X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=sensspeccommand.cpp;fp=sensspeccommand.cpp;h=b62bb00548f3e1ee66f0c1cf2b4bee117c5416cf;hb=6c2b1e530a5c0bb87040e58a3e410097acdfcc3d;hp=cfa1f5b6dc0649925ff4762abdef070e93fd7688;hpb=f509429e06e545bde69c97cacc0eb436775bd329;p=mothur.git diff --git a/sensspeccommand.cpp b/sensspeccommand.cpp index cfa1f5b..b62bb00 100644 --- a/sensspeccommand.cpp +++ b/sensspeccommand.cpp @@ -14,7 +14,6 @@ vector SensSpecCommand::setParameters(){ try { CommandParameter plist("list", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(plist); CommandParameter pphylip("phylip", "InputTypes", "", "", "PhylipColumn", "PhylipColumn", "none",false,false); parameters.push_back(pphylip); - //CommandParameter pname("name", "InputTypes", "", "", "none", "none", "ColumnName",false,false); parameters.push_back(pname); CommandParameter pcolumn("column", "InputTypes", "", "", "PhylipColumn", "PhylipColumn", "none",false,false); parameters.push_back(pcolumn); CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel); CommandParameter pcutoff("cutoff", "Number", "", "-1.00", "", "", "",false,false); parameters.push_back(pcutoff); @@ -136,16 +135,7 @@ SensSpecCommand::SensSpecCommand(string option) { path = m->hasPath(it->second); //if the user has not given a path then, add inputdir. else leave path alone. if (path == "") { parameters["column"] = 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; } - //} - + } } //check for required parameters listFile = validParameter.validFile(parameters, "list", true); @@ -196,12 +186,6 @@ SensSpecCommand::SensSpecCommand(string option) { else if(!m->isTrue(temp)) { hard = 0; } else if(m->isTrue(temp)) { hard = 1; } -// temp = validParameter.validFile(parameters, "name", true); -// if (temp == "not found") { nameFile = ""; } -// else if(temp == "not open") { abort = true; } -// else { nameFile = temp; } -// cout << "name:\t" << nameFile << endl; - temp = validParameter.validFile(parameters, "cutoff", false); if (temp == "not found") { temp = "-1.00"; } m->mothurConvert(temp, cutoff); // cout << cutoff << endl;