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;
}
}
if (it->second == "current") {
//look for file types
- if ((it->first == "fasta") || (it->first == "candidate")) {
+ if (it->first == "fasta") {
it->second = m->getFastaFile();
}else if (it->first == "qfile") {
it->second = m->getQualFile();
}
}else{ it++; }
}
-
+
return parameters;
}
catch(exception& e) {
}
}
+/***********************************************************************/
+//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 != "") {
+ 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);
+ }
+}
+
+
/***********************************************************************/