trim.seqs fix

[mothur.git] / mothur.h

diff --git a/mothur.h b/mothur.h
index b0ad51e6736159e738d83d08a418f6cdecaac767..190254a96e4c7d7830f8405035933efda4b003ea 100644 (file)
--- a/mothur.h
+++ b/mothur.h
@@ -57,6 +57,7 @@
        #include <sys/wait.h>
        #include <sys/time.h>
        #include <sys/resource.h>
+       #include <sys/types.h>
        #include <sys/stat.h>
        #include <unistd.h>
        
@@ -70,7 +71,7 @@
        #include <direct.h> //get cwd
        #include <windows.h>
        #include <psapi.h>
-
+       #include <direct.h>
 #endif
 
 using namespace std;
@@ -124,6 +125,23 @@ struct distlinePair {
        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){
@@ -221,5 +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