X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=mothur.h;h=53074eb1e146f28af23a87e6888d57bfaa5184fa;hb=d945488119ad368b180537f36ed40298ff170f39;hp=bfe0692cf035a8c96a933da2ce70ced46ca98429;hpb=260ae19c36cb11a53ddc5a75b5e507f8dd8b31d6;p=mothur.git

diff --git a/mothur.h b/mothur.h
index bfe0692..53074eb 100644
--- a/mothur.h
+++ b/mothur.h
@@ -36,6 +36,7 @@
 #include <map>
 #include <string>
 #include <list>
+#include <string.h>
 
 //math
 #include <cmath>
@@ -56,6 +57,8 @@
 	#include <sys/wait.h>
 	#include <sys/time.h>
 	#include <sys/resource.h>
+	#include <sys/types.h>
+	#include <sys/stat.h>
 	#include <unistd.h>
 	
 	#ifdef USE_READLINE
@@ -68,7 +71,7 @@
 	#include <direct.h> //get cwd
 	#include <windows.h>
 	#include <psapi.h>
-
+	#include <direct.h>
 #endif
 
 using namespace std;
@@ -116,6 +119,48 @@ struct seqDist {
 	seqDist(int s1, int s2, float d) : seq1(s1), seq2(s2), dist(d) {}
 	~seqDist() {}
 };
+/************************************************************/
+struct distlinePair {
+	int start;
+	int end;
+	
+};
+/************************************************************/
+struct seqPriorityNode {
+	int numIdentical;
+	string seq;
+	string name;
+	seqPriorityNode() {}
+	seqPriorityNode(int n, string s, string nm) : numIdentical(n), seq(s), name(nm) {}
+	~seqPriorityNode() {}
+};
+/***************************************************************/
+struct spearmanRank {
+	string name;
+	float score;
+	
+	spearmanRank(string n, float s) : name(n), score(s) {}
+};
+//********************************************************************************************************************
+//sorts highest to lowest
+inline bool compareSpearman(spearmanRank left, spearmanRank right){
+	return (left.score > right.score);	
+} 
+//********************************************************************************************************************
+//sorts highest to lowest
+inline bool compareSeqPriorityNodes(seqPriorityNode left, seqPriorityNode right){
+	return (left.numIdentical > right.numIdentical);	
+} 
+//********************************************************************************************************************
+//sorts lowest to highest
+inline bool compareSpearmanReverse(spearmanRank left, spearmanRank right){
+	return (left.score < right.score);	
+} 
+/************************************************************/
+//sorts lowest to highest
+inline bool compareDistLinePairs(distlinePair left, distlinePair right){
+	return (left.end < right.end);	
+} 
 //********************************************************************************************************************
 //sorts lowest to highest
 inline bool compareSequenceDistance(seqDist left, seqDist right){
@@ -208,5 +253,15 @@ string toString(const T&x, int i){
 }
 //**********************************************************************************************************************
 
+template<class T>
+T fromString(const string& s){
+	istringstream stream (s);
+	T t;
+	stream >> t;
+	return t;
+}
+
+//**********************************************************************************************************************
+
 #endif