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

[mothur.git] / chimera.h

diff --git a/chimera.h b/chimera.h
index e0e8944c6935afa6441b16c052b89b1fe2a51994..da908ce07571a54148f561e28c16b94e8b09f68b 100644 (file)
--- a/chimera.h
+++ b/chimera.h
@@ -12,11 +12,75 @@
 
 
 #include "mothur.h"
-#include "sparsematrix.hpp"
+#include "sequence.hpp"
 
-typedef list<PCell>::iterator MatData;
-typedef map<int, float> SeqMap;  //maps sequence to all distance for that seqeunce
+/***********************************************************************/
+struct Preference {
+               string name;
+               vector<string> leftParent; //keep the name of closest left associated with the two scores
+               vector<string> rightParent; //keep the name of closest right associated with the two scores
+               vector<float> score;  //so you can keep last score and calc this score and keep whichever is bigger.
+               vector<float> closestLeft;  //keep the closest left associated with the two scores
+               vector<float> closestRight; //keep the closest right associated with the two scores
+               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){
+       return (left.dist < right.dist);        
+} 
+//********************************************************************************************************************
+
+struct sim {
+               string leftParent;
+               string rightParent; 
+               float score;  
+               int midpoint;
+};
+
+struct linePair {
+                       int start;
+                       int end;
+                       linePair(int i, int j) : start(i), end(j) {}
+                       linePair(){}
+};
 
 /***********************************************************************/
 
@@ -26,27 +90,54 @@ class Chimera {
        
                Chimera(){};
                Chimera(string);
+               Chimera(string, bool, string);
                Chimera(string, string);
                virtual ~Chimera(){};
-               virtual void setFilter(bool f)                  {       filter = f;                     }
+               virtual void setFilter(bool f)                  {       filter = f;                     }
                virtual void setCorrection(bool c)              {       correction = c;         }
                virtual void setProcessors(int p)               {       processors = p;         }
                virtual void setWindow(int w)                   {       window = w;                     }
                virtual void setIncrement(int i)                {       increment = i;          }
+               virtual void setNumWanted(int n)                {       numWanted = n;          }
+               virtual void setKmerSize(int k)                 {       kmerSize = k;           }
+               virtual void setSVG(int s)                              {       svg = s;                        }
+               virtual void setName(string n)                  {       name = n;                       }
+               virtual void setMatch(int m)                    {       match = m;                      }
+               virtual void setMisMatch(int m)                 {       misMatch = m;           }
+               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 setCons(string){};
+               virtual void setQuantiles(string){};
+               virtual void doPrep(){};
+               virtual vector<Sequence*> readSeqs(string);
+               virtual vector< vector<float> > readQuantiles();
+               virtual void setMask(string);
+               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;
-               int processors, window, increment;
-                       
-
+               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, outputDir, templateFileName;
+               Sequence* getSequence(string);  //find sequence from name       
 };
 
 /***********************************************************************/