concatenates Proteins given as FASTAEntry to one big string separated by a unique character (by default $) More...
#include <OpenMS/DATASTRUCTURES/BigString.h>
Public Types | |
| typedef std::pair< String, String > | FASTAEntry |
Public Member Functions | |
| BigString () | |
| constructor More... | |
| BigString (const BigString &bs) | |
| copy constructor More... | |
| virtual | ~BigString () |
| desctructor More... | |
| void | add (FASTAEntry const &new_entry) |
| add new string to bigString More... | |
| void | setSeparator (const char sep) |
| setter for separator character by default $ More... | |
| char | getSeparator () |
| getter for separator character More... | |
| Size | size () |
| returns the number of strings More... | |
| Size | length () |
| length of bigString More... | |
| void | getPeptide (FASTAEntry &entry, Size start, Size length) |
| getPeptide from start position with given length this includes FASTAHeader More... | |
| const String & | getBigString () const |
| returns bigString More... | |
Protected Member Functions | |
| Size | getIndex_ (Size index, Size start, Size end) |
| private function to implement binary search More... | |
| Size | getIndex_ (Size index) |
| retrieves index of inserted protein by bigStringPosition More... | |
Protected Attributes | |
| String | big_string_ |
| concatenated String More... | |
| char | separator_ |
| separator sign More... | |
| Size | count_ |
| number of Strings added to big_string More... | |
| Size | len_ |
| length of the big_string More... | |
| std::vector< Size > | sep_indices_ |
| indices of separators More... | |
| std::vector< String > | FASTA_header_ |
| vector with headers of FASTAEntry More... | |
concatenates Proteins given as FASTAEntry to one big string separated by a unique character (by default $)
Concatenates the strings given as FASTAEntry separating them with a unique character and storing the headers of FASTAEntry as well as the position of separator characters. So a substring can be accessed easily and the corresponding header can be found fast by using bineary search.
| typedef std::pair<String, String> FASTAEntry |
| BigString | ( | ) |
constructor
|
virtual |
desctructor
| void add | ( | FASTAEntry const & | new_entry | ) |
add new string to bigString
| new_entry | FASTAEntry to be added to big_string |
| const String& getBigString | ( | ) | const |
returns bigString
private function to implement binary search
| index | |
| start | start index |
| end | end inxed |
retrieves index of inserted protein by bigStringPosition
| index |
| void getPeptide | ( | FASTAEntry & | entry, |
| Size | start, | ||
| Size | length | ||
| ) |
getPeptide from start position with given length this includes FASTAHeader
| entry | contains the entry of the given range after calling |
| start | start index |
| length | length of desired substring |
| InvalidValue | if a peptide is part of two different fasta entrys |
| char getSeparator | ( | ) |
getter for separator character
| Size length | ( | ) |
length of bigString
| void setSeparator | ( | const char | sep | ) |
setter for separator character by default $
| sep | separator character |
| Size size | ( | ) |
returns the number of strings
|
protected |
number of Strings added to big_string
|
protected |
vector with headers of FASTAEntry
|
protected |
length of the big_string
|
protected |
indices of separators
|
protected |
separator sign
| OpenMS / TOPP release 1.11.1 | Documentation generated on Thu Nov 14 2013 11:19:28 using doxygen 1.8.5 |