finished sub.sample command

[mothur.git] / mothurout.cpp

diff --git a/mothurout.cpp b/mothurout.cpp
index aab9945230f680e4ce106e4266ff66ba5ee7c34e..bd1a098c8d5662044552071c7c44a273214018ce 100644 (file)
--- a/mothurout.cpp
+++ b/mothurout.cpp
@@ -60,6 +60,16 @@ void MothurOut::setDefaultPath(string pathname)  {
        }
 }
 /*********************************************************************************************/
+void MothurOut::setOutputDir(string pathname)  {
+       try {
+               outputDir = pathname;
+       }
+       catch(exception& e) {
+               errorOut(e, "MothurOut", "setOutputDir");
+               exit(1);
+       }
+}
+/*********************************************************************************************/
 void MothurOut::closeLog()  {
        try {
                
@@ -502,19 +512,29 @@ string MothurOut::getFullPathName(string fileName){
                #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)   
                        
                        if (path.find("~") != -1) { //go to home directory
-                               string homeDir = getenv ("HOME");
+                               string homeDir;
+                       
+                               char *homepath = NULL;
+                               homepath = getenv ("HOME");
+                               if ( homepath != NULL) { homeDir = homepath; }
+                               else { homeDir = "";  }
+
                                newFileName = homeDir + fileName.substr(fileName.find("~")+1);
                                return newFileName;
                        }else { //find path
-                               if (path.rfind("./") == -1) { return fileName; } //already complete name
+                               if (path.rfind("./") == string::npos) { return fileName; } //already complete name
                                else { newFileName = fileName.substr(fileName.rfind("./")+2); } //save the complete part of the name
                                
-                               char* cwdpath = new char[1024];
+                               //char* cwdpath = new char[1024];
+                               //size_t size;
+                               //cwdpath=getcwd(cwdpath,size);
+                               //cwd = cwdpath;
+                               
+                               char *cwdpath = NULL;
+                               cwdpath = getcwd(NULL, 0); // or _getcwd
+                               if ( cwdpath != NULL) { cwd = cwdpath; }
+                               else { cwd = "";  }
 
-                               size_t size;
-                               cwdpath=getcwd(cwdpath,size);
-                       
-                               cwd = cwdpath;
                                
                                //rip off first '/'
                                string simpleCWD;
@@ -522,7 +542,7 @@ string MothurOut::getFullPathName(string fileName){
                                
                                //break apart the current working directory
                                vector<string> dirs;
-                               while (simpleCWD.find_first_of('/') != -1) {
+                               while (simpleCWD.find_first_of('/') != string::npos) {
                                        string dir = simpleCWD.substr(0,simpleCWD.find_first_of('/'));
                                        simpleCWD = simpleCWD.substr(simpleCWD.find_first_of('/')+1, simpleCWD.length());
                                        dirs.push_back(dir);
@@ -533,7 +553,7 @@ string MothurOut::getFullPathName(string fileName){
                        
                                int index = dirs.size()-1;
                
-                               while((pos = path.rfind("./")) != -1) { //while you don't have a complete path
+                               while((pos = path.rfind("./")) != string::npos) { //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);
@@ -553,12 +573,12 @@ string MothurOut::getFullPathName(string fileName){
                                return newFileName;
                        }       
                #else
-                       if (path.find("~") != -1) { //go to home directory
+                       if (path.find("~") != string::npos) { //go to home directory
                                string homeDir = getenv ("HOMEPATH");
                                newFileName = homeDir + fileName.substr(fileName.find("~")+1);
                                return newFileName;
                        }else { //find path
-                               if (path.rfind(".\\") == -1) { return fileName; } //already complete name
+                               if (path.rfind(".\\") == string::npos) { return fileName; } //already complete name
                                else { newFileName = fileName.substr(fileName.rfind(".\\")+2); } //save the complete part of the name
                                                        
                                char *cwdpath = NULL;
@@ -579,7 +599,7 @@ string MothurOut::getFullPathName(string fileName){
                                        
                                int index = dirs.size()-1;
                                        
-                               while((pos = path.rfind(".\\")) != -1) { //while you don't have a complete path
+                               while((pos = path.rfind(".\\")) != string::npos) { //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);
@@ -638,6 +658,7 @@ int MothurOut::openInputFile(string fileName, ifstream& fileHandle, string m){
 
                        fileHandle.open(completeFileName.c_str());
                        if(!fileHandle) {
+                               //mothurOut("[ERROR]: Could not open " + completeFileName); mothurOutEndLine();
                                return 1;
                        }else {
                                //check for blank file
@@ -781,6 +802,7 @@ void MothurOut::appendFiles(string temp, string filename) {
                //open output file in append mode
                openOutputFileAppend(filename, output);
                int ableToOpen = openInputFile(temp, input, "no error");
+               //int ableToOpen = openInputFile(temp, input);
                
                if (ableToOpen == 0) { //you opened it
                        while(char c = input.get()){
@@ -1018,7 +1040,7 @@ vector<unsigned long int> MothurOut::divideFile(string filename, int& proc) {
 
                //sanity check filePos
                for (int i = 0; i < (filePos.size()-1); i++) {
-                       if (filePos[(i+1)] <= filePos[i]) {  cout << "erasing " << (i+1) << endl; filePos.erase(filePos.begin()+(i+1)); i--; }
+                       if (filePos[(i+1)] <= filePos[i]) {  filePos.erase(filePos.begin()+(i+1)); i--; }
                }
 
                proc = (filePos.size() - 1);
@@ -1543,6 +1565,7 @@ bool MothurOut::checkReleaseVersion(ifstream& file, string version) {
                exit(1);
        }
 }
+
 /**************************************************************************************************/