| addToKISTable(vector< lightKIS< GENOME_TYPE > > &add, vector< lightKIS< GENOME_TYPE > > &kisTable) const | PREPRO< GENOME_TYPE > | |
| checkStitchedHits(vector< lightKIS< GENOME_TYPE > > &res) const | PREPRO< GENOME_TYPE > | [private] |
| extractBP(vector< vector< lightKIS< GENOME_TYPE > > * > &res) | PREPRO< GENOME_TYPE > | |
| extractBPCoords(vector< lightKIS< GENOME_TYPE > > &res) | PREPRO< GENOME_TYPE > | |
| extractGaps(string *results, vector< KIS< GENOME_TYPE > > &kisses) const | PREPRO< GENOME_TYPE > | |
| extractGapsFromHits(string *results, vector< lightKIS< GENOME_TYPE > > &hits) const | PREPRO< GENOME_TYPE > | |
| fileName1 | PREPRO< GENOME_TYPE > | [private] |
| fileName2 | PREPRO< GENOME_TYPE > | [private] |
| gAlign(vector< KIS< GENOME_TYPE > > &kisses, long &len) | PREPRO< GENOME_TYPE > | |
| GAOnStitchedHits(vector< lightKIS< GENOME_TYPE > > &stitchedHits) const | PREPRO< GENOME_TYPE > | |
| genome1 | PREPRO< GENOME_TYPE > | [private] |
| genome2 | PREPRO< GENOME_TYPE > | [private] |
| getGene(FILE *f, string &buff) | PREPRO< GENOME_TYPE > | [private] |
| getGenome(string &buff, int whichOne) const | PREPRO< GENOME_TYPE > | |
| labelIt(GENOME_TYPE i, long count, string name) const | PREPRO< GENOME_TYPE > | [private] |
| lAlign(string &chunks, int whichOne) const | PREPRO< GENOME_TYPE > | |
| PREPRO(string &f1, string &f2) | PREPRO< GENOME_TYPE > | [inline] |
| print(vector< lightKIS< GENOME_TYPE > > &vec) const | PREPRO< GENOME_TYPE > | |
| printToFile(vector< lightKIS< GENOME_TYPE > > &vec, string fileName) const | PREPRO< GENOME_TYPE > | |
| refineGapTable(long **gaps, long **gaps1, long **gaps2, long &len, string &seq1, string &seq2) const | PREPRO< GENOME_TYPE > | [private] |
| refineHitTable(vector< lightKIS< GENOME_TYPE > > &hits, long **gaps1, long **gaps2, long len, unsigned int i, vector< lightKIS< GENOME_TYPE > > &newhit) const | PREPRO< GENOME_TYPE > | [private] |
| refineKISTable(vector< KIS< GENOME_TYPE > > &kisses, long **gaps1, long **gaps2, long len, unsigned int i, vector< lightKIS< GENOME_TYPE > > &newkis) const | PREPRO< GENOME_TYPE > | [private] |
| stitch(vector< lightKIS< GENOME_TYPE > > &res) const | PREPRO< GENOME_TYPE > | [private] |
| stitchHits(vector< lightKIS< GENOME_TYPE > > &res) const | PREPRO< GENOME_TYPE > | |
| toString(unsigned long num, string &result) const | PREPRO< GENOME_TYPE > | |
| transformSeq(char *arr) const | PREPRO< GENOME_TYPE > | [private] |
| unionHits(lightKIS< GENOME_TYPE > &elm1, lightKIS< GENOME_TYPE > &elm2) const | PREPRO< GENOME_TYPE > | [private] |
