added sff.multiple command. fixed issue with windows paralellization in chimera...

[mothur.git] / mothurout.cpp

diff --git a/mothurout.cpp b/mothurout.cpp
index 1a3bf79f50dad4e0a66e9910bb4abfe8c2cff944..2debf843f7910e6e0d61c9092cd366f1be5b2161 100644 (file)
--- a/mothurout.cpp
+++ b/mothurout.cpp
@@ -939,7 +939,7 @@ string MothurOut::getFullPathName(string fileName){
                                }
                        
                                for (int i = index; i >= 0; i--) {
-                                       newFileName = dirs[i] +  "\\" + newFileName;            
+                                       newFileName = dirs[i] +  "\\\\" + newFileName;          
                                }
                                
                                return newFileName;
@@ -2431,30 +2431,29 @@ void MothurOut::splitAtDash(string& estim, vector<string>& container) {
        try {
                string individual = "";
                int estimLength = estim.size();
+               bool prevEscape = false;
                for(int i=0;i<estimLength;i++){
-                       if(estim[i] == '-'){
-                               container.push_back(individual);
-                               individual = "";                                
+                       if(prevEscape){
+                               individual += estim[i];
+                               prevEscape = false;
                        }
                        else{
-                               individual += estim[i];
+                               if(estim[i] == '\\'){
+                                       prevEscape = true;
+                               }
+                               else if(estim[i] == '-'){
+                                       container.push_back(individual);
+                                       individual = "";
+                                       prevEscape = false;                             
+                               }
+                               else{
+                                       individual += estim[i];
+                                       prevEscape = false;
+                               }
                        }
                }
                container.push_back(individual);
-
-       
-       /*      string individual;
-               
-               while (estim.find_first_of('-') != -1) {
-                       individual = estim.substr(0,estim.find_first_of('-'));
-                       if ((estim.find_first_of('-')+1) <= estim.length()) { //checks to make sure you don't have dash at end of string
-                               estim = estim.substr(estim.find_first_of('-')+1, estim.length());
-                               container.push_back(individual);
-                       }
-               }
-               //get last one
-               container.push_back(estim); */
-       }
+       }
        catch(exception& e) {
                errorOut(e, "MothurOut", "splitAtDash");
                exit(1);
@@ -2467,29 +2466,29 @@ void MothurOut::splitAtDash(string& estim, set<string>& container) {
        try {
                string individual = "";
                int estimLength = estim.size();
+               bool prevEscape = false;
                for(int i=0;i<estimLength;i++){
-                       if(estim[i] == '-'){
-                               container.insert(individual);
-                               individual = "";                                
+                       if(prevEscape){
+                               individual += estim[i];
+                               prevEscape = false;
                        }
                        else{
-                               individual += estim[i];
+                               if(estim[i] == '\\'){
+                                       prevEscape = true;
+                               }
+                               else if(estim[i] == '-'){
+                                       container.insert(individual);
+                                       individual = "";
+                                       prevEscape = false;                             
+                               }
+                               else{
+                                       individual += estim[i];
+                                       prevEscape = false;
+                               }
                        }
                }
                container.insert(individual);
-
-       //      string individual;
-               
-       //      while (estim.find_first_of('-') != -1) {
-       //              individual = estim.substr(0,estim.find_first_of('-'));
-       //              if ((estim.find_first_of('-')+1) <= estim.length()) { //checks to make sure you don't have dash at end of string
-       //                      estim = estim.substr(estim.find_first_of('-')+1, estim.length());
-       //                      container.insert(individual);
-       //              }
-       //      }
-               //get last one
-       //      container.insert(estim);
-       
+        
        }
        catch(exception& e) {
                errorOut(e, "MothurOut", "splitAtDash");
@@ -2500,19 +2499,32 @@ void MothurOut::splitAtDash(string& estim, set<string>& container) {
 //This function parses the line options and puts them in a set
 void MothurOut::splitAtDash(string& estim, set<int>& container) {
        try {
-               string individual;
+               string individual = "";
                int lineNum;
-               
-               while (estim.find_first_of('-') != -1) {
-                       individual = estim.substr(0,estim.find_first_of('-'));
-                       if ((estim.find_first_of('-')+1) <= estim.length()) { //checks to make sure you don't have dash at end of string
-                               estim = estim.substr(estim.find_first_of('-')+1, estim.length());
-                               convert(individual, lineNum); //convert the string to int
-                               container.insert(lineNum);
+               int estimLength = estim.size();
+               bool prevEscape = false;
+               for(int i=0;i<estimLength;i++){
+                       if(prevEscape){
+                               individual += estim[i];
+                               prevEscape = false;
+                       }
+                       else{
+                               if(estim[i] == '\\'){
+                                       prevEscape = true;
+                               }
+                               else if(estim[i] == '-'){
+                                       convert(individual, lineNum); //convert the string to int
+                                       container.insert(lineNum);
+                                       individual = "";
+                                       prevEscape = false;                             
+                               }
+                               else{
+                                       individual += estim[i];
+                                       prevEscape = false;
+                               }
                        }
                }
-               //get last one
-               convert(estim, lineNum); //convert the string to int
+               convert(individual, lineNum); //convert the string to int
                container.insert(lineNum);
        }
        catch(exception& e) {