fixed catchall PATH variable bug added trimera to chimera.slayer

[mothur.git] / slayer.h

diff --git a/slayer.h b/slayer.h
index 33ccc3fda70ad9e6dca595eb626c0bb9e5dedc1c..875e4a9d93c044339abfb71b8b3d0b009be0995a 100644 (file)
--- a/slayer.h
+++ b/slayer.h
@@ -11,46 +11,11 @@
 
  
 #include "sequence.hpp"
+#include "chimera.h"
 
 /***********************************************************************/
 //This class was modeled after the chimeraSlayer written by the Broad Institute
 /***********************************************************************/
-struct data_struct { //this is crazy big...but follow original.
-       float divr_qla_qrb;
-       float divr_qlb_qra;
-       float qla_qrb;
-       float qlb_qra;
-       float qla;
-       float qrb;
-       float ab; 
-       float qa;
-       float qb; 
-       float lab; 
-       float rab; 
-       float qra; 
-       float qlb; 
-       int winLStart;
-       int winLEnd; 
-       int winRStart; 
-       int winREnd; 
-       Sequence querySeq; 
-       Sequence parentA;
-       Sequence parentB;
-       float bsa;
-       float bsb;
-       float bsMax;
-       float chimeraMax;
-       
-};
-/***********************************************************************/
-//sorts lowest to highest first by bsMax, then if tie by chimeraMax
-inline bool compareDataStruct(data_struct left, data_struct right){
-       if (left.bsMax < right.bsMax) { return true; }
-       else if (left.bsMax == right.bsMax) {
-               return (left.chimeraMax < right.chimeraMax);
-       }else { return false;   }
-} 
-/***********************************************************************/
 struct snps { 
        char queryChar;
        char parentAChar;