileroot = outputDir + m->getRootName(m->getSimpleName(fastafile)); - string newFastaFile = fileroot + "precluster" + m->getExtension(fastafile); - string newNamesFile = fileroot + "precluster.names"; - string newMapFile = fileroot + "precluster.map"; //add group name if by group - outputNames.push_back(newFastaFile); outputTypes["fasta"].push_back(newFastaFile); - outputNames.push_back(newNamesFile); outputTypes["name"].push_back(newNamesFile); - - - if (bygroup) { - //clear out old files - ofstream outFasta; m->openOutputFile(newFastaFile, outFasta); outFasta.close(); - ofstream outNames; m->openOutputFile(newNamesFile, outNames); outNames.close(); - newMapFile = fileroot + "precluster."; - - //parse fasta and name file by group - SequenceParser* parser; - if (namefile != "") { parser = new SequenceParser(groupfile, fastafile, namefile); } - else { parser = new SequenceParser(groupfile, fastafile); } - - vector groups = parser->getNamesOfGroups(); - - if(processors == 1) { driverGroups(parser, newFastaFile, newNamesFile, newMapFile, 0, groups.size(), groups); } - else { createProcessesGroups(parser, newFastaFile, newNamesFile, newMapFile, groups); } - - delete parser; - - if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; } - - //run unique.seqs for deconvolute results - string inputString = "fasta=" + newFastaFile; - if (namefile != "") { inputString += ", name=" + newNamesFile; } - m->mothurOutEndLine(); - m->mothurOut("/******************************************/"); m->mothurOutEndLine(); - m->mothurOut("Running command: unique.seqs(" + inputString + ")"); m->mothurOutEndLine(); - m->mothurCalling = true; - - Command* uniqueCommand = new DeconvoluteCommand(inputString); - uniqueCommand->execute(); - - map > filenames = uniqueCommand->getOutputFiles(); - - delete uniqueCommand; - m->mothurCalling = false; - m->mothurOut("/******************************************/"); m->mothurOutEndLine(); - - m->renameFile(filenames["fasta"][0], newFastaFile); - m->renameFile(filenames["name"][0], newNamesFile); - - m->mothurOut("It took " + toString(time(NULL) - start) + " secs to run pre.cluster."); m->mothurOutEndLine(); - - }else { - if (namefile != "") { readNameFile(); } - - //reads fasta file and return number of seqs - int numSeqs = readFASTA(); //fills alignSeqs and makes all seqs active - - if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; } - - if (numSeqs == 0) { m->mothurOut("Error reading fasta file...please correct."); m->mothurOutEndLine(); return 0; } - if (diffs > length) { m->mothurOut("Error: diffs is greater than your sequence length."); m->mothurOutEndLine(); return 0; } - - int count = process(newMapFile); - outputNames.push_back(newMapFile); outputTypes["map"].push_back(newMapFile); - - if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; } - - m->mothurOut("Total number of sequences before precluster was " + toString(alignSeqs.size()) + "."); m->mothurOutEndLine(); - m->mothurOut("pre.cluster removed " + toString(count) + " sequences."); m->mothurOutEndLine(); m->mothurOutEndLine(); - printData(newFastaFile, newNamesFile); - - m->mothurOut("It took " + toString(time(NULL) - start) + " secs to cluster " + toString(numSeqs) + " sequences."); m->mothurOutEndLine(); - } - - if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; } - - m->mothurOutEndLine(); - m->mothurOut("Output File Names: "); m->mothurOutEndLine(); - for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); } - m->mothurOutEndLine(); - - //set fasta file as new current fastafile - string current = ""; - itTypes = outputTypes.find("fasta"); - if (itTypes != outputTypes.end()) { - if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setFastaFile(current); } - } - - itTypes = outputTypes.find("name"); - if (itTypes != outputTypes.end()) { - if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setNameFile(current); } - } - - return 0; - - } - catch(exception& e) { - m->errorOut(e, "PreClusterCommand", "execute"); - exit(1); - } -} -/**************************************************************************************************/ -int PreClusterCommand::createProcessesGroups(SequenceParser* parser, string newFName, string newNName, string newMFile, vector groups) { - try { - - vector processIDS; - int process = 1; - int num = 0; - - //sanity check - if (groups.size() < processors) { processors = groups.size(); } - - //divide the groups between the processors - vector lines; - int numGroupsPerProcessor = groups.size() / processors; - for (int i = 0; i < processors; i++) { - int startIndex = i * numGroupsPerProcessor; - int endIndex = (i+1) * numGroupsPerProcessor; - if(i == (processors - 1)){ endIndex = groups.size(); } - lines.push_back(linePair(startIndex, endIndex)); - } - -#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix) - - //loop through and create all the processes you want - while (process != processors) { - int pid = fork(); - - if (pid > 0) { - 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){ - outputNames.clear(); - num = driverGroups(parser, newFName + toString(getpid()) + ".temp", newNName + toString(getpid()) + ".temp", newMFile, lines[process].start, lines[process].end, groups); - - string tempFile = toString(getpid()) + ".outputNames.temp"; - ofstream outTemp; - m->openOutputFile(tempFile, outTemp); - - outTemp << outputNames.size(); - for (int i = 0; i < outputNames.size(); i++) { outTemp << outputNames[i] << endl; } - outTemp.close(); - - exit(0); - }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 - num = driverGroups(parser, newFName, newNName, newMFile, lines[0].start, lines[0].end, groups); - - //force parent to wait until all the processes are done - for (int i=0;iopenInputFile(tempFile, intemp); - - int num; - intemp >> num; - for (int k = 0; k < num; k++) { - string name = ""; - intemp >> name; m->gobble(intemp); - - outputNames.push_back(name); outputTypes["map"].push_back(name); - } - intemp.close(); - m->mothurRemove(tempFile); - } -#else - - ////////////////////////////////////////////////////////////////////////////////////////////////////// - //Windows version shared memory, so be careful when passing variables through the preClusterData struct. - //Above fork() will clone, so memory is separate, but that's not the case with windows, - ////////////////////////////////////////////////////////////////////////////////////////////////////// - - vector pDataArray; - DWORD dwThreadIdArray[processors-1]; - HANDLE hThreadArray[processors-1]; - - //Create processor worker threads. - for( int i=1; imapFileNames.size(); j++) { - outputNames.push_back(pDataArray[i]->mapFileNames[j]); outputTypes["map"].push_back(pDataArray[i]->mapFileNames[j]); - } - CloseHandle(hThreadArray[i]); - delete pDataArray[i]; - } - -#endif - - //append output files - for(int i=0;igetFullPathName(".\\" + newFName); - //newNName = m->getFullPathName(".\\" + newNName); - - m->appendFiles((newFName + toString(processIDS[i]) + ".temp"), newFName); - m->mothurRemove((newFName + toString(processIDS[i]) + ".temp")); - - m->appendFiles((newNName + toString(processIDS[i]) + ".temp"), newNName); - m->mothurRemove((newNName + toString(processIDS[i]) + ".temp")); - } - - return num; - - } - catch(exception& e) { - m->errorOut(e, "PreClusterCommand", "createProcessesGroups"); - exit(1); - } -} -/**************************************************************************************************/ -int PreClusterCommand::driverGroups(SequenceParser* parser, string newFFile, string newNFile, string newMFile, int start, int end, vector groups){ - try { - - int numSeqs = 0; - - //precluster each group - for (int i = start; i < end; i++) { - - start = time(NULL); - - if (m->control_pressed) { return 0; } - - m->mothurOutEndLine(); m->mothurOut("Processing group " + groups[i] + ":"); m->mothurOutEndLine(); - - map thisNameMap; - if (namefile != "") { thisNameMap = parser->getNameMap(groups[i]); } - vector thisSeqs = parser->getSeqs(groups[i]); - - //fill alignSeqs with this groups info. - numSeqs = loadSeqs(thisNameMap, thisSeqs); - - if (m->control_pressed) { return 0; } - - if (diffs > length) { m->mothurOut("Error: diffs is greater than your sequence length."); m->mothurOutEndLine(); m->control_pressed = true; return 0; } - - int count = process(newMFile+groups[i]+".map"); - outputNames.push_back(newMFile+groups[i]+".map"); outputTypes["map"].push_back(newMFile+groups[i]+".map"); - - if (m->control_pressed) { return 0; } - - m->mothurOut("Total number of sequences before pre.cluster was " + toString(alignSeqs.size()) + "."); m->mothurOutEndLine(); - m->mothurOut("pre.cluster removed " + toString(count) + " sequences."); m->mothurOutEndLine(); m->mothurOutEndLine(); - printData(newFFile, newNFile); - - m->mothurOut("It took " + toString(time(NULL) - start) + " secs to cluster " + toString(numSeqs) + " sequences."); m->mothurOutEndLine(); - - } - - return numSeqs; - } - catch(exception& e) { - m->errorOut(e, "PreClusterCommand", "driverGroups"); - exit(1); - } -} -/**************************************************************************************************/ -int PreClusterCommand::process(string newMapFile){ - try { - ofstream out; - m->openOutputFile(newMapFile, out); - - //sort seqs by number of identical seqs - sort(alignSeqs.begin(), alignSeqs.end(), comparePriority); - - int count = 0; - int numSeqs = alignSeqs.size(); - - //think about running through twice... - for (int i = 0; i < numSeqs; i++) { - - //are you active - // itActive = active.find(alignSeqs[i].seq.getName()); - - if (alignSeqs[i].active) { //this sequence has not been merged yet - - string chunk = alignSeqs[i].seq.getName() + "\t" + toString(alignSeqs[i].numIdentical) + "\t" + toString(0) + "\t" + alignSeqs[i].seq.getAligned() + "\n"; - - //try to merge it with all smaller seqs - for (int j = i+1; j < numSeqs; j++) { - - if (m->control_pressed) { out.close(); return 0; } - - if (alignSeqs[j].active) { //this sequence has not been merged yet - //are you within "diff" bases - int mismatch = calcMisMatches(alignSeqs[i].seq.getAligned(), alignSeqs[j].seq.getAligned()); - - if (mismatch <= diffs) { - //merge - alignSeqs[i].names += ',' + alignSeqs[j].names; - alignSeqs[i].numIdentical += alignSeqs[j].numIdentical; - - chunk += alignSeqs[j].seq.getName() + "\t" + toString(alignSeqs[j].numIdentical) + "\t" + toString(mismatch) + "\t" + alignSeqs[j].seq.getAligned() + "\n"; - - alignSeqs[j].active = 0; - alignSeqs[j].numIdentical = 0; - count++; - } - }//end if j active - }//end for loop j - - //remove from active list - alignSeqs[i].active = 0; - - out << "ideal_seq_" << (i+1) << '\t' << alignSeqs[i].numIdentical << endl << chunk << endl;; - - }//end if active i - if(i % 100 == 0) { m->mothurOut(toString(i) + "\t" + toString(numSeqs - count) + "\t" + toString(count)); m->mothurOutEndLine(); } - } - out.close(); - - if(numSeqs % 100 != 0) { m->mothurOut(toString(numSeqs) + "\t" + toString(numSeqs - count) + "\t" + toString(count)); m->mothurOutEndLine(); } - - return count; - - } - catch(exception& e) { - m->errorOut(e, "PreClusterCommand", "process"); - exit(1); - } -} -/**************************************************************************************************/ -int PreClusterCommand::readFASTA(){ - try { - //ifstream inNames; - ifstream inFasta; - - //m->openInputFile(namefile, inNames); - m->openInputFile(fastafile, inFasta); - - //string firstCol, secondCol, nameString; - set lengths; - - while (!inFasta.eof()) { - - if (m->control_pressed) { inFasta.close(); return 0; } - - //inNames >> firstCol >> secondCol; - //nameString = secondCol; - - //m->gobble(inNames); - //int size = 1; - //while (secondCol.find_first_of(',') != -1) { - // size++; - // secondCol = secondCol.substr(secondCol.find_first_of(',')+1, secondCol.length()); - //} - - Sequence seq(inFasta); m->gobble(inFasta); - - if (seq.getName() != "") { //can get "" if commented line is at end of fasta file - if (namefile != "") { - itSize = sizes.find(seq.getName()); - - if (itSize == sizes.end()) { m->mothurOut(seq.getName() + " is not in your names file, please correct."); m->mothurOutEndLine(); exit(1); } - else{ - seqPNode tempNode(itSize->second, seq, names[seq.getName()]); - alignSeqs.push_back(tempNode); - lengths.insert(seq.getAligned().length()); - } - }else { //no names file, you are identical to yourself - seqPNode tempNode(1, seq, seq.getName()); - alignSeqs.push_back(tempNode); - lengths.insert(seq.getAligned().length()); - } - } - } - inFasta.close(); - //inNames.close(); - - if (lengths.size() > 1) { m->control_pressed = true; m->mothurOut("[ERROR]: your sequences are not all the same length. pre.cluster requires sequences to be aligned."); m->mothurOutEndLine(); } - else if (lengths.size() == 1) { length = *(lengths.begin()); } - - return alignSeqs.size(); - } - - catch(exception& e) { - m->errorOut(e, "PreClusterCommand", "readFASTA"); - exit(1); - } -} -/**************************************************************************************************/ -int PreClusterCommand::loadSeqs(map& thisName, vector& thisSeqs){ - try { - set lengths; - alignSeqs.clear(); - map::iterator it; - bool error = false; - - for (int i = 0; i < thisSeqs.size(); i++) { - - if (m->control_pressed) { return 0; } - - if (namefile != "") { - it = thisName.find(thisSeqs[i].getName()); - - //should never be true since parser checks for this - if (it == thisName.end()) { m->mothurOut(thisSeqs[i].getName() + " is not in your names file, please correct."); m->mothurOutEndLine(); error = true; } - else{ - //get number of reps - int numReps = 1; - for(int j=0;j<(it->second).length();j++){ - if((it->second)[j] == ','){ numReps++; } - } - - seqPNode tempNode(numReps, thisSeqs[i], it->second); - alignSeqs.push_back(tempNode); - lengths.insert(thisSeqs[i].getAligned().length()); - } - }else { //no names file, you are identical to yourself - seqPNode tempNode(1, thisSeqs[i], thisSeqs[i].getName()); - alignSeqs.push_back(tempNode); - lengths.insert(thisSeqs[i].getAligned().length()); - } - } - - if (lengths.size() > 1) { error = true; m->mothurOut("[ERROR]: your sequences are not all the same length. pre.cluster requires sequences to be aligned."); m->mothurOutEndLine(); } - else if (lengths.size() == 1) { length = *(lengths.begin()); } - - //sanity check - if (error) { m->control_pressed = true; } - - thisSeqs.clear(); - - return alignSeqs.size(); - } - - catch(exception& e) { - m->errorOut(e, "PreClusterCommand", "loadSeqs"); - exit(1); - } -} - -/**************************************************************************************************/ - -int PreClusterCommand::calcMisMatches(string seq1, string seq2){ - try { - int numBad = 0; - - for (int i = 0; i < seq1.length(); i++) { - //do they match - if (seq1[i] != seq2[i]) { numBad++; } - if (numBad > diffs) { return length; } //to far to cluster - } - - return numBad; - } - catch(exception& e) { - m->errorOut(e, "PreClusterCommand", "calcMisMatches"); - exit(1); - } -} - -/**************************************************************************************************/ - -void PreClusterCommand::printData(string newfasta, string newname){ - try { - ofstream outFasta; - ofstream outNames; - - if (bygroup) { - m->openOutputFileAppend(newfasta, outFasta); - m->openOutputFileAppend(newname, outNames); - }else { - m->openOutputFile(newfasta, outFasta); - m->openOutputFile(newname, outNames); - } - - for (int i = 0; i < alignSeqs.size(); i++) { - if (alignSeqs[i].numIdentical != 0) { - alignSeqs[i].seq.printSequence(outFasta); - outNames << alignSeqs[i].seq.getName() << '\t' << alignSeqs[i].names << endl; - } - } - - outFasta.close(); - outNames.close(); - - } - catch(exception& e) { - m->errorOut(e, "PreClusterCommand", "printData"); - exit(1); - } -} -/**************************************************************************************************/ - -void PreClusterCommand::readNameFile(){ - try { - ifstream in; - m->openInputFile(namefile, in); - string firstCol, secondCol; - - while (!in.eof()) { - in >> firstCol >> secondCol; m->gobble(in); - names[firstCol] = secondCol; - int size = 1; - - for(int i=0;ierrorOut(e, "PreClusterCommand", "readNameFile"); - exit(1); - } -} - -/**************************************************************************************************/ - -