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/////////////////////////////////////////////////////////////////////////////
// File: gnTranslator.h
// Purpose: Filter for all Sequences
// Description: translates, converts sequence
// Changes:
// Version: libGenome 0.5.1
// Author: Aaron Darling
// Modified by:
// Copyright: (c) Aaron Darling
// Licenses: See COPYING file for details
/////////////////////////////////////////////////////////////////////////////
#ifdef HAVE_CONFIG_H
#include "config.h"
#endif
#include "libGenome/gnTranslator.h"
#include "libGenome/gnCompare.h"
#include <string>
using namespace std;
using namespace std;
namespace genome {
// static data access, avoids static initialization order fiasco
const gnTranslator *gnTranslator::ProteinDNATranslator(){
const static gnTranslator* t_trans = new gnTranslator(ProteinDNATranslatorType);
return t_trans;
}
const gnTranslator *gnTranslator::ProteinRNATranslator(){
const static gnTranslator* t_trans = new gnTranslator(ProteinRNATranslatorType);
return t_trans;
}
const gnTranslator *gnTranslator::DNAProteinTranslator(){
const static gnTranslator* t_trans = new gnTranslator(DNAProteinTranslatorType);
return t_trans;
}
const gnTranslator *gnTranslator::RNAProteinTranslator(){
const static gnTranslator* t_trans = new gnTranslator(RNAProteinTranslatorType);
return t_trans;
}
// public:
gnTranslator::gnTranslator()
{
use_default = false;
m_defaultChar = 0;
m_defaultInputWidth = 1;
}
gnTranslator::gnTranslator( const gnTranslator &sf )
{
m_name = sf.m_name;
use_default = sf.use_default;
m_defaultChar = sf.m_defaultChar;
compare = sf.compare;
m_inputTable = sf.m_inputTable;
m_outputTable = sf.m_outputTable;
m_defaultInputWidth = sf.m_defaultInputWidth;
}
gnTranslator::gnTranslator( gnTranslatorType t_type )
{
use_default = false;
m_defaultChar = 0;
switch(t_type){
case ProteinDNATranslatorType:
CreateProteinDNATranslator();
break;
case ProteinRNATranslatorType:
CreateProteinRNATranslator();
break;
case DNAProteinTranslatorType:
CreateDNAProteinTranslator();
break;
case RNAProteinTranslatorType:
CreateRNAProteinTranslator();
break;
}
}
// gnSeqC
gnSeqC gnTranslator::Filter( const gnSeqC ch ) const{
for(uint32 i=0; i < m_inputTable.size(); i++){
if(m_inputTable[i].length() == 1)
if(compare->Contains(m_inputTable[i][0], ch))
return m_outputTable[i][0];
}
return m_defaultChar;
}
void gnTranslator::Filter( gnSeqC** seq, gnSeqI& len ) const{
uint32 curpos = 0;
string output;
while(curpos < len){
uint32 i=0;
for(; i < m_inputTable.size(); i++){
//don't compare if there aren't enough chars
uint32 curlen = m_inputTable[i].length();
if(len - curpos < curlen)
continue;
if(compare->Contains(m_inputTable[i].data(), *seq + curpos, curlen)){
output += m_outputTable[i];
curpos += curlen;
break;
}
}
if(i == m_inputTable.size()){
//no match was found.
if(use_default) //fill with the default char?
output += m_defaultChar;
curpos += m_defaultInputWidth;
}
}
if(output.length() > len){
delete[] *seq;
*seq = new gnSeqC[output.length()];
}
len = output.length();
memcpy(*seq, output.data(), len);
}
// string
void gnTranslator::Filter( string &seq ) const{
uint32 curpos = 0;
uint32 len = seq.length();
string output;
while(curpos < len){
uint32 i=0;
for(; i < m_inputTable.size(); i++){
//don't compare if there aren't enough chars
uint32 curlen = m_inputTable[i].length();
if(len - curpos < curlen)
continue;
if(compare->Contains(m_inputTable[i], seq.substr(curpos, curlen))){
output += m_outputTable[i];
curpos += curlen;
break;
}
}
if(i == m_inputTable.size()){
//no match was found.
if(use_default) //fill with the default char?
output += m_defaultChar;
curpos += m_defaultInputWidth;
}
}
seq = output;
}
// fill map
void gnTranslator::SetPair( const string& ch1, const string& ch2 )
{
if(ch1.length() == 0)
return; //cant have an empty input, empty output is ok
m_inputTable.push_back(ch1);
m_outputTable.push_back(ch2);
}
void gnTranslator::RemovePair( const string& ch )
{
for(uint32 i=0; i < m_inputTable.size(); i++){
if(m_inputTable[i] == ch){
m_inputTable.erase(m_inputTable.begin()+i);
m_outputTable.erase(m_outputTable.begin()+i);
}
}
}
// standard comparators
void gnTranslator::CreateProteinDNATranslator(){
SetName( "Protein to DNA Translator" );
SetDefaultChar('X');
SetCompare(gnCompare::ProteinSeqCompare());
m_defaultInputWidth = 1;
SetPair( "F", "TTY" );
SetPair( "L", "YTX" ); //fix this somehow. how?
SetPair( "I", "ATH" );
SetPair( "M", "ATG" );
SetPair( "V", "GTX" );
SetPair( "P", "CCX" );
SetPair( "T", "ACX" );
SetPair( "A", "GCX" );
SetPair( "Y", "TAY" );
SetPair( ".", "TRR" );//fix this somehow. how?
SetPair( "H", "CAY" );
SetPair( "Q", "CAR" );
SetPair( "N", "AAY" );
SetPair( "K", "AAR" );
SetPair( "D", "GAY" );
SetPair( "E", "GAR" );
SetPair( "C", "TGY" );
SetPair( "W", "TGG" );
SetPair( "G", "GGX" );
SetPair( "S", "TCX" );
SetPair( "S", "AGY");
SetPair( "R", "CGX");
SetPair( "R", "AGR");
}
void gnTranslator::CreateProteinRNATranslator(){
SetName( "Protein to RNA Translator" );
SetDefaultChar('X');
SetCompare(gnCompare::ProteinSeqCompare());
m_defaultInputWidth = 1;
SetPair( "F", "UUY" );
SetPair( "L", "YUX" ); //fix this somehow. how?
SetPair( "I", "AUH" );
SetPair( "M", "AUG" );
SetPair( "V", "GUX" );
SetPair( "P", "CCX" );
SetPair( "U", "ACX" );
SetPair( "A", "GCX" );
SetPair( "Y", "UAY" );
SetPair( ".", "URR" );//fix this somehow. how?
SetPair( "H", "CAY" );
SetPair( "Q", "CAR" );
SetPair( "N", "AAY" );
SetPair( "K", "AAR" );
SetPair( "D", "GAY" );
SetPair( "E", "GAR" );
SetPair( "C", "UGY" );
SetPair( "W", "UGG" );
SetPair( "G", "GGX" );
SetPair( "S", "UCX" );
SetPair( "S", "AGY");
SetPair( "R", "CGX");
SetPair( "R", "AGR");
}
void gnTranslator::CreateDNAProteinTranslator(){
SetName( "DNA to Protein Translator" );
SetDefaultChar('X');
SetCompare(gnCompare::DNASeqCompare());
m_defaultInputWidth = 3;
use_default = true;
SetPair( "TTY", "F" );
SetPair( "CTX", "L" );
SetPair( "TTR", "L" );
SetPair( "ATH", "I" );
SetPair( "ATG", "M" );
SetPair( "GTX", "V" );
SetPair( "CCX", "P" );
SetPair( "ACX", "T" );
SetPair( "GCX", "A" );
SetPair( "TAY", "Y" );
SetPair( "TGG", "W" );
SetPair( "TGA", "." );
SetPair( "TAR", "." );
SetPair( "CAY", "H" );
SetPair( "CAR", "Q" );
SetPair( "AAY", "N" );
SetPair( "AAR", "K" );
SetPair( "GAY", "D" );
SetPair( "GAR", "E" );
SetPair( "TGY", "C" );
SetPair( "GGX", "G" );
SetPair( "TCX", "S" );
SetPair( "AGY", "S" );
SetPair( "CGX", "R" );
SetPair( "AGR", "R" );
SetPair( "tty", "F" );
SetPair( "ctx", "L" );
SetPair( "ttr", "L" );
SetPair( "ath", "I" );
SetPair( "atg", "M" );
SetPair( "gtx", "V" );
SetPair( "ccx", "P" );
SetPair( "acx", "T" );
SetPair( "gcx", "A" );
SetPair( "tay", "Y" );
SetPair( "tgg", "W" );
SetPair( "tga", "." );
SetPair( "tar", "." );
SetPair( "cay", "H" );
SetPair( "car", "Q" );
SetPair( "aay", "N" );
SetPair( "aar", "K" );
SetPair( "gay", "D" );
SetPair( "gar", "E" );
SetPair( "tgy", "C" );
SetPair( "ggx", "G" );
SetPair( "tcx", "S" );
SetPair( "agy", "S" );
SetPair( "cgx", "R" );
SetPair( "agr", "R" );
}
void gnTranslator::CreateRNAProteinTranslator(){
SetName( "RNA to Protein Translator" );
SetDefaultChar('X');
SetCompare(gnCompare::RNASeqCompare());
m_defaultInputWidth = 3;
use_default = true;
SetPair( "UUY", "F" );
SetPair( "CUX", "L" );
SetPair( "UUR", "L" );
SetPair( "AUH", "I" );
SetPair( "AUG", "M" );
SetPair( "GUX", "V" );
SetPair( "CCX", "P" );
SetPair( "ACX", "T" );
SetPair( "GCX", "A" );
SetPair( "UAY", "Y" );
SetPair( "UGG", "W" );
SetPair( "UGA", "." );
SetPair( "UAR", "." );
SetPair( "CAY", "H" );
SetPair( "CAR", "Q" );
SetPair( "AAY", "N" );
SetPair( "AAR", "K" );
SetPair( "GAY", "D" );
SetPair( "GAR", "E" );
SetPair( "UGY", "C" );
SetPair( "GGX", "G" );
SetPair( "UCX", "S" );
SetPair( "AGY", "S" );
SetPair( "CGX", "R" );
SetPair( "AGR", "R" );
SetPair( "uuy", "F" );
SetPair( "cux", "L" );
SetPair( "uur", "L" );
SetPair( "auh", "I" );
SetPair( "aug", "M" );
SetPair( "gux", "V" );
SetPair( "ccx", "P" );
SetPair( "acx", "T" );
SetPair( "gcx", "A" );
SetPair( "uay", "Y" );
SetPair( "ugg", "W" );
SetPair( "uga", "." );
SetPair( "uar", "." );
SetPair( "cay", "H" );
SetPair( "car", "Q" );
SetPair( "aay", "N" );
SetPair( "aar", "K" );
SetPair( "gay", "D" );
SetPair( "gar", "E" );
SetPair( "ugy", "C" );
SetPair( "ggx", "G" );
SetPair( "ucx", "S" );
SetPair( "agy", "S" );
SetPair( "cgx", "R" );
SetPair( "agr", "R" );
}
} // end namespace genome
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