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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; if (RepAtom(AtomOfTerm(t1))->StrOfAE[0] == 'f') mode = asserta;
else mode = assertz; else mode = assertz;
} else mode = IntegerOfTerm(t1); } else mode = IntegerOfTerm(t1);
if (mode == assertz && LOCAL_consult_level) /* separate assert in current file from reconsult
mode = consult; if (mode == assertz && LOCAL_consult_level && mod == CurrentModule)
mode = consult;
*/
old_optimize = optimizer_on; old_optimize = optimizer_on;
optimizer_on = FALSE; optimizer_on = FALSE;
YAPEnterCriticalSection(); YAPEnterCriticalSection();
@ -5635,6 +5637,233 @@ p_choicepoint_info( USES_REGS1 )
Yap_unify(ARG7,MkIntegerTerm(ClauseId(ncl,pe))); 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 void
Yap_InitCdMgr(void) Yap_InitCdMgr(void)
{ {
@ -5701,6 +5930,10 @@ Yap_InitCdMgr(void)
Yap_InitCPred("continuation", 4, p_env_info, HiddenPredFlag); Yap_InitCPred("continuation", 4, p_env_info, HiddenPredFlag);
Yap_InitCPred("cp_to_predicate", 5, p_cpc_info, HiddenPredFlag); Yap_InitCPred("cp_to_predicate", 5, p_cpc_info, HiddenPredFlag);
CurrentModule = cm; 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("$predicate_erased_statistics", 5, p_predicate_erased_statistics, SyncPredFlag); Yap_InitCPred("$predicate_erased_statistics", 5, p_predicate_erased_statistics, SyncPredFlag);
#ifdef DEBUG #ifdef DEBUG
Yap_InitCPred("$predicate_live_cps", 4, p_predicate_lu_cps, 0L); Yap_InitCPred("$predicate_live_cps", 4, p_predicate_lu_cps, 0L);

6
C/index.c
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@ -6864,8 +6864,8 @@ Yap_FollowIndexingCode(PredEntry *ap, yamop *ipc, Term Terms[3], yamop *ap_pc, y
break; break;
} }
} }
update_clause_choice_point(ipc->u.OtILl.n,ap_pc PASS_REGS); update_clause_choice_point(ipc->u.OtaLl.n,ap_pc PASS_REGS);
return ipc->u.OtILl.d; return ipc->u.OtaLl.d;
#if TABLING #if TABLING
case _table_try_single: case _table_try_single:
return (LogUpdClause *)ClauseCodeToStaticClause(ipc); 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 _count_trust_logical:
case _profiled_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; LogUpdIndex *cl = ipc->u.OtILl.block;
LogUpdClause *newpc; LogUpdClause *newpc;

1
C/modules.c
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@ -327,5 +327,6 @@ Yap_InitModules(void)
LookupModule(HACKS_MODULE); LookupModule(HACKS_MODULE);
LookupModule(ARG_MODULE); LookupModule(ARG_MODULE);
LookupModule(GLOBALS_MODULE); LookupModule(GLOBALS_MODULE);
LookupModule(DBLOAD_MODULE);
CurrentModule = PROLOG_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'; return '\n';
case 'r': case 'r':
return '\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': case 't':
return '\t'; return '\t';
case 'u': case 'u':
@ -357,6 +362,11 @@ read_quoted_char(int *scan_nextp, IOSTREAM *inp_stream)
} }
case 'v': case 'v':
return '\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 '\\': case '\\':
return '\\'; return '\\';
case '\'': case '\'':

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

1
H/iatoms.h
View File

@ -63,6 +63,7 @@
AtomCut = Yap_LookupAtom("!"); AtomCut = Yap_LookupAtom("!");
AtomCutBy = Yap_FullLookupAtom("$cut_by"); AtomCutBy = Yap_FullLookupAtom("$cut_by");
AtomDAbort = Yap_FullLookupAtom("$abort"); AtomDAbort = Yap_FullLookupAtom("$abort");
AtomDBLoad = Yap_FullLookupAtom("$db_load");
AtomDBREF = Yap_LookupAtom("DBRef"); AtomDBREF = Yap_LookupAtom("DBRef");
AtomDBReference = Yap_LookupAtom("db_reference"); AtomDBReference = Yap_LookupAtom("db_reference");
AtomDBTerm = Yap_LookupAtom("db_term"); 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->arg_module = MkAtomTerm(AtomArg);
Yap_heap_regs->globals_module = MkAtomTerm(AtomNb); Yap_heap_regs->globals_module = MkAtomTerm(AtomNb);
Yap_heap_regs->swi_module = MkAtomTerm(AtomSwi); Yap_heap_regs->swi_module = MkAtomTerm(AtomSwi);
Yap_heap_regs->dbload_module = MkAtomTerm(AtomDBLoad);

1
H/ratoms.h
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@ -63,6 +63,7 @@
AtomCut = AtomAdjust(AtomCut); AtomCut = AtomAdjust(AtomCut);
AtomCutBy = AtomAdjust(AtomCutBy); AtomCutBy = AtomAdjust(AtomCutBy);
AtomDAbort = AtomAdjust(AtomDAbort); AtomDAbort = AtomAdjust(AtomDAbort);
AtomDBLoad = AtomAdjust(AtomDBLoad);
AtomDBREF = AtomAdjust(AtomDBREF); AtomDBREF = AtomAdjust(AtomDBREF);
AtomDBReference = AtomAdjust(AtomDBReference); AtomDBReference = AtomAdjust(AtomDBReference);
AtomDBTerm = AtomAdjust(AtomDBTerm); 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->arg_module = AtomTermAdjust(Yap_heap_regs->arg_module);
Yap_heap_regs->globals_module = AtomTermAdjust(Yap_heap_regs->globals_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->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_ #define AtomCutBy Yap_heap_regs->AtomCutBy_
Atom AtomDAbort_; Atom AtomDAbort_;
#define AtomDAbort Yap_heap_regs->AtomDAbort_ #define AtomDAbort Yap_heap_regs->AtomDAbort_
Atom AtomDBLoad_;
#define AtomDBLoad Yap_heap_regs->AtomDBLoad_
Atom AtomDBREF_; Atom AtomDBREF_;
#define AtomDBREF Yap_heap_regs->AtomDBREF_ #define AtomDBREF Yap_heap_regs->AtomDBREF_
Atom AtomDBReference_; Atom AtomDBReference_;

7
Makefile.in
View File

@ -296,6 +296,7 @@ PL_SOURCES= \
$(srcdir)/pl/consult.yap \ $(srcdir)/pl/consult.yap \
$(srcdir)/pl/control.yap \ $(srcdir)/pl/control.yap \
$(srcdir)/pl/corout.yap $(srcdir)/pl/debug.yap \ $(srcdir)/pl/corout.yap $(srcdir)/pl/debug.yap \
$(srcdir)/pl/dbload.yap \
$(srcdir)/pl/depth_bound.yap \ $(srcdir)/pl/depth_bound.yap \
$(srcdir)/pl/dialect.yap \ $(srcdir)/pl/dialect.yap \
$(srcdir)/pl/directives.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 $@ $(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 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 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 $@ $(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@ yap@EXEC_SUFFIX@: $(HEADERS) yap.o @YAPLIB@
$(MPI_CC) $(EXECUTABLE_CFLAGS) $(LDFLAGS) -o yap yap.o @YAPLIB@ $(LIBS) @MPI_LIBS@ $(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)) (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) libYap.a: $(LIB_OBJECTS)
-rm -f libYap.a -rm -f libYap.a

4
docs/yap.tex
View File

@ -8505,7 +8505,9 @@ Stream currently being read in.
@item term_position @item term_position
@findex file (prolog_load_context/2 option) @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 @end table
@item source_location(?@var{FileName}, ?@var{Line}) @item source_location(?@var{FileName}, ?@var{Line})

1
misc/ATOMS
View File

@ -68,6 +68,7 @@ A CurrentModule F "$current_module"
A Cut N "!" A Cut N "!"
A CutBy F "$cut_by" A CutBy F "$cut_by"
A DAbort F "$abort" A DAbort F "$abort"
A DBLoad F "$db_load"
A DBREF N "DBRef" A DBREF N "DBRef"
A DBReference N "db_reference" A DBReference N "db_reference"
A DBTerm N "db_term" 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 arg_module ARG_MODULE MkAT AtomArg
Term globals_module GLOBALS_MODULE MkAT AtomNb Term globals_module GLOBALS_MODULE MkAT AtomNb
Term swi_module SWI_MODULE MkAT AtomSwi Term swi_module SWI_MODULE MkAT AtomSwi
Term dbload_module DBLOAD_MODULE MkAT AtomDBLoad
// //
// Module list // Module list

13
packages/CLPBN/Makefile.in
View File

@ -30,7 +30,7 @@ CLPBN_SRCDIR = $(srcdir)/clpbn
CLPBN_LEARNING_SRCDIR = $(srcdir)/learning CLPBN_LEARNING_SRCDIR = $(srcdir)/learning
CLPBN_EXDIR = $(srcdir)/clpbn/examples CLPBN_EXDIR = $(srcdir)/examples
CLPBN_PROGRAMS= \ CLPBN_PROGRAMS= \
$(CLPBN_SRCDIR)/aggregates.yap \ $(CLPBN_SRCDIR)/aggregates.yap \
@ -71,6 +71,15 @@ CLPBN_SCHOOL_EXAMPLES= \
$(CLPBN_EXDIR)/School/school_64.yap \ $(CLPBN_EXDIR)/School/school_64.yap \
$(CLPBN_EXDIR)/School/tables.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_EXAMPLES= \
$(CLPBN_EXDIR)/cg.yap \ $(CLPBN_EXDIR)/cg.yap \
$(CLPBN_EXDIR)/sprinkler.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
mkdir -p $(DESTDIR)$(SHAREDIR)/clpbn/learning mkdir -p $(DESTDIR)$(SHAREDIR)/clpbn/learning
mkdir -p $(DESTDIR)$(SHAREDIR)/clpbn/examples/School mkdir -p $(DESTDIR)$(SHAREDIR)/clpbn/examples/School
mkdir -p $(DESTDIR)$(SHAREDIR)/clpbn/examples/HMMer
for h in $(CLPBN_TOP); do $(INSTALL_DATA) $$h $(DESTDIR)$(SHAREDIR); done for h in $(CLPBN_TOP); do $(INSTALL_DATA) $$h $(DESTDIR)$(SHAREDIR); done
for h in $(CLPBN_PROGRAMS); do $(INSTALL_DATA) $$h $(DESTDIR)$(SHAREDIR)/clpbn; done for h in $(CLPBN_PROGRAMS); do $(INSTALL_DATA) $$h $(DESTDIR)$(SHAREDIR)/clpbn; done
for h in $(CLPBN_LEARNING_PROGRAMS); do $(INSTALL_DATA) $$h $(DESTDIR)$(SHAREDIR)/clpbn/learning; done for h in $(CLPBN_LEARNING_PROGRAMS); do $(INSTALL_DATA) $$h $(DESTDIR)$(SHAREDIR)/clpbn/learning; done
for h in $(CLPBN_EXAMPLES); do $(INSTALL_DATA) $$h $(DESTDIR)$(SHAREDIR)/clpbn/examples; done for h in $(CLPBN_EXAMPLES); do $(INSTALL_DATA) $$h $(DESTDIR)$(SHAREDIR)/clpbn/examples; done
for h in $(CLPBN_SCHOOL_EXAMPLES); do $(INSTALL_DATA) $$h $(DESTDIR)$(SHAREDIR)/clpbn/examples/School; done for h in $(CLPBN_SCHOOL_EXAMPLES); do $(INSTALL_DATA) $$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
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@ -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
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@ -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
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@ -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
NULE 595 -1558 85 338 -294 453 -1158 197 249 902 -1085 -142 -21 -313 45 531 201 384 -1998 -644
EVD -107.906906 0.177814
HMM A C D E F G H I K L M N P Q R S T V W Y
m->m m->i m->d i->m i->i d->m d->d b->m m->e
-110 * -3765
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- -18 -6914 -7956 -894 -1115 -3550 -129 * *
3 -818 -929 -1862 -1322 -641 -2171 -971 169 -964 1238 288 -1339 -2212 2240 -1140 -1236 -765 1496 -1363 -992 6
- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249
- -18 -6914 -7956 -894 -1115 -3550 -129 * *
4 1262 -2557 1921 2106 -2850 -1393 -477 -2640 -377 -2596 -1780 -22 -1759 -90 -1010 -778 -993 -2183 -2798 -1995 7
- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249
- -361 -6914 -2229 -894 -1115 -3550 -129 * *
5 1959 -737 -1983 -1620 -770 -1684 -1217 123 -1350 1511 129 -1398 -2018 -1217 -1464 -913 -639 108 -1537 -1163 8
- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249
- -23 -6575 -7617 -894 -1115 -3643 -120 * *
6 -909 3538 -2932 -2480 -462 -2247 -1584 420 -2070 1990 430 -2081 -2431 -1807 -2001 -1504 -963 293 -1408 -1050 9
- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249
- -23 -6575 -7617 -894 -1115 -2811 -222 * *
7 -447 -788 -2329 -2135 -1640 -1513 -1728 -244 -1943 -1307 -807 -1618 -2064 -1766 -2007 1427 -705 2813 -2213 -1812 10
- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249
- -18 -6914 -7956 -894 -1115 -3550 -129 * *
8 1580 -1167 -755 -683 -2613 1407 -1070 -2339 -947 -2479 -1637 2477 -1718 -763 -1344 -463 -616 -1669 -2725 -2220 11
- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249
- -18 -6914 -7956 -894 -1115 -3550 -129 * *
9 1791 -792 -2096 -2069 -2827 -1046 -1925 -2514 -2049 -2800 -1955 -1384 -1767 -1801 -2146 2767 -564 -1643 -3058 -2770 12
- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249
- -18 -6914 -7956 -894 -1115 -3550 -129 * *
10 1611 -700 -2005 -1664 -1754 -1223 -1383 -1052 -1498 -1589 -891 -1252 -1781 -1306 -1666 1925 -478 1539 -2138 -1780 13
- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249
- -18 -6914 -7956 -894 -1115 -3550 -129 * *
11 -678 -1254 -2027 -2203 -2902 -1430 -2171 -2966 -2329 -3184 -2473 -1697 -2138 -2150 -2383 3390 -1086 -2139 -3055 -2728 14
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- -18 -6914 -7956 -894 -1115 -1091 -914 * *
12 338 -2575 -727 524 -2888 211 3834 -2630 -381 -2596 -1699 -662 433 1123 -889 -1018 -1092 -2200 -2784 -2101 15
- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249
- -103 -8202 -3938 -894 -1115 -131 -3528 * *
13 -4706 -4011 -6464 -6215 -273 -6255 -3388 -1852 -5907 3081 -1113 -5432 -5593 -4660 -5340 -5591 -4543 -2675 3133 -1563 16
- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249
- -5 -8835 -9877 -894 -1115 -482 -1817 * *
14 -1995 -2562 -4756 -4903 948 -2899 -4002 -4323 -4709 -4557 -3803 -3536 -3665 -4271 -4506 2845 2539 -3465 -4401 -3785 17
- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249
- -5 -8893 -9935 -894 -1115 -701 -1378 * *
15 1974 -2894 1467 -816 -3309 781 -1179 -3058 963 -3017 -2101 -1116 189 -730 -1296 -776 170 -2597 -3194 -2516 18
- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249
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16 1383 -2883 585 1876 -3204 405 -1043 -2954 287 -2899 -1973 -61 -2477 990 -1132 -921 -518 -602 -3067 -2384 19
- -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 * *
17 -3444 -5495 2619 2744 -5608 -3223 -2646 -5588 -3024 -5423 -4830 874 -3800 1490 -3998 -3057 -3535 -5032 -5625 -4510 20
- -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 * *
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- -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 * *
19 1087 -2878 -1251 152 -3199 57 -1039 -2949 1245 -2894 -1968 1023 -478 1653 -1127 491 694 -2500 -3062 -2379 22
- -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 * *
20 998 -413 -1742 -198 -2292 -825 -1300 -1037 714 1062 420 2005 -2677 -395 -1494 -1541 -425 -661 -2537 -2029 23
- -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 * *
21 -3221 -2748 -5841 -5461 -3140 -5557 -5075 2551 -5338 -1071 -1986 -5198 -5343 -5155 -5383 -4856 -3201 2966 -4560 1098 24
- -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 * *
22 0 29 -1335 -786 -2969 -2418 -1085 -1608 1448 -65 -1823 700 -2509 1617 182 529 1205 -899 -2941 -2302 25
- -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 * *
23 1283 -2841 295 -428 -3146 56 -1049 -741 -636 -2850 -1935 1212 -2481 629 -1141 1467 446 -764 -3035 -2362 26
- -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 * *
24 615 -1463 -3974 -3342 -582 -3196 1142 1756 -2943 1380 -661 -2837 -3243 -2570 -2751 -2282 510 1530 -1938 -1595 27
- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249
- -88 -8959 -4135 -894 -1115 -701 -1378 * *
25 -5376 -4397 -5974 -6255 2051 -5819 -2124 -3799 -5814 -906 -3161 -4513 -5644 -4579 -5202 -5092 -5237 -4180 5849 -187 28
- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249
- -2316 -8876 -327 -894 -1115 -418 -1991 * *
26 -3400 -2532 -3998 -4210 2830 -3875 -263 -2335 -3796 -1766 -1796 -2595 -3766 -2689 -3273 -3120 -3283 -2481 476 4114 29
- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249
- -17 -6950 -7992 -894 -1115 -70 -4397 * *
27 -355 -2932 704 -32 -3235 2526 -1149 -2972 -758 -805 -2040 -1097 -2567 189 -1268 5 685 -2547 -3138 -2463 30
- -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 * *
28 -551 -3414 -2450 -1870 -3811 -3294 -400 969 3397 -3383 -2617 388 -3386 -1363 -1016 -2410 -2355 -3103 -3525 -3110 31
- -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 * *
29 -3385 -2869 -6061 -5728 -3309 -5904 -5809 2392 -5685 -657 -151 -5558 -5596 -5536 -5803 -5277 -3369 3170 -5065 -4654 32
- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249
- -505 -8959 -1768 -894 -1115 -701 -1378 * *
30 -175 -2400 -994 1422 -2661 1100 -750 -2369 1310 327 -1507 -745 -2175 -313 -851 3 -518 -1990 -2623 740 33
- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249
- -6 -8460 -9502 -894 -1115 -2614 -257 * *
31 472 -2516 -934 372 -2824 2028 -715 -2565 651 -2527 571 -695 -198 737 -805 380 -391 -2131 -2708 -2034 34
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- -126 -8460 -3635 -894 -1115 -155 -3291 * *
32 -689 1410 1891 -700 -3229 -2379 2645 -2979 1033 -2925 -2006 2170 -2489 626 -1156 -1316 -1381 -2533 -3094 -2410 35
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- -4 -8959 -10001 -894 -1115 -701 -1378 * *
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- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249
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- * * * * * * * * 0
//

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MSF: 171 Type: P Check: 4694 ..
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//
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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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packages/CLPBN/clpbn/examples/School/school_64.yap → packages/CLPBN/examples/School/school_64.yap
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0
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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 MALLOC PL_malloc
#define FREE PL_free #define FREE PL_free
#if defined(_REENTRANT)||defined(__YAP_PROLOG__) #if defined(_REENTRANT)
#define Long int /* 32-bits */ #define Long int /* 32-bits */
#define MULTIPLE_THREADS #define MULTIPLE_THREADS
@ -56,6 +56,8 @@ FREE_DTOA_LOCK(int n)
pthread_mutex_unlock(&mutex_1); pthread_mutex_unlock(&mutex_1);
} }
#elif defined(__YAP_PROLOG__)
#define Long int /* 32-bits */
#endif /*MULTIPLE_THREADS*/ #endif /*MULTIPLE_THREADS*/
#include "dtoa.c" #include "dtoa.c"

17
pl/boot.yap
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@ -144,18 +144,18 @@ true :- true.
*/ */
/* main execution loop */ /* main execution loop */
'$read_vars'(user_input, Goal, Mod, Pos, Bindings) :- '$read_vars'(user_input, Goal, Mod, Pos, Bindings, Prompt) :-
'$swi_current_prolog_flag'(readline, true), '$swi_current_prolog_flag'(readline, true),
read_history(h, '!h', read_history(h, '!h',
[trace, end_of_file], [trace, end_of_file],
' ?- ', Goal, Bindings), !, Prompt, Goal, Bindings), !,
(nonvar(Err) -> (nonvar(Err) ->
print_message(error,Err), fail print_message(error,Err), fail
; ;
true true
). ).
'$read_vars'(Stream,T,Mod,Pos,V) :- '$read_vars'(Stream, T, Mod, Pos, V, _Prompt) :-
'$read'(true,T,Mod,V,Pos,Err,Stream), '$read'(true, T, Mod, V, Pos, Err, Stream),
(nonvar(Err) -> (nonvar(Err) ->
print_message(error,Err), fail print_message(error,Err), fail
; ;
@ -195,13 +195,12 @@ true :- true.
prompt(_,'| '), prompt(_,'| '),
prompt1(' ?- '), prompt1(' ?- '),
'$run_toplevel_hooks', '$run_toplevel_hooks',
'$read_vars'(user_input,Command,_,Pos,Varnames), '$read_vars'(user_input,Command,_,Pos,Varnames, ' ?- '),
nb_setval('$spy_gn',1), nb_setval('$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_run',off),
nb_setval('$debug_jump',off), nb_setval('$debug_jump',off),
prompt(_,'|: '), prompt1('|: '),
'$command'(Command,Varnames,Pos,top), '$command'(Command,Varnames,Pos,top),
'$sync_mmapped_arrays', '$sync_mmapped_arrays',
set_value('$live','$false'). set_value('$live','$false').
@ -1141,7 +1140,7 @@ bootstrap(F) :-
!. !.
'$enter_command'(Stream,Status) :- '$enter_command'(Stream,Status) :-
'$read_vars'(Stream,Command,_,Pos,Vars), '$read_vars'(Stream,Command,_,Pos,Vars, '|: '),
'$command'(Command,Vars,Pos,Status). '$command'(Command,Vars,Pos,Status).
'$abort_loop'(Stream) :- '$abort_loop'(Stream) :-

8
pl/consult.yap
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@ -495,9 +495,11 @@ prolog_load_context(source, FileName) :-
nb_getval('$consulting_file',FileName). nb_getval('$consulting_file',FileName).
prolog_load_context(stream, Stream) :- prolog_load_context(stream, Stream) :-
'$fetch_stream_alias'(Stream,'$loop_stream'). '$fetch_stream_alias'(Stream,'$loop_stream').
prolog_load_context(term_position, Position) :- % return this term for SWI compatibility.
'$fetch_stream_alias'(Stream,'$loop_stream'), prolog_load_context(term_position, '$stream_position'(0,Line,0,0,0)) :-
stream_position(Stream, Position). '$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 % 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).
'$yap_flag_show_gc_tracing'(_, _, _, off). '$yap_flag_show_gc_tracing'(_, _, _, off).
'$flag_check_alias'(OUT, Alias) :- '$flag_check_alias'(OUT, Alias) :-
stream_property(OUT,[alias(Alias)]), !. stream_property(OUT,alias(Alias)), !.
current_prolog_flag(V,Out) :- current_prolog_flag(V,Out) :-
var(V), !, var(V), !,

1
pl/init.yap
View File

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

4
pl/yio.yap
View File

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