pat's ../ bug fix

[mothur.git] / mothur.h

diff --git a/mothur.h b/mothur.h
index a63d7ae055f8281bbfd0fda4ef03c3647419beea..8190152b8be3c15ee0a3559b93d846174d6c992d 100644 (file)
--- a/mothur.h
+++ b/mothur.h
@@ -487,7 +487,7 @@ inline bool isBlank(string fileName){
 /***********************************************************************/
 
 inline string getFullPathName(string fileName){
-       
+       try{
        string path = hasPath(fileName);
        string newFileName;
        int pos;
@@ -504,10 +504,12 @@ inline string getFullPathName(string fileName){
                        else { newFileName = fileName.substr(fileName.rfind("./")+2); } //save the complete part of the name
                        
                        char* cwdpath = new char[1024];
+
                        size_t size;
                        cwdpath=getcwd(cwdpath,size);
-                       cwd = cwdpath;
                
+                       cwd = cwdpath;
+                       
                        //rip off first '/'
                        string simpleCWD;
                        if (cwd.length() > 0) { simpleCWD = cwd.substr(1); }
@@ -521,9 +523,10 @@ inline string getFullPathName(string fileName){
                        }
                        //get last one              // ex. ../../../filename = /user/work/desktop/filename
                        dirs.push_back(simpleCWD);  //ex. dirs[0] = user, dirs[1] = work, dirs[2] = desktop
-                               
+                       
+               
                        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 ../
                                        path = path.substr(0, pos-1);
@@ -583,6 +586,12 @@ inline string getFullPathName(string fileName){
                        
                #endif
        }
+       }
+       catch(exception& e) {
+               errorOut(e, "getFullPathName", "getFullPathName");
+               exit(1);
+       }
+       
        
 }
 /***********************************************************************/
@@ -606,7 +615,7 @@ inline int openInputFile(string fileName, ifstream& fileHandle, string m){
 inline int openInputFile(string fileName, ifstream& fileHandle){
        //get full path name
        string completeFileName = getFullPathName(fileName);
-       
+
        fileHandle.open(completeFileName.c_str());
        if(!fileHandle) {
                mothurOut("Error: Could not open " + completeFileName);  mothurOutEndLine();