rc_t CC KMain(int argc, char* argv[]) {
rc_t rc = 0;
Args* args = NULL;
Params prm;
memset(&prm, 0, sizeof prm);
do {
uint32_t pcount = 0;
rc = ArgsMakeAndHandle(&args, argc, argv, 1,
Options, sizeof Options / sizeof (OptDef));
if (rc) {
LOGERR(klogErr, rc, "While calling ArgsMakeAndHandle");
break;
}
rc = ArgsParamCount(args, &pcount);
if (rc) {
LOGERR(klogErr, rc, "While calling ArgsParamCount");
break;
}
if (pcount < 1) {
MiniUsage(args);
DESTRUCT(Args, args);
exit(1);
break;
}
if (pcount > 1) {
rc = RC(rcExe, rcArgv, rcParsing, rcParam, rcAmbiguous);
LOGERR(klogErr, rc, "Too many database parameters");
break;
}
rc = ArgsParamValue(args, 0, &prm.dbPath);
if (rc) {
LOGERR(klogErr, rc, "Failure retrieving database name");
break;
}
rc = ArgsOptionCount (args, OPTION_ALL, &pcount);
if (rc) {
LOGERR(klogErr, rc, "Failure to get '" OPTION_ALL "' argument");
break;
}
if (pcount)
{ prm.paramBamHeader = prm.paramQuality = prm.paramRef = true; }
rc = ArgsOptionCount (args, OPTION_BAM, &pcount);
if (rc) {
LOGERR(klogErr, rc, "Failure to get '" OPTION_BAM "' argument");
break;
}
if (pcount)
{ prm.paramBamHeader = true; }
rc = ArgsOptionCount (args, OPTION_QUA, &pcount);
if (rc) {
LOGERR(klogErr, rc, "Failure to get '" OPTION_QUA "' argument");
break;
}
if (pcount)
{ prm.paramQuality = true; }
rc = ArgsOptionCount (args, OPTION_REF, &pcount);
if (rc) {
LOGERR(klogErr, rc, "Failure to get '" OPTION_REF "' argument");
break;
}
if (pcount)
{ prm.paramRef = true; }
if (!prm.paramBamHeader && !prm.paramQuality && !prm.paramRef)
{ prm.paramRef = true; }
} while (false);
if (rc == 0)
{ rc = align_info(&prm); }
DESTRUCT(Args, args);
return rc;
}
double lex_score(char *src,char * tr,char * al,align_info * al_info,LexMap * lmap)
{
double score=-1;
str_vec src_vec,
tr_vec;
aligns alignments;
// cout<<"Lexical score for ('"<<src<<"','"<<tr<<"')"<<endl;
tokenize_in_vec(src,&src_vec);
tokenize_in_vec(tr,&tr_vec);
// cout<<"Alignment: "<<al<<endl;
get_alignments(al,&alignments);
// cout<<"Extracted alignments:\n";
/*for(aligns::iterator i=alignments.begin();i!=alignments.end();++i)
cout<<i->first<<":"<<i->second <<endl;
*/
if (al_info)
*al_info= align_info(src_vec.size() ,tr_vec.size() ,&alignments);
ostringstream key;
short i=0;
for(str_vec::iterator src_itr=src_vec.begin();
src_itr !=src_vec.end();
++src_itr,++i){
if(alignments.count(i)==0){
// cout<<"the word '"<<*src_itr<<"' was unaligned"<<endl;
//cout<<(*lmap)[*src_itr]<<"<---from lex map"<<endl;
key.str(std::string());
key<<*src_itr<<STR_SEP<<UNALIGNED;
// cout<<"Looking for: "<<key.str()<<endl;
LexMap::iterator found=lmap->find(key.str());//src_itr->append(STR_SEP).append(UNALIGNED));
//lex_trans_type(*src_itr,UNALIGNED));
if(found!=lmap->end()){
// cout<<"Map('"<<*src_itr<<"','"<<UNALIGNED<<"')="<<found->second<<endl;
if(score<0)
score =found->second;
else
score *=found->second;//(*lmap)[lex_trans_type(*src_itr,UNALIGNED)];
}
/*
else
cout<<"the couple ('"<<*src_itr<<"',NULL) was not found in the lexical map"<<endl;
*/
}
else{
double sum=0;
unsigned npalign=0;
//cout<<"the word('"<<*src_itr<<"') was aligned at least once\n";
for(aligns::iterator al_itr=alignments.equal_range(i).first;
al_itr!=alignments.equal_range(i).second;
++al_itr){
key.str(std::string());
key<<*src_itr<<STR_SEP<<tr_vec[al_itr->second];
// cout<<"Looking for: "<<key.str()<<endl;
LexMap::iterator found=lmap->find(key.str());
if(found!=lmap->end()){
// cout<<"Map('"<<*src_itr<<"','"<<tr_vec[al_itr->second]<<"')="<<found->second<<endl;
sum+=found->second;//(*lmap)[lex_trans_type(*src_itr,tr_vec[(*al_itr).second])];
npalign++;
}else{
// cout<<"Couldn't find: '"<<*src_itr<<"','"<<tr_vec[al_itr->second]<<"' in the map\n";
}
}
if(npalign>0){
if(score<0)
score = sum/npalign;
else
score *= sum/npalign;
// score *= sum/alignments.count(i);
}
}
}
// cout<<"Score= "<<score<<endl;
return MAX(score,ZERO_PROB);
}
