Int2 Main (void)
{
Int2 argcount;
Boolean flagHaveNet;
Int4 gi;
SeqEntryPtr sep;
ComPatPtr cpp, cpph = NULL;
SeqAlignPtr sap, sapn;
StdSegPtr ssp;
SeqLocPtr slp, slpn;
Int4 start, stop;
FILE *fiop;
Char fastafile[256], namesfile[256];
CharPtr title;
CharPtr taxon;
FloatHi mw;
ValNodePtr namelist = NULL;
static CharPtr pattern_file = "ncbipros.dat";
static CharPtr protease_file = "ncbiendo.dat";
static CharPtr names_file = "ncbipnam.dat";
static GatherScope gs;
GatherScopePtr gsp;
static Gather_PBS gpbs;
Gather_PBSPtr gpbsp;
#ifndef NO_TAX_NET
Int4 i;
static Char taxdata[8];
static Gather_TaxId gti;
Gather_TaxIdPtr gtip;
#endif
#ifndef NO_TAX_NET
Int2 ia=4, ib=5, ic=6, id=7, ie=8, ig=9, ih=10, ii=11;
#else
Int2 ib=4, ic=5, id=6, ie=7, ig=8, ih=9, ii=10;
#endif
argcount = sizeof (myargs) / sizeof (Args);
if (!GetArgs ("ProSiteSearch", argcount, myargs))
return 1;
if (myargs[0].intvalue == 0 && myargs[1].strvalue == NULL)
{
ErrPostEx (SEV_ERROR, TOP_ERROR, 100,
"No gi or FastA file given :: for help : srchaa -");
ErrShow ();
exit (1);
}
gsp = &gs;
#ifndef NO_TAX_NET
gtip = >i;
#endif
gpbsp = &gpbs;
MemSet ((Pointer) gsp, 0, sizeof (GatherScope));
MemSet ((Pointer) gsp->ignore, (int) (TRUE),
(size_t) (OBJ_MAX * sizeof (Boolean)));
gsp->ignore[OBJ_SEQDESC] = TRUE;
gsp->ignore[OBJ_BIOSEQ] = FALSE;
gpbsp->bsp = NULL;
gi = myargs[0].intvalue;
if (myargs[1].strvalue != NULL)
StrCpy (fastafile, myargs[1].strvalue);
else
fastafile[0] = '\0';
if (gi > 0)
{
if (!EntrezInit ("srchaa", FALSE, &flagHaveNet))
{
ErrPostEx (SEV_ERROR, TOP_ERROR, 102,
"Entrez init failed");
ErrShow ();
exit (1);
}
}
#ifndef NO_TAX_NET
if (myargs[ia].intvalue)
{
if (!TaxArchInit ())
{
ErrPostEx (SEV_ERROR, TOP_ERROR, 103,
"Taxonomy init failed");
ErrShow ();
exit (1);
}
}
#endif
fiop = NULL;
if (gi > 0)
{
sep = EntrezSeqEntryGet (gi, SEQENTRY_READ_BIOSEQ);
}
else
{
if ((fiop = FileOpen (fastafile, "r")) == NULL)
{
ErrPostEx (SEV_ERROR, TOP_ERROR, 103,
"Failed to open FastA file: %s", fastafile);
ErrShow ();
exit (1);
}
sep = FastaToSeqEntry (fiop, FALSE);
}
if (sep == NULL)
{
ErrPostEx (SEV_ERROR, TOP_ERROR, 104,
"No seqentry found");
ErrShow ();
exit (1);
}
while (sep != NULL)
{
gsp->ignore[OBJ_SEQDESC] = TRUE;
gsp->ignore[OBJ_BIOSEQ] = FALSE;
gpbsp->bsp = NULL;
gpbsp->gi = gi;
GatherSeqEntry (sep, (Pointer) gpbsp, GetBioseq, (Pointer) gsp);
taxon = NULL;
#ifndef NO_TAX_NET
if (myargs[ia].intvalue)
{
for (i = 0; i < 8; i++)
taxdata[i] = '-';
taxon = taxdata;
gsp->ignore[OBJ_SEQDESC] = FALSE;
gsp->ignore[OBJ_BIOSEQ] = TRUE;
gtip->taxid = 0;
GatherSeqEntry (sep, (Pointer) gtip, GetTaxId, (Pointer) gsp);
if (gtip->taxid != 0)
WhatOrg (gtip->taxid, taxon);
else
taxon = NULL;
}
#endif
if (gpbsp->bsp != NULL)
{
if (ISA_aa (gpbsp->bsp->mol))
{
if (cpph == NULL)
{
namesfile[0] = '\0';
if (myargs[id].intvalue)
StrCpy (namesfile, names_file);
if (myargs[ie].strvalue != NULL)
StrCpy (namesfile, myargs[ie].strvalue);
if (myargs[ig].strvalue != NULL)
{
if ((cpph = CompilePattern (myargs[ig].strvalue, 1)) != NULL)
StrCpy (cpph->name, "User Pattern");
}
else
{
namelist = ReadPatternNames (namesfile);
if (myargs[ib].intvalue)
cpph = ReadPrositePattern (protease_file,
(Boolean) myargs[2].intvalue,
myargs[3].intvalue,
taxon, NULL);
else
cpph = ReadPrositePattern (pattern_file,
(Boolean) myargs[2].intvalue,
myargs[3].intvalue,
taxon, namelist);
}
}
if (!(Boolean) myargs[ih].intvalue)
{
title = FastaTitle (gpbsp->bsp, ">", NULL);
printf ("%s\n", title);
MemFree (title);
}
cpp = cpph;
while (cpp != NULL)
{
sap = PatternMatchBioseq (gpbsp->bsp, cpp,
(Int4)myargs[ii].intvalue);
if (myargs[ib].intvalue)
{
printf (">%s\n", cpp->name);
if (sap != NULL)
printf (" Start Stop M.W.\n");
}
if (myargs[ib].intvalue)
{
EmbedMolecularWeightInfo (sap, gpbsp->bsp);
if (myargs[ic].intvalue)
URK_SeqAlignSortByMolWt (&sap);
while (sap != NULL)
{
ssp = (StdSegPtr) sap->segs;
slp = ssp->loc;
start = SeqLocStart (slp);
stop = SeqLocStop (slp);
mw = ssp->scores->value.realvalue;
printf ("%8ld %8ld %9.2f\n",
(long) start+1, (long) stop+1, mw);
sapn = sap->next;
SeqAlignFree (sap);
sap = sapn;
}
}
else
{
slp = MatchSa2Sl (&sap);
if (myargs[ih].intvalue && slp != NULL)
{
title = FastaTitle (gpbsp->bsp, ">", NULL);
printf ("%s\n", title);
MemFree (title);
}
while (slp != NULL)
{
start = SeqLocStart (slp);
stop = SeqLocStop (slp);
printf ("%8ld %8ld %s\n",
(long) start+1, (long) stop+1, cpp->name);
slpn = slp->next;
SeqLocFree (slp);
slp = slpn;
}
}
cpp = cpp->nextpattern;
}
}
else
{
ErrPostEx (SEV_ERROR, TOP_ERROR, 106,
"Not a protein bioseq");
ErrShow ();
exit (1);
}
}
else
{
ErrPostEx (SEV_ERROR, TOP_ERROR, 105,
"No bioseq found");
ErrShow ();
exit (1);
}
SeqEntryFree (sep);
sep = NULL;
if (fiop != NULL)
sep = FastaToSeqEntry (fiop, FALSE);
}
ComPatFree (cpph);
ValNodeFreeData (namelist);
FileClose (fiop);
if (gi > 0)
EntrezFini ();
#ifndef NO_TAX_NET
if (myargs[ia].intvalue)
TaxArchFini ();
#endif
return 0;
}
CmdResult Handle (const std::vector<std::string>& parameters, User *user)
{
if (!parameters.size())
{
// no parameters, show the current silence list.
silencelist* sl = ext.get(user);
// if the user has a silence list associated with their user record, show it
if (sl)
{
for (silencelist::const_iterator c = sl->begin(); c != sl->end(); c++)
{
std::string decomppattern = DecompPattern(c->second);
user->WriteNumeric(271, "%s %s %s %s",user->nick.c_str(), user->nick.c_str(),c->first.c_str(), decomppattern.c_str());
}
}
user->WriteNumeric(272, "%s :End of Silence List",user->nick.c_str());
return CMD_SUCCESS;
}
else if (parameters.size() > 0)
{
// one or more parameters, add or delete entry from the list (only the first parameter is used)
std::string mask = parameters[0].substr(1);
char action = parameters[0][0];
// Default is private and notice so clients do not break
int pattern = CompilePattern("pn");
// if pattern supplied, use it
if (parameters.size() > 1) {
pattern = CompilePattern(parameters[1].c_str());
}
if (pattern == 0)
{
user->WriteServ("NOTICE %s :Bad SILENCE pattern",user->nick.c_str());
return CMD_INVALID;
}
if (!mask.length())
{
// 'SILENCE +' or 'SILENCE -', assume *!*@*
mask = "*!*@*";
}
ModeParser::CleanMask(mask);
if (action == '-')
{
std::string decomppattern = DecompPattern(pattern);
// fetch their silence list
silencelist* sl = ext.get(user);
// does it contain any entries and does it exist?
if (sl)
{
for (silencelist::iterator i = sl->begin(); i != sl->end(); i++)
{
// search through for the item
irc::string listitem = i->first.c_str();
if (listitem == mask && i->second == pattern)
{
sl->erase(i);
user->WriteNumeric(950, "%s %s :Removed %s %s from silence list",user->nick.c_str(), user->nick.c_str(), mask.c_str(), decomppattern.c_str());
if (!sl->size())
{
ext.unset(user);
}
return CMD_SUCCESS;
}
}
}
user->WriteNumeric(952, "%s %s :%s %s does not exist on your silence list",user->nick.c_str(), user->nick.c_str(), mask.c_str(), decomppattern.c_str());
}
else if (action == '+')
{
// fetch the user's current silence list
silencelist* sl = ext.get(user);
if (!sl)
{
sl = new silencelist;
ext.set(user, sl);
}
if (sl->size() > maxsilence)
{
user->WriteNumeric(952, "%s %s :Your silence list is full",user->nick.c_str(), user->nick.c_str());
return CMD_FAILURE;
}
std::string decomppattern = DecompPattern(pattern);
for (silencelist::iterator n = sl->begin(); n != sl->end(); n++)
{
irc::string listitem = n->first.c_str();
if (listitem == mask && n->second == pattern)
{
user->WriteNumeric(952, "%s %s :%s %s is already on your silence list",user->nick.c_str(), user->nick.c_str(), mask.c_str(), decomppattern.c_str());
return CMD_FAILURE;
}
}
if (((pattern & SILENCE_EXCLUDE) > 0))
{
sl->push_front(silenceset(mask,pattern));
}
else
{
sl->push_back(silenceset(mask,pattern));
}
user->WriteNumeric(951, "%s %s :Added %s %s to silence list",user->nick.c_str(), user->nick.c_str(), mask.c_str(), decomppattern.c_str());
return CMD_SUCCESS;
}
}
return CMD_SUCCESS;
}
CmdResult Handle (const std::vector<std::string>& parameters, User *user)
{
if (!parameters.size())
{
// no parameters, show the current silence list.
// Use Extensible::GetExt to fetch the silence list
silencelist* sl;
user->GetExt("silence_list", sl);
// if the user has a silence list associated with their user record, show it
if (sl)
{
for (silencelist::const_iterator c = sl->begin(); c != sl->end(); c++)
{
user->WriteNumeric(271, "%s %s %s %s",user->nick.c_str(), user->nick.c_str(),c->first.c_str(), DecompPattern(c->second).c_str());
}
}
user->WriteNumeric(272, "%s :End of Silence List",user->nick.c_str());
return CMD_LOCALONLY;
}
else if (parameters.size() > 0)
{
// one or more parameters, add or delete entry from the list (only the first parameter is used)
std::string mask = parameters[0].substr(1);
char action = parameters[0][0];
// Default is private and notice so clients do not break
int pattern = CompilePattern("pn");
// if pattern supplied, use it
if (parameters.size() > 1) {
pattern = CompilePattern(parameters[1].c_str());
}
if (!mask.length())
{
// 'SILENCE +' or 'SILENCE -', assume *!*@*
mask = "*!*@*";
}
ModeParser::CleanMask(mask);
if (action == '-')
{
// fetch their silence list
silencelist* sl;
user->GetExt("silence_list", sl);
// does it contain any entries and does it exist?
if (sl)
{
for (silencelist::iterator i = sl->begin(); i != sl->end(); i++)
{
// search through for the item
irc::string listitem = i->first.c_str();
if (listitem == mask && i->second == pattern)
{
sl->erase(i);
user->WriteNumeric(950, "%s %s :Removed %s %s from silence list",user->nick.c_str(), user->nick.c_str(), mask.c_str(), DecompPattern(pattern).c_str());
if (!sl->size())
{
delete sl;
user->Shrink("silence_list");
}
return CMD_SUCCESS;
}
}
}
user->WriteNumeric(952, "%s %s :%s %s does not exist on your silence list",user->nick.c_str(), user->nick.c_str(), mask.c_str(), DecompPattern(pattern).c_str());
}
else if (action == '+')
{
// fetch the user's current silence list
silencelist* sl;
user->GetExt("silence_list", sl);
// what, they dont have one??? WE'RE ALL GONNA DIE! ...no, we just create an empty one.
if (!sl)
{
sl = new silencelist;
user->Extend("silence_list", sl);
}
if (sl->size() > maxsilence)
{
user->WriteNumeric(952, "%s %s :Your silence list is full",user->nick.c_str(), user->nick.c_str());
return CMD_FAILURE;
}
for (silencelist::iterator n = sl->begin(); n != sl->end(); n++)
{
irc::string listitem = n->first.c_str();
if (listitem == mask && n->second == pattern)
{
user->WriteNumeric(952, "%s %s :%s %s is already on your silence list",user->nick.c_str(), user->nick.c_str(), mask.c_str(), DecompPattern(pattern).c_str());
return CMD_FAILURE;
}
}
if (((pattern & SILENCE_EXCLUDE) > 0))
{
sl->push_front(silenceset(mask,pattern));
}
else
{
sl->push_back(silenceset(mask,pattern));
}
user->WriteNumeric(951, "%s %s :Added %s %s to silence list",user->nick.c_str(), user->nick.c_str(), mask.c_str(), DecompPattern(pattern).c_str());
return CMD_SUCCESS;
}
}
return CMD_LOCALONLY;
}
