X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=optionparser.cpp;fp=optionparser.cpp;h=0000000000000000000000000000000000000000;hb=4a877efa127e56e81a21f53cfdbbfd3bfbe8c4ff;hp=0d6ed2d4d0bfa681a7aa30693bcb7ae30a9c77fb;hpb=a6cf29fa4dac0909c7582cb1094151d34093ee76;p=mothur.git

diff --git a/optionparser.cpp b/optionparser.cpp
deleted file mode 100644
index 0d6ed2d..0000000
--- a/optionparser.cpp
+++ /dev/null
@@ -1,168 +0,0 @@
-/*
- *  optionparser.cpp
- *  Mothur
- *
- *  Created by Sarah Westcott on 6/8/09.
- *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
- *
- */
-
-#include "optionparser.h"
-
-/***********************************************************************/
-
-OptionParser::OptionParser(string option) {
-	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;
-		}
-	}
-	catch(exception& e) {
-		m->errorOut(e, "OptionParser", "OptionParser");
-		exit(1);
-	}
-}
-
-/***********************************************************************/
-
-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 == "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++; }
-		}
-		
-		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);
-	}
-}
-
-				
-/***********************************************************************/