X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=getgroupcommand.cpp;h=529ed934d5b194d1a1d82869c44053ca4f7bbaf2;hp=b645517f938928c44eb5faa5871e4171c40fb800;hb=1a20e24ee786195ab0e1cccd4f5aede7a88f3f4e;hpb=74844a60d80c6dd06e3fb02ee9b928424f9019b0 diff --git a/getgroupcommand.cpp b/getgroupcommand.cpp index b645517..529ed93 100644 --- a/getgroupcommand.cpp +++ b/getgroupcommand.cpp @@ -8,46 +8,101 @@ */ #include "getgroupcommand.h" +#include "inputdata.h" +//********************************************************************************************************************** +vector GetgroupCommand::setParameters(){ + try { + CommandParameter pshared("shared", "InputTypes", "", "current", "none", "none", "none","",false,true, true); parameters.push_back(pshared); + 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, "GetgroupCommand", "setParameters"); + exit(1); + } +} +//********************************************************************************************************************** +string GetgroupCommand::getHelpString(){ + try { + string helpString = ""; + helpString += "The get.group command parameter is shared and it's required if you have no valid current file.\n"; + helpString += "You may not use any parameters with the get.group command.\n"; + helpString += "The get.group command should be in the following format: \n"; + helpString += "get.group()\n"; + helpString += "Example get.group().\n"; + return helpString; + } + catch(exception& e) { + m->errorOut(e, "GetgroupCommand", "getHelpString"); + exit(1); + } +} + +//********************************************************************************************************************** +GetgroupCommand::GetgroupCommand(){ + try { + abort = true; calledHelp = true; + setParameters(); + } + catch(exception& e) { + m->errorOut(e, "GetgroupCommand", "GetgroupCommand"); + exit(1); + } +} //********************************************************************************************************************** GetgroupCommand::GetgroupCommand(string option) { try { - globaldata = GlobalData::getInstance(); - abort = false; + abort = false; calledHelp = false; //allow user to run help - if(option == "help") { help(); abort = true; } + if(option == "help") { help(); abort = true; calledHelp = true; } + else if(option == "citation") { citation(); abort = true; calledHelp = true;} else { - //valid paramters for this command - string Array[] = {"outputdir","inputdir"}; - vector myArray (Array, Array+(sizeof(Array)/sizeof(string))); + vector myArray = setParameters(); OptionParser parser(option); map parameters = parser.getParameters(); + map::iterator it; ValidParameters validParameter; //check to make sure all parameters are valid for command - for (map::iterator it = parameters.begin(); it != parameters.end(); it++) { + for (it = parameters.begin(); it != parameters.end(); it++) { if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; } } - //if the user changes the output directory command factory will send this info to us in the output parameter - string outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){ outputDir = ""; } - - if ((globaldata->getSharedFile() == "")) { m->mothurOut("You must use the read.otu command to read a groupfile or a sharedfile before you can use the get.group command."); m->mothurOutEndLine(); abort = true; } - - if (abort == false) { - //open shared file - sharedfile = globaldata->getSharedFile(); - openInputFile(sharedfile, in); - - //open output file - if (outputDir == "") { outputDir += hasPath(sharedfile); } - outputFile = outputDir + getRootName(getSimpleName(sharedfile)) + "bootGroups"; - openOutputFile(outputFile, out); - + //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("shared"); + //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["shared"] = inputDir + it->second; } + } } + + //get shared file + sharedfile = validParameter.validFile(parameters, "shared", true); + if (sharedfile == "not open") { sharedfile = ""; abort = true; } + else if (sharedfile == "not found") { + //if there is a current shared file, use it + 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); } + + + //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 = m->hasPath(sharedfile); } } } catch(exception& e) { @@ -57,76 +112,21 @@ GetgroupCommand::GetgroupCommand(string option) { } //********************************************************************************************************************** -void GetgroupCommand::help(){ - try { - m->mothurOut("The get.group command can only be executed after a successful read.otu command.\n"); - //m->mothurOut("The get.group command outputs a .bootGroups file to you can use in addition to the tree file generated by the bootstrap.shared command to run the consensus command.\n"); - m->mothurOut("You may not use any parameters with the get.group command.\n"); - m->mothurOut("The get.group command should be in the following format: \n"); - m->mothurOut("get.group()\n"); - m->mothurOut("Example get.group().\n"); - - } - catch(exception& e) { - m->errorOut(e, "GetgroupCommand", "help"); - exit(1); - } -} - -//********************************************************************************************************************** - -GetgroupCommand::~GetgroupCommand(){ -} - -//********************************************************************************************************************** - int GetgroupCommand::execute(){ try { - if (abort == true) { return 0; } - - int num, inputData, count; - count = 0; - string holdLabel, nextLabel, groupN, label; - - //read in first row since you know there is at least 1 group. - in >> label >> groupN >> num; - holdLabel = label; + if (abort == true) { if (calledHelp) { return 0; } return 2; } + + InputData input(sharedfile, "sharedfile"); + vector lookup = input.getSharedRAbundVectors(); - //output first group - m->mothurOut(groupN); m->mothurOutEndLine(); - out << groupN << '\t' << groupN << endl; - - //get rest of line - for(int i=0;i> inputData; + for (int i = 0; i < lookup.size(); i++) { + m->mothurOut(lookup[i]->getGroup()); m->mothurOutEndLine(); + delete lookup[i]; } - - if (in.eof() != true) { in >> nextLabel; } - - //read the rest of the groups info in - while ((nextLabel == holdLabel) && (in.eof() != true)) { - in >> groupN >> num; - count++; - //output next group - m->mothurOut(groupN); m->mothurOutEndLine(); - out << groupN << '\t' << groupN << endl; - - //fill vector. - for(int i=0;i> inputData; - } - - if (in.eof() != true) { in >> nextLabel; } - } - - in.close(); - out.close(); - m->mothurOutEndLine(); - m->mothurOut("Output File Name: "); m->mothurOutEndLine(); - m->mothurOut(outputFile); m->mothurOutEndLine(); + m->mothurOut("Output File Names: "); m->mothurOutEndLine(); m->mothurOutEndLine(); return 0; @@ -137,5 +137,6 @@ int GetgroupCommand::execute(){ exit(1); } } +//**********************************************************************************************************************