chimeras, fix to sabundvector and sharedsabundvector that caused getRabundVector...

[mothur.git] / chimera.h

diff --git a/chimera.h b/chimera.h
index 41615733392988ceacec5531b908349157804ce5..da908ce07571a54148f561e28c16b94e8b09f68b 100644 (file)
--- a/chimera.h
+++ b/chimera.h
@@ -45,6 +45,7 @@ struct results {
        int nastRegionStart;
        int nastRegionEnd;
        string parent;
+       string parentAligned;
        float queryToParent;
        float queryToParentLocal;
        float divR;
@@ -53,6 +54,7 @@ struct results {
 struct SeqDist {
        Sequence* seq;
        float dist;
+       int index;
 };
 //********************************************************************************************************************
 //sorts lowest to highest
@@ -88,7 +90,7 @@ class Chimera {
        
                Chimera(){};
                Chimera(string);
-               Chimera(string, bool);
+               Chimera(string, bool, string);
                Chimera(string, string);
                virtual ~Chimera(){};
                virtual void setFilter(bool f)                  {       filter = f;                     }
@@ -119,8 +121,8 @@ class Chimera {
                virtual vector<Sequence*> readSeqs(string);
                virtual vector< vector<float> > readQuantiles();
                virtual void setMask(string);
-               virtual void runFilter(Sequence*);
-               virtual void createFilter(vector<Sequence*>);
+               virtual map<int, int> runFilter(Sequence*);
+               virtual string createFilter(vector<Sequence*>, float);
                
                virtual void printHeader(ostream&){};
                virtual int getChimeras(Sequence*){ return 0; }