#include <sstream>
#include <signal.h>
+
//exception
#include <stdexcept>
#include <exception>
//#include <readline/history.h>
#else
#include <conio.h> //allows unbuffered screen capture from stdin
+ #include <direct.h> //get cwd
#endif
using namespace std;
string simpleName = longName;
- if(longName.find_last_of("/") != longName.npos){
- int pos = longName.find_last_of('/')+1;
- simpleName = longName.substr(pos, longName.length());
- }
+ size_t found;
+ found=longName.find_last_of("/\\");
+ if(found != longName.npos){
+ simpleName = longName.substr(found+1);
+ }
+
+ //if(longName.find_last_of("/") != longName.npos){
+ // int pos = longName.find_last_of('/')+1;
+ // simpleName = longName.substr(pos, longName.length());
+ //}
+
return simpleName;
}
int pos = longName.find_last_of('/')+1;
rootPathName = longName.substr(0, pos);
}
-
+
return rootPathName;
}
+/***********************************************************************/
+
+inline string hasPath(string longName){
+
+ string path = "";
+
+ size_t found;
+ found=longName.find_last_of("/\\");
+
+ if(found != longName.npos){
+ path = longName.substr(0, found+1);
+ }
+
+ return path;
+}
/***********************************************************************/
}
/***********************************************************************/
+inline string getFullPathName(string fileName){
+
+ string path = hasPath(fileName);
+ string newFileName = getSimpleName(fileName);
+ int pos;
+
+ if (path == "") { return fileName; } //its a simple name
+ else { //we need to complete the pathname
+ // ex. ../../../filename
+ // cwd = /user/work/desktop
+
+ string cwd;
+ //get current working directory
+ #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+ if (path.rfind("./") == -1) { return fileName; } //already complete name
+
+ char* cwdpath;
+ size_t size;
+ cwdpath=getcwd(cwdpath,size);
+ cwd = cwdpath;
+
+ //rip off first '/'
+ string simpleCWD;
+ if (cwd.length() > 0) { simpleCWD = cwd.substr(1); }
+
+ //break apart the current working directory
+ vector<string> dirs;
+ while (simpleCWD.find_first_of('/') != -1) {
+ string dir = simpleCWD.substr(0,simpleCWD.find_first_of('/'));
+ simpleCWD = simpleCWD.substr(simpleCWD.find_first_of('/')+1, simpleCWD.length());
+ dirs.push_back(dir);
+ }
+ //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);
+ 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 { mothurOut("cannot resolve path for " + fileName); mothurOutEndLine(); return fileName; }
+ }
+
+ for (int i = index; i >= 0; i--) {
+ newFileName = dirs[i] + "/" + newFileName;
+ }
+
+ newFileName = "/" + newFileName;
+ return newFileName;
+
+ #else
+ if (path.rfind(".\\") == -1) { return fileName; } //already complete name
+
+ char *cwdpath = NULL;
+ cwdpath = getcwd(NULL, 0); // or _getcwd
+ if ( cwdpath != NULL) { cwd = cwdpath; }
+ else { cwd = ""; }
+
+ //break apart the current working directory
+ vector<string> dirs;
+ while (cwd.find_first_of('\\') != -1) {
+ string dir = cwd.substr(0,cwd.find_first_of('\\'));
+ cwd = cwd.substr(cwd.find_first_of('\\')+1, cwd.length());
+ dirs.push_back(dir);
+
+ }
+ //get last one
+ dirs.push_back(cwd); //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);
+ 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 { mothurOut("cannot resolve path for " + fileName); mothurOutEndLine(); return fileName; }
+ }
+
+ for (int i = index; i >= 0; i--) {
+ newFileName = dirs[i] + "\\" + newFileName;
+ }
+
+ return newFileName;
+
+ #endif
+ }
+
+}
+/***********************************************************************/
+
inline int openInputFile(string fileName, ifstream& fileHandle, string m){
+
+ //get full path name
+ string completeFileName = getFullPathName(fileName);
+ //string completeFileName = fileName;
- fileHandle.open(fileName.c_str());
+ fileHandle.open(completeFileName.c_str());
if(!fileHandle) {
- mothurOut("Error: Could not open " + fileName); mothurOutEndLine();
+ mothurOut("Error: Could not open " + completeFileName); mothurOutEndLine();
return 1;
}
else {
/***********************************************************************/
inline int openInputFile(string fileName, ifstream& fileHandle){
-
- fileHandle.open(fileName.c_str());
+ //get full path name
+ string completeFileName = getFullPathName(fileName);
+
+ fileHandle.open(completeFileName.c_str());
if(!fileHandle) {
- mothurOut("Error: Could not open " + fileName); mothurOutEndLine();
+ mothurOut("Error: Could not open " + completeFileName); mothurOutEndLine();
return 1;
}
else {
//check for blank file
gobble(fileHandle);
- if (fileHandle.eof()) { mothurOut(fileName + " is blank. Please correct."); mothurOutEndLine(); return 1; }
+ if (fileHandle.eof()) { mothurOut(completeFileName + " is blank. Please correct."); mothurOutEndLine(); return 1; }
return 0;
}
/***********************************************************************/
inline int openOutputFile(string fileName, ofstream& fileHandle){
+
+ string completeFileName = getFullPathName(fileName);
- fileHandle.open(fileName.c_str(), ios::trunc);
+ fileHandle.open(completeFileName.c_str(), ios::trunc);
if(!fileHandle) {
- mothurOut("Error: Could not open " + fileName); mothurOutEndLine();
+ mothurOut("Error: Could not open " + completeFileName); mothurOutEndLine();
return 1;
}
else {
projects / mothur.git / blobdiff