added oligos class. added check orient parameter to trim.flows, sffinfo, fastq.info...

[mothur.git] / mothur.h

diff --git a/mothur.h b/mothur.h
index 67c8ab3feaf7f7a82d611e2ed4b60c44fb86e86e..b4fc3ce1c41171c0cde75a83f6365e12873984bc 100644 (file)
--- a/mothur.h
+++ b/mothur.h
@@ -210,6 +210,16 @@ struct distlinePair {
        int end;
        
 };
+/************************************************************/
+struct oligosPair {
+       string forward;
+       string reverse;
+       
+       oligosPair() { forward = ""; reverse = "";  }
+       oligosPair(string f, string r) : forward(f), reverse(r) {}
+       ~oligosPair() {}
+};
+
 /************************************************************/
 struct seqPriorityNode {
        int numIdentical;
@@ -242,7 +252,24 @@ inline bool compareIndexes(PDistCell left, PDistCell right){
 //********************************************************************************************************************
 inline bool compareSpearman(spearmanRank left, spearmanRank right){
        return (left.score < right.score);      
-} 
+}
+//********************************************************************************************************************
+inline double max(double left, double right){
+    if (left > right) { return left; }
+    else { return right; }
+}
+//********************************************************************************************************************
+inline double max(int left, double right){
+    double value = left;
+    if (left > right) { return value; }
+    else { return right; }
+}
+//********************************************************************************************************************
+inline double max(double left, int right){
+    double value = right;
+    if (left > value) { return left; }
+    else { return value; }
+}
 //********************************************************************************************************************
 //sorts highest to lowest
 inline bool compareSeqPriorityNodes(seqPriorityNode left, seqPriorityNode right){