| BinarySearch(GENOME_TYPE S1, GENOME_TYPE E1, GENOME_TYPE S2, GENOME_TYPE E2, int orgNum) const | Table< GENOME_TYPE > | [private] |
| CleanDeleted() | Table< GENOME_TYPE > | |
| CleanDup() | Table< GENOME_TYPE > | |
| CleanProphages(ifstream &fd, int orgNum, double perc) | Table< GENOME_TYPE > | |
| CleanShortEntries() | Table< GENOME_TYPE > | |
| CleanTE(ifstream &fd, int orgNum, double perc) | Table< GENOME_TYPE > | |
| Clustering() | Table< GENOME_TYPE > | |
| deletedParalog1 | Table< GENOME_TYPE > | [private] |
| deletedParalog2 | Table< GENOME_TYPE > | [private] |
| deletedParalogCount1 | Table< GENOME_TYPE > | [private] |
| deletedParalogCount2 | Table< GENOME_TYPE > | [private] |
| DeleteEntry(unsigned long i) | Table< GENOME_TYPE > | [private] |
| dupPerc | Table< GENOME_TYPE > | [private] |
| entries | Table< GENOME_TYPE > | [private] |
| entryIter typedef | Table< GENOME_TYPE > | [private] |
| FillEnds(GENOME_TYPE *arr, int orgNum) const | Table< GENOME_TYPE > | [private] |
| FilterSet(set< Entry< GENOME_TYPE >, compare_entries_1< GENOME_TYPE > > &s, unsigned long j, int org, bool flag, bool sign=false) | Table< GENOME_TYPE > | [private] |
| firstCircOrg1 | Table< GENOME_TYPE > | [private] |
| firstCircOrg2 | Table< GENOME_TYPE > | [private] |
| GetDupGroup(unsigned long entry, int orgNum, GENOME_TYPE *endArr) | Table< GENOME_TYPE > | [private] |
| GetLength(GENOME_TYPE S, GENOME_TYPE E, int orgNum) const | Table< GENOME_TYPE > | [private] |
| InersecLen(GENOME_TYPE S, GENOME_TYPE E, GENOME_TYPE tmpS, GENOME_TYPE tmpE, int orgNum) const | Table< GENOME_TYPE > | [private] |
| InsertEntries(ifstream &fd) | Table< GENOME_TYPE > | [private] |
| Intersec(unsigned long entry, GENOME_TYPE S, GENOME_TYPE E, int orgNum) const | Table< GENOME_TYPE > | [private] |
| IsDuplication(unsigned long entry, unsigned ofEntry, int orgNum) const | Table< GENOME_TYPE > | [private] |
| IterativeRemoveOverlaps() | Table< GENOME_TYPE > | |
| Join(unsigned long *arr) | Table< GENOME_TYPE > | [private] |
| JoinForDeletedParalogs(unsigned long i, unsigned long j, int orgNum) | Table< GENOME_TYPE > | [private] |
| JoinForOverlap(unsigned long i, unsigned long j) | Table< GENOME_TYPE > | [private] |
| lastCircOrg1 | Table< GENOME_TYPE > | [private] |
| lastCircOrg2 | Table< GENOME_TYPE > | [private] |
| Loop(double orthPerc, const char *deletedParFile1, const char *deletedParFile2) | Table< GENOME_TYPE > | |
| ManipulateStartsAndEnds(GENOME_TYPE &S1, GENOME_TYPE &E1, GENOME_TYPE &S2, GENOME_TYPE &E2, int orgNum) const | Table< GENOME_TYPE > | [private] |
| minLen | Table< GENOME_TYPE > | [private] |
| numOfEntries | Table< GENOME_TYPE > | [private] |
| organism1 | Table< GENOME_TYPE > | [private] |
| organism2 | Table< GENOME_TYPE > | [private] |
| PrintDeletedParalogs(ofstream &file1, ofstream &file2) | Table< GENOME_TYPE > | [private] |
| PrintTable(ofstream &ofs, int org) | Table< GENOME_TYPE > | |
| ReadFromProbFile(ifstream &fileName, string &genumName, GENOME_TYPE &genumLen, bool &circ) | Table< GENOME_TYPE > | [private] |
| RemoveFinalConflicts() | Table< GENOME_TYPE > | |
| RemoveFinalOverlaping() | Table< GENOME_TYPE > | |
| RemoveNuisances(double orthPerc) | Table< GENOME_TYPE > | |
| RemoveOverlaps() | Table< GENOME_TYPE > | |
| RemoveParalogs(double orthPerc) | Table< GENOME_TYPE > | |
| SortBy(int org) | Table< GENOME_TYPE > | [private] |
| SwapEntries(unsigned long i, unsigned long j) | Table< GENOME_TYPE > | [private] |
| Table() | Table< GENOME_TYPE > | [inline] |
| Table(ifstream &fd, long numOfRows, long cleanMinLen, double dupPerc, ifstream &orag1DataFile, ifstream &org2DataFile) | Table< GENOME_TYPE > | |
| Table(const Table< GENOME_TYPE > &t) | Table< GENOME_TYPE > | |
| tableSize | Table< GENOME_TYPE > | [private] |
| UpDateCircInfo() | Table< GENOME_TYPE > | [private] |
| ~Table() | Table< GENOME_TYPE > | [inline] |
