X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=readdistcommand.cpp;h=744a35d6715867e64697461d88d648982479f0f5;hb=163b300cfd7d4ca4e70c454be20f07b1d8346650;hp=4feddfde47e51b6564e2da9b414009709fade4e8;hpb=d5c8caf2d08b7ac6de30e33b1d19cfd246d08f03;p=mothur.git diff --git a/readdistcommand.cpp b/readdistcommand.cpp index 4feddfd..744a35d 100644 --- a/readdistcommand.cpp +++ b/readdistcommand.cpp @@ -8,35 +8,109 @@ */ #include "readdistcommand.h" +#include "readphylip.h" +#include "readcolumn.h" +#include "readmatrix.hpp" -ReadDistCommand::ReadDistCommand(){ +ReadDistCommand::ReadDistCommand(string option){ try { globaldata = GlobalData::getInstance(); + abort = false; - filename = globaldata->inputFileName; - format = globaldata->getFormat(); + //allow user to run help + if(option == "help") { help(); abort = true; } - if (format == "column") { read = new ReadColumnMatrix(filename); } - else if (format == "phylip") { read = new ReadPhylipMatrix(filename); } + else { + //valid paramters for this command + string Array[] = {"phylip", "column", "name", "cutoff", "precision", "group"}; + vector myArray (Array, Array+(sizeof(Array)/sizeof(string))); - if(globaldata->getPrecision() != ""){ - convert(globaldata->getPrecision(), precision); - } + OptionParser parser(option); + map parameters = parser.getParameters(); + + ValidParameters validParameter; + + //check to make sure all parameters are valid for command + for (map::iterator it = parameters.begin(); it != parameters.end(); it++) { + if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; } + } + + globaldata->newRead(); + + //check for required parameters + phylipfile = validParameter.validFile(parameters, "phylip", true); + if (phylipfile == "not open") { abort = true; } + else if (phylipfile == "not found") { phylipfile = ""; } + else { globaldata->setPhylipFile(phylipfile); globaldata->setFormat("phylip"); } + + columnfile = validParameter.validFile(parameters, "column", true); + if (columnfile == "not open") { abort = true; } + else if (columnfile == "not found") { columnfile = ""; } + else { globaldata->setColumnFile(columnfile); globaldata->setFormat("column"); } + + groupfile = validParameter.validFile(parameters, "group", true); + if (groupfile == "not open") { abort = true; } + else if (groupfile == "not found") { groupfile = ""; } + else { + globaldata->setGroupFile(groupfile); + //groupMap = new GroupMap(groupfile); + //groupMap->readMap(); + } + + namefile = validParameter.validFile(parameters, "name", true); + if (namefile == "not open") { abort = true; } + else if (namefile == "not found") { namefile = ""; } + else { globaldata->setNameFile(namefile); } + + //you are doing a list and group shared + if ((phylipfile != "") && (groupfile != "")) { + globaldata->setFormat("matrix"); } + + if ((phylipfile == "") && (columnfile == "")) { cout << "When executing a read.dist command you must enter a phylip or a column." << endl; abort = true; } + else if ((phylipfile != "") && (columnfile != "")) { cout << "When executing a read.dist command you must enter ONLY ONE of the following: phylip or column." << endl; abort = true; } - if(globaldata->getCutOff() != ""){ - convert(globaldata->getCutOff(), cutoff); + if (columnfile != "") { + if (namefile == "") { cout << "You need to provide a namefile if you are going to use the column format." << endl; abort = true; } + } + + //check for optional parameter and set defaults + // ...at some point should added some additional type checking... + //get user cutoff and precision or use defaults + string temp; + temp = validParameter.validFile(parameters, "precision", false); if (temp == "not found") { temp = "100"; } + convert(temp, precision); + + temp = validParameter.validFile(parameters, "cutoff", false); if (temp == "not found") { temp = "10"; } + convert(temp, cutoff); cutoff += (5 / (precision * 10.0)); - } - read->setCutoff(cutoff); + + if (abort == false) { + distFileName = globaldata->inputFileName; + format = globaldata->getFormat(); + + if (format == "column") { read = new ReadColumnMatrix(distFileName); } + else if (format == "phylip") { read = new ReadPhylipMatrix(distFileName); } + else if (format == "matrix") { + groupMap = new GroupMap(groupfile); + groupMap->readMap(); + if (globaldata->gGroupmap != NULL) { delete globaldata->gGroupmap; } + globaldata->gGroupmap = groupMap; + } + + if (format != "matrix" ) { + read->setCutoff(cutoff); - if(globaldata->getNameFile() != ""){ - nameMap = new NameAssignment(globaldata->getNameFile()); - nameMap->readMap(1,2); - } - else{ - nameMap = NULL; + if(namefile != ""){ + nameMap = new NameAssignment(namefile); + nameMap->readMap(); + }else{ + nameMap = NULL; + } + } + } + } - + } catch(exception& e) { cout << "Standard Error: " << e.what() << " has occurred in the ReadDistCommand class Function ReadDistCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; @@ -47,19 +121,64 @@ ReadDistCommand::ReadDistCommand(){ exit(1); } } +//********************************************************************************************************************** + +void ReadDistCommand::help(){ + try { + cout << "The read.dist command parameter options are phylip or column, group, name, cutoff and precision" << "\n"; + cout << "The read.dist command can be used in two ways. The first is to read a phylip or column and run the cluster command" << "\n"; + cout << "For this use the read.dist command should be in the following format: " << "\n"; + cout << "read.dist(phylip=yourDistFile, name=yourNameFile, cutoff=yourCutoff, precision=yourPrecision) " << "\n"; + cout << "The phylip or column parameter is required, but only one may be used. If you use a column file the name filename is required. " << "\n"; + cout << "If you do not provide a cutoff value 10.00 is assumed. If you do not provide a precision value then 100 is assumed." << "\n"; + cout << "The second way to use the read.dist command is to read a phylip or column and a group, so you can use the libshuff command." << "\n"; + cout << "For this use the read.dist command should be in the following format: " << "\n"; + cout << "read.dist(phylip=yourPhylipfile, group=yourGroupFile). The cutoff and precision parameters are not valid with this use. " << "\n"; + cout << "Note: No spaces between parameter labels (i.e. phylip), '=' and parameters (i.e.yourPhylipfile)." << "\n" << "\n"; + } + catch(exception& e) { + cout << "Standard Error: " << e.what() << " has occurred in the ReadDistCommand class Function help. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + exit(1); + } + catch(...) { + cout << "An unknown error has occurred in the ReadDistCommand class function help. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + exit(1); + } +} //********************************************************************************************************************** + ReadDistCommand::~ReadDistCommand(){ - delete read; - delete nameMap; + if (abort == false) { + if (format != "matrix") { delete read; delete nameMap; } + } } //********************************************************************************************************************** int ReadDistCommand::execute(){ try { - read->read(nameMap); - globaldata->setListVector(read->getListVector()); - globaldata->setSparseMatrix(read->getMatrix()); + + if (abort == true) { return 0; } + + if (format == "matrix") { + ifstream in; + openInputFile(distFileName, in); + matrix = new FullMatrix(in); //reads the matrix file + in.close(); + //memory leak prevention + if (globaldata->gMatrix != NULL) { delete globaldata->gMatrix; } + globaldata->gMatrix = matrix; //save matrix for coverage commands + }else { + read->read(nameMap); + //to prevent memory leak + + if (globaldata->gListVector != NULL) { delete globaldata->gListVector; } + globaldata->gListVector = read->getListVector(); + + if (globaldata->gSparseMatrix != NULL) { delete globaldata->gSparseMatrix; } + globaldata->gSparseMatrix = read->getMatrix(); + + } return 0; } catch(exception& e) { @@ -70,4 +189,4 @@ int ReadDistCommand::execute(){ cout << "An unknown error has occurred in the ReadDistCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; exit(1); } -} \ No newline at end of file +}