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

[mothur.git] / chimera.h

diff --git a/chimera.h b/chimera.h
index 33e514b0f05d424740f2a660066e1ace6d99d40d..da908ce07571a54148f561e28c16b94e8b09f68b 100644 (file)
--- a/chimera.h
+++ b/chimera.h
@@ -14,7 +14,7 @@
 #include "mothur.h"
 #include "sequence.hpp"
 
-
+/***********************************************************************/
 struct Preference {
                string name;
                vector<string> leftParent; //keep the name of closest left associated with the two scores
@@ -25,12 +25,42 @@ struct Preference {
                int midpoint;
 
 };
-
+/***********************************************************************/
+struct score_struct {
+       int prev;
+       int score;
+       int row;
+       int col;
+};
+/***********************************************************************/
+struct trace_struct {
+       int col;
+       int oldCol;
+       int row;
+};
+/***********************************************************************/
+struct results {
+       int regionStart;
+       int regionEnd;
+       int nastRegionStart;
+       int nastRegionEnd;
+       string parent;
+       string parentAligned;
+       float queryToParent;
+       float queryToParentLocal;
+       float divR;
+};
+/***********************************************************************/
 struct SeqDist {
        Sequence* seq;
        float dist;
+       int index;
 };
-
+//********************************************************************************************************************
+//sorts lowest to highest
+inline bool compareRegionStart(results left, results right){
+       return (left.nastRegionStart < right.nastRegionStart);  
+} 
 //********************************************************************************************************************
 //sorts lowest to highest
 inline bool compareSeqDist(SeqDist left, SeqDist right){
@@ -60,6 +90,7 @@ class Chimera {
        
                Chimera(){};
                Chimera(string);
+               Chimera(string, bool, string);
                Chimera(string, string);
                virtual ~Chimera(){};
                virtual void setFilter(bool f)                  {       filter = f;                     }
@@ -76,30 +107,37 @@ class Chimera {
                virtual void setDivR(float d)                   {       divR = d;                       }
                virtual void setParents(int p)                  {       parents = p;            }
                virtual void setMinSim(int s)                   {       minSim = s;                     }
+               virtual void setMinCoverage(int c)              {       minCov = c;                     }
+               virtual void setMinBS(int b)                    {       minBS = b;                      }
+               virtual void setMinSNP(int s)                   {       minSNP = s;                     }
                virtual void setIters(int i)                    {       iters = i;                      }
-
+               virtual void setTemplateSeqs(vector<Sequence*> t)       {       templateSeqs = t;       }
+               virtual bool getUnaligned()                             {       return unaligned;                       }
+               virtual void setTemplateFile(string t)  {   templateFileName = t;       }
                
                virtual void setCons(string){};
                virtual void setQuantiles(string){};
+               virtual void doPrep(){};
                virtual vector<Sequence*> readSeqs(string);
                virtual vector< vector<float> > readQuantiles();
                virtual void setMask(string);
-               virtual void runFilter(vector<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&){}; 
                
-               //pure functions
-               virtual void getChimeras() = 0; 
-               virtual void print(ostream&) = 0;       
                
        protected:
                
-               bool filter, correction, svg;
-               int processors, window, increment, numWanted, kmerSize, match, misMatch, minSim, parents, iters;
+               vector<Sequence*> templateSeqs;
+               bool filter, correction, svg, unaligned;
+               int processors, window, increment, numWanted, kmerSize, match, misMatch, minSim, minCov, minBS, minSNP, parents, iters;
                float divR;
-               string seqMask, quanfile, filterString, name;
-                       
-
+               string seqMask, quanfile, filterString, name, outputDir, templateFileName;
+               Sequence* getSequence(string);  //find sequence from name       
 };
 
 /***********************************************************************/