void
FE_Utils::create_uses_multiple_stuff (AST_Component *c,
AST_Uses *u,
const char *prefix)
{
ACE_CString struct_name (prefix);
if (!struct_name.empty ())
{
struct_name += '_';
}
struct_name += u->local_name ()->get_string ();
struct_name += "Connection";
Identifier struct_id (struct_name.c_str ());
UTL_ScopedName sn (&struct_id, 0);
// In case this call comes from the backend. We
// will pop the scope before returning.
idl_global->scopes ().push (c);
AST_Structure *connection =
idl_global->gen ()->create_structure (&sn, 0, 0);
struct_id.destroy ();
/// If the field type is a param holder, we want
/// to use the lookup to create a fresh one,
/// since the field will own it and destroy it.
UTL_ScopedName *fn = u->uses_type ()->name ();
AST_Decl *d =
idl_global->root ()->lookup_by_name (fn, true, false);
AST_Type *ft = AST_Type::narrow_from_decl (d);
Identifier object_id ("objref");
UTL_ScopedName object_name (&object_id,
0);
AST_Field *object_field =
idl_global->gen ()->create_field (ft,
&object_name,
AST_Field::vis_NA);
(void) DeclAsScope (connection)->fe_add_field (object_field);
object_id.destroy ();
Identifier local_id ("Cookie");
UTL_ScopedName local_name (&local_id,
0);
Identifier module_id ("Components");
UTL_ScopedName scoped_name (&module_id,
&local_name);
d = c->lookup_by_name (&scoped_name, true);
local_id.destroy ();
module_id.destroy ();
if (d == 0)
{
// This would happen if we haven't included Components.idl.
idl_global->err ()->lookup_error (&scoped_name);
return;
}
AST_ValueType *cookie = AST_ValueType::narrow_from_decl (d);
Identifier cookie_id ("ck");
UTL_ScopedName cookie_name (&cookie_id,
0);
AST_Field *cookie_field =
idl_global->gen ()->create_field (cookie,
&cookie_name,
AST_Field::vis_NA);
(void) DeclAsScope (connection)->fe_add_field (cookie_field);
cookie_id.destroy ();
(void) c->fe_add_structure (connection);
ACE_CDR::ULong bound = 0;
AST_Expression *bound_expr =
idl_global->gen ()->create_expr (bound,
AST_Expression::EV_ulong);
AST_Sequence *sequence =
idl_global->gen ()->create_sequence (bound_expr,
connection,
0,
0,
0);
ACE_CString seq_string (struct_name);
seq_string += 's';
Identifier seq_id (seq_string.c_str ());
UTL_ScopedName seq_name (&seq_id,
0);
AST_Typedef *connections =
idl_global->gen ()->create_typedef (sequence,
&seq_name,
0,
0);
seq_id.destroy ();
(void) c->fe_add_typedef (connections);
// In case this call comes from the backend.
idl_global->scopes ().pop ();
}
bool Spectrum::read_from_MGF_stream(const Config *_config, FILE *stream, int _charge, bool verbose)
{
config_ = _config;
totalPeakIntensity_ = 0;
char buff[1024];
peaks_ = new Peak[5000];
localAllocationSize_ = 5000;
/* while (1)
{
if( ! fgets(buff, 1024, stream) )
return false;
if (strlen(buff)<3)
continue;
if (strncmp(buff,"BEGIN IONS",10) )
continue;
break;
}*/
scanNumber_ =-1;
retentionTime_ =-1;
clusterSize_ =-1;
charge_ =-1;
mOverZ_ =-1;
originalPmWith19_=-1;
// read header info and first peak
while (1)
{
if( ! fgets(buff, 1024, stream))
return false;
if (strlen(buff)<3)
continue;
if (strncmp(buff,"BEGIN IONS",10) )
continue;
if (! strncmp(buff,"END IONS",7))
return false;
if (! strncmp(buff,"TITLE=",6) )
{
buff[strlen(buff)-1]='\0';
title_ = static_cast<string>(buff+6);
continue;
}
else
if (! strncmp(buff,"SEQ=",4) )
{
string seq_string(buff+4);
peptide_.parseFromString(config_,seq_string);
peptide_.calc_mass(config_);
continue;
}
else
if (! strncmp(buff,"SCAN=",5) )
{
if (sscanf(buff+5,"%d",&scanNumber_) != 1)
{
cout << "Error: couldn't read scan number!" << endl;
exit(1);
}
continue;
}
if (! strncmp(buff,"SCANS=",6) )
{
if (sscanf(buff+6,"%d",&scanNumber_) != 1)
{
cout << "Error: couldn't read scan number!" << endl;
exit(1);
}
continue;
}
else
if (! strncmp(buff,"RT=",3) )
{
if (sscanf(buff+3,"%f",&retentionTime_) != 1)
{
cout << "Error: couldn't read retention_time!" << endl;
exit(1);
}
continue;
}
else
if (! strncmp(buff,"CLUSTER_SIZE=",13) )
{
if (sscanf(buff+13,"%d",&clusterSize_) != 1)
{
cout << "Error: couldn't read cluster size!" << endl;
exit(1);
}
continue;
}
else
if ( ! strncmp(buff,"CHARGE=",6))
{
if (sscanf(buff,"CHARGE=%d",&charge_) != 1)
{
cout << "Error: couldn't read charge!" << endl;
return false;
}
}
else
if (! strncmp(buff,"PEPMASS=",8))
{
istringstream is(buff+8);
is >> mOverZ_;
if (mOverZ_ < 0)
{
cout << "Error: reading pepmass:" << mOverZ_ << endl;
return false;
}
}
else
{
