X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=mothur.h;h=f1b13920d0a4c8941214dbf3e42c96ed4ce39486;hb=1d18c13c5d71e92ee850a0d8d7cda4f0ef530bf7;hp=93f96df30c73fa91b7119b07eadb27a89dc5109d;hpb=a86aff4f80701bf0d436f02c0095920114e1cba2;p=mothur.git

diff --git a/mothur.h b/mothur.h
index 93f96df..f1b1392 100644
--- a/mothur.h
+++ b/mothur.h
@@ -54,6 +54,8 @@
 
 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 	#include <sys/wait.h>
+	#include <sys/time.h>
+	#include <sys/resource.h>
 	#include <unistd.h>
 	
 	#ifdef USE_READLINE
@@ -660,6 +662,29 @@ inline bool inVector(string member, vector<string> group){
 }
 /***********************************************************************/
 
+//This function parses the estimator options and puts them in a vector
+inline void splitAtChar(string& estim, vector<string>& container, char symbol) {
+	try {
+		string individual;
+		
+		while (estim.find_first_of(symbol) != -1) {
+			individual = estim.substr(0,estim.find_first_of(symbol));
+			if ((estim.find_first_of(symbol)+1) <= estim.length()) { //checks to make sure you don't have dash at end of string
+				estim = estim.substr(estim.find_first_of(symbol)+1, estim.length());
+				container.push_back(individual);
+			}
+		}
+		//get last one
+		container.push_back(estim);
+	}
+	catch(exception& e) {
+		cout << "Standard Error: " << e.what() << " has occurred in the mothur.h function splitAtDash. Please contact Pat Schloss at mothur.bugs@gmail.com." << "\n";
+		exit(1);
+	}	
+}
+
+/***********************************************************************/
+
 //This function parses the estimator options and puts them in a vector
 inline void splitAtDash(string& estim, vector<string>& container) {
 	try {
@@ -786,6 +811,7 @@ inline void splitAtEquals(string& key, string& value){
 		exit(1);
 	}	
 }
+
 /**************************************************************************************************/
 
 inline bool inUsersGroups(string groupname, vector<string> Groups) {
@@ -990,9 +1016,9 @@ inline string sortFile(string distFile, string outputDir){
 	}	
 }
 /**************************************************************************************************/
-inline vector<long> setFilePosFasta(string filename, int& num) {
+inline vector<unsigned long int> setFilePosFasta(string filename, int& num) {
 
-			vector<long> positions;
+			vector<unsigned long int> positions;
 			ifstream inFASTA;
 			openInputFile(filename, inFASTA);
 				
@@ -1000,7 +1026,7 @@ inline vector<long> setFilePosFasta(string filename, int& num) {
 			while(!inFASTA.eof()){
 				input = getline(inFASTA); gobble(inFASTA);
 				if (input.length() != 0) {
-					if(input[0] == '>'){	long pos = inFASTA.tellg(); positions.push_back(pos - input.length() - 1);	}
+					if(input[0] == '>'){	unsigned long int pos = inFASTA.tellg(); positions.push_back(pos - input.length() - 1);	}
 				}
 			}
 			inFASTA.close();
@@ -1019,7 +1045,7 @@ inline vector<long> setFilePosFasta(string filename, int& num) {
 				fclose (pFile);
 			}*/
 			
-			long size = positions[(positions.size()-1)];
+			unsigned long int size = positions[(positions.size()-1)];
 			ifstream in;
 			openInputFile(filename, in);
 			
@@ -1036,18 +1062,18 @@ inline vector<long> setFilePosFasta(string filename, int& num) {
 			return positions;
 }
 /**************************************************************************************************/
-inline vector<long> setFilePosEachLine(string filename, int& num) {
+inline vector<unsigned long int> setFilePosEachLine(string filename, int& num) {
 
-			vector<long> positions;
+			vector<unsigned long int> positions;
 			ifstream in;
 			openInputFile(filename, in);
 				
 			string input;
 			while(!in.eof()){
-				long lastpos = in.tellg();
+				unsigned long int lastpos = in.tellg();
 				input = getline(in); gobble(in);
 				if (input.length() != 0) {
-					long pos = in.tellg(); 
+					unsigned long int pos = in.tellg(); 
 					if (pos != -1) { positions.push_back(pos - input.length() - 1);	}
 					else {  positions.push_back(lastpos);  }
 				}
@@ -1057,7 +1083,7 @@ inline vector<long> setFilePosEachLine(string filename, int& num) {
 			num = positions.size();
 		
 			FILE * pFile;
-			long size;
+			unsigned long int size;
 		
 			//get num bytes in file
 			pFile = fopen (filename.c_str(),"rb");