| bandExtension_ | MatchAligner | [protected] |
| createAlignment(Alignment &alignment, const char *pQuery, int queryStart, int queryEnd, const char *pSubject, int subjectStart, int subjectEnd) | MatchAligner | [virtual] |
| formatAlignment(Alignment &alignment, const char *pQuery, int queryStart, int queryEnd, const char *pSubject, int subjectStart, int subjectEnd) | MatchAligner | [virtual] |
| MatchAligner(int numCols, int bandExtension, ScoreTable *pTable, ostream &outputStream) | MatchAligner | |
| matchChar(const char a, const char b) | MatchAligner | [inline] |
| numCols_ | MatchAligner | [protected] |
| operator()(const char *pQuery, int queryStart, int queryEnd, const char *pSubject, int subjectStart, int subjectEnd) | MatchAligner | |
| outputAlignmentColumn(const char queryChar, const char AlignChar, const char subjectChar, int queryNext, int subjectNext) | MatchAligner | |
| outputAlignmentLine(void) | MatchAligner | |
| outputStream_ | MatchAligner | [protected] |
| pBufAlign_ | MatchAligner | [protected] |
| pBufSeq1_ | MatchAligner | [protected] |
| pBufSeq2_ | MatchAligner | [protected] |
| pCursorAlign_ | MatchAligner | [protected] |
| pCursorSeq1_ | MatchAligner | [protected] |
| pCursorSeq2_ | MatchAligner | [protected] |
| pTable_ | MatchAligner | [protected] |
| tableBlosum62_ | MatchAligner | [protected, static] |
| tableDNA_ | MatchAligner | [protected, static] |
| ~MatchAligner() | MatchAligner | [virtual] |
