chimeracode

[mothur.git] / mothur.h

diff --git a/mothur.h b/mothur.h
index fdaa06362db6ecda7054fe4ff9b21442487c19d4..5f8a2fe75b41d57e345d50cb63606921c866ff67 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;
@@ -503,11 +503,13 @@ inline string getFullPathName(string fileName){
                        if (path.rfind("./") == -1) { return fileName; } //already complete name
                        else { newFileName = fileName.substr(fileName.rfind("./")+2); } //save the complete part of the name
                        
-                       char* cwdpath;
+                       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();
@@ -639,7 +648,7 @@ inline int renameFile(string oldName, string newName){
        system(command.c_str());
 #else
        remove(newName.c_str());
-       renameOk = rename(oldName.c_str(), newName.c_str());
+       int renameOk = rename(oldName.c_str(), newName.c_str());
 #endif
        return 0;
 }
@@ -822,6 +831,21 @@ inline bool inUsersGroups(string groupname, vector<string> Groups) {
                exit(1);
        }
 }
+/**************************************************************************************************/
+//returns true if any of the strings in first vector are in second vector
+inline bool inUsersGroups(vector<string> groupnames, vector<string> Groups) {
+       try {
+               
+               for (int i = 0; i < groupnames.size(); i++) {
+                       if (inUsersGroups(groupnames[i], Groups)) { return true; }
+               }
+               return false;
+       }
+       catch(exception& e) {
+               errorOut(e, "mothur", "inUsersGroups");
+               exit(1);
+       }
+}
 
 /**************************************************************************************************/