Kmer* kmer;
vector< vector<sim> > IS; //IS[0] is the vector of IS values for each window for querySeqs[0]
+ float chimeraCutoff;
- //map of vector of maps- I know its a little convaluted but I am trying to save time
- //I think that since the window is only sliding 10 bases there is a good probability that the closest seq to each fragment
- //will be the same for several windows so I want to save the vector of maps containing its kmer info rather than regenerating it.
- //So...
- map<string, vector< map<int, int> > > seqKmerInfo; // outer map - sequence name -> kmer info
- // kmer info: inner vector of maps - each entry in the vector is a map of the kmers up to that spot in the unaligned seq
- //example: seqKmerInfo["ecoli"][50] = map containing the kmers found in the first 50 + kmersize characters of ecoli.
- //i chose to store the kmers numbers in a map so you wouldn't have to check for dupilcate entries and could easily find the
- //kmers 2 seqs had in common. There may be a better way to do this thats why I am leaving so many comments...
- map<string, vector< map<int, int> > >:: iterator it;
- map<int, int>::iterator it2;
+
+ //map<string, vector< map<int, int> > >:: iterator it;
+ //map<int, int>::iterator it2;
vector<Sequence> closest; //closest[0] is the closest overall seq to querySeqs[0].
string fastafile, templateFile;
-
+ map<string, string> names;
vector<sim> findIS(int);
- int calcKmers(map<int, int>, map<int, int>);
- vector< vector<sim> > createProcessesIS(vector<Sequence*>, vector<linePair*>);
+ int calcKmers(map<int, int>, map<int, int>);
+ void getCutoff();
+ void makeSVGpic(vector<sim>, int);
+ void readName(string);
+
+ void createProcessesIS();
};