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Merge branch 'master' of ssh://yap.git.sourceforge.net/gitroot/yap/yap-6.3

Browse Source 
Conflicts:
	C/cdmgr.c
This commit is contained in:
Joao 2011-05-04 11:10:20 +01:00
commit d9cee607e9
42 changed files with 5223 additions and 26 deletions
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237
C/cdmgr.c
View File

@ -2507,8 +2507,10 @@ p_compile_dynamic( USES_REGS1 )
if (RepAtom(AtomOfTerm(t1))->StrOfAE[0] == 'f') mode = asserta;
else mode = assertz;
} else mode = IntegerOfTerm(t1);
if (mode == assertz && LOCAL_consult_level)
mode = consult;
/* separate assert in current file from reconsult
if (mode == assertz && LOCAL_consult_level && mod == CurrentModule)
mode = consult;
*/
old_optimize = optimizer_on;
optimizer_on = FALSE;
YAPEnterCriticalSection();
@ -5635,6 +5637,233 @@ p_choicepoint_info( USES_REGS1 )
Yap_unify(ARG7,MkIntegerTerm(ClauseId(ncl,pe)));
}
static UInt
compute_dbcl_size(UInt arity)
{
UInt sz;
switch(arity) {
case 2:
sz = (UInt)NEXTOP((yamop *)NULL,cc);
break;
case 3:
sz = (UInt)NEXTOP((yamop *)NULL,ccc);
break;
case 4:
sz = (UInt)NEXTOP((yamop *)NULL,cccc);
break;
case 5:
sz = (UInt)NEXTOP((yamop *)NULL,ccccc);
break;
case 6:
sz = (UInt)NEXTOP((yamop *)NULL,cccccc);
break;
default:
sz = arity*(UInt)NEXTOP((yamop *)NULL,xc);
break;
}
return (UInt)NEXTOP((yamop *)sz,p);
}
#define DerefAndCheck(t, V) \
t = Deref(V); if(IsVarTerm(t) || !(IsAtomOrIntTerm(t))) Yap_Error(TYPE_ERROR_ATOM, t0, "load_db");
static int
store_dbcl_size(yamop *pc, UInt arity, Term t0, PredEntry *pe)
{
Term t;
CELL *tp = RepAppl(t0)+1;
switch(arity) {
case 2:
pc->opc = Yap_opcode(_get_2atoms);
DerefAndCheck(t, tp[0]);
pc->u.cc.c1 = t;
DerefAndCheck(t, tp[1]);
pc->u.cc.c2 = t;
pc = NEXTOP(pc,cc);
break;
case 3:
pc->opc = Yap_opcode(_get_3atoms);
DerefAndCheck(t, tp[0]);
pc->u.ccc.c1 = t;
DerefAndCheck(t, tp[1]);
pc->u.ccc.c2 = t;
DerefAndCheck(t, tp[2]);
pc->u.ccc.c3 = t;
pc = NEXTOP(pc,ccc);
break;
case 4:
pc->opc = Yap_opcode(_get_4atoms);
DerefAndCheck(t, tp[0]);
pc->u.cccc.c1 = t;
DerefAndCheck(t, tp[1]);
pc->u.cccc.c2 = t;
DerefAndCheck(t, tp[2]);
pc->u.cccc.c3 = t;
DerefAndCheck(t, tp[3]);
pc->u.cccc.c4 = t;
pc = NEXTOP(pc,cccc);
break;
case 5:
pc->opc = Yap_opcode(_get_5atoms);
DerefAndCheck(t, tp[0]);
pc->u.ccccc.c1 = t;
DerefAndCheck(t, tp[1]);
pc->u.ccccc.c2 = t;
DerefAndCheck(t, tp[2]);
pc->u.ccccc.c3 = t;
DerefAndCheck(t, tp[3]);
pc->u.ccccc.c4 = t;
DerefAndCheck(t, tp[4]);
pc->u.ccccc.c5 = t;
pc = NEXTOP(pc,ccccc);
break;
case 6:
pc->opc = Yap_opcode(_get_6atoms);
DerefAndCheck(t, tp[0]);
pc->u.cccccc.c1 = t;
DerefAndCheck(t, tp[1]);
pc->u.cccccc.c2 = t;
DerefAndCheck(t, tp[2]);
pc->u.cccccc.c3 = t;
DerefAndCheck(t, tp[3]);
pc->u.cccccc.c4 = t;
DerefAndCheck(t, tp[4]);
pc->u.cccccc.c5 = t;
DerefAndCheck(t, tp[5]);
pc->u.cccccc.c6 = t;
pc = NEXTOP(pc,cccccc);
break;
default:
{
UInt i;
for (i = 0; i< arity; i++) {
pc->opc = Yap_opcode(_get_atom);
#if PRECOMPUTE_REGADDRESS
pc->u.xc.x = (CELL) (XREGS + (i+1));
#else
pc->u.xc.x = i+1;
#endif
DerefAndCheck(t, tp[0]);
pc->u.xc.c = t;
tp++;
pc = NEXTOP(pc,xc);
}
}
break;
}
pc->opc = Yap_opcode(_procceed);
pc->u.p.p = pe;
return TRUE;
}
static Int
p_dbload_get_space( USES_REGS1 )
{ /* '$number_of_clauses'(Predicate,M,N) */
Term t = Deref(ARG1);
Term mod = Deref(ARG2);
Term tn = Deref(ARG3);
UInt arity;
Prop pe;
PredEntry *ap;
UInt sz;
MegaClause *mcl;
yamop *ptr;
UInt ncls;
UInt required;
if (IsVarTerm(mod) || !IsAtomTerm(mod)) {
return(FALSE);
}
if (IsAtomTerm(t)) {
Atom a = AtomOfTerm(t);
arity = 0;
pe = PredPropByAtom(a, mod);
} else if (IsApplTerm(t)) {
register Functor f = FunctorOfTerm(t);
arity = ArityOfFunctor(f);
pe = PredPropByFunc(f, mod);
} else {
return FALSE;
}
if (EndOfPAEntr(pe))
return FALSE;
ap = RepPredProp(pe);
if (ap->PredFlags & (DynamicPredFlag|LogUpdatePredFlag
#ifdef TABLING
|TabledPredFlag
#endif /* TABLING */
)) {
Yap_Error(PERMISSION_ERROR_MODIFY_STATIC_PROCEDURE,t,"dbload_get_space/4");
return FALSE;
}
if (IsVarTerm(tn) || !IsIntegerTerm(tn)) {
return FALSE;
}
ncls = IntegerOfTerm(tn);
if (ncls <= 1) {
return FALSE;
}
sz = compute_dbcl_size(arity);
required = sz*ncls+sizeof(MegaClause)+(UInt)NEXTOP((yamop *)NULL,l);
#ifdef DEBUG
total_megaclause += required;
nof_megaclauses++;
#endif
while (!(mcl = (MegaClause *)Yap_AllocCodeSpace(required))) {
if (!Yap_growheap(FALSE, required, NULL)) {
/* just fail, the system will keep on going */
return FALSE;
}
}
Yap_ClauseSpace += required;
/* cool, it's our turn to do the conversion */
mcl->ClFlags = MegaMask;
mcl->ClSize = sz*ncls;
mcl->ClPred = ap;
mcl->ClItemSize = sz;
mcl->ClNext = NULL;
ap->cs.p_code.FirstClause =
ap->cs.p_code.LastClause =
mcl->ClCode;
ap->PredFlags |= MegaClausePredFlag;
ap->cs.p_code.NOfClauses = ncls;
if (ap->PredFlags & (SpiedPredFlag|CountPredFlag|ProfiledPredFlag)) {
ap->OpcodeOfPred = Yap_opcode(_spy_pred);
} else {
ap->OpcodeOfPred = INDEX_OPCODE;
}
ap->CodeOfPred = ap->cs.p_code.TrueCodeOfPred = (yamop *)(&(ap->OpcodeOfPred));
ptr = (yamop *)((ADDR)mcl->ClCode+ncls*sz);
ptr->opc = Yap_opcode(_Ystop);
return Yap_unify(ARG4, MkIntegerTerm((Int)mcl));
}
static Int
p_dbassert( USES_REGS1 )
{ /* '$number_of_clauses'(Predicate,M,N) */
Term thandle = Deref(ARG2);
Term tn = Deref(ARG3);
PredEntry *pe;
MegaClause *mcl;
Int n;
if (IsVarTerm(thandle) || !IsIntegerTerm(thandle)) {
return FALSE;
}
mcl = (MegaClause *)IntegerOfTerm(thandle);
if (IsVarTerm(tn) || !IsIntegerTerm(tn)) {
return FALSE;
}
n = IntegerOfTerm(tn);
pe = mcl->ClPred;
return store_dbcl_size((yamop *)((ADDR)mcl->ClCode+n*(mcl->ClItemSize)),pe->ArityOfPE,Deref(ARG1),pe);
}
void
Yap_InitCdMgr(void)
{
@ -5701,6 +5930,10 @@ Yap_InitCdMgr(void)
Yap_InitCPred("continuation", 4, p_env_info, HiddenPredFlag);
Yap_InitCPred("cp_to_predicate", 5, p_cpc_info, HiddenPredFlag);
CurrentModule = cm;
CurrentModule = DBLOAD_MODULE;
Yap_InitCPred("dbload_get_space", 4, p_dbload_get_space, 0L);
Yap_InitCPred("dbassert", 3, p_dbassert, 0L);
CurrentModule = cm;
Yap_InitCPred("$predicate_erased_statistics", 5, p_predicate_erased_statistics, SyncPredFlag);
#ifdef DEBUG
Yap_InitCPred("$predicate_live_cps", 4, p_predicate_lu_cps, 0L);

6
C/index.c
View File

@ -6864,8 +6864,8 @@ Yap_FollowIndexingCode(PredEntry *ap, yamop *ipc, Term Terms[3], yamop *ap_pc, y
break;
}
}
update_clause_choice_point(ipc->u.OtILl.n,ap_pc PASS_REGS);
return ipc->u.OtILl.d;
update_clause_choice_point(ipc->u.OtaLl.n,ap_pc PASS_REGS);
return ipc->u.OtaLl.d;
#if TABLING
case _table_try_single:
return (LogUpdClause *)ClauseCodeToStaticClause(ipc);
@ -6874,7 +6874,7 @@ Yap_FollowIndexingCode(PredEntry *ap, yamop *ipc, Term Terms[3], yamop *ap_pc, y
case _count_trust_logical:
case _profiled_trust_logical:
{
UInt timestamp = ((CELL *)(B+1))[5];
UInt timestamp = IntegerOfTerm(((CELL *)(B+1))[5]);
LogUpdIndex *cl = ipc->u.OtILl.block;
LogUpdClause *newpc;

1
C/modules.c
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@ -327,5 +327,6 @@ Yap_InitModules(void)
LookupModule(HACKS_MODULE);
LookupModule(ARG_MODULE);
LookupModule(GLOBALS_MODULE);
LookupModule(DBLOAD_MODULE);
CurrentModule = PROLOG_MODULE;
}

10
C/scanner.c
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@ -315,6 +315,11 @@ read_quoted_char(int *scan_nextp, IOSTREAM *inp_stream)
return '\n';
case 'r':
return '\r';
case 's': /* space */
if (yap_flags[CHARACTER_ESCAPE_FLAG] == ISO_CHARACTER_ESCAPES) {
return send_error_message("invalid escape sequence \\s");
} else
return ' ';
case 't':
return '\t';
case 'u':
@ -357,6 +362,11 @@ read_quoted_char(int *scan_nextp, IOSTREAM *inp_stream)
}
case 'v':
return '\v';
case 'z': /* Prolog end-of-file */
if (yap_flags[CHARACTER_ESCAPE_FLAG] == ISO_CHARACTER_ESCAPES) {
return send_error_message("invalid escape sequence \\z");
} else
return -1;
case '\\':
return '\\';
case '\'':

1
H/dhstruct.h
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@ -96,6 +96,7 @@
#define ARG_MODULE Yap_heap_regs->arg_module
#define GLOBALS_MODULE Yap_heap_regs->globals_module
#define SWI_MODULE Yap_heap_regs->swi_module
#define DBLOAD_MODULE Yap_heap_regs->dbload_module

1
H/hstruct.h
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@ -96,6 +96,7 @@
Term arg_module;
Term globals_module;
Term swi_module;
Term dbload_module;

1
H/iatoms.h
View File

@ -63,6 +63,7 @@
AtomCut = Yap_LookupAtom("!");
AtomCutBy = Yap_FullLookupAtom("$cut_by");
AtomDAbort = Yap_FullLookupAtom("$abort");
AtomDBLoad = Yap_FullLookupAtom("$db_load");
AtomDBREF = Yap_LookupAtom("DBRef");
AtomDBReference = Yap_LookupAtom("db_reference");
AtomDBTerm = Yap_LookupAtom("db_term");

1
H/ihstruct.h
View File

@ -96,6 +96,7 @@
Yap_heap_regs->arg_module = MkAtomTerm(AtomArg);
Yap_heap_regs->globals_module = MkAtomTerm(AtomNb);
Yap_heap_regs->swi_module = MkAtomTerm(AtomSwi);
Yap_heap_regs->dbload_module = MkAtomTerm(AtomDBLoad);

1
H/ratoms.h
View File

@ -63,6 +63,7 @@
AtomCut = AtomAdjust(AtomCut);
AtomCutBy = AtomAdjust(AtomCutBy);
AtomDAbort = AtomAdjust(AtomDAbort);
AtomDBLoad = AtomAdjust(AtomDBLoad);
AtomDBREF = AtomAdjust(AtomDBREF);
AtomDBReference = AtomAdjust(AtomDBReference);
AtomDBTerm = AtomAdjust(AtomDBTerm);

1
H/rhstruct.h
View File

@ -96,6 +96,7 @@
Yap_heap_regs->arg_module = AtomTermAdjust(Yap_heap_regs->arg_module);
Yap_heap_regs->globals_module = AtomTermAdjust(Yap_heap_regs->globals_module);
Yap_heap_regs->swi_module = AtomTermAdjust(Yap_heap_regs->swi_module);
Yap_heap_regs->dbload_module = AtomTermAdjust(Yap_heap_regs->dbload_module);

2
H/tatoms.h
View File

@ -124,6 +124,8 @@
#define AtomCutBy Yap_heap_regs->AtomCutBy_
Atom AtomDAbort_;
#define AtomDAbort Yap_heap_regs->AtomDAbort_
Atom AtomDBLoad_;
#define AtomDBLoad Yap_heap_regs->AtomDBLoad_
Atom AtomDBREF_;
#define AtomDBREF Yap_heap_regs->AtomDBREF_
Atom AtomDBReference_;

7
Makefile.in
View File

@ -296,6 +296,7 @@ PL_SOURCES= \
$(srcdir)/pl/consult.yap \
$(srcdir)/pl/control.yap \
$(srcdir)/pl/corout.yap $(srcdir)/pl/debug.yap \
$(srcdir)/pl/dbload.yap \
$(srcdir)/pl/depth_bound.yap \
$(srcdir)/pl/dialect.yap \
$(srcdir)/pl/directives.yap \
@ -570,7 +571,7 @@ pl-ntconsole.o: $(srcdir)/console/LGPL/pl-ntconsole.c config.h
$(CC) -c $(CFLAGS) -I$(srcdir) -I$(srcdir)/include -I$(srcdir)/packages/PLStream @EXTRA_INCLUDES_FOR_WIN32@ $(srcdir)/console/LGPL/pl-ntconsole.c -o $@
pl-ntmain.o: $(srcdir)/console/LGPL/pl-ntmain.c config.h
$(CC) -c $(CFLAGS) -I$(srcdir)/include -I$(srcdir) -I$(srcdir)/packages/PLStream @EXTRA_INCLUDES_FOR_WIN32@ < $(srcdir)/console/LGPL/pl-ntmain.c -o $@
$(CC) -c $(CFLAGS) -I$(srcdir)/include -I$(srcdir) -I$(srcdir)/packages/PLStream @EXTRA_INCLUDES_FOR_WIN32@ $(srcdir)/console/LGPL/pl-ntmain.c -o $@
pl-buffer.o: $(srcdir)/packages/PLStream/pl-buffer.c config.h
$(CC) -c $(CFLAGS) -I$(srcdir)/include -I$(srcdir) -I$(srcdir)/packages/PLStream @EXTRA_INCLUDES_FOR_WIN32@ $(srcdir)/packages/PLStream/pl-buffer.c -o $@
@ -702,9 +703,9 @@ startup.yss: yap@EXEC_SUFFIX@ $(PL_SOURCES)
yap@EXEC_SUFFIX@: $(HEADERS) yap.o @YAPLIB@
$(MPI_CC) $(EXECUTABLE_CFLAGS) $(LDFLAGS) -o yap yap.o @YAPLIB@ $(LIBS) @MPI_LIBS@
pl-yap@EXEC_SUFFIX@: $(PLCONS_OBJECTS) LGPL/swi_console/plterm.dll packages/PLSTream/libplstream.dll
plyap@EXEC_SUFFIX@: $(PLCONS_OBJECTS) $(HEADERS) @YAPLIB@ LGPL/swi_console/plterm.dll
(cd LGPL/swi_console; $(MAKE))
$(MPI_CC) $(EXECUTABLE_CFLAGS) $(LDFLAGS) -o pl-yap $(PLCONS_OBJECTS) LGPL/swi_console/plterm.dll packages/PLSTream/libplstream.dll @YAPLIB@ $(LIBS) @MPI_LIBS@
$(MPI_CC) $(EXECUTABLE_CFLAGS) $(LDFLAGS) -o pl-yap $(PLCONS_OBJECTS) LGPL/swi_console/plterm.dll @YAPLIB@ $(LIBS) @MPI_LIBS@
libYap.a: $(LIB_OBJECTS)
-rm -f libYap.a

4
docs/yap.tex
View File

@ -8505,7 +8505,9 @@ Stream currently being read in.
@item term_position
@findex file (prolog_load_context/2 option)
@*
Stream position at the stream currently being read in.
Stream position at the stream currently being read in. For SWI
compatibility, it is a term of the form
@code{'$stream_position'(0,Line,0,0,0)}.
@end table
@item source_location(?@var{FileName}, ?@var{Line})

1
misc/ATOMS
View File

@ -68,6 +68,7 @@ A CurrentModule F "$current_module"
A Cut N "!"
A CutBy F "$cut_by"
A DAbort F "$abort"
A DBLoad F "$db_load"
A DBREF N "DBRef"
A DBReference N "db_reference"
A DBTerm N "db_term"

1
misc/HEAPFIELDS
View File

@ -99,6 +99,7 @@ Term hacks_module HACKS_MODULE MkAT AtomYapHacks
Term arg_module ARG_MODULE MkAT AtomArg
Term globals_module GLOBALS_MODULE MkAT AtomNb
Term swi_module SWI_MODULE MkAT AtomSwi
Term dbload_module DBLOAD_MODULE MkAT AtomDBLoad
//
// Module list

13
packages/CLPBN/Makefile.in
View File

@ -30,7 +30,7 @@ CLPBN_SRCDIR = $(srcdir)/clpbn
CLPBN_LEARNING_SRCDIR = $(srcdir)/learning
CLPBN_EXDIR = $(srcdir)/clpbn/examples
CLPBN_EXDIR = $(srcdir)/examples
CLPBN_PROGRAMS= \
$(CLPBN_SRCDIR)/aggregates.yap \
@ -71,6 +71,15 @@ CLPBN_SCHOOL_EXAMPLES= \
$(CLPBN_EXDIR)/School/school_64.yap \
$(CLPBN_EXDIR)/School/tables.yap
CLPBN_HMMER_EXAMPLES= \
$(CLPBN_EXDIR)/HMMer/Artemia.fa \
$(CLPBN_EXDIR)/HMMer/fasta.yap \
$(CLPBN_EXDIR)/HMMer/globin.hmm \
$(CLPBN_EXDIR)/HMMer/globin.yap \
$(CLPBN_EXDIR)/HMMer/plan7.yap \
$(CLPBN_EXDIR)/HMMer/scan.yap \
$(CLPBN_EXDIR)/HMMer/score.yap
CLPBN_EXAMPLES= \
$(CLPBN_EXDIR)/cg.yap \
$(CLPBN_EXDIR)/sprinkler.yap
@ -80,9 +89,11 @@ install: $(CLBN_TOP) $(CLBN_PROGRAMS) $(CLPBN_PROGRAMS)
mkdir -p $(DESTDIR)$(SHAREDIR)/clpbn
mkdir -p $(DESTDIR)$(SHAREDIR)/clpbn/learning
mkdir -p $(DESTDIR)$(SHAREDIR)/clpbn/examples/School
mkdir -p $(DESTDIR)$(SHAREDIR)/clpbn/examples/HMMer
for h in $(CLPBN_TOP); do $(INSTALL_DATA) $$h $(DESTDIR)$(SHAREDIR); done
for h in $(CLPBN_PROGRAMS); do $(INSTALL_DATA) $$h $(DESTDIR)$(SHAREDIR)/clpbn; done
for h in $(CLPBN_LEARNING_PROGRAMS); do $(INSTALL_DATA) $$h $(DESTDIR)$(SHAREDIR)/clpbn/learning; done
for h in $(CLPBN_EXAMPLES); do $(INSTALL_DATA) $$h $(DESTDIR)$(SHAREDIR)/clpbn/examples; done
for h in $(CLPBN_SCHOOL_EXAMPLES); do $(INSTALL_DATA) $$h $(DESTDIR)$(SHAREDIR)/clpbn/examples/School; done
for h in $(CLPBN_HMMER_EXAMPLES); do $(INSTALL_DATA) $$h $(DESTDIR)$(SHAREDIR)/clpbn/examples/HMMer; done

48
packages/CLPBN/examples/HMMer/Artemia.fa Normal file
View File

@ -0,0 +1,48 @@
>S13421 S13421 GLOBIN - BRINE SHRIMP
DKATIKRTWATVTDLPSFGRNVFLSVFAAK
PEYKNLFVEFRNIPASELASSERLLYHGGR
VLSSIDEAIAGIDTPDRAVKTLLALGERHI
SRGTVRRHFEAFSYAFIDELKQRGVESADL
AAWRRGWDNIVNVLEAGLLRRQIDLEVTGL
SCVDVANIQESWSKVSGDLKTTGSVVFQRM
INGHPEYQQLFRQFRDVDLDKLGESNSFVA
HVFRVVAAFDGIIHELDNNQFIVSTLKKLG
EQHIARGTDISHFQNFRVTLLEYLKENGMN
GAQKASWNKAFDAFEKYISMGLSSLKRVDP
ITGLSGLEKNAILSTWGKVRGNLQEVGKAT
FGKLFTAHPEYQQMFRFSQGMPLASLVESP
KFAAHTQRVVSALDQTLLALNRPSDFVYMI
KELGLDHINRGTDRSHFENYQVVFIEYLKE
TLGDSLDEFTVKSFNHVFEVIISFLNEGLR
QADIVDPVTHLTGRQKEMIKASWSKARTDL
RSLGQELFMRMFKAHPEYQTLFVNKGFADV
PLVSLREDERFISHMANVLGGFDTLLQNLD
ESSYFIYSLRNLGDAHIQRKAGTQHFRSFE
AILIPILQESQGLDAASVEAWKKFFDVSIG
VIAQGLKVATSEEADPVTGLYGKEIVALRQ
AFAAVTPRNVEIGKRVFAKLFAAHPEYKNL
FKKFEQYSVEELPSTDAFHYHISLVMNRFS
SIGKVIDDNVSFVYLLKKLGREHIKRGLSR
KQFDQFVELYIAEISSELSDTGRNGLEKVL
TFATGVIEQGLFQLGQVDSNTLTALEKQSI
QDIWSNLRSTGLQDLAVKIFTRLFSAHPEY
KLLFTGRFGNVDNINENAPFKAHLHRVLSA
FDIVISTLDDSEHLIRQLKDLGLFHTRLGM
TRSHFDNFATAFLSVAQDIAPNQLTVLGRE
SLNKGFKLMHGVIEEGLLQLERINPITGLS
AREVAVVKQTWNLVKPDLMGVGMRIFKSLF
EAFPAYQAVFPKFSDVPLDKLEDTPAVGKH
SISVTTKLDELIQTLDEPANLALLARQLGE
DHIVLRVNKPMFKSFGKVLVRLLENDLGQR
FSSFASRSWHKAYDVIVEYIEEGLQQSYKQ
DPVTGITDAEKALVQESWDLLKPDLLGLGR
KIFTKVFTKHPDYQILFTRTGFGDTPLTKL
DDNPAFGTHIIKVMRAFDHVIQILGKPKTL
MAYLRSVGADHIATNVERRHFQAFSNALIP
VMQHDLKAQLRPDAVAAWRKGLDRIIGIID
QGLIGLKEVNPQNAFSAYDIQAVQRTWALA
KPDLMGKGAMVFKQLFTDHGYQPLFSNLAQ
YEITGLEGSPELNTHARNVMAQLDTLVGSL
QNSIELGQSLAQLGKDHVPRKVNRVHFKDF
AEHFIPLMKADLGDEFTPLAESAWKRAFDV
MIATIEQGQEGSSHALSSFLTNPVA

47
packages/CLPBN/examples/HMMer/fasta.yap Normal file
View File

@ -0,0 +1,47 @@
%
% Preliminary support for FASTA format.
% Just convert sequence into string of atoms.
%
% support for a single sequence.
%
:- module(fasta, [fa2atoms/2,fa2atoms/3]).
fa2atoms(F, L) :-
fa2atoms(F, L, []).
fa2atoms(F,L,L0) :-
open(F,read,S),
get0(S,C0),
skip_header(C0,S),
get0(S,C),
read_chars(C, S, L, L0),
close(S).
read_chars(-1,_) --> [].
read_chars(10,S) --> !,
{ get0(S,MC) },
read_chars(MC,S).
read_chars(C,S) -->
[AC],
{
cvt_c(C,AC),
get0(S,MC)
},
read_chars(MC, S).
cvt_c(C,A) :-
C >= 0'A, C =< 0'Z, !,
AC is C-(0'A-0'a),
atom_codes(A,[AC]).
cvt_c(C,A) :-
C >= 0'a, C =< 0'z,
atom_codes(A,[C]).
skip_header(10,_) :- !.
skip_header(_,S) :-
get0(S,C),
skip_header(C,S).

506
packages/CLPBN/examples/HMMer/globin.hmm Normal file
View File

@ -0,0 +1,506 @@
HMMER2.0
NAME globins50
LENG 162
ALPH Amino
RF no
CS no
MAP yes
COM hmmbuild globin.hmm globins50.msf
COM hmmcalibrate globin.hmm
NSEQ 50
DATE Tue Aug 16 16:12:11 2005
CKSUM 8939
XT -8455 -4 -1000 -1000 -8455 -4 -8455 -4
NULT -4 -8455
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EVD -107.906906 0.177814
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147 -1696 -3203 2107 1686 -3513 508 -1292 -3276 -98 -3215 -2304 -545 -2698 2093 -1462 197 -974 -2821 -3384 -2676 150
- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249
- -4 -8959 -10001 -894 -1115 -701 -1378 * *
148 -206 -3207 301 -1311 -3800 -540 -1754 -3505 3357 -3525 -2667 -1586 -3037 -1345 -1850 -1908 -2007 106 -3732 -3091 151
- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249
- -4 -8959 -10001 -894 -1115 -701 -1378 * *
149 1654 -1721 -4245 -3631 2645 -3462 -2390 -910 -3244 1144 -791 -3131 -3508 -2856 -3053 -2564 87 891 -2223 -1892 152
- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249
- -4 -8959 -10001 -894 -1115 -701 -1378 * *
150 -137 -1432 -3948 -3313 1581 -3155 -2026 -114 -2909 1428 2225 -648 -3203 -2531 -2710 -2240 -1547 1624 -1889 1109 153
- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249
- -4 -8959 -10001 -894 -1115 -701 -1378 * *
151 1325 1101 1112 721 -3197 -363 -1036 -2947 702 -1945 -1965 -289 -2471 375 -257 1183 -1037 -2498 -3059 -2377 154
- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249
- -4 -8959 -10001 -894 -1115 -701 -1378 * *
152 1277 -1469 -3536 -2925 -1430 1509 -1928 601 -2600 216 1186 -1524 -3132 -175 -2535 -508 -85 1083 -1920 -1568 155
- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249
- -4 -8959 -10001 -894 -1115 -701 -1378 * *
153 -3610 -3121 -6153 -5690 1786 -5837 -5020 1076 -5518 1386 -1290 -5502 -5406 -4901 -5339 -5127 -3551 2808 -4105 -3986 156
- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249
- -4 -8959 -10001 -894 -1115 -701 -1378 * *
154 2030 2259 -3344 -2779 473 -514 -2054 -1307 -2515 -1647 -982 -2529 -3154 -2266 681 1110 -1625 881 -2225 -1864 157
- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249
- -4 -8959 -10001 -894 -1115 -701 -1378 * *
155 502 -2761 -339 -762 -3031 -384 1988 -18 -326 -1254 -1863 1897 -2499 -629 -1172 471 1548 -2356 -2975 -2324 158
- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249
- -4 -8959 -10001 -894 -1115 -701 -1378 * *
156 2557 -2132 1224 -2787 -2497 -3049 -2499 -1705 -2776 -586 -1671 -2638 -3386 -2536 -2949 -1127 -1982 1773 -2964 -2581 159
- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249
- -4 -8959 -10001 -894 -1115 -701 -1378 * *
157 -4284 -3705 -6735 -6190 -2138 -6510 -5341 1840 -6011 2724 1723 -6217 -5667 -4910 -5578 -5867 -4158 115 -3948 -4121 160
- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249
- -5 -8875 -9917 -894 -1115 -701 -1378 * *
158 1959 -2667 -1304 160 207 -440 -1064 -2658 652 -2686 -1806 -1057 -2476 -630 -1169 822 1391 -2278 -2923 -2284 161
- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249
- -5 -8816 -9858 -894 -1115 -701 -1378 * *
159 1365 -2863 -1251 1036 -3195 -2373 3163 -2932 818 -2872 -1957 -1010 -2467 -558 298 930 -1351 -2492 -3031 -2370 162
- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249
- -5 -8816 -9858 -894 -1115 -701 -1378 * *
160 360 -3058 -1454 144 -3448 -36 -1205 -3163 3161 -3086 -2193 -1228 -2682 -756 -274 -567 -1600 -2731 -3220 -2602 163
- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249
- -5 -8724 -9766 -894 -1115 -701 -1378 * *
161 -5001 -4245 -5636 -5890 -650 -5388 -2113 -3919 -5374 -3258 935 -4373 -5399 -4454 -4899 -4809 -4973 -4162 -1378 4785 164
- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249
- -6 -8565 -9607 -894 -1115 -701 -1378 * *
162 -3220 -3923 -3873 -2549 -201 -3790 3575 -4055 2069 -3728 -3058 -2457 -3723 -1277 2773 -3101 -2911 -3829 -3495 -3253 165
- * * * * * * * * * * * * * * * * * * * *
- * * * * * * * * 0
//

3281
packages/CLPBN/examples/HMMer/globin.yap Normal file
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packages/CLPBN/examples/HMMer/globins50.msf Normal file
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@ -0,0 +1,266 @@
MSF: 171 Type: P Check: 4694 ..
Name: GLB2_MORMR oo Len: 171 Check: 6522 Weight: 2.7687
Name: GLBZ_CHITH oo Len: 171 Check: 6733 Weight: 2.9329
Name: HBA2_BOSMU oo Len: 171 Check: 5006 Weight: 0.6394
Name: HBA2_GALCR oo Len: 171 Check: 6652 Weight: 0.5183
Name: HBA4_SALIR oo Len: 171 Check: 5434 Weight: 1.9511
Name: HBAD_CHLME oo Len: 171 Check: 6621 Weight: 1.2927
Name: HBAD_PASMO oo Len: 171 Check: 8118 Weight: 1.2927
Name: HBAZ_HORSE oo Len: 171 Check: 8382 Weight: 1.6223
Name: HBA_AILME oo Len: 171 Check: 5402 Weight: 0.4145
Name: HBA_ANSSE oo Len: 171 Check: 3688 Weight: 0.8315
Name: HBA_COLLI oo Len: 171 Check: 4420 Weight: 0.8557
Name: HBA_ERIEU oo Len: 171 Check: 5528 Weight: 0.8390
Name: HBA_FRAPO oo Len: 171 Check: 4136 Weight: 0.5014
Name: HBA_MACFA oo Len: 171 Check: 5986 Weight: 0.2233
Name: HBA_MACSI oo Len: 171 Check: 6064 Weight: 0.2233
Name: HBA_MESAU oo Len: 171 Check: 5499 Weight: 0.6722
Name: HBA_PAGLA oo Len: 171 Check: 6189 Weight: 0.5388
Name: HBA_PHACO oo Len: 171 Check: 5129 Weight: 0.5014
Name: HBA_PONPY oo Len: 171 Check: 5894 Weight: 0.3907
Name: HBA_PROLO oo Len: 171 Check: 5810 Weight: 0.4145
Name: HBA_TRIOC oo Len: 171 Check: 6427 Weight: 0.6883
Name: HBB1_VAREX oo Len: 171 Check: 7239 Weight: 1.1252
Name: HBB2_TRICR oo Len: 171 Check: 7790 Weight: 1.9629
Name: HBB2_XENTR oo Len: 171 Check: 9537 Weight: 1.4685
Name: HBBL_RANCA oo Len: 171 Check: 7490 Weight: 1.4685
Name: HBB_CALAR oo Len: 171 Check: 6568 Weight: 0.4226
Name: HBB_COLLI oo Len: 171 Check: 5043 Weight: 0.7672
Name: HBB_EQUHE oo Len: 171 Check: 6101 Weight: 0.6734
Name: HBB_LARRI oo Len: 171 Check: 5673 Weight: 0.7672
Name: HBB_MANSP oo Len: 171 Check: 7148 Weight: 0.4226
Name: HBB_ORNAN oo Len: 171 Check: 6249 Weight: 0.6615
Name: HBB_RABIT oo Len: 171 Check: 7043 Weight: 0.5259
Name: HBB_SPECI oo Len: 171 Check: 3680 Weight: 0.5422
Name: HBB_SPETO oo Len: 171 Check: 4246 Weight: 0.5422
Name: HBB_SUNMU oo Len: 171 Check: 5601 Weight: 0.6734
Name: HBB_TACAC oo Len: 171 Check: 7133 Weight: 0.6615
Name: HBB_TRIIN oo Len: 171 Check: 4009 Weight: 0.8445
Name: HBB_TUPGL oo Len: 171 Check: 7197 Weight: 0.7375
Name: HBB_URSMA oo Len: 171 Check: 7200 Weight: 0.4695
Name: HBE_PONPY oo Len: 171 Check: 5902 Weight: 1.0101
Name: HBF1_URECA oo Len: 171 Check: 6462 Weight: 2.9329
Name: LGB1_PEA oo Len: 171 Check: 4791 Weight: 2.0005
Name: LGB1_VICFA oo Len: 171 Check: 7426 Weight: 2.0005
Name: MYG_ESCGI oo Len: 171 Check: 9170 Weight: 0.7432
Name: MYG_HORSE oo Len: 171 Check: 1290 Weight: 0.7432
Name: MYG_LYCPI oo Len: 171 Check: 1107 Weight: 0.8773
Name: MYG_MOUSE oo Len: 171 Check: 1320 Weight: 1.0018
Name: MYG_MUSAN oo Len: 171 Check: 5461 Weight: 2.3158
Name: MYG_PROGU oo Len: 171 Check: 1450 Weight: 0.7629
Name: MYG_SAISC oo Len: 171 Check: 1728 Weight: 0.7629
//
GLB2_MORMR ...PIVD..S GSVSPLSDAE KNKIRAAW.D IVYKNYEKNG VDILVKFFTG
GLBZ_CHITH MKFIILALCV AAASALSGDQ IGLVQST.YG KVKG....DS VGILYAVFKA
HBA2_BOSMU ...V...... .....LSAAD KGNVKAAW.G KVGGHAAEYG AEALERMFLS
HBA2_GALCR ...V...... .....LSPTD KSNVKAAW.E KVGAHAGDYG AEALERMFLS
HBA4_SALIR ...S...... .....LSAKD KANVKAIW.G KILPKSDEIG EQALSRMLVV
HBAD_CHLME ...M...... .....LTADD KKLLTQLW.E KVAGHQEEFG SEALQRMFLT
HBAD_PASMO ...M...... .....LTAED KKLIQQIW.G KLGGAEEEIG ADALWRMFHS
HBAZ_HORSE ...S...... .....LTKAE RTMVVSIW.G KISMQADAVG TEALQRLFSS
HBA_AILME ...V...... .....LSPAD KTNVKATW.D KIGGHAGEYG GEALERTFAS
HBA_ANSSE ...V...... .....LSAAD KGNVKTVF.G KIGGHAEEYG AETLQRMFQT
HBA_COLLI ...V...... .....LSAND KSNVKAVF.A KIGGQAGDLG GEALERLFIT
HBA_ERIEU ...V...... .....LSATD KANVKTFW.G KLGGHGGEYG GEALDRMFQA
HBA_FRAPO ...V...... .....LSAAD KNNVKGIF.G KISSHAEDYG AEALERMFIT
HBA_MACFA ...V...... .....LSPAD KTNVKAAW.G KVGGHAGEYG AEALERMFLS
HBA_MACSI ...V...... .....LSPAD KTNVKDAW.G KVGGHAGEYG AEALERMFLS
HBA_MESAU ...V...... .....LSAKD KTNISEAW.G KIGGHAGEYG AEALERMFFV
HBA_PAGLA ...V...... .....LSSAD KNNIKATW.D KIGSHAGEYG AEALERTFIS
HBA_PHACO ...V...... .....LSAAD KNNVKGIF.T KIAGHAEEYG AEALERMFIT
HBA_PONPY ...V...... .....LSPAD KTNVKTAW.G KVGAHAGDYG AEALERMFLS
HBA_PROLO ...V...... .....LSPAD KANIKATW.D KIGGHAGEYG GEALERTFAS
HBA_TRIOC ...V...... .....LSAND KTNVKTVF.T KITGHAEDYG AETLERMFIT
HBB1_VAREX ...V...... ....HWTAEE KQLICSLW.G KI..DVGLIG GETLAGLLVI
HBB2_TRICR ...V...... ....HLTAED RKEIAAIL.G KV..NVDSLG GQCLARLIVV
HBB2_XENTR ...V...... ....HWTAEE KATIASVW.G KV..DIEQDG HDALSRLLVV
HBBL_RANCA ...V...... ....HWTAEE KAVINSVW.Q KV..DVEQDG HEALTRLFIV
HBB_CALAR ...V...... ....HLTGEE KSAVTALW.G KV..NVDEVG GEALGRLLVV
HBB_COLLI ...V...... ....HWSAEE KQLITSIW.G KV..NVADCG AEALARLLIV
HBB_EQUHE ...V...... ....QLSGEE KAAVLALW.D KV..NEEEVG GEALGRLLVV
HBB_LARRI ...V...... ....HWSAEE KQLITGLW.G KV..NVADCG AEALARLLIV
HBB_MANSP ...V...... ....HLTPEE KTAVTTLW.G KV..NVDEVG GEALGRLLVV
HBB_ORNAN ...V...... ....HLSGGE KSAVTNLW.G KV..NINELG GEALGRLLVV
HBB_RABIT ...V...... ....HLSSEE KSAVTALW.G KV..NVEEVG GEALGRLLVV
HBB_SPECI ...V...... ....HLSDGE KNAISTAW.G KV..HAAEVG AEALGRLLVV
HBB_SPETO ...V...... ....HLTDGE KNAISTAW.G KV..NAAEIG AEALGRLLVV
HBB_SUNMU ...V...... ....HLSGEE KACVTGLW.G KV..NEDEVG AEALGRLLVV
HBB_TACAC ...V...... ....HLSGSE KTAVTNLW.G HV..NVNELG GEALGRLLVV
HBB_TRIIN ...V...... ....HLTPEE KALVIGLW.A KV..NVKEYG GEALGRLLVV
HBB_TUPGL ...V...... ....HLSGEE KAAVTGLW.G KV..DLEKVG GQSLGSLLIV
HBB_URSMA ...V...... ....HLTGEE KSLVTGLW.G KV..NVDEVG GEALGRLLVV
HBE_PONPY ...V...... ....HFTAEE KAAVTSLW.S KM..NVEEAG GEALGRLLVV
HBF1_URECA .......... ....GLTTAQ IKAIQDHWFL NIKGCLQAAA DSIFFKYLTA
LGB1_PEA GFTDKQEALV NSSSE.FKQN LPGYSILFYT IVLEKAP..A AKGL......
LGB1_VICFA GFTEKQEALV NSSSQLFKQN PSNYSVLFYT IILQKAP..T AKAM......
MYG_ESCGI ...V...... .....LSDAE WQLVLNIW.A KVEADVAGHG QDILIRLFKG
MYG_HORSE ...G...... .....LSDGE WQQVLNVW.G KVEADIAGHG QEVLIRLFTG
MYG_LYCPI ...G...... .....LSDGE WQIVLNIW.G KVETDLAGHG QEVLIRLFKN
MYG_MOUSE ...G...... .....LSDGE WQLVLNVW.G KVEADLAGHG QEVLIGLFKT
MYG_MUSAN .......... ........VD WEKVNSVW.S AVESDLTAIG QNILLRLFEQ
MYG_PROGU ...G...... .....LSDGE WQLVLNVW.G KVEGDLSGHG QEVLIRLFKG
MYG_SAISC ...G...... .....LSDGE WQLVLNIW.G KVEADIPSHG QEVLISLFKG
GLB2_MORMR TPAAQAFFPK FKGLTTADAL KKSSDVRWHA ERIINAVNDA VKSMDDTEKM
GLBZ_CHITH DPTIQAAFPQ FVGK.DLDAI KGGAEFSTHA GRIVGFLGGV IDDLP...NI
HBA2_BOSMU FPTTKTYFPH FD.LSH.... .GSAQVKGHG AKVAAALTKA VGHLDD...L
HBA2_GALCR FPTTKTYFPH FD.LSH.... .GSTQVKGHG KKVADALTNA VLHVDD...M
HBA4_SALIR YPQTKAYFSH WASVAP.... .GSAPVKKHG ITIMNQIDDC VGHMDD...L
HBAD_CHLME YPQTKTYFPH FD.LHP.... .GSEQVRGHG KKVAAALGNA VKSLDN...L
HBAD_PASMO YPSTKTYFPH FD.LSQ.... .GSDQIRGHG KKVVAALSNA IKNLDN...L
HBAZ_HORSE YPQTKTYFPH FD.LHE.... .GSPQLRAHG SKVAAAVGDA VKSIDN...V
HBA_AILME FPTTKTYFPH FD.LSP.... .GSAQVKAHG KKVADALTTA VGHLDD...L
HBA_ANSSE FPQTKTYFPH FD.LQP.... .GSAQIKAHG KKVAAALVEA ANHIDD...I
HBA_COLLI YPQTKTYFPH FD.LSH.... .GSAQIKGHG KKVAEALVEA ANHIDD...I
HBA_ERIEU HPTTKTYFPH FD.LNP.... .GSAQVKGHG KKVADALTTA VNNLDD...V
HBA_FRAPO YPSTKTYFPH FD.LSH.... .GSAQVKGHG KKVVAALIEA ANHIDD...I
HBA_MACFA FPTTKTYFPH FD.LSH.... .GSAQVKGHG KKVADALTLA VGHVDD...M
HBA_MACSI FPTTKTYFPH FD.LSH.... .GSAQVKGHG KKVADALTLA VGHVDD...M
HBA_MESAU YPTTKTYFPH FD.VSH.... .GSAQVKGHG KKVADALTNA VGHLDD...L
HBA_PAGLA FPTTKTYFPH FD.LSH.... .GSAQVKAHG KKVADALTLA VGHLED...L
HBA_PHACO YPSTKTYFPH FD.LSH.... .GSAQIKGHG KKVVAALIEA VNHIDD...I
HBA_PONPY FPTTKTYFPH FD.LSH.... .GSAQVKDHG KKVADALTNA VAHVDD...M
HBA_PROLO FPTTKTYFPH FD.LSP.... .GSAQVKAHG KKVADALTLA VGHLDD...L
HBA_TRIOC YPPTKTYFPH FD.LHH.... .GSAQIKAHG KKVVGALIEA VNHIDD...I
HBB1_VAREX YPWTQRQFSH FGNLSSPTAI AGNPRVKAHG KKVLTSFGDA IKNLDN...I
HBB2_TRICR NPWSRRYFHD FGDLSSCDAI CRNPKVLAHG AKVMRSIVEA TKHLDN...L
HBB2_XENTR YPWTQRYFSS FGNLSNVSAV SGNVKVKAHG NKVLSAVGSA IQHLDD...V
HBBL_RANCA YPWTQRYFST FGDLSSPAAI AGNPKVHAHG KKILGAIDNA IHNLDD...V
HBB_CALAR YPWTQRFFES FGDLSTPDAV MNNPKVKAHG KKVLGAFSDG LTHLDN...L
HBB_COLLI YPWTQRFFSS FGNLSSATAI SGNPNVKAHG KKVLTSFGDA VKNLDN...I
HBB_EQUHE YPWTQRFFDS FGDLSNPAAV MGNPKVKAHG KKVLHSFGEG VHHLDN...L
HBB_LARRI YPWTQRFFAS FGNLSSPTAI NGNPMVRAHG KKVLTSFGEA VKNLDN...I
HBB_MANSP YPWTQRFFDS FGDLSSPDAV MGNPKVKAHG KKVLGAFSDG LNHLDN...L
HBB_ORNAN YPWTQRFFEA FGDLSSAGAV MGNPKVKAHG AKVLTSFGDA LKNLDD...L
HBB_RABIT YPWTQRFFES FGDLSSANAV MNNPKVKAHG KKVLAAFSEG LSHLDN...L
HBB_SPECI YPWTQRFFDS FGDLSSASAV MGNAKVKAHG KKVIDSFSNG LKHLDN...L
HBB_SPETO YPWTQRFFDS FGDLSSASAV MGNAKVKAHG KKVIDSFSNG LKHLDN...L
HBB_SUNMU YPWTQRFFDS FGDLSSASAV MGNPKVKAHG KKVLHSLGEG VANLDN...L
HBB_TACAC YPWTQRFFES FGDLSSADAV MGNAKVKAHG AKVLTSFGDA LKNLDN...L
HBB_TRIIN YPWTQRFFEH FGDLSSASAI MNNPKVKAHG EKVFTSFGDG LKHLED...L
HBB_TUPGL YPWTQRFFDS FGDLSSPSAV MSNPKVKAHG KKVLTSFSDG LNHLDN...L
HBB_URSMA YPWTQRFFDS FGDLSSADAI MNNPKVKAHG KKVLNSFSDG LKNLDN...L
HBE_PONPY YPWTQRFFDS FGNLSSPSAI LGNPKVKAHG KKVLTSFGDA IKNMDN...L
HBF1_URECA YPGDLAFFHK FSSV.PLYGL RSNPAYKAQT LTVINYLDKV VDALGG..NA
LGB1_PEA .......... FSFLKDTAGV EDSPKLQAHA EQVFGLVRDS AAQLRTKGEV
LGB1_VICFA .......... FSFLKDSAGV VDSPKLGAHA EKVFGMVRDS AVQLRATGEV
MYG_ESCGI HPETLEKFDK FKHLKTEAEM KASEDLKKHG NTVLTALGGI LKKKGH...H
MYG_HORSE HPETLEKFDK FKHLKTEAEM KASEDLKKHG TVVLTALGGI LKKKGH...H
MYG_LYCPI HPETLDKFDK FKHLKTEDEM KGSEDLKKHG NTVLTALGGI LKKKGH...H
MYG_MOUSE HPETLDKFDK FKNLKSEEDM KGSEDLKKHG CTVLTALGTI LKKKGQ...H
MYG_MUSAN YPESQNHFPK FKN.KSLGEL KDTADIKAQA DTVLSALGNI VKKKGS...H
MYG_PROGU HPETLEKFDK FKHLKAEDEM RASEELKKHG TTVLTALGGI LKKKGQ...H
MYG_SAISC HPETLEKFDK FKHLKSEDEM KASEELKKHG TTVLTALGGI LKKKGQ...H
GLB2_MORMR SMKLQELSVK HAQSFYVDRQ YFKVLAGII. ........AD TTAPGDAGFE
GLBZ_CHITH GKHVDALVAT H.KPRGVTHA QFNNFRAAFI AYLKGHV..D YTAAVEAAWG
HBA2_BOSMU PGALSELSDL HAHKLRVDPV NFKLLSHSLL VTLASHLPSD FTPAVHASLD
HBA2_GALCR PSALSALSDL HAHKLRVDPV NFKLLRHCLL VTLACHHPAE FTPAVHASLD
HBA4_SALIR FGFLTKLSEL HATKLRVDPT NFKILAHNLI VVIAAYFPAE FTPEIHLSVD
HBAD_CHLME SQALSELSNL HAYNLRVDPA NFKLLAQCFQ VVLATHLGKD YSPEMHAAFD
HBAD_PASMO SQALSELSNL HAYNLRVDPV NFKFLSQCLQ VSLATRLGKE YSPEVHSAVD
HBAZ_HORSE AGALAKLSEL HAYILRVDPV NFKFLSHCLL VTLASRLPAD FTADAHAAWD
HBA_AILME PGALSALSDL HAHKLRVDPV NFKLLSHCLL VTLASHHPAE FTPAVHASLD
HBA_ANSSE AGALSKLSDL HAQKLRVDPV NFKFLGHCFL VVLAIHHPSL LTPEVHASMD
HBA_COLLI AGALSKLSDL HAQKLRVDPV NFKLLGHCFL VVVAVHFPSL LTPEVHASLD
HBA_ERIEU PGALSALSDL HAHKLRVDPV NFKLLSHCLL VTLALHHPAD FTPAVHASLD
HBA_FRAPO AGTLSKLSDL HAHKLRVDPV NFKLLGQCFL VVVAIHHPSA LTPEVHASLD
HBA_MACFA PQALSALSDL HAHKLRVDPV NFKLLSHCLL VTLAAHLPAE FTPAVHASLD
HBA_MACSI PQALSALSDL HAHKLRVDPV NFKLLSHCLL VTLAAHLPAE FTPAVHASLD
HBA_MESAU PGALSALSDL HAHKLRVDPV NFKLLSHCLL VTLANHHPAD FTPAVHASLD
HBA_PAGLA PNALSALSDL HAYKLRVDPV NFKLLSHCLL VTLACHHPAE FTPAVHSALD
HBA_PHACO TGTLSKLSDL HAHKLRVDPV NFKLLGQCFL VVVAIHHPSA LTPEVHASLD
HBA_PONPY PNALSALSDL HAHKLRVDPV NFKLLSHCLL VTLAAHLPAE FTPAVHASLD
HBA_PROLO PGALSALSDL HAYKLRVDPV NFKLLSHCLL VTLACHHPAE FTPAVHASLD
HBA_TRIOC AGALSKLSDL HAQKLRVDPV NFKLLGQCFL VVVAIHHPSV LTPEVHASLD
HBB1_VAREX KDTFAKLSEL HCDKLHVDPT NFKLLGNVLV IVLADHHGKE FTPAHHAAYQ
HBB2_TRICR REYYADLSVT HSLKFYVDPE NFKLFSGIVI VCLALTLQTD FSCHKQLAFE
HBB2_XENTR KSHLKGLSKS HAEDLHVDPE NFKRLADVLV IVLAAKLGSA FTPQVQAVWE
HBBL_RANCA KGTLHDLSEE HANELHVDPE NFRRLGEVLI VVLGAKLGKA FSPQVQHVWE
HBB_CALAR KGTFAHLSEL HCDKLHVDPE NFRLLGNVLV CVLAHHFGKE FTPVVQAAYQ
HBB_COLLI KGTFAQLSEL HCDKLHVDPE NFRLLGDILV IILAAHFGKD FTPECQAAWQ
HBB_EQUHE KGTFAQLSEL HCDKLHVDPE NFRLLGNVLV VVLARHFGKD FTPELQASYQ
HBB_LARRI KNTFAQLSEL HCDKLHVDPE NFRLLGDILI IVLAAHFAKD FTPDSQAAWQ
HBB_MANSP KGTFAQLSEL HCDKLHVDPE NFKLLGNVLV CVLAHHFGKE FTPQVQAAYQ
HBB_ORNAN KGTFAKLSEL HCDKLHVDPE NFNRLGNVLI VVLARHFSKD FSPEVQAAWQ
HBB_RABIT KGTFAKLSEL HCDKLHVDPE NFRLLGNVLV IVLSHHFGKE FTPQVQAAYQ
HBB_SPECI KGTFASLSEL HCDKLHVDPE NFKLLGNMIV IVMAHHLGKD FTPEAQAAFQ
HBB_SPETO KGTFASLSEL HCDKLHVDPE NFKLLGNMIV IVMAHHLGKD FTPEAQAAFQ
HBB_SUNMU KGTFAKLSEL HCDKLHVDPE NFRLLGNVLV VVLASKFGKE FTPPVQAAFQ
HBB_TACAC KGTFAKLSEL HCDKLHVDPE NFNRLGNVLV VVLARHFSKE FTPEAQAAWQ
HBB_TRIIN KGAFAELSEL HCDKLHVDPE NFRLLGNVLV CVLARHFGKE FSPEAQAAYQ
HBB_TUPGL KGTFAKLSEL HCDKLHVDPE NFRLLGNVLV RVLACNFGPE FTPQVQAAFQ
HBB_URSMA KGTFAKLSEL HCDKLHVDPE NFKLLGNVLV CVLAHHFGKE FTPQVQAAYQ
HBE_PONPY KTTFAKLSEL HCDKLHVDPE NFKLLGNVMV IILATHFGKE FTPEVQAAWQ
HBF1_URECA GALMKAKVPS H.DAMGITPK HFGQLLKLVG GVFQEEF..S ADPTTVAAWG
LGB1_PEA VLGNATLGAI HVQKGVTNP. HFVVVKEALL QTIKKASGNN WSEELNTAWE
LGB1_VICFA VLDGKD.GSI HIQKGVLDP. HFVVVKEALL KTIKEASGDK WSEELSAAWE
MYG_ESCGI EAELKPLAQS HATKHKIPIK YLEFISDAII HVLHSRHPGD FGADAQAAMN
MYG_HORSE EAELKPLAQS HATKHKIPIK YLEFISDAII HVLHSKHPGN FGADAQGAMT
MYG_LYCPI EAELKPLAQS HATKHKIPVK YLEFISDAII QVLQNKHSGD FHADTEAAMK
MYG_MOUSE AAEIQPLAQS HATKHKIPVK YLEFISEIII EVLKKRHSGD FGADAQGAMS
MYG_MUSAN SQPVKALAAT HITTHKIPPH YFTKITTIAV DVLSEMYPSE MNAQVQAAFS
MYG_PROGU AAELAPLAQS HATKHKIPVK YLEFISEAII QVLQSKHPGD FGADAQGAMS
MYG_SAISC EAELKPLAQS HATKHKIPVK YLELISDAIV HVLQKKHPGD FGADAQGAMK
GLB2_MORMR KLMSMICILL SSAY...... .
GLBZ_CHITH ATFDAFFGAV FAK....... M
HBA2_BOSMU KFLANVSTVL TSKYR..... .
HBA2_GALCR KFMASVSTVL TSKYR..... .
HBA4_SALIR KFLQQLALAL AEKYR..... .
HBAD_CHLME KFLSAVAAVL AEKYR..... .
HBAD_PASMO KFMSAVASVL AEKYR..... .
HBAZ_HORSE KFLSIVSSVL TEKYR..... .
HBA_AILME KFFSAVSTVL TSKYR..... .
HBA_ANSSE KFLCAVATVL TAKYR..... .
HBA_COLLI KFVLAVGTVL TAKYR..... .
HBA_ERIEU KFLATVATVL TSKYR..... .
HBA_FRAPO KFLCAVGNVL TAKYR..... .
HBA_MACFA KFLASVSTVL TSKYR..... .
HBA_MACSI KFLASVSTVL TSKYR..... .
HBA_MESAU KFFASVSTVL TSKYR..... .
HBA_PAGLA KFFSAVSTVL TSKYR..... .
HBA_PHACO KFLCAVGTVL TAKYR..... .
HBA_PONPY KFLASVSTVL TSKYR..... .
HBA_PROLO KFFTSVSTVL TSKYR..... .
HBA_TRIOC KFLCAVGNVL SAKYR..... .
HBB1_VAREX KLVNVVSHSL ARRYH..... .
HBB2_TRICR KLMKGVSHAL GHGY...... .
HBB2_XENTR KLNATLVAAL SHGYF..... .
HBBL_RANCA KFIAVLVDAL SHSYH..... .
HBB_CALAR KVVAGVANAL AHKYH..... .
HBB_COLLI KLVRVVAHAL ARKYH..... .
HBB_EQUHE KVVAGVANAL AHKYH..... .
HBB_LARRI KLVRVVAHAL ARKYH..... .
HBB_MANSP KVVAGVANAL AHKYH..... .
HBB_ORNAN KLVSGVAHAL GHKYH..... .
HBB_RABIT KVVAGVANAL AHKYH..... .
HBB_SPECI KVVAGVANAL AHKYH..... .
HBB_SPETO KVVAGVANAL SHKYH..... .
HBB_SUNMU KVVAGVANAL AHKYH..... .
HBB_TACAC KLVSGVSHAL AHKYH..... .
HBB_TRIIN KVVAGVANAL AHKYH..... .
HBB_TUPGL KVVAGVANAL AHKYH..... .
HBB_URSMA KVVAGVANAL AHKYH..... .
HBE_PONPY KLVSAVAIAL AHKYH..... .
HBF1_URECA DAAGVLVAAM .......... K
LGB1_PEA VAYDGLATAI KKAMKT.... A
LGB1_VICFA VAYDGLATAI K....A.... A
MYG_ESCGI KALELFRKDI AAKYKELGFQ G
MYG_HORSE KALELFRNDI AAKYKELGFQ G
MYG_LYCPI KALELFRNDI AAKYKELGFQ G
MYG_MOUSE KALELFRNDI AAKYKELGFQ G
MYG_MUSAN GAFKIICSDI EKEYKAANFQ G
MYG_PROGU KALELFRNDI AAKYKELGFQ G
MYG_SAISC KALELFRNDM AAKYKELGFQ G

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:- ensure_loaded(library(clpbn)).
:- ensure_loaded(library('clpbn/hmm')).
:- hmm_state((m/3, i/3, d/3, t/2, b/2, n/2, j/2, e/2, s/2, c/2)).
/*
We represent a plan7 HMMer as a recursive program. There are two parameters:
i represents position on a string
j slice in the HMMer: probability distributions are different for each slice.
An HMM has 10 states (M, I, D are the core states):
S -> begin
N -> before match
B -> begin a match
M -> match state
I -> insertion
D -> deletion
E -> end of match
C -> continuation after matches done
T -> end of sequence
J -> go back to match start.
S, B, E, and T do not emit.
Each state will be represented as a binary random variable.
Also, you'll see terms of the form
{ S = m(I) with p([t,f], trans([MMCPT,IMCPT,DMCPT]), [M0,I0,D0]) }.
the sum function is as examplified:
P(S=t) = P(MMCPT|M0)P(M0=t)+P(IMCPT|M0)P(I0=t)+P(IDCPT|M0)P(D0=t)
P(S=f) = 1-P(S=t)
With sum a single element may be true so if
k1\=k2, P(A_k1=t,A_k2=t) = 0.
*/
% now this is our nice DBN: notice that CPTs depend on slide,
% so this is really an "irregular" DBN.
% first, the emission probabilities (they are easier ;-).
% we look at the core first: m, and i emissions
% next, go to inner states (state transitions).
% the first m-state
m(I,J,M) :-
slices(J), !,
I1 is I+1,
e(I1,E),
{ M = m(I,J) with p(bool, trans([0]),[E]) },
emitting(M).
% standard m-state
m(I,J,M) :-
I1 is I+1,
J1 is J+1,
i(I1,J,NI),
m(I1,J1,NM),
d(I1,J1,ND),
e(I1,NE),
m_i_cpt(J,MICPT),
m_m_cpt(J,MMCPT),
m_d_cpt(J,MDCPT),
m_e_cpt(J,MECPT),
{ M = m(I,J) with p(bool, trans([MICPT,MMCPT,MDCPT,MECPT]),[NI,NM,ND,NE]) },
emitting(M).
i(I,J,S) :-
I1 is I+1,
J1 is J+1,
m(I1,J1,M),
i(I1,J,IS),
i_i_cpt(J,IICPT),
i_m_cpt(J,IMCPT),
{ S = i(I,J) with p(bool, trans([IMCPT,IICPT]), [M,IS]) },
emitting(S).
d(I,J,D) :-
slices(J), !,
e(I,E),
{ D = d(I,J) with p(bool, trans([0]), [E]) }.
d(I,J,S) :-
J1 is J+1,
m(I,J1,M),
d(I,J1,ND),
m_d_cpt(J,MDCPT),
d_d_cpt(J,DDCPT),
{ S = d(I,J) with p(bool, trans([MDCPT,DDCPT]), [M,ND]) }.
e_evidence([],_).
e_evidence([Emission|Es],Emission) :-
e_evidence(Es,Emission).
%
% N, C, and J states can also emit.
%
% and they have transitions.
% initial state
s(0,S) :-
n(0,N),
{ S = s(0) with p(bool, trans([0]),[N]) }.
n(I,S) :-
I1 is I+1,
b(I1, B0),
n(I1, N0),
n_n_cpt(NNCPT),
n_b_cpt(NBCPT),
{ S = n(I) with p(bool, trans([NBCPT,NNCPT]), [B0,N0]) },
emitting(S).
b(I,S) :-
slices(Ss),
b_m_transitions(0,Ss,I,Ms,MCPTs),
d(I,1, D),
b_d_cpt(BMCPT),
{ S = b(I) with p(bool, trans([BMCPT|MCPTs]), [D|Ms]) }.
b_m_transitions(Ss,Ss,_,[],[]) :- !.
b_m_transitions(J0,Ss,I,[M|Ms],[CPT|MCPTs]) :-
J is J0+1,
m(I,J,M),
b_m_cpt(J,CPT),
b_m_transitions(J,Ss,I,Ms,MCPTs).
j(I,S) :-
I1 is I+1,
b(I1, NB),
j(I1, NJ),
j_b_cpt(JBCPT),
j_j_cpt(JJCPT),
{ S = j(I) with p(bool, trans([JBCPT,JJCPT]), [NB,NJ]) },
emitting(S).
e(I,S) :-
c(I, NC),
j(I, NJ),
e_c_cpt(ECCPT),
e_j_cpt(EJCPT),
{ S = e(I) with p(bool, trans([ECCPT,EJCPT]), [NC,NJ]) }.
c(I,S) :-
I1 is I+1,
t(I1, T),
c(I1, NC),
c_t_cpt(CTCPT),
c_c_cpt(CCCPT),
{ S = c(I) with p(bool, trans([CCCPT,CTCPT]),[NC,T]) },
emitting(S).
t(I,S) :-
% I < IMax
{ S = t(I) with p(bool, trans([]), []) }.
% the item I at slice J is a random variable P.
emitting(M) :-
emission(M).
emission_cpt(Key, CPT) :-
Key=..[A,_,Slice], !,
emission_cpt(A, Slice, CPT).
emission_cpt(_, CPT) :-
nule_cpt(CPT).
emission_cpt(m,J,CPT) :- !, me_cpt(J,CPT).
emission_cpt(i,J,CPT) :- !, ie_cpt(J,CPT).
emission_cpt(_,_,CPT) :- nule_cpt(CPT).
ie_cpt(I,Logs) :- ie_cpt(I,Logs,_,_).
me_cpt(I,Logs) :- me_cpt(I,Logs,_,_).
nule_cpt(Logs) :- nule_cpt(Logs,_,_).
b_m_cpt(I,Log) :- b_m_cpt(I,Log,_,_).
b_d_cpt(Log) :- b_d_cpt(Log,_,_).
c_c_cpt(Log) :- c_c_cpt(Log,_,_).
c_t_cpt(Log) :- c_t_cpt(Log,_,_).
d_d_cpt(I,Log) :- d_d_cpt(I,Log,_,_).
d_m_cpt(I,Log) :- d_m_cpt(I,Log,_,_).
e_c_cpt(Log) :- e_c_cpt(Log,_,_).
e_j_cpt(Log) :- e_j_cpt(Log,_,_).
i_i_cpt(I,Log) :- i_i_cpt(I,Log,_,_).
i_m_cpt(I,Log) :- i_m_cpt(I,Log,_,_).
j_b_cpt(Log) :- j_b_cpt(Log,_,_).
j_j_cpt(Log) :- j_j_cpt(Log,_,_).
m_d_cpt(I,Log) :- m_d_cpt(I,Log,_,_).
m_e_cpt(I,Log) :- m_e_cpt(I,Log,_,_).
m_i_cpt(I,Log) :- m_i_cpt(I,Log,_,_).
m_m_cpt(I,Log) :- m_m_cpt(I,Log,_,_).
n_b_cpt(Log) :- n_b_cpt(Log,_,_).
n_n_cpt(Log) :- n_n_cpt(Log,_,_).
%hmm_domain([a, c, d, e, f, g, h, i, k, l, m, n, p, q, r, s, t, v, w, y]).
hmm_domain(aminoacids).

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%
% Convert HMMer model to CLP(BN) program
%
main :-
open('hmmer_b.1.18.1.hmm', read, S),
open('hmmer_b.1.18.1.yap', write, W),
% open('globin.hmm', read, S),
catch(parse_model(S,_),done(Info),stop(S,W,Info)),
close(S),
close(W).
stop(S,W,Info) :-
ground(Info),
gen_program(W, Info).
stop(_,_,_) :-
format(user_error,"Bad HMM~n", []).
parse_model(S,Info) :-
get_line(S, Line, Info),
% format('~s~n',[Line]),
match_field(Info, S, Line, []),
parse_model(S, Info).
get_line(S, Out, Info) :-
get0(S, C),
(
C == 10 -> Out = [] ;
C == -1 -> throw(done(Info)) ;
Out = [C|Line], get_line(S, Line, Info)
).
match_field(hmmer(2,_,_,_,_,_,_,_), _) --> "HMMER", !,
scanner_skip. % mandatory field, should be ground
match_field(hmmer(_,Name,_,_,_,_,_,_),_) --> "NAME", !, % mandatory field
scanner_skip_blanks,
get_name(String), {atom_codes(Name,String) }.
match_field(_,_) --> "ACC", !. % accession id, used to track DB accesses
match_field(hmmer(_,_,NOfStates,_,_,_,_,_),_) --> "LENG", !, % number of states
scanner_skip_blanks,
get_number(NOfStates, 0).
match_field(hmmer(_,_,_,Alph,_,_,_,_),_) --> "ALPH", !, % aminos or bases
scanner_skip_blanks,
check_alphabet(Alph).
match_field(_,_) --> "RF", !, scanner_skip.
match_field(_,_) --> "CS", !, scanner_skip.
match_field(hmmer(_,_,_,_,_,_,_,MAP),_) --> "MAP", !,
scanner_skip_blanks,
to_lower(Codes),
{ map_code(Codes,MAP) }.
match_field(_,_) --> "COM", !, scanner_skip.
match_field(_,_) --> "CKSUM", !, scanner_skip.
match_field(_,_) --> "GA", !, scanner_skip.
match_field(_,_) --> "TC", !, scanner_skip.
match_field(_,_) --> "NC", !, scanner_skip.
match_field(_,_) --> "NSEQ", !, scanner_skip.
match_field(_,_) --> "DATE", !, scanner_skip.
match_field(hmmer(_,_,_,_,special(NB,NN,EC,EJ,CT,CC,JB,JJ,_,_),_,_,_),_) --> "XT", !,
scan_transition(NB),
scan_transition(NN),
scan_transition(EC),
scan_transition(EJ),
scan_transition(CT),
scan_transition(CC),
scan_transition(JB),
scan_transition(JJ).
match_field(hmmer(_,_,_,_,special(_,_,_,_,_,_,_,_,GG,GF),_,_,_),_) --> "NULT", !,
scan_transition(GG),
scan_transition(GF).
match_field(hmmer(_,_,_,Alph,_,NULE,_,_),_) --> "NULE", !,
{ nof_symbols(Alph,N) },
scan_transitions(N,Transitions),
{ NULE =.. [null|Transitions] }.
match_field(_,_) --> "EVD", !,
scanner_skip. % optional, but should do later.x
match_field(Info,S) --> "HMM", !,
scanner_skip,
{
get_line(S,_,Info),
Info = hmmer(_,_,NOfStates,Alph,_,_,model(BD,NBD,Transitions),MAP),
nof_symbols(Alph,N),
scan_model(S,NOfStates,N,BD,NBD,Transitions,MAP,Info),
throw(done(Info))
}.
scan_model(S,NOfStates,N,BD,NBD,Transitions,MAP,Info) :-
get_line(S,Line, Info),
scan_bd(BD, NBD, Line, []),
scan_states(NOfStates, N, S, MAP, Transitions, Info).
scan_states(0, _, _, MAP, [], _) :- !, close_map(MAP).
scan_states(NOfStates, N, Stream, MAP, [t(E,I,S)|Transitions], Info) :-
NOfStates1 is NOfStates-1,
scan_state(Stream, E, I, MAP, S, N, NMAP, Info),
scan_states(NOfStates1, N, Stream, NMAP, Transitions, Info).
scan_state(Stream, E,I,MAP,s(MM,MI,MD,IM,II,DM,DD,BM,ME), N, NMAP, Info) :-
get_line(Stream, ELine, Info),
get_line(Stream, ILine, Info),
get_line(Stream, SLine, Info),
% format('~s~n~s~n~s~n',[ELine,ILine,SLine]),
scanner_skip_field(ELine,Eline1),
scan_transitions(N, E, Eline1, EMap),
scan_map(MAP,NMAP,EMap, []),
scanner_skip_field(ILine,ILine1),
scan_transitions(N, I, ILine1, []),
scanner_skip_field(SLine,SLine1),
scan_transitions(MM, MI, MD, IM, II, DM, DD, BM, ME, SLine1, []).
scan_transitions(MM, MI, MD, IM, II, DM, DD, BM, ME) -->
scan_transition(MM),
scan_transition(MI),
scan_transition(MD),
scan_transition(IM),
scan_transition(II),
scan_transition(DM),
scan_transition(DD),
scan_transition(BM),
scan_transition(ME).
scan_transitions(0, []) --> !.
scan_transitions(N, [T|Ts]) -->
{ N1 is N-1 },
scan_transition(T),
scan_transitions(N1, Ts).
scan_transition(T) -->
scanner_skip_blanks,
get_transition(T).
get_transition('*') --> "*", !, scanner_skip_blanks.
get_transition(N) --> [C],
{ C >= 0'0, C =< 0'9, !, C0 is C-0'0 },
get_number(N, C0 ).
get_transition(N) --> "-",
get_number(C0, 0 ),
{ N is -C0}.
get_number(Nf, N0) --> [C], !,
( { C >= 0'0, C =< 0'9 } -> { Ni is N0*10+(C-0'0) }, get_number(Nf,Ni) ;
{ Nf = N0 }
).
get_number(N, N) --> [].
scanner_skip_blanks --> " ", !, scanner_skip_blanks.
scanner_skip_blanks --> " ", !, scanner_skip_blanks.
scanner_skip_blanks --> [].
scanner_skip_field --> scan_transition(_).
scan_bd(BD, NBD) -->
scan_transition(BD),
scanner_skip_field,
scan_transition(NBD).
check_alphabet(Alph) -->
to_lower(Lower),
{ get_alph(Lower, Alph) }.
to_lower([CF|Lower]) --> [C], !,
{ ( C >= 0'A, C =< 0'Z -> CF is C+(0'a-0'A) ; CF = C) },
to_lower(Lower).
to_lower([]) --> [].
get_alph("amino", amino).
get_alph("nucleic", nucleic).
map_code("yes", yes(_)).
map_code("no", no).
nof_symbols(amino,20).
nof_symbols(nucleic,4).
scanner_skip(_,_).
get_name(L,L,[]).
scan_map(yes([Id|Next]),yes(Next)) -->
scan_transition(Id).
scan_map(no,no) --> [].
close_map(yes([])) :- !.
close_map(no).
gen_program(W, hmmer(VersionId,Name,NOfStates,Alphabet,SpecialTransitions,NULE,Model,MAP)) :-
format(W, '~n% HMMer Version ~d (Plan 7) using ~a~n',[VersionId,Alphabet]),
format(W, '~n% Name: ~a~n',[Name]),
format(W, '~n% Size: ~d~n',[NOfStates]),
format(W, 'slices(~d).~n',[NOfStates]),
gen_specials(W, SpecialTransitions),
gen_nule(W, NULE,Alphabet,NULEProbs),
gen_model(W, Model,NULEProbs),
gen_map(W, MAP).
%
% special nodes in graph.
%
gen_specials(W, special(NB,NN,EC,EJ,CT,CC,JB,JJ,GG,GF)) :-
% reaching state N
normalize(NN,1.0,NNCPT),
format(W, '~n%Reaching state N.~n',[]),
format(W, 'n_n_cpt(~w,1.0,~w).~n',[NN,NNCPT]),
% reaching state B
normalize(JB,1.0,JBCPT),
format(W, '~n%Reaching state B.~n',[]),
format(W, 'j_b_cpt(~w,1.0,~w).~n',[JB,JBCPT]),
normalize(NB,1.0,NBCPT),
format(W, 'n_b_cpt(~w,1.0,~w).~n',[NB,NBCPT]),
% reaching state J
format(W, '~n%Reaching state J.~n',[]),
normalize(EJ,1.0,EJCPT),
format(W, 'e_j_cpt(~w,1.0,~w).~n',[EJ,EJCPT]),
normalize(JJ,1.0,JJCPT),
format(W, 'j_j_cpt(~w,1.0,~w).~n',[JJ,JJCPT]),
% reaching state C
format(W, '~n%Reaching state C.~n',[]),
normalize(EC,1.0,ECCPT),
format(W, 'e_c_cpt(~w,1.0,~w).~n',[EC,ECCPT]),
normalize(CC,1.0,CCCPT),
format(W, 'c_c_cpt(~w,1.0,~w).~n',[CC,CCCPT]),
% reaching state T
format(W, '~n%Reaching state T.~n',[]),
normalize(CT,1.0,CTCPT),
format(W, 'c_t_cpt(~w,1.0,~w).~n',[CT,CTCPT]),
% null model
format(W, '~n%Reaching state G (Null Model).~n',[]),
normalize(GG,1.0,GGCPT),
format(W, 'g_g_cpt(~w,1.0,~w).~n',[GG,GGCPT]),
format(W, '~n%Reaching state F (Null Model).~n',[]),
normalize(GF,1.0,GFCPT),
format(W, 'g_f_cpt(~w,1.0,~w).~n',[GF,GFCPT]).
normalize(*,_,0.0) :- !.
normalize(Score,NULL,Prob) :-
Prob is NULL * exp(2.0, (Score/1000)).
normalizel([],_,[]).
normalizel([Score|Scores],NULL,[Prob|Probs]) :-
normalize(Score, NULL, Prob),
normalizel(Scores,NULL,Probs).
normalizell([],[],[]).
normalizell([Score|Scores],[Norm|Norms],[Prob|Probs]) :-
normalize(Score, Norm, Prob),
normalizell(Scores,Norms,Probs).
% null emission CPT
gen_nule(W, NULE,Alph,PsCPT) :-
NULE =.. [_|Ps],
nof_symbols(Alph,Size),
Norm is 1/Size,
normalizel(Ps,Norm,PsCPT),
E0s =.. [e|Ps],
Es =.. [e|PsCPT],
format(W, '~n%Null state emission CPT.~n',[]),
format(W, 'nule_cpt(~n ~w,~n ~w,~n ~w).~n',[E0s,Norm,Es]).
gen_model(W, model(BD,NBD,States),PsCPT) :-
normalize_bd(BD,NBD,BDCPT),
format(W, '~n%Reaching first D.~n',[]),
format(W, 'b_d_cpt(~w,~w,~w).~n',[BD,NBD,BDCPT]),
gen_states(W, States,1,PsCPT).
gen_states(_, [],_,_).
gen_states(W, [State|States],StateNo,PsCPT) :-
gen_state(W, State,StateNo,PsCPT),
NStateNo is StateNo+1,
gen_states(W, States,NStateNo,PsCPT).
gen_state(W, t(E,I,s(MM,MI,MD,IM,II,DM,DD,BM,ME)),StateNo,PsCPT) :-
format(W, '~n%State ~d.~n',[StateNo]),
Norm =.. [e|PsCPT],
normalizell(E,PsCPT,ECPT),
E0s =.. [e|E],
Es =.. [e|ECPT],
find_consensus(W,StateNo,ECPT),
sum(ECPT,0,TE),
format(W, 'me_cpt(~d,~n ~w,~n ~w,~n ~w). % ~w~n',[StateNo,E0s,Norm,Es,TE]),
normalizell(I,PsCPT,ICPT),
I0s =.. [e|ICPT],
Is =.. [e|ICPT],
sum(ICPT,0,TI),
format(W, 'ie_cpt(~d,~n ~w,~n ~w,~n ~w). %~w~n',[StateNo,I0s,Norm,Is,TI]),
normalize(MM,1.0,MMCPT),
format(W, 'm_m_cpt(~d,~w,~w,~w).~n',[StateNo,MM,1.0,MMCPT]),
normalize(MI,1.0,MICPT),
format(W, 'm_i_cpt(~d,~w,~w,~w).~n',[StateNo,MI,1.0,MICPT]),
normalize(MD,1.0,MDCPT),
format(W, 'm_d_cpt(~d,~w,~w,~w).~n',[StateNo,MD,1.0,MDCPT]),
normalize(II,1.0,IICPT),
format(W, 'i_i_cpt(~d,~w,~w,~w).~n',[StateNo,II,1.0,IICPT]),
normalize(IM,1.0,IMCPT),
format(W, 'i_m_cpt(~d,~w,~w,~w).~n',[StateNo,IM,1.0,IMCPT]),
normalize(DM,1.0,DMCPT),
format(W, 'd_m_cpt(~d,~w,~w,~w).~n',[StateNo,DM,1.0,DMCPT]),
normalize(DD,1.0,DDCPT),
format(W, 'd_d_cpt(~d,~w,~w,~w).~n',[StateNo,DD,1.0,DDCPT]),
normalize(BM,1.0,BMCPT),
format(W, 'b_m_cpt(~d,~w,~w,~w).~n',[StateNo,BM,1.0,BMCPT]),
normalize(ME,1.0,MECPT),
format(W, 'm_e_cpt(~d,~w,~w,~w).~n',[StateNo,ME,1.0,MECPT]).
gen_map(_,_).
normalize_bd(A,B,A).
sum([],S,S).
sum([P|Ps],S0,S) :-
Si is S0+P,
sum(Ps,Si,S).
find_consensus(W, StateNo,ECPT) :-
max_index(ECPT,1,0,-1,_,MaxIndex),
format(W, 'consensus(~d,~d).~n',[StateNo,MaxIndex]).
max_index([],_,Max,MaxIndex,Max,MaxIndex).
max_index([H|L],I0,Max0,MaxIndex0,Max,MaxIndex) :-
H > Max0, !,
I is I0+1,
max_index(L,I,H,I0,Max,MaxIndex).
max_index([_|L],I0,Max0,MaxIndex0,Max,MaxIndex) :-
I is I0+1,
max_index(L,I,Max0,MaxIndex0,Max,MaxIndex).

121
packages/CLPBN/examples/HMMer/score.yap Normal file
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@ -0,0 +1,121 @@
#!/usr/bin/yap -L --
#.
:- initialization(main).
:- ensure_loaded(library('clpbn/viterbi')).
:- use_module(fasta,
[fa2atoms/3]).
:- use_module(library(lists),
[
nth/3,
append/3
]).
:- [plan7].
:- ['globin.yap'].
%:- ['hmmer_b.1.18.1.yap'].
:- dynamic len/1, emission/2.
main :-
unix(argv([Sequence])),
fa2atoms(Sequence, L, [a]),
run_model([a|L],_Trace).
artemia :-
fa2atoms('Artemia.fa', L, [a]),
run_model([a|L],_Trace).
% given a string, construct a model
run_model(String,Trace) :-
viterbi(s(0,_),t(_,_),String,Trace),
out(Trace,String).
write_keys([]).
write_keys([V|Vars0]) :-
clpbn:get_atts(V,[key(K)]), !,
write(K), nl,
write_keys(Vars0).
write_keys([_|Vars0]) :-
write(no_key),nl,
write_keys(Vars0).
convert2emissions([],_).
convert2emissions([E|String],I0) :-
I is I0+1,
assert(emission(I,E)),
convert2emissions(String, I).
out([],_).
out([State|Trace],String) :-
out_state(State,String,RString),
out(Trace,RString).
out_state(s(_),String,String).
out_state(n(_),[_|String],String).
out_state(j(_),[_|String],String).
out_state(c(_),[_|String],String).
out_state(t(_),String,String).
out_state(b(Pos),String,String) :-
format('START MATCH at ~d~n', [Pos]).
out_state(d(_,State),String,String) :-
find_consensus(State,Consensus),
format(' -~a~n', [Consensus]).
out_state(i(_,_),[Code|String],String) :-
to_upper(Code,UCode),
format(' ~a+~n', [UCode]).
out_state(m(_,State),[Code|String],String) :-
to_upper(Code,UCode),
find_consensus(State,Consensus),
find_match_type(State,Code,Consensus,MatchType),
format(' ~a~a~a~n', [UCode,MatchType,Consensus]).
out_state(e(Pos),String,String) :-
format('END MATCH at ~d~n', [Pos]).
to_upper(A,U) :-
atom_codes(A,[C]),
( C =< "A", C>="Z" ->
U = A
;
NC is C + ("A"-"a"),
atom_codes(U,[NC])
).
find_consensus(State,Consensus) :-
consensus(State,I),
hmm_domain(Type),
domain_vals(Type,Vals),
arg(I, Vals, Consensus).
find_match_type(_,Code,Code,'=') :- !.
find_match_type(State,Code,_,'^') :-
me_cpt(State,Probs,_,_),
hmm_domain(Type),
domain_vals(Type,Vals),
find_prob_for_code(Vals,Code,Probs,Prob),
Prob >= 0, !.
find_match_type(_,_,_,' ').
find_prob_for_code(Vals,Code,Probs,Prob) :-
Vals =.. [_|L],
once(nth(I,L,Code)),
arg(I,Probs,Prob).
domain_vals(aminoacids,domain(a, c, d, e, f, g, h, i, k, l, m, n, p, q, r, s, t, v, w, y)).
domain_vals(bool,domain(t,f)).
domain_vals(bases,domain(a,c,g,t)).
domain_vals([A|B],Domain) :-
Domain =.. [domain,A|B].
start(S) :-
s_state(0,S).
end(Items,E) :-
t_state(Items,E).

0
packages/CLPBN/clpbn/examples/School/README → packages/CLPBN/examples/School/README
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0
packages/CLPBN/clpbn/examples/School/evidence_128.yap → packages/CLPBN/examples/School/evidence_128.yap
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0
packages/CLPBN/clpbn/examples/School/parlearn.yap → packages/CLPBN/examples/School/parlearn.yap
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0
packages/CLPBN/clpbn/examples/School/sample32.yap → packages/CLPBN/examples/School/sample32.yap
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0
packages/CLPBN/clpbn/examples/School/schema.yap → packages/CLPBN/examples/School/schema.yap
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0
packages/CLPBN/clpbn/examples/School/school_128.yap → packages/CLPBN/examples/School/school_128.yap
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0
packages/CLPBN/clpbn/examples/School/school_32.yap → packages/CLPBN/examples/School/school_32.yap
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0
packages/CLPBN/clpbn/examples/School/school_64.yap → packages/CLPBN/examples/School/school_64.yap
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0
packages/CLPBN/clpbn/examples/School/tables.yap → packages/CLPBN/examples/School/tables.yap
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0
packages/CLPBN/clpbn/examples/cg.yap → packages/CLPBN/examples/cg.yap
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0
packages/CLPBN/clpbn/examples/sprinkler.yap → packages/CLPBN/examples/sprinkler.yap
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4
packages/PLStream/pl-dtoa.c
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@ -30,7 +30,7 @@
#define MALLOC PL_malloc
#define FREE PL_free
#if defined(_REENTRANT)||defined(__YAP_PROLOG__)
#if defined(_REENTRANT)
#define Long int /* 32-bits */
#define MULTIPLE_THREADS
@ -56,6 +56,8 @@ FREE_DTOA_LOCK(int n)
pthread_mutex_unlock(&mutex_1);
}
#elif defined(__YAP_PROLOG__)
#define Long int /* 32-bits */
#endif /*MULTIPLE_THREADS*/
#include "dtoa.c"

17
pl/boot.yap
View File

@ -144,18 +144,18 @@ true :- true.
*/
/* main execution loop */
'$read_vars'(user_input, Goal, Mod, Pos, Bindings) :-
'$read_vars'(user_input, Goal, Mod, Pos, Bindings, Prompt) :-
'$swi_current_prolog_flag'(readline, true),
read_history(h, '!h',
[trace, end_of_file],
' ?- ', Goal, Bindings), !,
Prompt, Goal, Bindings), !,
(nonvar(Err) ->
print_message(error,Err), fail
;
true
).
'$read_vars'(Stream,T,Mod,Pos,V) :-
'$read'(true,T,Mod,V,Pos,Err,Stream),
'$read_vars'(Stream, T, Mod, Pos, V, _Prompt) :-
'$read'(true, T, Mod, V, Pos, Err, Stream),
(nonvar(Err) ->
print_message(error,Err), fail
;
@ -195,13 +195,12 @@ true :- true.
prompt(_,'| '),
prompt1(' ?- '),
'$run_toplevel_hooks',
'$read_vars'(user_input,Command,_,Pos,Varnames),
'$read_vars'(user_input,Command,_,Pos,Varnames, ' ?- '),
nb_setval('$spy_gn',1),
% stop at spy-points if debugging is on.
% stop at spy-points if debugging is on.
nb_setval('$debug_run',off),
nb_setval('$debug_jump',off),
prompt(_,'|: '),
prompt1('|: '),
'$command'(Command,Varnames,Pos,top),
'$sync_mmapped_arrays',
set_value('$live','$false').
@ -1141,7 +1140,7 @@ bootstrap(F) :-
!.
'$enter_command'(Stream,Status) :-
'$read_vars'(Stream,Command,_,Pos,Vars),
'$read_vars'(Stream,Command,_,Pos,Vars, '|: '),
'$command'(Command,Vars,Pos,Status).
'$abort_loop'(Stream) :-

8
pl/consult.yap
View File

@ -495,9 +495,11 @@ prolog_load_context(source, FileName) :-
nb_getval('$consulting_file',FileName).
prolog_load_context(stream, Stream) :-
'$fetch_stream_alias'(Stream,'$loop_stream').
prolog_load_context(term_position, Position) :-
'$fetch_stream_alias'(Stream,'$loop_stream'),
stream_position(Stream, Position).
% return this term for SWI compatibility.
prolog_load_context(term_position, '$stream_position'(0,Line,0,0,0)) :-
'$fetch_stream_alias'(Stream,'$loop_stream'), !,
stream_property(Stream, position(Position)),
stream_position_data(line_count, Position, Line).
% if the file exports a module, then we can

119
pl/dbload.yap Normal file
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@ -0,0 +1,119 @@
/*************************************************************************
* *
* YAP Prolog *
* *
* Yap Prolog was developed at NCCUP - Universidade do Porto *
* *
* Copyright L.Damas, V.S.Costa and Universidade do Porto 1985-1997 *
* *
**************************************************************************
* *
* File: dbload.yap *
* Last rev: 8/2/88 *
* mods: *
* comments: Compact Loading of Facts in YAP *
* *
*************************************************************************/
:- module('$db_load',
[]).
:- dynamic dbloading/6, dbprocess/2.
prolog:load_db(Fs) :-
'$current_module'(M0),
prolog_flag(agc_margin,Old,0),
dbload(Fs,M0,load_db(Fs)),
load_facts,
prolog_flag(agc_margin,_,Old),
clean_up.
dbload(Fs, _, G) :-
var(Fs),
'$do_error'(instantiation_error,G).
dbload([], _, _).
dbload([F|Fs], M0, G) :-
dbload(F, M0, G),
dbload(Fs, M0, G).
dbload(M:F, _M0, G) :-
dbload(F, M, G).
dbload(F, M0, G) :-
atom(F), !,
do_dbload(F, M0, G).
dbload(F, _, G) :-
'$do_error'(type_error(atom,F),G).
do_dbload(F0, M0, G) :-
'$find_in_path'(F0,F,G),
assert(dbprocess(F, M0)),
open(F, read, R),
check_dbload_stream(R, M0),
close(R).
check_dbload_stream(R, M0) :-
repeat,
read(R,T),
( T = end_of_file -> !;
dbload_count(T, M0),
fail
).
dbload_count(T0, M0) :-
get_module(T0,M0,T,M),
functor(T,Na,Arity),
% dbload_check_term(T),
(
dbloading(Na,Arity,M,_,NaAr,_) ->
nb_getval(NaAr,I0),
I is I0+1,
nb_setval(NaAr,I)
;
atomic_concat([Na,'__',Arity,'__',M],NaAr),
assert(dbloading(Na,Arity,M,T,NaAr,0)),
nb_setval(NaAr,1)
).
get_module(M1:T0,_,T,M) :- !,
get_module(T0, M1, T , M).
get_module(T,M,T,M).
load_facts :-
retract(dbloading(Na,Arity,M,T,NaAr,_)),
nb_getval(NaAr,Size),
dbload_get_space(T, M, Size, Handle),
assertz(dbloading(Na,Arity,M,T,NaAr,Handle)),
nb_setval(NaAr,0),
fail.
load_facts :-
dbprocess(F, M),
open(F, read, R),
dbload_add_facts(R, M),
close(R),
fail.
load_facts.
dbload_add_facts(R, M) :-
repeat,
read(R,T),
( T = end_of_file -> !;
dbload_add_fact(T, M),
fail
).
dbload_add_fact(T0, M0) :-
get_module(T0,M0,T,M),
functor(T,Na,Arity),
Na \= gene_product,
dbloading(Na,Arity,M,_,NaAr,Handle),
nb_getval(NaAr,I0),
I is I0+1,
nb_setval(NaAr,I),
dbassert(T,Handle,I0).
clean_up :-
retractall(dbloading(_,_,_,_,_,_)),
retractall(dbprocess(_,_)),
fail.
clean_up.

2
pl/flags.yap
View File

@ -958,7 +958,7 @@ yap_flag(dialect,yap).
'$yap_flag_show_gc_tracing'(_, _, _, off).
'$flag_check_alias'(OUT, Alias) :-
stream_property(OUT,[alias(Alias)]), !.
stream_property(OUT,alias(Alias)), !.
current_prolog_flag(V,Out) :-
var(V), !,

1
pl/init.yap
View File

@ -114,6 +114,7 @@ system_mode(verbose,off) :- set_value('$verbose',off).
:- use_module('corout.yap').
:- use_module('dialect.yap').
:- use_module('history.pl').
:- use_module('dbload.yap').
'$system_module'('$messages').
'$system_module'('$hacks').

4
pl/yio.yap
View File

@ -116,13 +116,13 @@ read_term(T, Options) :-
'$check_io_opts'(Options,read_term(T, Options)),
current_input(S),
'$preprocess_read_terms_options'(Options,Module),
'$read_vars'(S,T,Module,Pos,VL),
'$read_vars'(S,T,Module,Pos,VL,'|: '),
'$postprocess_read_terms_options'(Options, T, VL, Pos).
read_term(Stream, T, Options) :-
'$check_io_opts'(Options,read_term(T, Options)),
'$preprocess_read_terms_options'(Options,Module),
'$read_vars'(Stream,T,Module,Pos,VL),
'$read_vars'(Stream,T,Module,Pos,VL,'|: '),
'$postprocess_read_terms_options'(Options, T, VL, Pos).
%