some changes while testing 1.9

[mothur.git] / mothur.h

diff --git a/mothur.h b/mothur.h
index dcb026c310ef7052116bb61f5b3517e24ae1e39e..062c4814dfa4addeeb923f586c601717daca7c66 100644 (file)
--- a/mothur.h
+++ b/mothur.h
@@ -459,15 +459,16 @@ inline string getFullPathName(string fileName){
                        
                
                        int index = dirs.size()-1;
-               
+       
                        while((pos = path.rfind("./")) != -1) { //while you don't have a complete path
-                               if (path[(pos-1)] == '.') { //you want your parent directory ../
+                               if (pos == 0) { break;  //you are at the end
+                               }else if (path[(pos-1)] == '.') { //you want your parent directory ../
                                        path = path.substr(0, pos-1);
                                        index--;
                                        if (index == 0) {  break; }
                                }else if (path[(pos-1)] == '/') { //you want the current working dir ./
                                        path = path.substr(0, pos);
-                               }else if (pos == 1) { break; 
+                               }else if (pos == 1) { break;  //you are at the end
                                }else { cout << "cannot resolve path for " <<  fileName << endl; return fileName; }
                        }
                
@@ -501,14 +502,15 @@ inline string getFullPathName(string fileName){
                        int index = dirs.size()-1;
                                
                        while((pos = path.rfind(".\\")) != -1) { //while you don't have a complete path
-                               if (path[(pos-1)] == '.') { //you want your parent directory ../
+                               if (pos == 0) { break;  //you are at the end
+                               }else if (path[(pos-1)] == '.') { //you want your parent directory ../
                                        path = path.substr(0, pos-1);
                                        index--;
                                        if (index == 0) {  break; }
                                }else if (path[(pos-1)] == '\\') { //you want the current working dir ./
                                        path = path.substr(0, pos);
-                               }else if (pos == 1) { break; 
-                               }else {  cout << "cannot resolve path for " <<  fileName << endl;  return fileName; }
+                               }else if (pos == 1) { break;  //you are at the end
+                               }else { cout << "cannot resolve path for " <<  fileName << endl; return fileName; }
                        }
                
                        for (int i = index; i >= 0; i--) {
@@ -880,9 +882,12 @@ inline void appendFiles(string temp, string filename) {
 }
 
 /**************************************************************************************************/
-inline string sortFile(string distFile){
+inline string sortFile(string distFile, string outputDir){
        try {   
+       
+               //if (outputDir == "") {  outputDir += hasPath(distFile);  }
                string outfile = getRootName(distFile) + "sorted.dist";
+
                
                //if you can, use the unix sort since its been optimized for years
                #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)