added MPI code, broke up chimera.seqs into 5 separated commands, added parse.sff...

[mothur.git] / chimera.h

diff --git a/chimera.h b/chimera.h
index ef62b5357981272c93cd2c9869c5b507f0c1daaa..11bc435938b99d63df86958667b801f34318a63a 100644 (file)
--- a/chimera.h
+++ b/chimera.h
@@ -17,13 +17,14 @@
 /***********************************************************************/
 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
+               string leftParent; //keep the name of closest left 
+               string rightParent; //keep the name of closest 
+               float score;  //preference score
+               float closestLeft;  //keep the closest left 
+               float closestRight; //keep the closest right 
                int midpoint;
-
+               Preference() { name = ""; leftParent = ""; rightParent = ""; score = 0.0; closestLeft = 10000.0; closestRight = 10000.0; midpoint = 0;  }
+               ~Preference() {}
 };
 /***********************************************************************/
 struct score_struct {
@@ -88,38 +89,38 @@ class Chimera {
 
        public:
        
-               Chimera(){ m = MothurOut::getInstance(); }
-               Chimera(string) { m = MothurOut::getInstance(); }
-               Chimera(string, bool, string) { m = MothurOut::getInstance(); }
-               Chimera(string, string) { m = MothurOut::getInstance(); }
+               Chimera(){ m = MothurOut::getInstance(); length = 0; unaligned = false; }
+               //Chimera(string) { m = MothurOut::getInstance(); }
+               //Chimera(string, bool, string) { m = MothurOut::getInstance(); }
+               //Chimera(string, string) { m = MothurOut::getInstance(); }
                virtual ~Chimera(){     for (int i = 0; i < templateSeqs.size(); i++) { delete templateSeqs[i];  } };
-               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 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 bool getUnaligned()                             {       return unaligned;                       }
-               virtual void setTemplateFile(string t)  {   templateFileName = t;       templateSeqs = readSeqs(t);  }
+               //virtual void setTemplateFile(string t)        {   templateFileName = t;       templateSeqs = readSeqs(t);  }
                virtual int getLength()                                 {   return length;      }
                
-               virtual void setCons(string){};
-               virtual void setQuantiles(string){};
-               virtual int doPrep(){ return 0; }
+               //virtual void setCons(string){};
+               //virtual void setQuantiles(string){};
+               //virtual int doPrep(){ return 0; }
                virtual vector<Sequence*> readSeqs(string);
-               virtual vector< vector<float> > readQuantiles();
+               //virtual vector< vector<float> > readQuantiles();
                virtual void setMask(string);
                virtual map<int, int> runFilter(Sequence*);
                virtual string createFilter(vector<Sequence*>, float);
@@ -127,16 +128,20 @@ class Chimera {
                virtual void printHeader(ostream&){};
                virtual int getChimeras(Sequence*){ return 0; }
                virtual int getChimeras(){ return 0; }
-               virtual int print(ostream&, ostream&){ return 0; }
+               virtual int print(ostream&, ostream&){  return 0; }
+               
+               #ifdef USE_MPI
+               virtual int print(MPI_File&, MPI_File&){  return 0; }
+               #endif
                
                
        protected:
                
                vector<Sequence*> templateSeqs;
-               bool filter, correction, svg, unaligned;
-               int processors, window, increment, numWanted, kmerSize, match, misMatch, minSim, minCov, minBS, minSNP, parents, iters, length;
-               float divR;
-               string seqMask, quanfile, filterString, name, outputDir, templateFileName;
+               bool filter, unaligned; //  correction, svg,
+               int length; //processors, window, increment, numWanted, kmerSize, match, misMatch, minSim, minCov, minBS, minSNP, parents, iters,
+               //float divR;
+               string seqMask, filterString, outputDir, templateFileName; //quanfile, name, 
                Sequence* getSequence(string);  //find sequence from name       
                MothurOut* m;
 };