added modify names parameter to set.dir

[mothur.git] / mothur.h

diff --git a/mothur.h b/mothur.h
index 6e5833f7032aafba146f8b92cd30bacc149ab931..98b34c31c58c88b614412be4e9ba6874ec1cbe36 100644 (file)
--- a/mothur.h
+++ b/mothur.h
@@ -42,6 +42,7 @@
 #include <cmath>
 #include <math.h>
 #include <algorithm>
+#include <numeric>
 
 //misc
 #include <cerrno>
@@ -53,10 +54,11 @@
 #endif
 /***********************************************************************/
 
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
        #include <sys/wait.h>
        #include <sys/time.h>
        #include <sys/resource.h>
+       #include <sys/types.h>
        #include <sys/stat.h>
        #include <unistd.h>
        
@@ -70,6 +72,8 @@
        #include <direct.h> //get cwd
        #include <windows.h>
        #include <psapi.h>
+       #include <direct.h>
+       #include <tchar.h>
 
 #endif
 
@@ -82,7 +86,9 @@ using namespace std;
 #define isnan(x) ((x) != (x))
 #define isinf(x) (fabs(x) == std::numeric_limits<double>::infinity())
 
+
 typedef unsigned long ull;
+typedef unsigned short intDist;
 
 struct IntNode {
        int lvalue;
@@ -102,6 +108,25 @@ struct ThreadNode {
        IntNode* right;
 };
 
+struct diffPair {
+       float   prob;
+       float   reverseProb;
+       
+       diffPair() {
+               prob = 0; reverseProb = 0;
+       }
+       diffPair(float p, float rp) {
+               prob = p;
+               reverseProb = rp;
+       }
+};
+/***********************************************************************/
+struct PDistCell{
+       ull index;
+       float dist;
+       PDistCell() :  index(0), dist(0) {};
+       PDistCell(ull c, float d) :  index(c), dist(d) {}
+};
 /************************************************************/
 struct clusterNode {
        int numSeq;
@@ -113,9 +138,9 @@ struct clusterNode {
 struct seqDist {
        int seq1;
        int seq2;
-       float dist;
+       double dist;
        seqDist() {}
-       seqDist(int s1, int s2, float d) : seq1(s1), seq2(s2), dist(d) {}
+       seqDist(int s1, int s2, double d) : seq1(s1), seq2(s2), dist(d) {}
        ~seqDist() {}
 };
 /************************************************************/
@@ -124,6 +149,15 @@ struct distlinePair {
        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;
@@ -131,16 +165,26 @@ struct spearmanRank {
        
        spearmanRank(string n, float s) : name(n), score(s) {}
 };
+//***********************************************************************
+inline bool compareIndexes(PDistCell left, PDistCell right){
+       return (left.index > right.index);      
+}
 //********************************************************************************************************************
-//sorts highest to lowest
 inline bool compareSpearman(spearmanRank left, spearmanRank right){
-       return (left.score > right.score);      
+       return (left.score < right.score);      
 } 
 //********************************************************************************************************************
-//sorts lowest to highest
-inline bool compareSpearmanReverse(spearmanRank left, spearmanRank right){
-       return (left.score < right.score);      
+//sorts highest to lowest
+inline bool compareSeqPriorityNodes(seqPriorityNode left, seqPriorityNode right){
+       if (left.numIdentical > right.numIdentical) {
+        return true;
+    }else if (left.numIdentical == right.numIdentical) {
+        if (left.seq > right.seq) { return true; }
+        else { return false; }
+    }
+    return false;      
 } 
+ 
 /************************************************************/
 //sorts lowest to highest
 inline bool compareDistLinePairs(distlinePair left, distlinePair right){
@@ -171,7 +215,8 @@ void convert(const string& s, T& x, bool failIfLeftoverChars = true){
                        throw BadConversion(s);
        
 }
-
+//**********************************************************************************************************************
+template <typename T> int sgn(T val){ return (val > T(0)) - (val < T(0)); }
 //**********************************************************************************************************************
 
 template<typename T>
@@ -238,5 +283,15 @@ 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