Protein Class Reference
#include <bioseq.h>
Public Member Functions | |
| Protein () | |
| Protein (const Protein &s) | |
| Protein (const string &str) | |
| Protein (const bioseq &s) | |
| Protein (const string &n, const string &s) | |
| Protein | subseq (int b, int e) const |
| ~Protein () | |
| Protein & | operator= (const Protein &p) |
| Protein & | operator= (const string &str) |
| double | relativeEntropy () const |
| double | relativeEntropyUniform () const |
| const double * | getCodeFrequence () |
| sequenceType | getSequenceType () const |
| bool | hasStart () const |
| bool | hasStop () const |
| bool | hasInternalStop () const |
| int | countInternalStops () |
Static Public Member Functions | |
| static const char * | threeLetterCode (const char A) |
| static const char * | aminoAcidFullName (const char A) |
Static Public Attributes | |
| static const int | numcodes = 27 |
| static const char * | oneLetterSymbols = "ABCDEFGHIKLMNPQRSTUVWXYZ*" |
Private Attributes | |
| double | codefreq [27] |
Static Private Attributes | |
| static const char * | symbols [] |
| static const double | aafreq [] |
Detailed Description
all protein single letter code use upper case The most recent version of amino acid code is stored in this class.Constructor & Destructor Documentation
| Protein::Protein | ( | ) | [inline] |
References codefreq.
| Protein::Protein | ( | const string & | str | ) | [inline] |
References codefreq.
| Protein::Protein | ( | const string & | n, | |
| const string & | s | |||
| ) | [inline] |
References codefreq.
| Protein::~Protein | ( | ) | [inline] |
Member Function Documentation
| Protein Protein::subseq | ( | int | b, | |
| int | e | |||
| ) | const [inline] |
performance is very bad if sequence is long. 1-based index, inclusive [b, e]
Reimplemented from bioseq.
References bioseq::subseq().
References codefreq, numcodes, and bioseq::operator=().
| Protein & Protein::operator= | ( | const string & | str | ) |
| static const char* Protein::threeLetterCode | ( | const char | A | ) | [inline, static] |
| static const char* Protein::aminoAcidFullName | ( | const char | A | ) | [inline, static] |
| double Protein::relativeEntropy | ( | ) | const |
relative to SwissProt statistics
References aafreq, bioseq::getFrequency(), and toupper().
Referenced by main().
| double Protein::relativeEntropyUniform | ( | ) | const |
References codon::getAAUniformFrequency(), bioseq::getFrequency(), and toupper().
Referenced by main().
| const double * Protein::getCodeFrequence | ( | ) |
return a pointer to the internally stored int array that is terminated by -1, all legal code for aa range from 0-26 it has one extra element than the sequence length calling this before calling encode will return the array is according the 26 letter codes Note: all letters are used.
References codefreq, bioseq::getcode(), and bioseq::length().
| sequenceType Protein::getSequenceType | ( | ) | const [inline, virtual] |
| bool Protein::hasStart | ( | ) | const [inline] |
References bioseq::seq.
| bool Protein::hasStop | ( | ) | const [inline] |
| bool Protein::hasInternalStop | ( | ) | const |
References bioseq::seq.
| int Protein::countInternalStops | ( | ) |
Member Data Documentation
const int Protein::numcodes = 27 [static] |
Referenced by operator=(), and Protein().
const char * Protein::oneLetterSymbols = "ABCDEFGHIKLMNPQRSTUVWXYZ*" [static] |
double Protein::codefreq[27] [mutable, private] |
stores the amino acid frequence as an array A in zero, B in one .... Calling computeEntropy will fill this array The first element is set to -1 to indicate that this array has not been set. Not occuring letters have frequency of zero. # 27 is the stop codon "*"
Referenced by getCodeFrequence(), operator=(), and Protein().
const char * Protein::symbols [static, private] |
Initial value:
{
"Ala", "alanine",
"Asx", "aspartic acid or asparagine",
"Cys", "cysteine",
"Asp", "aspartic acid",
"Glu", "glutamic acid",
"Phe", "phenylalanine",
"Gly", "glycine",
"His", "histidine",
"Ile", "isoleucine",
"NUL", "not defined",
"Lys", "lysine",
"Leu", "leucine",
"Met", "methionine",
"Asn", "asparagine",
"NUL", "not defined",
"Pro", "proline",
"Gln", "glutamine",
"Arg", "arginine",
"Ser", "serine",
"Thr", "threonine",
"Sec", "selenocysteine",
"Val", "valine",
"Trp", "tryptophan",
"Xaa", "unknown or 'other' amino acid",
"Tyr", "tyrosine",
"Glx", "glutamic acid or glutamine (or substances such as 4-carboxyglutamic acid and 5-oxoproline that yield glutamic acid on acid hydrolysis of peptides)",
"Stp", "stop codon"}
Referenced by aminoAcidFullName(), and threeLetterCode().
const double Protein::aafreq [static, private] |
Initial value:
{
0.0783, 0.0000, 0.0152, 0.0532, 0.0664,
0.0400, 0.0693, 0.0229, 0.0591, 0.0000,
0.0593, 0.0964, 0.0238, 0.0418, 0.0000,
0.0483, 0.0395, 0.0535, 0.0686, 0.0542,
0.0000, 0.0671, 0.0115, 0.0000, 0.0306, 0.0000}
Referenced by relativeEntropy().
The documentation for this class was generated from the following files:
- bioseq/bioseq.h
- bioseq/bioseq.cpp
