double
get_hapscore(hap_set_t& hap_set) {
std::sort(hap_set.begin(),hap_set.end());
std::vector<hinfo> haps;
typedef hap_set_t::const_iterator hiter;
{
hiter i(hap_set.begin()), i_end(hap_set.end());
for (; i!=i_end; ++i) {
// 1: check if we match any types; add new type if not
bool is_match(false);
const unsigned hs(haps.size());
for (unsigned j(0); j<hs; ++j) {
if (is_hap_match(*i,haps[j])) {
is_match=true;
break;
}
}
if (! is_match) haps.push_back(hinfo(*i));
}
}
const bool is_2hap(haps.size()>1);
// 2: get two most likely haplotypes:
if (is_2hap) {
std::partial_sort(haps.begin(),haps.begin()+2,haps.end());
}
// 3: calculate average read alignment score restricted to two best haplotypes:
//static const double neginf(std::log(0));
double ln2hapratio(0);
{
hiter i(hap_set.begin()), i_end(hap_set.end());
for (; i!=i_end; ++i) {
double als(get_align_score(*i,haps[0]));
if (is_2hap) {
als=std::max(als,get_align_score(*i,haps[1]));
}
//ln2hapratio = log_sum(ln2hapratio,als);
ln2hapratio += als;
}
// target is log(avg(read_prob_ratio)), not avg(log(read_prob_ratio)):
//
//ln2hapratio -= std::log(static_cast<double>(hap_set.size()));
ln2hapratio /= static_cast<double>(hap_set.size());
}
return ln2hapratio;
}
void PluginGeneratorGUI::save( const QString& filepath,const bool generatecpp)
{
MLXMLTree tree;
collectInfo(tree);
if (generatecpp)
{
QDir dir(finfo.absolutePath());
QString cppcode = MLXMLUtilityFunctions::generateCPP(finfo.baseName(),tree);
QFileInfo cppinfo(finfo.absolutePath() + "/" +finfo.baseName() + ".cpp");
QString cppoldfilename = UsefulGUIFunctions::generateBackupName(cppinfo);
dir.rename(cppinfo.fileName(),cppoldfilename);
QFile cppfile(cppinfo.absoluteFilePath());
if (!cppfile.open(QIODevice::WriteOnly | QIODevice::Text))
return;
QTextStream outcpp(&cppfile);
outcpp << cppcode;
cppfile.close();
QString hcode = MLXMLUtilityFunctions::generateH(finfo.baseName(),tree);
QFileInfo hinfo(finfo.absolutePath() + "/" +finfo.baseName() + ".h");
QString holdfilename = UsefulGUIFunctions::generateBackupName(hinfo);
dir.rename(hinfo.fileName(),holdfilename);
QFile hfile(hinfo.absoluteFilePath());
if (!hfile.open(QIODevice::WriteOnly | QIODevice::Text))
return;
QTextStream outh(&hfile);
outh << hcode;
hfile.close();
}
QString xml = generateXML(tree);
//QDomDocument has been introduced only in order to indent the xml code
QDomDocument doc;
doc.setContent(xml,false);
xml = doc.toString();
QFile file(filepath);
if (!file.open(QIODevice::WriteOnly | QIODevice::Text))
return;
QTextStream out(&file);
out << xml;
file.close();
finfo.setFile(filepath);
}
