- 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") {