X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=mothurout.cpp;h=de6da8c217a36a17368be48c21a7116d36a43108;hb=6cf9539162b0fb0b5c0b99673e999df3cd717c55;hp=0c3ef3d9cddf5cc90544d9a6d0117882d60db6b6;hpb=7bf581f8c46b08eb3bb40715dac94695edee4a67;p=mothur.git

diff --git a/mothurout.cpp b/mothurout.cpp
index 0c3ef3d..de6da8c 100644
--- 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);
 	}
 }
+
 /**************************************************************************************************/