fixed catchall "clunky" names

[mothur.git] / mothur.h

diff --git a/mothur.h b/mothur.h
index bfe0692cf035a8c96a933da2ce70ced46ca98429..190254a96e4c7d7830f8405035933efda4b003ea 100644 (file)
--- 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 +119,34 @@ struct seqDist {
        seqDist(int s1, int s2, float d) : seq1(s1), seq2(s2), dist(d) {}
        ~seqDist() {}
 };
+/************************************************************/
+struct distlinePair {
+       int start;
+       int end;
+       
+};
+/***************************************************************/
+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 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 +239,15 @@ 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