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 |