X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=optionparser.cpp;h=262ac88286b0639ace8cb3bff4fe10a091ec4748;hp=0d6ed2d4d0bfa681a7aa30693bcb7ae30a9c77fb;hb=b206f634aae1b4ce13978d203247fb64757d5482;hpb=0caf3fbabaa3ece404f8ce77f4c883dc5b1bf1dc

diff --git a/optionparser.cpp b/optionparser.cpp
index 0d6ed2d..262ac88 100644
--- a/optionparser.cpp
+++ b/optionparser.cpp
@@ -38,7 +38,37 @@ OptionParser::OptionParser(string option) {
 		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() {	
@@ -47,65 +77,72 @@ 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;	
 	}