X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=mothur.h;h=ec56c506c8c0c7654c4e436afa16222f14b1224f;hb=e7fe6dd9db877b98c362f9524c3130bbbd037200;hp=07bb971347d974066ab5449614172c5e68d4c2a6;hpb=a8f5a612bba54ceb74e17efc027d3a7f5aa93c9a;p=mothur.git

diff --git a/mothur.h b/mothur.h
index 07bb971..ec56c50 100644
--- a/mothur.h
+++ b/mothur.h
@@ -40,6 +40,15 @@ using namespace std;
 #include <cmath>
 #include <math.h>
 #include <algorithm>
+#include <ctime>
+
+#ifdef _WIN32
+	#define exp(x) (exp((double) x))
+	#define sqrt(x) (sqrt((double) x))
+	#define log10(x) (log10((double) x))
+	#define log2(x) (log10(x)/log10(2))
+#endif
+
 
 typedef unsigned long long ull;
 
@@ -51,7 +60,13 @@ struct IntNode {
 	IntNode* left;
 	IntNode* right;
 };
-	
+
+struct ThreadNode {
+	int* pid;
+	IntNode* left;
+	IntNode* right;
+};
+
 /***********************************************************************/
 
 // snagged from http://www.parashift.com/c++-faq-lite/misc-technical-issues.html#faq-39.2
@@ -139,6 +154,13 @@ inline void gobble(istream& f){
 	f.putback(d);
 	
 }
+/***********************************************************************/
+
+inline bool isTrue(string f){
+	
+	if ((f == "TRUE") || (f == "T")	|| (f == "true") || (f == "t")) {	return true;	}
+	else {	return false;  }
+}
 
 /***********************************************************************/
 
@@ -224,6 +246,7 @@ inline string getSimpleName(string longName){
 
 	return simpleName;
 }
+
 /***********************************************************************/
 
 inline int factorial(int num){
@@ -249,7 +272,7 @@ inline string getPathName(string longName){
  
 	string rootPathName = longName;
 	
-	if(longName.find_last_of("/") != longName.npos){
+	if(longName.find_last_of('/') != longName.npos){
 		int pos = longName.find_last_of('/')+1;
 		rootPathName = longName.substr(0, pos);
 	}
@@ -259,6 +282,20 @@ inline string getPathName(string longName){
 
 /***********************************************************************/
 
+inline string getExtension(string longName){
+	
+	string extension = longName;
+	
+	if(longName.find_last_of('.') != longName.npos){
+		int pos = longName.find_last_of('.');
+		extension = longName.substr(pos, longName.length());
+	}
+	
+	return extension;
+}
+
+/***********************************************************************/
+
 inline int openInputFile(string fileName, ifstream& fileHandle){
 
 	fileHandle.open(fileName.c_str());
@@ -302,6 +339,16 @@ inline int openOutputFileAppend(string fileName, ofstream& fileHandle){
 }
 
 
+/***********************************************************************/
+
+inline int getNumSeqs(ifstream& file){
+	
+	int numSeqs = count(istreambuf_iterator<char>(file),istreambuf_iterator<char>(), '>');
+	file.seekg(0);
+	return numSeqs;
+
+}
+
 /***********************************************************************/
 
 //This function parses the estimator options and puts them in a vector