//**********************************************************************************************************************
vector<string> RemoveOtuLabelsCommand::setParameters(){
try {
- CommandParameter paccnos("accnos", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(paccnos);
- CommandParameter pconstaxonomy("constaxonomy", "InputTypes", "", "", "none", "FNGLT", "none",false,false); parameters.push_back(pconstaxonomy);
- CommandParameter potucorr("otucorr", "InputTypes", "", "", "none", "FNGLT", "none",false,false); parameters.push_back(potucorr);
- CommandParameter pcorraxes("corraxes", "InputTypes", "", "", "none", "FNGLT", "none",false,false); parameters.push_back(pcorraxes);
- CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
- CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+ CommandParameter paccnos("accnos", "InputTypes", "", "", "none", "none", "none","",false,true,true); parameters.push_back(paccnos);
+ CommandParameter pconstaxonomy("constaxonomy", "InputTypes", "", "", "none", "FNGLT", "none","constaxonomy",false,false); parameters.push_back(pconstaxonomy);
+ CommandParameter potucorr("otucorr", "InputTypes", "", "", "none", "FNGLT", "none","otucorr",false,false); parameters.push_back(potucorr);
+ CommandParameter pcorraxes("corraxes", "InputTypes", "", "", "none", "FNGLT", "none","corraxes",false,false); parameters.push_back(pcorraxes);
+ CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
+ CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
vector<string> myArray;
for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
}
}
//**********************************************************************************************************************
-string RemoveOtuLabelsCommand::getOutputFileNameTag(string type, string inputName=""){
- try {
- string outputFileName = "";
- map<string, vector<string> >::iterator it;
+string RemoveOtuLabelsCommand::getOutputPattern(string type) {
+ try {
+ string pattern = "";
- //is this a type this command creates
- it = outputTypes.find(type);
- if (it == outputTypes.end()) { m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
- else {
- if (type == "constaxonomy") { outputFileName = "pick.taxonomy"; }
- else if (type == "otucorr") { outputFileName = "pick.corr"; }
- else if (type == "corraxes") { outputFileName = "pick.axes"; }
- else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true; }
- }
- return outputFileName;
- }
- catch(exception& e) {
- m->errorOut(e, "RemoveOtuLabelsCommand", "getOutputFileNameTag");
- exit(1);
- }
+ if (type == "constaxonomy") { pattern = "[filename],pick,[extension]"; }
+ else if (type == "otucorr") { pattern = "[filename],pick,[extension]"; }
+ else if (type == "corraxes") { pattern = "[filename],pick,[extension]"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
+
+ return pattern;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "RemoveOtuLabelsCommand", "getOutputPattern");
+ exit(1);
+ }
}
//**********************************************************************************************************************
RemoveOtuLabelsCommand::RemoveOtuLabelsCommand(){
abort = true; calledHelp = true;
setParameters();
vector<string> tempOutNames;
- outputTypes["contaxonomy"] = tempOutNames;
+ outputTypes["constaxonomy"] = tempOutNames;
outputTypes["otucorr"] = tempOutNames;
outputTypes["corraxes"] = tempOutNames;
}
try {
string thisOutputDir = outputDir;
if (outputDir == "") { thisOutputDir += m->hasPath(constaxonomyfile); }
- string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(constaxonomyfile)) + getOutputFileNameTag("constaxonomy");
+ map<string, string> variables;
+ variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(constaxonomyfile));
+ variables["[extension]"] = m->getExtension(constaxonomyfile);
+ string outputFileName = getOutputFileName("constaxonomy", variables);
ofstream out;
m->openOutputFile(outputFileName, out);
try {
string thisOutputDir = outputDir;
if (outputDir == "") { thisOutputDir += m->hasPath(otucorrfile); }
- string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(otucorrfile)) + getOutputFileNameTag("otucorr");
+ map<string, string> variables;
+ variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(otucorrfile));
+ variables["[extension]"] = m->getExtension(otucorrfile);
+ string outputFileName = getOutputFileName("otucorr", variables);
ofstream out;
m->openOutputFile(outputFileName, out);
try {
string thisOutputDir = outputDir;
if (outputDir == "") { thisOutputDir += m->hasPath(corraxesfile); }
- string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(corraxesfile)) + getOutputFileNameTag("corraxes");
+ map<string, string> variables;
+ variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(corraxesfile));
+ variables["[extension]"] = m->getExtension(corraxesfile);
+ string outputFileName = getOutputFileName("corraxes", variables);
ofstream out;
m->openOutputFile(outputFileName, out);