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/////////////////////////////////////////////////////////////////////////////
// File: gnFastTranslator.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/gnFastTranslator.h"
#include <iostream>
#include <cstring>
using namespace std;
namespace genome {
// static data access, avoids static initialization order fiasco
const gnFastTranslator *gnFastTranslator::ProteinDNATranslator(){
const static gnFastTranslator* t_trans = new gnFastTranslator(ProteinDNATranslatorType);
return t_trans;
}
const gnFastTranslator *gnFastTranslator::DNAProteinTranslator(){
const static gnFastTranslator* t_trans = new gnFastTranslator(DNAProteinTranslatorType);
return t_trans;
}
// public:
gnFastTranslator::gnFastTranslator()
{
use_default = false;
m_defaultChar = 0;
}
gnFastTranslator::gnFastTranslator( const gnFastTranslator &sf )
{
m_name = sf.m_name;
use_default = sf.use_default;
m_defaultChar = sf.m_defaultChar;
m_transCache = sf.m_transCache;
}
gnFastTranslator::gnFastTranslator( gnTranslatorType t_type )
{
use_default = false;
m_defaultChar = 0;
switch(t_type){
case ProteinDNATranslatorType:
CacheTranslator(gnTranslator::ProteinDNATranslator(), "FLIMVPTAY.HQNKDECGSR", 1);
break;
case DNAProteinTranslatorType:
CacheTranslator(gnTranslator::DNAProteinTranslator(), "ACGTRYKMBVDHSWNX", 3);
break;
}
}
// gnSeqC
gnSeqC gnFastTranslator::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 gnFastTranslator::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++;
}
}
if(output.length() > len){
delete[] *seq;
*seq = new gnSeqC[output.length()];
}
len = output.length();
memcpy(*seq, output.data(), len);
*/}
// string
void gnFastTranslator::Filter( string &seq ) const{
uint32 curpos = 0, outpos = 0;
uint32 len = seq.length();
uint32 width = m_transCache.begin()->first.length();
uint32 out_width = m_transCache.begin()->second.length();
uint32 out_size = (seq.length() / width) * out_width + seq.length() % width + 1;
gnSeqC* output_array = new gnSeqC[out_size];
output_array[out_size-1] = 0;
string seq_upper;
while(curpos < len){
//transform to upper case
seq_upper = seq.substr(curpos, width);
for(uint32 i=0; i < seq_upper.size(); i++)
seq_upper[i] = toupper(seq_upper[i]);
map<string, string>::const_iterator iter = m_transCache.find(seq_upper);
if(iter == m_transCache.end()){
//no match was found.
if(use_default) //fill with the default char?
output_array[curpos] = m_defaultChar;
curpos++;
}else{
strcpy( output_array + outpos, iter->second.c_str() );
curpos += width;
outpos += out_width;
}
}
seq = output_array;
}
void gnFastTranslator::CacheTranslator(const gnTranslator* tranny, string inputs, const gnSeqI input_width){
string cur_input;
string cur_trans;
vector<gnSeqI> index;
gnSeqI cur_index = input_width;
//fill the index array with input_width 0's
for(gnSeqI curI = 0; curI < input_width; curI++)
index.push_back(0);
while(true){
//ensure the validity of our indices
cur_index = input_width - 1;
while(index[cur_index] == inputs.length()){
if(cur_index == 0){
return;
}
index[cur_index] = 0;
cur_index--;
index[cur_index]++;
continue;
}
//create a sequence to cache.
for(gnSeqI i = 0; i < input_width; i++){
cur_input += inputs[index[i]];
}
cur_trans = cur_input;
tranny->Filter(cur_trans);
m_transCache[cur_input] = cur_trans;
// m_transCache.insert(map<string, string>::value_type(cur_input, cur_trans));
// prepare for next time thru the loop
cur_input = "";
index[input_width - 1]++;
}
}
} // end namespace genome
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