| bandExtension_ | MatchAligner | [protected] |
| codonize(const char *pSeq, int seqSize, int finalFrame, vector< vector< char > > &translatedSeqs) | MatchAlignerTranslated | |
| createAlignment(Alignment &alignment, const char *pQuery, int queryStart, int queryEnd, const char *pSubject, int subjectStart, int subjectEnd) | MatchAlignerTranslated | [virtual] |
| formatAlignment(Alignment &alignment, const char *pQuery, int queryStart, int queryEnd, const char *pSubject, int subjectStart, int subjectEnd) | MatchAlignerTranslatedProtein | [virtual] |
| getCodon(const char *pChar) | MatchAlignerTranslated | [inline, static] |
| isQueryProtein_ | MatchAlignerTranslated | [protected] |
| isSubjectProtein_ | MatchAlignerTranslated | [protected] |
| MatchAligner(int numCols, int bandExtension, ScoreTable *pTable, ostream &outputStream) | MatchAligner | |
| MatchAlignerTranslated(int numCols, int bandExtension, bool isQueryProtein, bool isSubjectProtein, ostream &outputStream) | MatchAlignerTranslated | |
| MatchAlignerTranslatedProtein(int isQueryProtein=true, int numCols=80, int bandExtension=0, ostream &outputStream=cout) | MatchAlignerTranslatedProtein | |
| 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] |
