QFrameWorkConfig.cc

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#include "QFrameWorkConfig.hh"
#include <fstream>
#include <set>
 
QObjectImp(QFrameWorkConfig);
 
QError QFrameWorkConfig::GetModuleByLabel(const std::string& label, QModuleConfig& mod) const
{
    
    std::vector<QSequenceConfig*>::const_reverse_iterator iter = fSequences.rbegin();
    while(iter!= fSequences.rend()) {
        if((*iter)->GetModuleByLabel(label,mod) == QERR_SUCCESS) {
            return QERR_SUCCESS;
        }
        iter++;
    }
    return QERR_OUT_OF_RANGE;
}
 
 
void QFrameWorkConfig::Dump(std::ostream& o) const
{
    for(size_t s = 0; s < fSequences.size(); s++) {
            o<<"sequence "<<fSequences[s]->fName<<std::endl;
            o<<std::endl;
            fSequences[s]->Dump(o);
            o<<"endseq"<<std::endl;
            o<<std::endl;
    }
}
void QFrameWorkConfig::List() const
{
    std::cout<<"Sequence  / Original filename"<<std::endl;
    for(size_t s = 0; s < fSequences.size(); s++) {
        std::cout<<fSequences[s]->fName<<" / "<<fSequences[s]->fFilename<<std::endl;
    }
}
bool QFrameWorkConfig::SaveSequence(const std::string& seq, const std::string& outputfile, bool append) const
{
    QSequenceConfig* sc = 0;
    for(size_t s = 0; s < fSequences.size(); s++) {
        if(fSequences[s]->fName == seq) {
            sc = fSequences[s];
            break;
        }
    }
    if(!sc) {
        std::cerr<<"Error: sequence name not found"<<std::endl;
        return false;
    }
 
    std::string outname = outputfile;
    if(outname.empty()) outname = sc->fFilename;
    std::ofstream of;
    if(append)
        of.open(outname.c_str(),std::ios::app);
    else
        of.open(outname.c_str());
    if(of.fail()) {
        std::cerr<<"Cannot open file \""<<outname<<std::endl;
        return false;
    }
    of<<"# Dumped by QFramework config. Original filename: "<<sc->fFilename<<std::endl;
 
    of<<"sequence "<<sc->fName<<std::endl;
    of<<std::endl;
    sc->Dump(of);
    of<<"endseq"<<std::endl;
    of<<std::endl;
 
    of.close();
 
    return true;
}
 
bool QFrameWorkConfig::SaveAllSequences(const std::string& outputfilename) const
{
    if(fSequences.empty()) {
        std::cerr<<"Error: no sequence available"<<std::endl;
        return false;
    }
    bool ok = true;
     for(size_t s = 0; s < fSequences.size(); s++) {
         ok = SaveSequence(fSequences[s]->fName,outputfilename,s!=0); 
         if(!ok) return false;
     } 
    return true;
}
 
bool QFrameWorkConfig::SaveFile(const std::string& origfilename, const std::string& outputfile) const
{
     std::vector<QSequenceConfig*> selected;
     for(size_t s = 0; s < fSequences.size(); s++) {
        if(fSequences[s]->fFilename == origfilename) {
            selected.push_back(fSequences[s]);
        }
    }
    if(selected.empty()) {
        std::cerr<<"Error: filename not found"<<std::endl;
        return false;
    }
 
    std::string outname = outputfile;
    if(outname.empty()) outname = origfilename;
 
 
    bool ok = true;
     for(size_t s = 0; s < selected.size(); s++) {
         ok = SaveSequence(selected[s]->fName,outname,s!=0); 
         if(!ok) return false;
     } 
     return true;
}
 
bool QFrameWorkConfig::SaveAllFiles(const std::string& outputdir, const std::string& prefix) const
{
     std::set<std::string> selected;
 
     for(size_t s = 0; s < fSequences.size(); s++) {
         selected.insert(fSequences[s]->fFilename);
     }
     if(selected.empty()) {
         std::cerr<<"Error: filename not found"<<std::endl;
         return false;
     }
    bool ok = true;
     std::set<std::string>::iterator iter = selected.begin();
     while(iter != selected.end()) {
        std::string file = outputdir + "/";
        file += prefix;
        file += *iter;
        ok = SaveFile(*iter,file);
         if(!ok) return false;
        iter++;
    }
     return true;
}