string key, value;
//reads in parameters and values
while((option.find_first_of(',') != -1)) { //while there are parameters
- splitAtComma(value, option);
- splitAtEquals(key, value);
+ 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
- splitAtEquals(key, option);
+ m->splitAtEquals(key, option);
+ if ((key == "candidate") || (key == "query")) { key = "fasta"; }
+ if (key == "template") { key = "reference"; }
parameters[key] = option;
}
}
catch(exception& e) {
- m->errorOut(e, "OptionParser", "parse");
+ m->errorOut(e, "OptionParser", "OptionParser");
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() { return parameters; }
+map<string, string> OptionParser::getParameters() {
+ try {
+
+ //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 == "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 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;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "OptionParser", "getParameters");
+ exit(1);
+ }
+}
+
+/***********************************************************************/
+//pass a vector of filenames that may match the current namefile.
+//this function will look at each one, if the rootnames match, mothur will warn
+//the user that they may have neglected to provide a namefile.
+//stops when it finds a match.
+bool OptionParser::getNameFile(vector<string> files) {
+ try {
+ string namefile = m->getNameFile();
+ bool match = false;
+
+ if ((namefile != "")&&(!m->mothurCalling)) {
+ string temp = m->getRootName(m->getSimpleName(namefile));
+ vector<string> rootName;
+ m->splitAtChar(temp, rootName, '.');
+
+ for (int i = 0; i < files.size(); i++) {
+ temp = m->getRootName(m->getSimpleName(files[i]));
+ vector<string> root;
+ m->splitAtChar(temp, root, '.');
+
+ int smallest = rootName.size();
+ if (root.size() < smallest) { smallest = root.size(); }
+
+ int numMatches = 0;
+ for(int j = 0; j < smallest; j++) {
+ if (root[j] == rootName[j]) { numMatches++; }
+ }
+
+ if (smallest > 0) {
+ if ((numMatches >= (smallest-2)) && (root[0] == rootName[0])) {
+ m->mothurOut("[WARNING]: This command can take a namefile and you did not provide one. The current namefile is " + namefile + " which seems to match " + files[i] + ".");
+ m->mothurOutEndLine();
+ match = true;
+ break;
+ }
+ }
+ }
+
+ }
+
+
+ return match;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "OptionParser", "getNameFile");
+ exit(1);
+ }
+}
+
/***********************************************************************/
projects / mothur.git / blobdiff