added warning about merging with something above cutoff to cluster. working on chimeras

[mothur.git] / chimera.h

diff --git a/chimera.h b/chimera.h
index a968a02fa61cb06d7bef2d92386db5d55cf020f3..f893d63ed9c57e7d53d84843cb3b647cc9dd89d6 100644 (file)
--- a/chimera.h
+++ b/chimera.h
@@ -45,28 +45,18 @@ struct results {
        int nastRegionStart;
        int nastRegionEnd;
        string parent;
+       string parentAligned;
        float queryToParent;
        float queryToParentLocal;
        float divR;
 };
 /***********************************************************************/
-struct rank {
-               int num;
-               float score;
-               rank(int n, float s) : num(n), score(s) {}
-};
-/***********************************************************************/
-
 struct SeqDist {
        Sequence* seq;
        float dist;
+       int index;
 };
 //********************************************************************************************************************
-//sorts highest to lowest
-inline bool compareMembers(rank left, rank right){
-       return (left.score > right.score);      
-} 
-//********************************************************************************************************************
 //sorts lowest to highest
 inline bool compareRegionStart(results left, results right){
        return (left.nastRegionStart < right.nastRegionStart);  
@@ -100,6 +90,7 @@ class Chimera {
        
                Chimera(){};
                Chimera(string);
+               Chimera(string, bool, string);
                Chimera(string, string);
                virtual ~Chimera(){};
                virtual void setFilter(bool f)                  {       filter = f;                     }
@@ -123,6 +114,7 @@ class Chimera {
                virtual void setTemplateSeqs(vector<Sequence*> t)       {       templateSeqs = t;       }
                virtual bool getUnaligned()                             {       return unaligned;                       }
                virtual void setTemplateFile(string t)  {   templateFileName = t;       }
+               virtual int getLength()                                 {   return length;      }
                
                virtual void setCons(string){};
                virtual void setQuantiles(string){};
@@ -130,20 +122,20 @@ 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; }
                virtual int getChimeras(){ return 0; }
-               virtual void print(ostream&){}; 
+               virtual void print(ostream&, ostream&){};       
                
                
        protected:
                
                vector<Sequence*> templateSeqs;
                bool filter, correction, svg, unaligned;
-               int processors, window, increment, numWanted, kmerSize, match, misMatch, minSim, minCov, minBS, minSNP, parents, iters;
+               int processors, window, increment, numWanted, kmerSize, match, misMatch, minSim, minCov, minBS, minSNP, parents, iters, length;
                float divR;
                string seqMask, quanfile, filterString, name, outputDir, templateFileName;
                Sequence* getSequence(string);  //find sequence from name