X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=setcurrentcommand.cpp;h=9d277f3e71ae3635d5f14cf468822fa3e1181e8c;hp=a4f5c5c1f7ac756c1803bb25dfd7a95133477580;hb=1a20e24ee786195ab0e1cccd4f5aede7a88f3f4e;hpb=348de0f8b17d84ede77081dcf67bd6ef43496677 diff --git a/setcurrentcommand.cpp b/setcurrentcommand.cpp index a4f5c5c..9d277f3 100644 --- a/setcurrentcommand.cpp +++ b/setcurrentcommand.cpp @@ -10,47 +10,71 @@ #include "setcurrentcommand.h" //********************************************************************************************************************** -vector SetCurrentCommand::getValidParameters(){ +vector SetCurrentCommand::setParameters(){ try { - string Array[] = {"outputdir","inputdir","clear", "phylip", "column", "list","rabund","sabund","name","group", - "design","order","tree","shared","ordergroup","relabund","fasta","qfile","sff","oligos","accnos","taxonomy"}; - vector myArray (Array, Array+(sizeof(Array)/sizeof(string))); + + CommandParameter pprocessors("processors", "Number", "", "1", "", "", "","",false,false,true); parameters.push_back(pprocessors); + CommandParameter pflow("flow", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(pflow); + CommandParameter pbiom("biom", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(pbiom); + CommandParameter pphylip("phylip", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(pphylip); + CommandParameter pcolumn("column", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(pcolumn); + CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none","",false,false); 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 plist("list", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(plist); + CommandParameter ptaxonomy("taxonomy", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(ptaxonomy); + CommandParameter pqfile("qfile", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(pqfile); + CommandParameter paccnos("accnos", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(paccnos); + CommandParameter prabund("rabund", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(prabund); + CommandParameter psabund("sabund", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(psabund); + CommandParameter pdesign("design", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(pdesign); + CommandParameter porder("order", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(porder); + CommandParameter ptree("tree", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(ptree); + CommandParameter pshared("shared", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(pshared); + CommandParameter pordergroup("ordergroup", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(pordergroup); + CommandParameter pcount("count", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(pcount); + CommandParameter prelabund("relabund", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(prelabund); + CommandParameter psff("sff", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(psff); + CommandParameter poligos("oligos", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(poligos); + CommandParameter pclear("clear", "String", "", "", "", "", "","",false,false); parameters.push_back(pclear); + 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, "SetCurrentCommand", "getValidParameters"); + m->errorOut(e, "SetCurrentCommand", "setParameters"); exit(1); } } //********************************************************************************************************************** -SetCurrentCommand::SetCurrentCommand(){ +string SetCurrentCommand::getHelpString(){ try { - abort = true; calledHelp = true; + string helpString = ""; + helpString += "The set.current command allows you to set the current files saved by mothur.\n"; + helpString += "The set.current command parameters are: clear, phylip, column, list, rabund, sabund, name, group, design, order, tree, shared, ordergroup, relabund, fasta, qfile, sff, oligos, accnos, biom, count and taxonomy.\n"; + helpString += "The clear paramter is used to indicate which file types you would like to clear values for, multiple types can be separated by dashes.\n"; + helpString += "The set.current command should be in the following format: \n"; + helpString += "set.current(fasta=yourFastaFile) or set.current(fasta=amazon.fasta, clear=name-accnos)\n"; + return helpString; } catch(exception& e) { - m->errorOut(e, "SetCurrentCommand", "SetCurrentCommand"); - exit(1); - } -} -//********************************************************************************************************************** -vector SetCurrentCommand::getRequiredParameters(){ - try { - vector myArray; - return myArray; - } - catch(exception& e) { - m->errorOut(e, "SetCurrentCommand", "getRequiredParameters"); + m->errorOut(e, "SetCurrentCommand", "getHelpString"); exit(1); } } + + //********************************************************************************************************************** -vector SetCurrentCommand::getRequiredFiles(){ +SetCurrentCommand::SetCurrentCommand(){ try { - vector myArray; - return myArray; + abort = true; calledHelp = true; + setParameters(); } catch(exception& e) { - m->errorOut(e, "SetCurrentCommand", "getRequiredFiles"); + m->errorOut(e, "SetCurrentCommand", "SetCurrentCommand"); exit(1); } } @@ -61,12 +85,11 @@ SetCurrentCommand::SetCurrentCommand(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 { //valid paramters for this command - string Array[] = {"outputdir","inputdir","clear", "phylip", "column", "list","rabund","sabund","name","group", - "design","order","tree","shared","ordergroup","relabund","fasta","qfile","sff","oligos","accnos","taxonomy"}; - vector myArray (Array, Array+(sizeof(Array)/sizeof(string))); + vector myArray = setParameters(); OptionParser parser(option); map parameters = parser.getParameters(); @@ -188,6 +211,14 @@ SetCurrentCommand::SetCurrentCommand(string option) { if (path == "") { parameters["ordergroup"] = inputDir + it->second; } } + it = parameters.find("count"); + //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["count"] = inputDir + it->second; } + } + it = parameters.find("relabund"); //user has given a template file if(it != parameters.end()){ @@ -243,6 +274,22 @@ SetCurrentCommand::SetCurrentCommand(string option) { //if the user has not given a path then, add inputdir. else leave path alone. if (path == "") { parameters["taxonomy"] = inputDir + it->second; } } + + it = parameters.find("flow"); + //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["flow"] = inputDir + it->second; } + } + + it = parameters.find("biom"); + //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["biom"] = inputDir + it->second; } + } } //check for parameters @@ -280,6 +327,11 @@ SetCurrentCommand::SetCurrentCommand(string option) { if (groupfile == "not open") { m->mothurOut("Ignoring: " + parameters["group"]); m->mothurOutEndLine(); groupfile = ""; } else if (groupfile == "not found") { groupfile = ""; } if (groupfile != "") { m->setGroupFile(groupfile); } + + countfile = validParameter.validFile(parameters, "count", true); + if (countfile == "not open") { m->mothurOut("Ignoring: " + parameters["count"]); m->mothurOutEndLine(); countfile = ""; } + else if (countfile == "not found") { countfile = ""; } + if (countfile != "") { m->setCountTableFile(countfile); } designfile = validParameter.validFile(parameters, "design", true); if (designfile == "not open") { m->mothurOut("Ignoring: " + parameters["design"]); m->mothurOutEndLine(); designfile = ""; } @@ -341,6 +393,20 @@ SetCurrentCommand::SetCurrentCommand(string option) { else if (taxonomyfile == "not found") { taxonomyfile = ""; } if (taxonomyfile != "") { m->setTaxonomyFile(taxonomyfile); } + flowfile = validParameter.validFile(parameters, "flow", true); + if (flowfile == "not open") { m->mothurOut("Ignoring: " + parameters["flow"]); m->mothurOutEndLine(); flowfile = ""; } + else if (flowfile == "not found") { flowfile = ""; } + if (flowfile != "") { m->setFlowFile(flowfile); } + + biomfile = validParameter.validFile(parameters, "biom", true); + if (biomfile == "not open") { m->mothurOut("Ignoring: " + parameters["biom"]); m->mothurOutEndLine(); biomfile = ""; } + else if (biomfile == "not found") { biomfile = ""; } + if (biomfile != "") { m->setBiomFile(biomfile); } + + processors = validParameter.validFile(parameters, "processors", false); + if (processors == "not found") { processors = "1"; } + if (processors != "") { m->setProcessors(processors); } + clearTypes = validParameter.validFile(parameters, "clear", false); if (clearTypes == "not found") { clearTypes = ""; } else { m->splitAtDash(clearTypes, types); } @@ -354,25 +420,6 @@ SetCurrentCommand::SetCurrentCommand(string option) { } //********************************************************************************************************************** -void SetCurrentCommand::help(){ - try { - m->mothurOut("The set.current command allows you to set the current files saved by mothur.\n"); - m->mothurOut("The set.current command parameters are: clear, phylip, column, list, rabund, sabund, name, group, design, order, tree, shared, ordergroup, relabund, fasta, qfile, sff, oligos, accnos, taxonomy.\n"); - m->mothurOut("The clear paramter is used to indicate which file types you would like to clear values for, multiple types can be separated by dashes.\n"); - m->mothurOut("The set.current command should be in the following format: \n"); - m->mothurOut("set.current(fasta=yourFastaFile) or set.current(fasta=amazon.fasta, clear=name-accnos)\n"); - - } - catch(exception& e) { - m->errorOut(e, "SetCurrentCommand", "help"); - exit(1); - } -} - -//********************************************************************************************************************** -SetCurrentCommand::~SetCurrentCommand(){} -//********************************************************************************************************************** - int SetCurrentCommand::execute(){ try { @@ -423,6 +470,14 @@ int SetCurrentCommand::execute(){ m->setAccnosFile(""); }else if (types[i] == "taxonomy") { m->setTaxonomyFile(""); + }else if (types[i] == "flow") { + m->setFlowFile(""); + }else if (types[i] == "biom") { + m->setBiomFile(""); + }else if (types[i] == "count") { + m->setCountTableFile(""); + }else if (types[i] == "processors") { + m->setProcessors("1"); }else if (types[i] == "all") { m->clearCurrentFiles(); }else {