exit(1);
}
}
+/***********************************************************************/
+OptionParser::OptionParser(string option, map<string, string>& copy) {
+ try {
+ m = MothurOut::getInstance();
+ if (option != "") {
+
+ string key, value;
+ //reads in parameters and values
+ while((option.find_first_of(',') != -1)) { //while there are parameters
+ m->splitAtComma(value, option);
+ m->splitAtEquals(key, value);
+ if ((key == "candidate") || (key == "query")) { key = "fasta"; }
+ if (key == "template") { key = "reference"; }
+ parameters[key] = value;
+ }
+
+ //in case there is no comma and to get last parameter after comma
+ m->splitAtEquals(key, option);
+ if ((key == "candidate") || (key == "query")) { key = "fasta"; }
+ if (key == "template") { key = "reference"; }
+ parameters[key] = option;
+ }
+
+ copy = parameters;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "OptionParser", "OptionParser");
+ exit(1);
+ }
+}
/***********************************************************************/
map<string, string> OptionParser::getParameters() {
//loop through parameters and look for "current" so you can return the appropriate file
//doing it here to avoid code duplication in each of the commands
- map<string, string>::iterator it;
- for (it = parameters.begin(); it != parameters.end();) {
-
- if (it->second == "current") {
-
- //look for file types
- if (it->first == "fasta") {
- it->second = m->getFastaFile();
- }else if (it->first == "qfile") {
- it->second = m->getQualFile();
- }else if (it->first == "phylip") {
- it->second = m->getPhylipFile();
- }else if (it->first == "column") {
- it->second = m->getColumnFile();
- }else if (it->first == "list") {
- it->second = m->getListFile();
- }else if (it->first == "rabund") {
- it->second = m->getRabundFile();
- }else if (it->first == "sabund") {
- it->second = m->getSabundFile();
- }else if (it->first == "name") {
- it->second = m->getNameFile();
- }else if (it->first == "group") {
- it->second = m->getGroupFile();
- }else if (it->first == "order") {
- it->second = m->getOrderFile();
- }else if (it->first == "ordergroup") {
- it->second = m->getOrderGroupFile();
- }else if (it->first == "tree") {
- it->second = m->getTreeFile();
- }else if (it->first == "shared") {
- it->second = m->getSharedFile();
- }else if (it->first == "relabund") {
- it->second = m->getRelAbundFile();
- }else if (it->first == "design") {
- it->second = m->getDesignFile();
- }else if (it->first == "sff") {
- it->second = m->getSFFFile();
- }else if (it->first == "oligos") {
- it->second = m->getOligosFile();
- }else if (it->first == "accnos") {
- it->second = m->getAccnosFile();
- }else if (it->first == "taxonomy") {
- it->second = m->getTaxonomyFile();
- }else if (it->first == "biom") {
+
+ map<string, string>::iterator it;
+ for (it = parameters.begin(); it != parameters.end();) {
+
+ if (it->second == "current") {
+
+ //look for file types
+ if (it->first == "fasta") {
+ it->second = m->getFastaFile();
+ }else if (it->first == "qfile") {
+ it->second = m->getQualFile();
+ }else if (it->first == "phylip") {
+ it->second = m->getPhylipFile();
+ }else if (it->first == "column") {
+ it->second = m->getColumnFile();
+ }else if (it->first == "list") {
+ it->second = m->getListFile();
+ }else if (it->first == "rabund") {
+ it->second = m->getRabundFile();
+ }else if (it->first == "sabund") {
+ it->second = m->getSabundFile();
+ }else if (it->first == "name") {
+ it->second = m->getNameFile();
+ }else if (it->first == "group") {
+ it->second = m->getGroupFile();
+ }else if (it->first == "order") {
+ it->second = m->getOrderFile();
+ }else if (it->first == "ordergroup") {
+ it->second = m->getOrderGroupFile();
+ }else if (it->first == "tree") {
+ it->second = m->getTreeFile();
+ }else if (it->first == "shared") {
+ it->second = m->getSharedFile();
+ }else if (it->first == "relabund") {
+ it->second = m->getRelAbundFile();
+ }else if (it->first == "design") {
+ it->second = m->getDesignFile();
+ }else if (it->first == "sff") {
+ it->second = m->getSFFFile();
+ }else if (it->first == "flow") {
+ it->second = m->getFlowFile();
+ }else if (it->first == "oligos") {
+ it->second = m->getOligosFile();
+ }else if (it->first == "accnos") {
+ it->second = m->getAccnosFile();
+ }else if (it->first == "taxonomy") {
+ it->second = m->getTaxonomyFile();
+ }else if (it->first == "biom") {
it->second = m->getBiomFile();
- }else {
- m->mothurOut("[ERROR]: mothur does not save a current file for " + it->first); m->mothurOutEndLine();
- }
-
- if (it->second == "") { //no file was saved for that type, warn and remove from parameters
- m->mothurOut("[WARNING]: no file was saved for " + it->first + " parameter."); m->mothurOutEndLine();
- parameters.erase(it++);
- }else {
- m->mothurOut("Using " + it->second + " as input file for the " + it->first + " parameter."); m->mothurOutEndLine();
- it++;
- }
- }else{ it++; }
- }
+ }else if (it->first == "count") {
+ it->second = m->getCountTableFile();
+ }else if (it->first == "summary") {
+ it->second = m->getSummaryFile();
+ }else {
+ m->mothurOut("[ERROR]: mothur does not save a current file for " + it->first); m->mothurOutEndLine();
+ }
+
+ if (it->second == "") { //no file was saved for that type, warn and remove from parameters
+ m->mothurOut("[WARNING]: no file was saved for " + it->first + " parameter."); m->mothurOutEndLine();
+ parameters.erase(it++);
+ }else {
+ m->mothurOut("Using " + it->second + " as input file for the " + it->first + " parameter."); m->mothurOutEndLine();
+ it++;
+ }
+ }else{ it++; }
+ }
return parameters;
}
projects / mothur.git / blobdiff