enabled ~

diff --git a/mothur.h b/mothur.h
index 7f3608e73ee8770d8d777bde1be399c61027b515..f101d1f808fdb22d0fac7795dcc6388be6dacaf2 100644 (file)
--- a/mothur.h
+++ b/mothur.h
@@ -379,7 +379,7 @@ inline string hasPath(string longName){
        string path = "";
        
        size_t found;
-       found=longName.find_last_of("/\\");
+       found=longName.find_last_of("~/\\");
 
        if(found != longName.npos){
                path = longName.substr(0, found+1);
@@ -433,91 +433,103 @@ inline string getFullPathName(string fileName){
                string cwd;
                //get current working directory 
                #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)   
-                       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 = new char[1024];
+                       if (path.find("~") != -1) { //go to home directory
+                               string homeDir = getenv ("HOME");
+                               newFileName = homeDir + fileName.substr(fileName.find("~")+1);
+                               return newFileName;
+                       }else { //find path
+                               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 = new char[1024];
 
-                       size_t size;
-                       cwdpath=getcwd(cwdpath,size);
-               
-                       cwd = cwdpath;
-                       
-                       //rip off first '/'
-                       string simpleCWD;
-                       if (cwd.length() > 0) { simpleCWD = cwd.substr(1); }
+                               size_t size;
+                               cwdpath=getcwd(cwdpath,size);
                        
-                       //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
+                               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;
                
-                       int index = dirs.size()-1;
-       
-                       while((pos = path.rfind("./")) != -1) { //while you don't have a complete path
-                               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;  //you are at the end
-                               }else { cout << "cannot resolve path for " <<  fileName << endl; return fileName; }
-                       }
-               
-                       for (int i = index; i >= 0; i--) {
-                               newFileName = dirs[i] +  "/" + newFileName;             
-                       }
+                               while((pos = path.rfind("./")) != -1) { //while you don't have a complete path
+                                       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;  //you are at the end
+                                       }else { cout << "cannot resolve path for " <<  fileName << endl; return fileName; }
+                               }
                        
-                       newFileName =  "/" +  newFileName;
-                       return newFileName;
+                               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
-                       else { newFileName = fileName.substr(fileName.rfind(".\\")+2); } //save the complete part of the 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;
+                       if (path.find("~") != -1) { //go to home directory
+                               string homeDir = getenv ("HOME");
+                               newFileName = homeDir + fileName.substr(fileName.find("~")+1);
+                               return newFileName;
+                       }else { //find path
+                               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 = NULL;
+                               cwdpath = getcwd(NULL, 0); // or _getcwd
+                               if ( cwdpath != NULL) { cwd = cwdpath; }
+                               else { cwd = "";  }
                                
-                       while((pos = path.rfind(".\\")) != -1) { //while you don't have a complete path
-                               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;  //you are at the end
-                               }else { cout << "cannot resolve path for " <<  fileName << endl; return fileName; }
-                       }
+                               //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);
                
-                       for (int i = index; i >= 0; i--) {
-                               newFileName = dirs[i] +  "\\" + newFileName;            
-                       }
+                               }
+                               //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 (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;  //you are at the end
+                                       }else { cout << "cannot resolve path for " <<  fileName << endl; return fileName; }
+                               }
                        
-                       return newFileName;
+                               for (int i = index; i >= 0; i--) {
+                                       newFileName = dirs[i] +  "\\" + newFileName;            
+                               }
+                               
+                               return newFileName;
+                       }
                        
                #endif
        }

diff --git a/nocommands.cpp b/nocommands.cpp
index 459ac5cfe8d0d79ff86569c4c090a0ae84d6c52c..1a01d3718f33fa02ee7f475323d704e135130fea 100644 (file)
--- a/nocommands.cpp
+++ b/nocommands.cpp
@@ -22,8 +22,8 @@ NoCommand::~NoCommand(){}
 int NoCommand::execute(){
        //Could choose to give more help here?fdsah
        cout << "Invalid command.\n";
-       
-       CommandFactory* valid =  CommandFactory::getInstance();
+   
+               CommandFactory* valid =  CommandFactory::getInstance();
        valid->printCommands(cout);
        
        return 0;