class Ccode : public Chimera {
public:
- Ccode(string, string);
+ Ccode(string, string, bool, string, int, int, string); //fasta, template, filter, mask, window, numWanted, outputDir
~Ccode();
- void getChimeras();
- void print(ostream&);
-
- void setCons(string c) {}
- void setQuantiles(string q) {}
-
+ int getChimeras(Sequence* query);
+ Sequence print(ostream&, ostream&);
+ #ifdef USE_MPI
+ Sequence print(MPI_File&, MPI_File&);
+ #endif
private:
Dist* distCalc;
DeCalculator* decalc;
- int iters;
- string fastafile, templateFile;
+ int iters, window, numWanted;
+ string fastafile, mapInfo;
+ Sequence* querySeq;
- vector<linePair*> lines;
- vector<Sequence*> querySeqs;
- vector<Sequence*> templateSeqs;
- vector< map<int, int> > spotMap;
+ map<int, int> spotMap;
map<int, int>::iterator it;
- vector< vector<int> > windows; //windows[0] is the vector of window breaks for querySeqs[0]
- vector<int> windowSizes; //windowSizes[0] is the size of the windows for querySeqs[0]
- vector< map<int, int> > trim; //trim[0] is the map containing the starting and ending positions for querySeqs[0] set of seqs
- vector< vector<SeqDist> > closest; //closest[0] is a vector of sequence at are closest to queryseqs[0]...
- vector< vector<float> > averageRef; //averageRef[0] is the average distance at each window for the references for querySeqs[0]
- vector< vector<float> > averageQuery; //averageQuery[0] is the average distance at each winow for the query for querySeqs[0]
- vector< vector<float> > sumRef; //sumRef[0] is the sum of distances at each window for the references for querySeqs[0]
- vector< vector<float> > sumSquaredRef; //sumSquaredRef[0] is the sum of squared distances at each window for the references for querySeqs[0]
- vector< vector<float> > sumQuery; //sumQuery[0] is the sum of distances at each window for the comparison of query to references for querySeqs[0]
- vector< vector<float> > sumSquaredQuery; //sumSquaredQuery[0] is the sum of squared distances at each window for the comparison of query to references for querySeqs[0]
- vector< vector<float> > varRef; //varRef[0] is the variance among references seqs at each window for querySeqs[0]
- vector< vector<float> > varQuery; //varQuery[0] is the variance among references and querySeqs[0] at each window
- vector< vector<float> > sdRef; //sdRef[0] is the standard deviation of references seqs at each window for querySeqs[0]
- vector< vector<float> > sdQuery; //sdQuery[0] is the standard deviation of references and querySeqs[0] at each window
- vector< vector<float> > anova; //anova[0] is the vector of anova scores for each window for querySeqs[0]
- vector<int> refCombo; //refCombo[0] is the number of reference sequences combinations for querySeqs[0]
- vector< vector<bool> > isChimericConfidence; //isChimericConfidence[0] indicates whether querySeqs[0] is chimeric at a given window according to the confidence limits
- vector< vector<bool> > isChimericTStudent; //isChimericConfidence[0] indicates whether querySeqs[0] is chimeric at a given window according to the confidence limits
- vector< vector<bool> > isChimericANOVA; //isChimericConfidence[0] indicates whether querySeqs[0] is chimeric at a given window according to the confidence limits
+ vector<int> windows; //windows is the vector of window breaks for query
+ int windowSizes; //windowSizes is the size of the windows for query
+ map<int, int> trim; //trim is the map containing the starting and ending positions for query
+ vector<SeqDist> closest; //closest is a vector of sequence at are closest to query
+ vector<float> averageRef; //averageRef is the average distance at each window for the references for query
+ vector<float> averageQuery; //averageQuery is the average distance at each winow for the query for query
+ vector<float> sumRef; //sumRef is the sum of distances at each window for the references for query
+ vector<float> sumSquaredRef; //sumSquaredRef is the sum of squared distances at each window for the references for query
+ vector<float> sumQuery; //sumQuery is the sum of distances at each window for the comparison of query to references for query
+ vector<float> sumSquaredQuery; //sumSquaredQuery is the sum of squared distances at each window for the comparison of query to references for query
+ vector<float> varRef; //varRef is the variance among references seqs at each window for query
+ vector<float> varQuery; //varQuery is the variance among references and query at each window
+ vector<float> sdRef; //sdRef is the standard deviation of references seqs at each window for query
+ vector<float> sdQuery; //sdQuery is the standard deviation of references and query at each window
+ vector<float> anova; //anova is the vector of anova scores for each window for query
+ int refCombo; //refCombo is the number of reference sequences combinations for query
+ vector<bool> isChimericConfidence; //isChimericConfidence indicates whether query is chimeric at a given window according to the confidence limits
+ vector<bool> isChimericTStudent; //isChimericConfidence indicates whether query is chimeric at a given window according to the confidence limits
+ vector<bool> isChimericANOVA; //isChimericConfidence indicates whether query is chimeric at a given window according to the confidence limits
- vector< vector<SeqDist> > findClosest(int, int, int);
- void removeBadReferenceSeqs(vector<SeqDist>&, int); //removes sequences from closest that are to different of too similar to eachother.
- void trimSequences(int);
- vector<int> findWindows(int);
- void getAverageRef(vector<SeqDist>, int); //fills sumRef[i], averageRef[i], sumSquaredRef[i] and refCombo[i].
- void getAverageQuery (vector<SeqDist>, int); //fills sumQuery[i], averageQuery[i], sumSquaredQuery[i].
- void findVarianceRef (int); //fills varRef[i] and sdRef[i] also sets minimum error rate to 0.001 to avoid divide by 0.
- void findVarianceQuery (int); //fills varQuery[i] and sdQuery[i]
- void determineChimeras (int); //fills anova, isChimericConfidence[i], isChimericTStudent[i] and isChimericANOVA[i].
+ vector<SeqDist> findClosest(Sequence*, int);
+ void removeBadReferenceSeqs(vector<SeqDist>&); //removes sequences from closest that are to different of too similar to eachother.
+ void trimSequences(Sequence*);
+ vector<int> findWindows();
+ void getAverageRef(vector<SeqDist>); //fills sumRef, averageRef, sumSquaredRef and refCombo.
+ void getAverageQuery (vector<SeqDist>, Sequence*); //fills sumQuery, averageQuery, sumSquaredQuery.
+ void findVarianceRef (); //fills varRef and sdRef also sets minimum error rate to 0.001 to avoid divide by 0.
+ void findVarianceQuery (); //fills varQuery and sdQuery
+ void determineChimeras (); //fills anova, isChimericConfidence, isChimericTStudent and isChimericANOVA.
int getDiff(string, string); //return number of mismatched bases, a gap to base is not counted as a mismatch
float getT(int);
float getF(int);
- void createProcessesClosest();
- void createProcessesRemoveBad();
- void createProcessesAverages();
- void createProcessesVariances();
- void createProcessesDetermine();
-
+ #ifdef USE_MPI
+ int printMapping(string&);
+ MPI_File outMap;
+ #endif
+
};
/***********************************************************/
projects / mothur.git / blobdiff