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#include<algorithm>
#include "TranscriptExpression.h"
#include "FileHeader.h"
#include "common.h"
TE_FileType TranscriptExpression::guessFileType(const string &fileName){//{{{
string extension = fileName.substr(fileName.rfind(".")+1);
if(extension == "thetaMeans") return SAMPLER_MEANS;
if(extension == "m_alphas") return M_ALPHAS;
// Ends with 'mean' or 'variance' or 'var'
if((extension.rfind("mean") == extension.size() - 4) ||
(extension.rfind("variance") == extension.size() - 8) ||
(extension.rfind("var") == extension.size() - 3)) return MEAN_VARIANCE;
// Default is SAMPLER_MEANS.
return SAMPLER_MEANS;
}//}}}
TranscriptExpression::TranscriptExpression(){//{{{
M=0;
logged=false;
}//}}}
TranscriptExpression::TranscriptExpression(const string &fileName, TE_FileType fileType){//{{{
TranscriptExpression();
readExpression(fileName,fileType);
}//}}}
bool TranscriptExpression::readExpression(const string &fileName, TE_FileType fileType){//{{{
long i;
if(fileType == GUESS)fileType = guessFileType(fileName);
ifstream varFile(fileName.c_str());
FileHeader fh(&varFile);
if((!fh.varianceHeader(&M,&logged))||(M==0)){
error("TranscriptExpression: Problem loading variance file %s\n",(fileName).c_str());
return false;
}
// M_ALPHAS file contains nosie transcript.
if(fileType == M_ALPHAS) M--;
trs.resize(M);
if(fileType == SAMPLER_MEANS){
double count,mean2;
for(i=0;i<M;i++){
varFile>>trs[i].id>>trs[i].exp>>count>>mean2>>trs[i].var;
// IDs in SAMPLER_MEANS file are shifted by 1
trs[i].id--;
varFile.ignore(1000,'\n');
if(varFile.bad()){
error("TranscriptExpression: Problem reading transcript %ld.\n",i);
return false;
}
}
}else if(fileType == MEAN_VARIANCE){
for(i=0;i<M;i++){
trs[i].id=i;
varFile>>trs[i].exp>>trs[i].var;
varFile.ignore(1000,'\n');
if(varFile.bad()){
error("TranscriptExpression: Problem reading transcript %ld.\n",i);
return false;
}
}
}else if(fileType == M_ALPHAS){
double alpha, beta, beta0;
// Skip first entry - noise transcript.
varFile>>trs[0].exp>>alpha>>beta0;
varFile.ignore(1000,'\n');
for(i=0;i<M;i++){
trs[i].id=i;
varFile>>trs[i].exp>>alpha>>beta;
// Beta0 is the sum of all except noise.
trs[i].exp = alpha / beta0;
trs[i].var = alpha * (beta0-alpha) / (beta0 * beta0 * (beta0 + 1));
varFile.ignore(1000,'\n');
if(varFile.bad()){
error("TranscriptExpression: Problem reading transcript %ld.\n",i);
return false;
}
}
}
fh.close();
return true;
}//}}}
void TranscriptExpression::doSort(bool reverse){//{{{
if(! reverse)
sort(trs.begin(),trs.end());
else
sort(trs.rbegin(),trs.rend());
}//}}}
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