added cluster.classic command

[mothur.git] / mothurout.cpp

diff --git a/mothurout.cpp b/mothurout.cpp
index 0c3ef3d9cddf5cc90544d9a6d0117882d60db6b6..de6da8c217a36a17368be48c21a7116d36a43108 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 {
                
@@ -276,8 +286,9 @@ int MothurOut::openOutputFileAppend(string fileName, ofstream& fileHandle){
 /***********************************************************************/
 void MothurOut::gobble(istream& f){
        try {
+               
                char d;
-               while(isspace(d=f.get()))               {;}
+               while(isspace(d=f.get()))               { ;}
                f.putback(d);
        }
        catch(exception& e) {
@@ -501,19 +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
                                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;
@@ -984,7 +1005,7 @@ vector<unsigned long int> MothurOut::divideFile(string filename, int& proc) {
                //estimate file breaks
                unsigned long int chunkSize = 0;
                chunkSize = size / proc;
-       
+
                //file to small to divide by processors
                if (chunkSize == 0)  {  proc = 1;       filePos.push_back(size); return filePos;        }
        
@@ -1002,7 +1023,7 @@ vector<unsigned long int> MothurOut::divideFile(string filename, int& proc) {
                           char c = in.get();
                           if (c == '>') {   in.putback(c); newSpot = in.tellg(); break;  }
                        }
-                       
+               
                        //there was not another sequence before the end of the file
                        unsigned long int sanityPos = in.tellg();
 
@@ -1017,7 +1038,7 @@ 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]) {  filePos.erase(filePos.begin()+(i+1)); i--; }
+                       if (filePos[(i+1)] <= filePos[i]) {  cout << "erasing " << (i+1) << endl; filePos.erase(filePos.begin()+(i+1)); i--; }
                }
 
                proc = (filePos.size() - 1);
@@ -1181,7 +1202,20 @@ void MothurOut::getNumSeqs(ifstream& file, int& numSeqs){
 //This function parses the estimator options and puts them in a vector
 void MothurOut::splitAtChar(string& estim, vector<string>& container, char symbol) {
        try {
-               string individual;
+               string individual = "";
+               int estimLength = estim.size();
+               for(int i=0;i<estimLength;i++){
+                       if(estim[i] == symbol){
+                               container.push_back(individual);
+                               individual = "";                                
+                       }
+                       else{
+                               individual += estim[i];
+                       }
+               }
+               container.push_back(individual);
+
+               /*
                
                while (estim.find_first_of(symbol) != -1) {
                        individual = estim.substr(0,estim.find_first_of(symbol));
@@ -1191,7 +1225,7 @@ void MothurOut::splitAtChar(string& estim, vector<string>& container, char symbo
                        }
                }
                //get last one
-               container.push_back(estim);
+               container.push_back(estim); */
        }
        catch(exception& e) {
                errorOut(e, "MothurOut", "splitAtChar");
@@ -1529,6 +1563,7 @@ bool MothurOut::checkReleaseVersion(ifstream& file, string version) {
                exit(1);
        }
 }
+
 /**************************************************************************************************/