changes while testing

[mothur.git] / mothur.h

diff --git a/mothur.h b/mothur.h
index cd14056b21ba82f9d6c07e650fcf210616e7a882..32f4778a7c1ee19db25eeb4e1eafaf74fabcd617 100644 (file)
--- a/mothur.h
+++ b/mothur.h
@@ -127,6 +127,21 @@ struct PDistCell{
        PDistCell() :  index(0), dist(0) {};
        PDistCell(ull c, float d) :  index(c), dist(d) {}
 };
+/***********************************************************************/
+struct consTax{
+       string name;
+    string taxonomy;
+    int abundance;
+       consTax() :  name(""), taxonomy("unknown"), abundance(0) {};
+       consTax(string n, string t, int a) :  name(n), taxonomy(t), abundance(a) {}
+};
+/***********************************************************************/
+struct consTax2{
+    string taxonomy;
+    int abundance;
+       consTax2() :  taxonomy("unknown"), abundance(0) {};
+       consTax2(string t, int a) :  taxonomy(t), abundance(a) {}
+};
 /************************************************************/
 struct clusterNode {
        int numSeq;
@@ -158,6 +173,15 @@ struct seqPriorityNode {
        seqPriorityNode(int n, string s, string nm) : numIdentical(n), seq(s), name(nm) {}
        ~seqPriorityNode() {}
 };
+/************************************************************/
+struct compGroup {
+       string group1;
+       string group2;
+       compGroup() {}
+       compGroup(string s, string nm) : group1(s), group2(nm) {}
+    string getCombo() { return group1+"-"+group2; }
+       ~compGroup() {}
+};
 /***************************************************************/
 struct spearmanRank {
        string name;
@@ -170,7 +194,6 @@ 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);      
 } 
@@ -185,11 +208,7 @@ inline bool compareSeqPriorityNodes(seqPriorityNode left, seqPriorityNode right)
     }
     return false;      
 } 
-//********************************************************************************************************************
-//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){
@@ -199,7 +218,15 @@ inline bool compareDistLinePairs(distlinePair left, distlinePair right){
 //sorts lowest to highest
 inline bool compareSequenceDistance(seqDist left, seqDist right){
        return (left.dist < right.dist);        
-} 
+}
+//********************************************************************************************************************
+//returns sign of double
+inline double sign(double temp){
+       //find sign
+    if (temp > 0)       { return 1.0;   }
+    else if (temp < 0)  { return -1.0;  }
+    return 0;
+}
 /***********************************************************************/
 
 // snagged from http://www.parashift.com/c++-faq-lite/misc-technical-issues.html#faq-39.2