#include <Cassiopee.h>
Main constructor
- Parameters
-
index_ref | Indexer for sequence |
bool CassieSearch::isequal |
( |
char |
a, |
|
|
char |
b |
|
) |
| |
Compare two chars, with ambiguity is option is set
void CassieSearch::removeDuplicates |
( |
| ) |
|
Remove matches with same position and same length.
void CassieSearch::search |
( |
string |
suffix, |
|
|
bool |
clear |
|
) |
| |
Search for a string in the indexed sequence
- Parameters
-
suffix | pattern to search |
clear | Clear existing matches? |
void CassieSearch::search |
( |
string |
suffix | ) |
|
Search for a string in the indexed sequence. Clear all previous matches.
- Parameters
-
void CassieSearch::search |
( |
string |
suffixes[] | ) |
|
Search for multiple strings
- Parameters
-
array | of patterns to search |
void CassieSearch::sort |
( |
| ) |
|
Sort matches according to positions i nascending order
bool CassieSearch::ambiguity |
Allow alphabet ambiguity search. False by default. N are by default ignored. To allow N matching, the nmax attribute must be set
Match* CassieSearch::match_limits |
Used to store max errors allowed
list<Match*> CassieSearch::matches |
List of positions in original sequence matching the search
int CassieSearch::max_indel |
Maximum number of insertion or deletion
int CassieSearch::max_subst |
Maximum number of substitution
Allow N matching with alphabet ambiguity. nmax defines the maximum number of consecutive N allowed in match.
The documentation for this class was generated from the following files: