X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=optionparser.cpp;h=262ac88286b0639ace8cb3bff4fe10a091ec4748;hp=0506da6ff441c5a85e296c1fd6f3033110622335;hb=050a3ff02473a3d4c0980964e1a9ebe52e55d6b8;hpb=348de0f8b17d84ede77081dcf67bd6ef43496677

diff --git a/optionparser.cpp b/optionparser.cpp
index 0506da6..262ac88 100644
--- a/optionparser.cpp
+++ b/optionparser.cpp
@@ -21,11 +21,15 @@ OptionParser::OptionParser(string option) {
 			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;
 		}
 	}
@@ -34,7 +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() {	
@@ -43,70 +77,129 @@ 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();) {
+       
+            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, '.');
 			
-			if (it->second == "current") {
+			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(); }
 				
-				//look for file types
-				if ((it->first == "fasta") || (it->first == "candidate")) {
-					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 {
-					m->mothurOut("[ERROR]: mothur does not save a current file for " + it->first); m->mothurOutEndLine();
+				int numMatches = 0;
+				for(int j = 0; j < smallest; j++) {
+					if (root[j] == rootName[j]) { numMatches++; }
 				}
 				
-				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++;
+				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;
+					}
 				}
-			}else{ it++; }
+			}
+			
 		}
-	
-		return parameters;	
+		
+		
+		return match;
 	}
 	catch(exception& e) {
-		m->errorOut(e, "OptionParser", "getParameters");
+		m->errorOut(e, "OptionParser", "getNameFile");
 		exit(1);
 	}
 }
 
+				
 /***********************************************************************/