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git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPrimers/trunk@179 60f365c0-8329-0410-b2a4-ec073aeeaa1d
This commit is contained in:
Eric Coissac
2009-03-04 22:22:48 +00:00
parent f9410e5aee
commit 6d8bb449d5
40 changed files with 0 additions and 6741 deletions
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63
src/Makefile
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EXEC=ecoPrimer
PRIMER_SRC= ecoprimer.c
PRIMER_OBJ= $(patsubst %.c,%.o,$(PRIMER_SRC))
SRCS= $(PRIMER_SRC)
LIB= -lecoPCR -lapat -lKMRK -lz -lm
LIBFILE= libapat/libapat.a \
libecoPCR/libecoPCR.a \
libKMRK/libKMRK.a
include global.mk
all: $(EXEC)
########
#
# ecoPrimer compilation
#
########
# executable compilation and link
ecoPrimer: $(PRIMER_OBJ) $(LIBFILE)
$(CC) $(LDFLAGS) -o $@ $< $(LIBPATH) $(LIB)
########
#
# library compilation
#
########
libapat/libapat.a:
$(MAKE) -C libapat
libecoPCR/libecoPCR.a:
$(MAKE) -C libecoPCR
libKMRK/libKMRK.a:
$(MAKE) -C libKMRK
########
#
# project management
#
########
clean:
rm -f *.o
rm -f $(EXEC)
$(MAKE) -C libapat clean
$(MAKE) -C libecoPCR clean
$(MAKE) -C libKMRK clean

0
src/ecoprimer.c
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18
src/global.mk
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MACHINE=MAC_OS_X
LIBPATH= -Llibapat -LlibecoPCR -LlibKMRK
MAKEDEPEND = gcc -D$(MACHINE) -M $(CPPFLAGS) -o $*.d $<
CC=gcc
CFLAGS= -W -Wall -O2 -g
default: all
%.o: %.c
$(CC) -D$(MACHINE) $(CFLAGS) -c -o $@ $<
%.P : %.c
$(MAKEDEPEND)
@sed 's/\($*\)\.o[ :]*/\1.o $@ : /g' < $*.d > $@; \
rm -f $*.d; [ -s $@ ] || rm -f $@
include $(SRCS:.c=.P)

1009
src/libKMRK/KMRK.c
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309
src/libKMRK/KMRK.h
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#ifndef _KMRK_H_
#define _KMRK_H_
/********************************************
********************************************
**
** Declaration of struct
**
********************************************
********************************************/
#include <stdint.h>
#include "repseek_types.h"
#include "KMRK_mask.h"
/**
* Structure used to manipulate simultanously
* the v and n vector
*
*/
typedef struct {
int32_t size; /**< size of vectors */
int32_t seqCount; /**< count of concatenated sequences */
int32_t complement; /**< if seqCount > 1 and complement !=0
* then second sequence is the inverted complement
* strand of first one */
int32_t symbmax;
int32_t* v; /**< sequence vector */
int32_t* n; /**< linked list vector */
int32_t limits[1]; /**< array of end limits of concatenated
* sequences in v (array size is seqCount) */
} vn_type;
/********************************************
********************************************
**
** Declaration of public macro
**
********************************************
********************************************/
// Return a pointer to a vector from a vn_type structure
#define GETVECTOR(x,vector) (((x)->vector) - 1)
#define IS_MARKED(x,i) ((x)[i] < 0)
#define MARK(x,i) ((x)[i]) = -ABS((x)[i])
#define UNMARK(x,i) ((x)[i]) = ABS((x)[i])
#define SET(x,i,v) ((x)[i]) = (v)
// set and mark in one operation
#define SETMARKED(x,i,v) ((x)[i]) = -(v)
//internal macro
#define GET(x,i) ABS((x)[i])
// get symbole at position i in vector x
#define SYMBOLE(x,i) ((IS_MARKED((x),(i))) ? (i): (GET(x,i)))
/**
* Macro used to declare a pointer to a quorum function.
*
* @param name name of the pointer
*
*/
#define KMRK_QUORUM_FUNC_PTR(name) int32_t (*name)(vn_type* x, \
int32_t pos, \
int32_t count, \
int32_t countSeq)
/**
* Macro used to declare a pointer to an initialisation function.
*
* @param name name of the pointer
* @param quorum name used for the quorum assiciated function
*
* @see KMRK_QUORUM_FUNC_PTR
*
*/
#define KMRK_INIT_FUNC_PTR(name,quorum) vn_type* (*name)(char *sequence, \
int32_t complement, \
int32_t count, \
int32_t countSeq, \
int32_t *k, \
KMRK_QUORUM_FUNC_PTR(quorum),\
masked_area_table_t *mask)
/********************************************
********************************************
**
** Declaration of public functions
**
********************************************
********************************************/
/**
* Initialise a vn_type record from one sequence to run KMRK algorithm
*
* @param sequence pointer to a C string containing the sequence
* @param complement != 0 means that seq one and two are the two strands of
* the same sequence.
* @param count parameter count passed to the quorun function
* @param countSeq parametter countSeq passed to the quorun function
* @param k length of the word represented by each symbole of v.
* k is an output parametter
* @param quorum pointer to a quorum function
*
* @return a pointer to vn_type structure correctly initialized
* to be used by KMRK_RunKMRK
*
* @see KMRK_HashOneSequence
*/
vn_type* KMRK_InitOneSequence(char *sequence,
int32_t complement,
int32_t count,
int32_t countSeq,
int32_t *k,
KMRK_QUORUM_FUNC_PTR(quorum),
masked_area_table_t *mask);
/**
* Initialise a vn_type record from one sequence to run KMRK algorithme.
* In more than KMRK_InitOneSequence, KMRK_HashOneSequence construct
* word of len k with an hash algorithm. k used is a function of
* sequence size and alphabet size. If calculed k is superior to lmax
* then k = lmax.
*
* @param sequence pointer to a C string containing the sequence
* @param complement != 0 means that seq one and two are the two strands of
* the same sequence.
* @param count parametter count passed to the quorun function
* @param countSeq parametter countSeq passed to the quorun function
* @param k maximum length of the created word (input)
* length of the word represented by each symbole
* of v (output).
* @param quorum pointer to a quorum function
*
* @return a pointer to vn_type structure correctly initialized
* to be used by KMRK_RunKMRK
*
* @see KMRK_InitOneSequence
*/
vn_type* KMRK_HashOneSequence(char *sequence,
int32_t complement,
int32_t count,
int32_t countSeq,
int32_t *k,
KMRK_QUORUM_FUNC_PTR(quorum),
masked_area_table_t *mask);
/**
* An example of quorum function testing than a factor is
* present a least two times. Because of definition of this
* quorum function count and countSeq parametter have no meanning
* in this instance of quorum function
*
* @param x a pointer to vn_type structure to check
* @param pos position in n of the beginning of the linked list to test
* @param count minimal number of occurence of factor
* @param countSeq minimal number of sequences concerned
*
* @return 1 if quorum is ok 0 otherwise.
*/
int32_t KMRK_CoupleQuorum(vn_type* x,
int32_t pos,
int32_t count,
int32_t countSeq);
/**
* An example of quorum function testing than a factor is
* present a least two times in the direct strand of a sequence or
* at least one time in the direct strand and one time in the reverse
* strand. Because of definition of this
* quorum function count and countSeq parametter have no meanning
* in this instance of quorum function
*
* @param x a pointer to vn_type structure to check
* @param pos position in n of the beginning of the linked list to test
* @param count minimal number of occurence of factor
* @param countSeq minimal number of sequences concerned
*
* @return 1 if quorum is ok 0 otherwise.
*/
int32_t KMRK_DirInvQuorum(vn_type* x,
int32_t pos,
int32_t count,
int32_t countSeq);
/**
* An example of quorum function testing than a factor is
* present a least one time in the direct strand and one time in the reverse
* strand. Because of definition of this
* quorum function count and countSeq parametter have no meanning
* in this instance of quorum function
*
* @param x a pointer to vn_type structure to check
* @param pos position in n of the beginning of the linked list to test
* @param count minimal number of occurence of factor
* @param countSeq minimal number of sequences concerned
*
* @return 1 if quorum is ok 0 otherwise.
*/
int32_t KMRK_InvQuorum(vn_type* x,
int32_t pos,
int32_t count,
int32_t countSeq);
int32_t KMRK_Int12Quorum(vn_type* x,
int32_t pos,
int32_t count,
int32_t countSeq);
int32_t KMRK_IntInv12Quorum(vn_type* x,
int32_t pos,
int32_t count,
int32_t countSeq);
int32_t KMRK_IntDirInv12Quorum(vn_type* x,
int32_t pos,
int32_t count,
int32_t countSeq);
/**
* realize one cycle of KMR.
*
* @param x a pointer to vn_type created by an intialisation
* function or returned by this function.
* @param k step used to join two words
* @param count parametter count passed to the quorun function
* @param countSeq parametter countSeq passed to the quorun function
* @param KMRK_QUORUM_FUNC_PTR quorum pointer to a quorum function
*/
void KMRK_RunKMRK(vn_type *x,
int32_t k,
int32_t count,
int32_t countSeq,
KMRK_QUORUM_FUNC_PTR(quorum));
/**
* realises serveral run of KMR cycle to make from a sequence
* a vn_type structure describing sequences of factors of a precise size.
*
* @param sequence pointer to a C string containing the sequence
* @param size word size to construct
* @param count parametter count passed to the quorun function
* @param countSeq parametter countSeq passed to the quorun function
* @param quorum pointer to a quorum function
* @param init pointer to a initialisation function
*
* @return a vn_type pointer to a structure containing sequences of factors
*/
vn_type *KMRK_RunTo(char *sequence,
int32_t size,
int32_t complement,
int32_t count,
int32_t countSeq,
KMRK_QUORUM_FUNC_PTR(quorum),
KMRK_INIT_FUNC_PTR(init,quorum),
masked_area_table_t *mask);
/**
* free memory associated to a vn_type pointer
*
* @param x a pointer to vn_type structure
*/
void KMRK_FreeVN(vn_type *x);
int32_t KMRK_upperCoupleCount(vn_type *x);
int32_t KMRK_upperInvertedCount(vn_type* x,int32_t wordsize);
int32_t KMRK_upperInterCount(vn_type* x,int32_t seq1,int32_t seq2,int32_t wordsize);
void KMRK_markStart(vn_type* x);
#endif //_KMRK_H_

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src/libKMRK/KMRK_Seeds.c
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#include "KMRK_Seeds.h"
#include "memory.h"
#include <stdlib.h>
#include <string.h>
#include "sequence.h"
static void SetMultipleLenInvSeeds(SmallSeed_type* seeds,
int32_t nseeds,
int32_t wordSize,
int8_t same,
AllSeeds_type *PtrAllSeeds);
/*
Concatenate
DirSeq\0InvSeq\0
*/
static char* makeDirInvSeq(char* seq, int32_t size)
{
char *SeqInv;
seq = (char *)MyRealloc( (void *)seq, (size*2+2)*sizeof(char),
(size+1)* sizeof(char), "Cannot allocate space for reverse sequence");
SeqInv= seq + size + 1;
seq[size]=0;
invseq(seq, SeqInv);
seq[size]='@';
SeqInv[size]=0;
return seq;
}
/*
Merge the seq1 with seq2
*/
static char *merge2seq(char* seq1, char* seq2,
int32_t size1, int32_t size2)
{
char * dest;
seq1 = (char *)MyRealloc((void *)seq1, (size1+size2+2) *sizeof(char),
(size1+1)*sizeof(char), "Cannot allocate space for reverse sequence");
dest = seq1 + size1 + 1;
seq1[size1]='@';
memcpy(dest,seq2,size2);
dest[size2]=0;
return seq1;
}
static int32_t dirDelta(SmallSeed_type* seed)
{
return seed->pos2 - seed->pos1;
}
void KMRK_SetMultipleLenDirSeeds(SmallSeed_type* seeds,
int32_t nseeds,
int32_t wordSize,
AllSeeds_type *PtrAllSeeds)
{
int32_t i,j; /* dummy counters j=kept seeds ; i = current seed */
int32_t curLen=wordSize; /* Length of the current seed */
int32_t delta;
SmallSeed_type *mainSeed;
SmallSeed_type *curSeed;
int32_t add;
/* fprintf(stderr,"New Version\n");*/
KMRK_sortSeeds(seeds,nseeds,KMRK_cmpDeltaSeedsPos);
for(j=0,mainSeed=seeds ;
j < nseeds;
j=i,mainSeed=curSeed)
{
/* foreach seed */
delta = dirDelta(mainSeed);
curLen=wordSize;
for (i=j+1,curSeed=mainSeed+1;
i < nseeds &&
dirDelta(curSeed)==delta &&
(curSeed->pos1 - mainSeed->pos1) <= curLen;
i++,curSeed++)
{
add=wordSize - mainSeed->pos1 - curLen + curSeed->pos1;
if (add < 0) add = 0;
curLen+=add;
}
KMRK_pushSeed(PtrAllSeeds,
seeds[j].pos1,seeds[j].pos2,
curLen,
1);
}
}
static int32_t invDelta(SmallSeed_type* seed)
{
return seed->pos2 + seed->pos1;
}
static void SetMultipleLenInvSeeds(SmallSeed_type* seeds,
int32_t nseeds,
int32_t wordSize,
int8_t same,
AllSeeds_type *PtrAllSeeds)
{
int32_t i,j; /* dummy counters j=kept seeds ; i = current seed */
int32_t curLen=wordSize; /* Length of the current seed */
int32_t delta;
int32_t pos2;
SmallSeed_type *mainSeed;
SmallSeed_type *curSeed;
int32_t add;
/* fprintf(stderr,"New Version\n");*/
KMRK_sortSeeds(seeds,nseeds,KMRK_cmpDeltaInvSeedsPos);
for(j=0,mainSeed=seeds ;
j < nseeds;
j=i,mainSeed=curSeed)
{
/* foreach seed */
delta = invDelta(mainSeed);
curLen=wordSize;
for (i=j+1,curSeed=mainSeed+1;
i < nseeds &&
invDelta(curSeed)==delta &&
(curSeed->pos1 - mainSeed->pos1) <= curLen;
i++,curSeed++)
{
add=wordSize - mainSeed->pos1 - curLen + curSeed->pos1;
if (add < 0) add = 0;
curLen+=add;
}
if ( same && (seeds[j].pos1+curLen>= seeds[i-1].pos2))
{
curLen = (seeds[i-1].pos2 - seeds[j].pos1 + 1) * 2;
pos2 = seeds[j].pos1;
}
else
pos2 = seeds[i-1].pos2;
KMRK_pushSeed(PtrAllSeeds,
seeds[j].pos1,pos2,
curLen,
0);
}
}
AllSeeds_type *KMRK_allocSeeds(AllSeeds_type *AllSeeds,
int32_t size,
int8_t opt_dir,
int8_t opt_inv)
{
AllSeeds_type *reponse;
if(opt_inv != 1 && opt_dir != 1)
{
fprintf(stderr,"AllocSeeds: requiere at least "
"one of opt_dir and opt_inv to be 1\n");
exit(4);
}
reponse = AllSeeds;
if (!reponse)
reponse = MyCalloc( 1, sizeof(AllSeeds_type),"KMRK_allocSeeds: cannot allocate new data structure");
if(opt_dir)
{
if (reponse->dirSeeds==NULL)
reponse->dirSeeds = (Seed_type *)MyCalloc( size,sizeof(Seed_type),"KMRK_allocSeeds: cannot allocate new data structure");
else
{
if(size)
reponse->dirSeeds = (Seed_type *)MyRealloc( (void *)reponse->dirSeeds,
size*sizeof(Seed_type), reponse->cDirSeeds*sizeof(Seed_type),
"allocSeeds: cannot reallocate data structure" );
else
{
MyFree(reponse->dirSeeds, reponse->cDirSeeds*sizeof(Seed_type));
reponse->dirSeeds=NULL;
reponse->cDirSeeds=0;
}
}
reponse->cDirSeeds=size;
}
if(opt_inv)
{
if (reponse->invSeeds==NULL)
reponse->invSeeds = (Seed_type *)MyCalloc( size, sizeof(Seed_type),"KMRK_allocSeeds: cannot allocate new data structure");
else
{
if(size)
reponse->invSeeds = (Seed_type *)MyRealloc( (void *)reponse->invSeeds,
size*sizeof(Seed_type), reponse->cInvSeeds*sizeof(Seed_type),
"allocSeeds: cannot reallocate data structure" );
else
{
MyFree(reponse->invSeeds, reponse->cInvSeeds*sizeof(Seed_type));
reponse->invSeeds=NULL;
reponse->cInvSeeds=0;
}
}
reponse->cInvSeeds=size;
}
return reponse;
}
void KMRK_freeSeeds(AllSeeds_type *AllSeeds)
{
if (!AllSeeds)
return;
if (AllSeeds->dirSeeds)
MyFree(AllSeeds->dirSeeds, AllSeeds->cDirSeeds*sizeof(Seed_type) );
AllSeeds->dirSeeds=NULL;
if (AllSeeds->invSeeds)
MyFree(AllSeeds->invSeeds, AllSeeds->cInvSeeds*sizeof(Seed_type) );
AllSeeds->dirSeeds=NULL;
MyFree(AllSeeds, 1*sizeof( AllSeeds_type ) );
}
void KMRK_compactSeeds(AllSeeds_type *AllSeeds)
{
if (AllSeeds)
{
if (AllSeeds->dirSeeds)
KMRK_allocSeeds(AllSeeds,
AllSeeds->nDirSeeds,
1,
0);
if (AllSeeds->invSeeds)
KMRK_allocSeeds(AllSeeds,
AllSeeds->nInvSeeds,
0,
1);
}
}
void KMRK_pushSeed(AllSeeds_type *AllSeeds,
int32_t pos1,
int32_t pos2,
int32_t length,
int8_t dir)
{
Seed_type* stack;
int32_t maxcount;
int32_t index;
if (dir)
{
dir = 1;
stack = AllSeeds->dirSeeds;
maxcount = AllSeeds->cDirSeeds;
index = AllSeeds->nDirSeeds;
}
else
{
dir = 0;
stack = AllSeeds->invSeeds;
maxcount = AllSeeds->cInvSeeds;
index = AllSeeds->nInvSeeds;
}
if (index == maxcount)
{
(void) KMRK_allocSeeds(AllSeeds,
maxcount * 2,
dir,
!dir);
if (dir)
stack = AllSeeds->dirSeeds;
else
stack = AllSeeds->invSeeds;
}
stack+=index;
stack->pos1 = pos1;
stack->pos2 = pos2;
stack->length = length;
if (dir)
AllSeeds->nDirSeeds++;
else
AllSeeds->nInvSeeds++;
}
AllSeeds_type* KMRK_enumerateDirectCouple(AllSeeds_type* Seeds,
int32_t expected,
int32_t wordSize,
vn_type* stack,
int32_t seq)
{
int32_t xmin;
int32_t xmax;
int32_t i;
int32_t j;
int32_t k;
int32_t next;
int32_t* n;
int32_t nseeds;
SmallSeed_type *list;
list = (SmallSeed_type *)MyCalloc( expected, sizeof(SmallSeed_type) ,
"KMRK_enumerateDirectCouple: cannot allocate DirectCouple memory");
nseeds = 0;
n = GETVECTOR(stack,n);
if (seq)
xmin = stack->limits[seq-1];
else
xmin = 0;
xmax = stack->limits[seq];
for (i=1; i <= xmax; i++)
if (IS_MARKED(n,i)) /* Check begining of chained list */
{
/* Look for begining of sequence of interest */
for( ;(i <= xmin) && (i != GET(n,i));
i=GET(n,i));
/* for each factor in sequence of interest */
for (j=i;
(j != GET(n,j)) && (j <= xmax);
j = GET(n,j))
{
next = GET(n,j);
if (next <= xmax)
do
{
k = next;
next = GET(n,k);
list[nseeds].pos1 = j-1;
list[nseeds].pos2 = k-1;
nseeds++;
} while ((k!=next) && (next <= xmax));
}
} ;
Seeds = KMRK_allocSeeds(Seeds,
expected/20+1,
1,0);
/* fprintf(stderr,"Expected direct couple : %d\n",expected);*/
KMRK_SetMultipleLenDirSeeds(list,nseeds,wordSize,Seeds);
MyFree(list, expected*sizeof(SmallSeed_type) );
KMRK_compactSeeds(Seeds);
return Seeds;
}
/*
From KMR-K Stacks to SmallSeeds
*/
AllSeeds_type* KMRK_enumerateInvertedCouple(AllSeeds_type* Seeds,
int32_t expected,
int32_t wordSize,
vn_type* stack)
{
int32_t xmax;
int32_t invmax;
int32_t posinv;
int32_t i;
int32_t j;
int32_t k;
int32_t memk;
int32_t* n;
int32_t next;
int32_t nseeds; /* number of seeds */
SmallSeed_type *list; /* seed list with only pos1 and pos2 --simple output from kmrk */
list = (SmallSeed_type *)MyCalloc( expected, sizeof(SmallSeed_type) ,
"KMRK_enumerateInvertedCouple: cannot allocate InvertedCouple memory");
nseeds = 0;
n = GETVECTOR(stack,n);
xmax = stack->limits[0];
invmax = stack->limits[1];
for (i=1; i <= xmax; i++)
if (IS_MARKED(n,i))
{
for(memk=i ;
(memk < xmax) &&
memk != GET(n,memk) &&
(memk <= invmax);
memk=GET(n,memk));
if ((memk > xmax) && (memk <= invmax))
for (j=i;
(j <= xmax) && (j != GET(n,j));
j=GET(n,j))
{
next = memk;
do
{
k = next;
next = GET(n,k);
posinv = 2 * xmax - k -wordSize + 3;
if (j <= posinv)
{
list[nseeds].pos1=j-1;
list[nseeds].pos2=posinv-1;
nseeds++;
}
} while ((next <= invmax) && (k != next));
}
}
Seeds = KMRK_allocSeeds(Seeds,
expected/20+1,
0,1);
/* fprintf(stderr,"Expected inverted couple : %d\n",expected);*/
SetMultipleLenInvSeeds(list,nseeds,wordSize,1,Seeds); /* turn the Small seeds into merged seeds */
MyFree(list, expected*sizeof(SmallSeed_type) );
KMRK_compactSeeds(Seeds);
return Seeds;
}
AllSeeds_type* KMRK_enumerateInterCouple(AllSeeds_type* Seeds,
int32_t seq1,
int32_t seq2,
int32_t expected,
int32_t wordSize,
vn_type* stack)
{
int32_t xmin;
int32_t xmax;
int32_t ymax;
int32_t ymin;
int32_t pos1;
int32_t pos2;
int32_t i;
int32_t j;
int32_t k;
int32_t memj;
int32_t memk;
int32_t* n;
int32_t next;
int32_t nseeds;
SmallSeed_type *list;
nseeds=0;
list = (SmallSeed_type *)MyCalloc( expected, sizeof(SmallSeed_type) ,
"KMRK_enumerateInterCouple: cannot allocate InterCouple memory");
n = GETVECTOR(stack,n);
if (seq1==0)
xmin=0;
else
xmin = stack->limits[seq1-1];
xmax = stack->limits[seq1];
ymin = stack->limits[seq2-1];
ymax = stack->limits[seq2];
for (i=1; i <= xmax; i++)
if (IS_MARKED(n,i))
{
for(memj=i ;
(memj < xmin) &&
memj != GET(n,memj);
memj=GET(n,memj));
if ((memj > xmin) && (memj <= xmax))
{
for(memk=memj ;
(memk < ymin) &&
memk != GET(n,memk);
memk=GET(n,memk));
if ((memk > ymin) && (memk <= ymax))
for (j=memj;
(j <= xmax) && (j != GET(n,j));
j=GET(n,j))
{
next = memk;
do
{
k = next;
next = GET(n,k);
if (seq1 > 0)
pos1 = j - xmin - 1;
else
pos1 = j;
pos2 = k - ymin - 1;
list[nseeds].pos1 = pos1 - 1;
list[nseeds].pos2 = pos2 - 1;
nseeds++;
} while ((next <= ymax) && (k != next));
}
}
}
Seeds = KMRK_allocSeeds(Seeds,
expected/20+1,
1,0);
/* fprintf(stderr,"Expected inter-direct couple : %d\n",expected);*/
KMRK_SetMultipleLenDirSeeds(list,nseeds,wordSize,Seeds);
MyFree(list, expected*sizeof(SmallSeed_type) );
KMRK_compactSeeds(Seeds);
return Seeds;
}
AllSeeds_type* KMRK_enumerateInterInvertedCouple(AllSeeds_type* Seeds,
int32_t seq2,
int32_t expected,
int32_t wordSize,
vn_type* stack)
{
int32_t xmin;
int32_t xmax;
int32_t ymax;
int32_t ymin;
int32_t posinv;
int32_t pos2;
int32_t i;
int32_t j;
int32_t k;
int32_t memj;
int32_t memk;
int32_t* n;
int32_t next;
int32_t nseeds;
SmallSeed_type *list;
list = (SmallSeed_type *)MyCalloc( expected, sizeof(SmallSeed_type) ,
"KMRK_enumerateInterCouple: cannot allocate InterCouple memory");
nseeds = 0;
n = GETVECTOR(stack,n);
if (seq2 < 2)
{
fprintf(stderr,"enumerateInterInvertedCouple: seq2 must be differente to 0");
exit(4);
}
xmin = stack->limits[0];
xmax = stack->limits[1];
ymin = stack->limits[seq2-1];
ymax = stack->limits[seq2];
Seeds = KMRK_allocSeeds(Seeds,
expected,
0,1);
for (i=1; i <= xmax; i++)
if (IS_MARKED(n,i))
{
for(memj=i ;
(memj < xmin) &&
memj != GET(n,memj);
memj=GET(n,memj));
if ((memj > xmin) && (memj <= xmax))
{
for(memk=memj ;
(memk < ymin) &&
memk != GET(n,memk);
memk=GET(n,memk));
if ((memk > ymin) && (memk <= ymax))
for (j=memj;
(j <= xmax) && (j != GET(n,j));
j=GET(n,j))
{
next = memk;
do
{
k = next;
next = GET(n,k);
posinv = 2 * xmin - j -wordSize + 3;
pos2 = k - ymin - 1;
list[nseeds].pos1=posinv-1;
list[nseeds].pos2=pos2-1;
nseeds++;
} while ((next <= ymax) && (k != next));
}
}
}
Seeds = KMRK_allocSeeds(Seeds,
expected/20+1,
0,1);
/* fprintf(stderr,"Expected inter-inverted couple : %d\n",expected);*/
SetMultipleLenInvSeeds(list,nseeds,wordSize,0,Seeds);
MyFree(list, expected* sizeof(SmallSeed_type) );
KMRK_compactSeeds(Seeds);
return Seeds;
}
int32_t KMRK_cmpSeedsPos(SmallSeed_type *s1, SmallSeed_type *s2)
{
if (s1->pos1==s2->pos1)
return s1->pos2 - s2->pos2;
else
return s1->pos1 - s2->pos1;
}
int32_t KMRK_cmpDeltaSeedsPos(SmallSeed_type *s1, SmallSeed_type *s2)
{
int32_t delta1 = s1->pos2-s1->pos1;
int32_t delta2 = s2->pos2-s2->pos1;
if (delta1==delta2)
return s1->pos1 - s2->pos1;
else
return delta1 - delta2;
}
int32_t KMRK_cmpDeltaInvSeedsPos(SmallSeed_type *s1, SmallSeed_type *s2)
{
int32_t delta1 = s1->pos2+s1->pos1;
int32_t delta2 = s2->pos2+s2->pos1;
if (delta1==delta2)
return s1->pos1 - s2->pos1;
else
return delta1 - delta2;
}
void KMRK_sortSeeds(SmallSeed_type* seeds,
int32_t nseeds,
KMRK_SORT_SEEDS_FUNC_PTR(compare))
{
qsort(seeds,
nseeds,
sizeof(SmallSeed_type),
(int (*)(const void *, const void *))compare);
}
AllSeeds_type* KMRK_get_seeds(char **seq,
int32_t SimpleSeqLen,
int16_t Lmin,
int8_t opt_dir,
int8_t opt_inv,
int8_t opt_verbose,
masked_area_table_t *mask)
{
AllSeeds_type* AllSeeds;
char *SeqDir = *seq;
vn_type * stacks;
int32_t dirExpect=0;
int32_t invExpect=0;
KMRK_QUORUM_FUNC_PTR(quorum);
if(opt_inv != 1 &&
opt_dir != 1)
{
fprintf(stderr,
"get_seeds: requiered at least "
"opt_dir or opt_inv to be 1\n");
exit(4);
}
if(opt_inv)
SeqDir = makeDirInvSeq(SeqDir,SimpleSeqLen); /* create a sequence with "DirSeq\0InvSeq\0" */
if (opt_inv){ /* Are we interested in dir, inv or both ? */
if (opt_dir)
quorum = KMRK_DirInvQuorum;
else
quorum = KMRK_InvQuorum;
}
else
quorum = KMRK_CoupleQuorum;
stacks = KMRK_RunTo(SeqDir,
Lmin,
opt_inv,
2,
1,
quorum,
KMRK_HashOneSequence,
mask);
invExpect =0;
KMRK_markStart(stacks);
if (opt_inv)
{
SeqDir = (char *)MyRealloc( (void *)SeqDir, (SimpleSeqLen+1)*sizeof(char),
(2*SimpleSeqLen+2)*sizeof(char) , "KRMK_get_seeds: Cannot shrink memory"); /* reset mem to a sigle sequence */
SeqDir[SimpleSeqLen]=0;
}
if(opt_inv)
invExpect = KMRK_upperInvertedCount(stacks,Lmin);
if(opt_dir)
dirExpect = KMRK_upperCoupleCount(stacks);
AllSeeds = NULL;
MyFree(stacks->v, stacks->size * sizeof(int32_t));
stacks->v=NULL;
if (opt_dir)
AllSeeds = KMRK_enumerateDirectCouple(AllSeeds,dirExpect,Lmin ,stacks,0);
if (opt_inv)
AllSeeds = KMRK_enumerateInvertedCouple(AllSeeds,invExpect,Lmin,stacks);
KMRK_FreeVN(stacks);
*seq = SeqDir;
return AllSeeds;
}
AllSeeds_type* KMRK_get_seeds_2seqs(char **seq1,
char **seq2,
int32_t size1,
int32_t size2,
int16_t Lmin,
int8_t opt_dir,
int8_t opt_inv,
int8_t opt_verbose,
masked_area_table_t *mask)
{
AllSeeds_type* AllSeeds;
char *sequence1 = *seq1;
char *sequence2 = *seq2;
vn_type * stacks;
int32_t dirExpect=0;
int32_t invExpect=0;
KMRK_QUORUM_FUNC_PTR(quorum);
int32_t sizef;
if(opt_inv != 1 &&
opt_dir != 1)
{
fprintf(stderr,
"get_seeds_2seqs: requiered at least "
"opt_dir or opt_inv to be 1\n");
exit(4);
}
sizef = size1;
if(opt_inv)
{
sequence1 = makeDirInvSeq(sequence1,size1);
sizef+=(1+size1);
}
sequence1 = merge2seq(sequence1,sequence2,sizef,size2);
if (opt_inv)
if (opt_dir)
quorum = KMRK_IntDirInv12Quorum;
else
quorum = KMRK_IntInv12Quorum;
else
quorum = KMRK_Int12Quorum;
stacks = KMRK_RunTo(sequence1,
Lmin,
opt_inv,
2,
2,
quorum,
KMRK_HashOneSequence,
mask);
KMRK_markStart(stacks);
sequence1= (char *)MyRealloc(
(void *)sequence1,
(size1+1)*sizeof(char),
(sizef+size2+2)*sizeof(char),
"KMRK_get_seeds_2seqs: shrink memory from 3N to 1N... ???");
sequence1[size1]=0;
if (opt_dir){
if (opt_inv)
dirExpect = KMRK_upperInterCount(stacks,0,2,Lmin);
else
dirExpect = KMRK_upperInterCount(stacks,0,1,Lmin);
}
if (opt_inv)
invExpect = KMRK_upperInterCount(stacks,1,2,Lmin);
AllSeeds = NULL;
MyFree(stacks->v, stacks->size*sizeof(int32_t));
stacks->v=NULL;
if (opt_dir){
if (opt_inv)
AllSeeds = KMRK_enumerateInterCouple(AllSeeds,
0,2,
dirExpect,
Lmin ,
stacks);
else
AllSeeds = KMRK_enumerateInterCouple(AllSeeds,
0,1,
dirExpect,
Lmin ,
stacks);
}
if (opt_inv)
AllSeeds = KMRK_enumerateInterInvertedCouple(AllSeeds,
2,
invExpect,
Lmin ,
stacks);
KMRK_FreeVN(stacks);
*seq1 = sequence1;
return AllSeeds;
}
#define SIGN(x) (((x)<0) ? -1:(((x)>0) ? 1:0))
static int32_t compareSeedsByPos(Seed_type* s1,Seed_type* s2)
{
if (s1->pos1 == s2->pos1)
return SIGN(s1->pos2 - s2->pos2);
else
return SIGN(s1->pos1 - s2->pos1);
}
void KMRK_sortSeedsByPos(Seed_type* seeds, int32_t count)
{
qsort(seeds,
count,
sizeof(Seed_type),
(int (*)(const void *, const void *))compareSeedsByPos);
};

126
src/libKMRK/KMRK_Seeds.h
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@ -1,126 +0,0 @@
#ifndef KMRK_Seeds_h
#define KMRK_Seeds_h
/********************************************
********************************************
**
** Declaration of struct
**
********************************************
********************************************/
#include <stdint.h>
#include <stdio.h>
#include "KMRK.h"
#define KMRK_SORT_SEEDS_FUNC_PTR(name) int32_t (*name)(SmallSeed_type*, \
SmallSeed_type*)
#define KMRK_DELTA_SEEDS_FUNC_PTR(name) int32_t (*name)(SmallSeed_type*)
/********************************************
********************************************
**
** Declaration of public functions
**
********************************************
********************************************/
AllSeeds_type *KMRK_allocSeeds(AllSeeds_type *AllSeeds,
int32_t size,
int8_t opt_dir,
int8_t opt_inv);
void KMRK_SetMultipleLenDirSeeds(SmallSeed_type* seeds,
int32_t nseeds,
int32_t wordSize,
AllSeeds_type *PtrAllSeeds);
void KMRK_freeSeeds(AllSeeds_type *AllSeeds);
void KMRK_compactSeeds(AllSeeds_type *AllSeeds);
void KMRK_pushSeed(AllSeeds_type *AllSeeds,
int32_t pos1,
int32_t pos2,
int32_t length,
int8_t dir);
AllSeeds_type* KMRK_enumerateDirectCouple(AllSeeds_type* Seeds,
int32_t expected,
int32_t wordSize,
vn_type* stack,
int32_t seq);
AllSeeds_type* KMRK_enumerateInvertedCouple(AllSeeds_type* Seeds,
int32_t expected,
int32_t wordSize,
vn_type* stack);
AllSeeds_type* KMRK_enumerateInterCouple(AllSeeds_type* Seeds,
int32_t seq1,
int32_t seq2,
int32_t expected,
int32_t wordSize,
vn_type* stack);
AllSeeds_type* KMRK_enumerateInterInvertedCouple(AllSeeds_type* Seeds,
int32_t seq2,
int32_t expected,
int32_t wordSize,
vn_type* stack);
/**
* Compare two seeds and return an integer less than, equal to or greater
* than zero considering the relative order of the two seeds. This
* version take into account only pos1 and pos2 of seeds without taking
* account of the sequences or of the relative direction
*
* @param s1 pointer to seed one
* @param s2 pointer to seed two
*
* @return a integer less than, equal to or greater than zero
*/
int32_t KMRK_cmpSeedsPos(SmallSeed_type *s1, SmallSeed_type *s2);
int32_t KMRK_cmpDeltaSeedsPos(SmallSeed_type *s1, SmallSeed_type *s2);
int32_t KMRK_cmpDeltaInvSeedsPos(SmallSeed_type *s1, SmallSeed_type *s2);
void KMRK_sortSeeds(SmallSeed_type* seeds,
int32_t nseeds,
KMRK_SORT_SEEDS_FUNC_PTR(compare));
AllSeeds_type* KMRK_get_seeds(char **seq,
int32_t SimpleSeqLen,
int16_t Lmin,
int8_t opt_dir,
int8_t opt_inv,
int8_t opt_verbose,
masked_area_table_t *mask);
AllSeeds_type* KMRK_get_seeds_2seqs(char **seq1,
char **seq2,
int32_t size1,
int32_t size2,
int16_t Lmin,
int8_t opt_dir,
int8_t opt_inv,
int8_t opt_verbose,
masked_area_table_t *mask);
/**
* Order an array of seeds by pos1,pos2
*
* @param seeds pointer to an array of Seed_type object to sort
* @param count count of element in the array
*/
void KMRK_sortSeedsByPos(Seed_type* seeds, int32_t count);
#endif /* KMRK_Seeds_h */

259
src/libKMRK/KMRK_mask.c
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@ -1,259 +0,0 @@
/*
* KMRK_mask.c
* repseek
*
* Created by Eric Coissac on 04/12/04.
* Copyright 2004 __MyCompanyName__. All rights reserved.
*
*/
#include "KMRK_mask.h"
#include <stdio.h>
#include <stdlib.h>
#include "memory.h"
#define MASKED_AREA_TABLE_SIZE(seqcount) (sizeof(masked_area_table_t) + (sizeof(masked_area_list_t*) * ((seqcount)-1)))
#define MASKED_AREA_LIST_SIZE(areacount) (sizeof(masked_area_list_t) + (sizeof(masked_area_t) * ((areacount)-1)))
#define AREA_COUNT_INIT (1000)
static masked_area_table_t *new_masked_area_table(int32_t seqcount, int32_t areacount);
static masked_area_list_t *new_masked_area_list(int32_t areacount);
static masked_area_list_t *realloc_masked_area_list(masked_area_list_t *list,int32_t areacount);
static int32_t push_area(masked_area_table_t* table,int32_t sequence,int32_t begin,int32_t end);
static void sort_area_table(masked_area_table_t* table);
static int32_t compare_area(const masked_area_t* v1,const masked_area_t* v2);
static int32_t search_area(const masked_area_t* v1,const masked_area_t* v2);
static masked_area_list_t *strip_area_list(masked_area_list_t* list);
static void strip_area_table(masked_area_table_t* table);
static masked_area_list_t *new_masked_area_list(int32_t areacount)
{
masked_area_list_t *list;
list = MyCalloc(1,MASKED_AREA_LIST_SIZE(areacount),"Not enougth memory for mask table");
list->reserved=areacount;
return list;
}
static masked_area_list_t *realloc_masked_area_list(masked_area_list_t *list,int32_t areacount)
{
list = MyRealloc(list,
MASKED_AREA_LIST_SIZE(areacount),
MASKED_AREA_LIST_SIZE(list->reserved),
"Not enougth memory for mask table");
list->reserved=areacount;
return list;
}
static masked_area_table_t *new_masked_area_table(int32_t seqcount, int32_t areacount)
{
masked_area_table_t *table;
int32_t i;
table = MyCalloc(1,MASKED_AREA_TABLE_SIZE(seqcount),"Not enougth memory for mask table");
table->seqcount=seqcount;
for (i=0;i<seqcount;i++)
table->sequence[i]=new_masked_area_list(areacount);
return table;
}
static int32_t push_area(masked_area_table_t* table,int32_t sequence,int32_t begin,int32_t end)
{
masked_area_list_t * list;
if (sequence >= table->seqcount)
return -1;
list = table->sequence[sequence];
if (list->reserved == list->count)
{
list = realloc_masked_area_list(list,list->reserved*2);
table->sequence[sequence]=list;
}
list->area[list->count].begin=begin;
list->area[list->count].end=end;
list->count++;
table->total++;
return table->total;
}
static int32_t compare_area(const masked_area_t* v1,const masked_area_t* v2)
{
return v1->begin - v2->begin;
}
static void sort_area_table(masked_area_table_t* table)
{
int32_t i;
for (i=0; i<table->seqcount;i++)
{
qsort(table->sequence[i]->area,
table->sequence[i]->count,
sizeof(masked_area_t),
(int (*)(const void *, const void *))compare_area);
}
}
static masked_area_list_t *strip_area_list(masked_area_list_t* list)
{
int32_t i;
int32_t j;
int32_t count;
int32_t newcount;
count = list->count;
newcount=count;
for (i=1;i<count;i++)
{
/* fprintf(stderr,"\n%d->%d %d->%d ==>",list->area[i-1].begin,list->area[i-1].end,list->area[i].begin,list->area[i].end); */
if ((list->area[i].begin-1) <= list->area[i-1].end)
{
/* fprintf(stderr," joined"); */
list->area[i].begin=list->area[i-1].begin;
list->area[i-1].begin=-1;
newcount--;
}
}
list->count=newcount;
for (i=0,j=0;i<count;i++)
{
if (list->area[i].begin>=0)
{
if (i!=j)
list->area[j]=list->area[i];
j++;
}
}
return realloc_masked_area_list(list,newcount);
}
static void strip_area_table(masked_area_table_t* table)
{
int32_t seq;
int32_t oldcount;
masked_area_list_t* list;
sort_area_table(table);
for (seq=0; seq < table->seqcount;seq++)
{
list = table->sequence[seq];
oldcount = list->count;
table->sequence[seq]=strip_area_list(list);
table->total-=oldcount - table->sequence[seq]->count;
}
}
static int32_t search_area(const masked_area_t* v1,const masked_area_t* v2)
{
int32_t pos;
pos = v1->begin;
if (pos < v2->begin)
return -1;
if (pos > v2->end)
return 1;
return 0;
}
masked_area_table_t *KMRK_ReadMaskArea(char *areafile,int32_t seqcount,int32_t complement)
{
FILE* area;
char buffer[1000];
char *ok;
int32_t begin;
int32_t end;
int32_t sequence;
int32_t column;
int32_t linecount;
masked_area_table_t *table;
if (complement > 0)
seqcount++;
else
complement=0;
area = fopen(areafile,"r");
linecount=0;
table=new_masked_area_table(seqcount,AREA_COUNT_INIT);
do {
linecount++;
ok = fgets(buffer,999,area);
if (ok)
{
column = sscanf(buffer,"%d %d %d",&begin,&end,&sequence);
if (column > 1 && begin <= end)
{
begin--;
end--;
if (column==3)
sequence--;
else
sequence=0;
if (sequence && complement)
sequence++;
push_area(table,sequence,begin,end);
if (!sequence && complement)
push_area(table,1,complement -1 - end,complement -1 -begin);
}
if (column==1)
fprintf(stderr,"WARNING in mask file reading line %d\n",linecount);
}
} while (ok);
fprintf(stderr,"\nread %d masked areas from file\n",table->total);
strip_area_table(table);
fprintf(stderr,"strip to %d non overlaping areas\n",table->total);
return table;
}
char KMRK_isMasked(masked_area_table_t *mask,int32_t seq, int32_t position)
{
masked_area_t input;
int32_t result;
masked_area_list_t *list;
if (! mask || (seq >= mask->seqcount))
return 0;
list = mask->sequence[seq];
input.begin=position;
result = bsearch(&input,
list->area,
list->count,
sizeof(masked_area_t),
(int (*)(const void *, const void *))search_area) != NULL;
return result;
}

37
src/libKMRK/KMRK_mask.h
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@ -1,37 +0,0 @@
/*
* KMRK_mask.h
* repseek
*
* Created by Eric Coissac on 04/12/04.
* Copyright 2004 __MyCompanyName__. All rights reserved.
*
*/
#include <stdint.h>
#ifndef _KMRK_MASK_H_
#define _KMRK_MASK_H_
typedef struct {
int32_t begin;
int32_t end;
} masked_area_t;
typedef struct {
int32_t reserved;
int32_t count;
masked_area_t area[1];
} masked_area_list_t;
typedef struct {
int32_t seqcount;
int32_t total;
masked_area_list_t *sequence[1];
} masked_area_table_t;
masked_area_table_t *KMRK_ReadMaskArea(char *areafile,int32_t seqcount,int32_t complement);
char KMRK_isMasked(masked_area_table_t *mask,int32_t seq, int32_t position);
#endif

123
src/libKMRK/KMRK_merge_seeds.c
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@ -1,123 +0,0 @@
/**
* @file KMRK_merge_seeds.c
* @author Eric Coissac <coissac@inrialpes.fr>
* @date Wed Mar 3 11:15:57 2004
*
* @brief Merge function of overlapping seeds
*
*
*/
#include "KMRK_merge_seeds.h"
void KMRK_MergeSeeds(AllSeeds_type *AllSeeds,
int8_t opt_dir,
int8_t opt_inv)
{
int32_t i; /* the current seed */
int32_t j; /* the checked seed */
int32_t N; /* the kept ones */
Seed_type* seeds;
if(opt_dir){
seeds = AllSeeds->dirSeeds;
for(i=0, N=0 ;i<AllSeeds->nDirSeeds; i++){
if(seeds[i].pos1==-1) /* any seed at -1 is removed */
continue;
j=i+1;
while( (seeds[j].pos1!=-1) &&
(seeds[i].pos1!=-1) &&
(j < AllSeeds->nDirSeeds) &&
(seeds[j].pos1 < seeds[i].pos1+ seeds[i].length))
{
if(
((seeds[j].pos2 >= seeds[i].pos2) &&
(seeds[j].pos2 < seeds[i].pos2 + seeds[i].length)) || /* if the seeds are overlapping */
((seeds[j].pos2 + seeds[j].length >= seeds[i].pos2) &&
(seeds[j].pos2 + seeds[j].length < seeds[i].pos2 + seeds[i].length)))
{
if(seeds[j].length <= seeds[i].length)
seeds[j].pos1=seeds[j].pos2=seeds[j].length=-1; /* removed the smallest */
else
seeds[i].pos1=seeds[i].pos2=seeds[i].length=-1;
}
j++;
}
if(seeds[i].pos1 !=-1)
{ /* if this seed is not out, store it */
seeds[N].pos1 = seeds[i].pos1;
seeds[N].pos2 = seeds[i].pos2;
seeds[N].length = seeds[i].length;
N++;
}
}
AllSeeds->nFilteredDirSeeds += AllSeeds->nDirSeeds-N;
AllSeeds->nDirSeeds=N;
}
if(opt_inv){
seeds = AllSeeds->invSeeds;
for(i=0, N=0 ;i<AllSeeds->nInvSeeds; i++){
if(seeds[i].pos1==-1)
continue;
j=i+1;
while( (seeds[j].pos1!=-1 ) &&
(seeds[i].pos1!=-1 ) &&
(j < AllSeeds->nInvSeeds) &&
(seeds[j].pos1 < seeds[i].pos1+seeds[i].length))
{
if(
((seeds[j].pos2 >= seeds[i].pos2) && /* if the seeds are overlapping */
(seeds[j].pos2 < seeds[i].pos2+seeds[i].length)) ||
((seeds[j].pos2 + seeds[j].length >= seeds[i].pos2) &&
(seeds[j].pos2 + seeds[j].length < seeds[i].pos2+seeds[i].length)))
{
if(seeds[j].length <= seeds[i].length)
seeds[j].pos1=seeds[j].pos2=seeds[j].length=-1; /* removed the smallest */
else
seeds[i].pos1=seeds[i].pos2=seeds[i].length=-1;
}
j++;
}
if(seeds[i].pos1!=-1)
{ /* if this seed is not out, store it */
seeds[N].pos1 = seeds[i].pos1;
seeds[N].pos2 = seeds[i].pos2;
seeds[N].length = seeds[i].length;
N++;
}
}
AllSeeds->nFilteredInvSeeds += AllSeeds->nInvSeeds-N;
AllSeeds->nInvSeeds=N;
}
KMRK_compactSeeds(AllSeeds);
}

11
src/libKMRK/KMRK_merge_seeds.h
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@ -1,11 +0,0 @@
#ifndef KMRK_merge_seeds_h
#define KMRK_merge_seeds_h
#include "KMRK_Seeds.h"
void KMRK_MergeSeeds(AllSeeds_type *AllSeeds,
int8_t opt_dir,
int8_t opt_inv);
#endif /* KMRK_MergeSeeds */

25
src/libKMRK/Makefile
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@ -1,25 +0,0 @@
SOURCES = KMRK.c \
KMRK_mask.c \
KMRK_merge_seeds.c \
KMRK_Seeds.c
SRCS=$(SOURCES)
OBJECTS= $(patsubst %.c,%.o,$(SOURCES))
LIBFILE= libKMRK.a
RANLIB= ranlib
include ../global.mk
all: $(LIBFILE)
clean:
rm -rf $(OBJECTS) $(LIBFILE)
$(LIBFILE): $(OBJECTS)
ar -cr $@ $?
$(RANLIB) $@

224
src/libKMRK/memory.c
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@ -1,224 +0,0 @@
/******
file : memory.c
function : All about memory of the KMR, Seeds and Repeats
All MyMalloc() series is about follwoing how mauch memory has been used
created : 19 Sep 2003
modif : Oct 2003, Feb 2004
modif : Dec 2004 <EC> ; Corrected Memory declaration
author : amikezor
*****/
#include <stdio.h>
#include <stdlib.h>
#include "repseek_types.h"
#include "memory.h"
MemUsage Memory;
/*
Functions to count the memory usage all along
dybamic allocation and free
*/
void PrintMem(char *Comment){
extern MemUsage Memory;
fprintf(stderr,"\n%s\nMemory Usage\n\t* Max is: %d bytes, %.2f Kb, %.2f Mb\n\t* Cur is: %d bytes, %.2f Kb, %.2f Mb\n",
Comment,
Memory.Max, (float)Memory.Max/1024, (float)Memory.Max/(1024*1024),
Memory.Current, (float)Memory.Current/1024, (float)Memory.Current/(1024*1024));
}
void PrintMaxMem( void ){
extern MemUsage Memory;
if(Memory.Max < 1024)
fprintf(stderr,"Max Memory Usage.. %d bytes\n", Memory.Max);
else if(Memory.Max < 1024*1024)
fprintf(stderr,"Max Memory Usage.. %.2f Kilobytes\n", (float)Memory.Max/1024);
else if(Memory.Max < 1024*1024*1024)
fprintf(stderr,"Max Memory Usage.. %.2f Megabytes\n", (float)Memory.Max/(1024*1024));
else
fprintf(stderr,"Max Memory Usage.. %.2f Gigabytes\n", (float)Memory.Max/(1024*1024*1024));
}
void Update_Mem(int32_t Value){
extern MemUsage Memory;
Memory.Current += Value;
Memory.Max = (Memory.Current>Memory.Max)?Memory.Current:Memory.Max;
}
void Init_Mem(int32_t Value){
extern MemUsage Memory;
Memory.Current = Value;
Memory.Max = Value;
}
/*
Replace functions of dynamic allocation
to allow the tracking of memory usage
*/
void *MyMalloc( int32_t size , char *Error ){
void *pointer;
pointer = malloc(size);
if(!pointer)fprintf(stderr,"%s\n",Error),exit(3);
Update_Mem(size);
return pointer;
}
void *MyCalloc( int32_t number, int32_t TypeSize , char *Error ){
void *pointer;
pointer = calloc(number, TypeSize);
if(!pointer)fprintf(stderr,"%s\n",Error),exit(3);
Update_Mem(number*TypeSize );
return pointer;
}
void MyFree( void *Pointer, int32_t size){
free(Pointer);
Pointer=NULL;
Update_Mem(-size);
}
void *MyRealloc( void *Pointer, int32_t newsize, int32_t oldsize, char *Error){
Pointer = realloc(Pointer,newsize);
if(!Pointer)fprintf(stderr,"%s\n",Error),exit(3);
Update_Mem( newsize-oldsize );
return Pointer;
}
/*
Deal with Stacks structure for KMR
void MallocStack(Stacks *s, int32_t number, int32_t *histo, int32_t AllValues){
int32_t i;
s->nStacks = number;
s->nValues = AllValues;
s->ppStacks = (int32_t **)MyMalloc( number * sizeof(int32_t *),
"MallocStack: ppStacks malloc error, bye\n");
s->lenStacks = (int32_t *)MyMalloc( number * sizeof(int32_t),
"MallocStack: lenStacks malloc error, bye\n");
s->ppStacks[0] = (int32_t *)MyMalloc( AllValues * sizeof(int32_t),
"MallocStack: ppStacks[0] malloc error, bye\n");
s->lenStacks[0]=0;
for(i=1;i < number; i++){
s->lenStacks[i]=0;
s->ppStacks[i] = s->ppStacks[i-1] + histo[i] ;
}
}
void FreeStack( Stacks *p){
MyFree(p->ppStacks[0] , p->nValues*sizeof(int32_t) );
MyFree(p->ppStacks , p->nStacks*sizeof(int32_t *) );
MyFree(p->lenStacks , p->nStacks*sizeof(int32_t));
}
*/
/*
Deal with the Seeds part
void free_Seeds(Seeds AllSeeds)
{
if( AllSeeds.nDirSeeds ){
MyFree(AllSeeds.DirPos1, AllSeeds.nDirSeeds*sizeof(int32_t));
MyFree(AllSeeds.DirPos2, AllSeeds.nDirSeeds*sizeof(int32_t));
MyFree(AllSeeds.DirLen, AllSeeds.nDirSeeds*sizeof(int32_t));
MyFree(AllSeeds.DirMeanR, AllSeeds.nDirSeeds*sizeof(float));
}
if(AllSeeds.nInvSeeds ){
MyFree(AllSeeds.InvPos1, AllSeeds.nInvSeeds*sizeof(int32_t));
MyFree(AllSeeds.InvPos2, AllSeeds.nInvSeeds*sizeof(int32_t));
MyFree(AllSeeds.InvLen, AllSeeds.nInvSeeds*sizeof(int32_t));
MyFree(AllSeeds.InvMeanR, AllSeeds.nInvSeeds*sizeof(float));
}
}
*/
/*
Malloc if it is the first time otherwise readjust
void AllocSeeds(Seeds *AllSeeds, int32_t size, int32_t old_size, int8_t opt_dir, int8_t opt_inv){
if(opt_inv != 1 && opt_dir != 1)
fprintf(stderr,"AllocSeeds: requiere at least one of opt_dir and opt_inv to be 1\n"),exit(4);
if(opt_dir == 1){
if( AllSeeds->DirPos1 == NULL){
AllSeeds->DirPos1 = (int32_t *)MyCalloc(size , sizeof(int32_t),"AllocSeeds: Alloc for DirPos1 failed, bye");
AllSeeds->DirPos2 = (int32_t *)MyCalloc(size , sizeof(int32_t),"AllocSeeds: Alloc for DirPos2 failed, bye");
}
else{
AllSeeds->DirPos1 = (int32_t *)MyRealloc(AllSeeds->DirPos1, size * sizeof(int32_t), old_size* sizeof(int32_t),
"AllocSeeds: realloc for DirPos1 failed, bye");
AllSeeds->DirPos2 = (int32_t *)MyRealloc(AllSeeds->DirPos2, size * sizeof(int32_t), old_size* sizeof(int32_t),
"AllocSeeds: realloc for DirPos2 failed, bye");
}
}
if(opt_inv == 1){
if( AllSeeds->InvPos1 == NULL){
AllSeeds->InvPos1 = (int32_t *)MyCalloc(size , sizeof(int32_t), "AllocSeeds: Alloc for InvPos1 failed, bye");
AllSeeds->InvPos2 = (int32_t *)MyCalloc(size , sizeof(int32_t), "AllocSeeds: Alloc for InvPos2 failed, bye");
}
else{
AllSeeds->InvPos1 = (int32_t *)MyRealloc(AllSeeds->InvPos1, size * sizeof(int32_t), old_size* sizeof(int32_t),
"AllocSeeds: realloc for InvPos1 failed, bye");
AllSeeds->InvPos2 = (int32_t *)MyRealloc(AllSeeds->InvPos2, size * sizeof(int32_t), old_size* sizeof(int32_t),
"AllocSeeds: realloc for InvPos2 failed, bye");
}
}
}
*/
/*
Deal with the Repeats structure
*/
Repeats mem_Repeats(int32_t Ndir, int32_t Ninv){
Repeats AllRepeats; /* All Repeats structure */
AllRepeats.nDirRep = Ndir; /* set the number of repeats to the number of seeds */
AllRepeats.nInvRep = Ninv;
AllRepeats.nDirBadRep = 0; /* set the "bad" repet (included into another rep) as 0 */
AllRepeats.nInvBadRep = 0;
if(AllRepeats.nDirRep)
AllRepeats.DirRep = (Rep *)MyMalloc( (AllRepeats.nDirRep)*sizeof(Rep), "init_Repeats: repdir malloc error" );
else
AllRepeats.DirRep = NULL;
if(AllRepeats.nInvRep)
AllRepeats.InvRep = (Rep *)MyMalloc( (AllRepeats.nInvRep)*sizeof(Rep), "init_Repeats: repinv malloc error" );
else
AllRepeats.InvRep = NULL;
return AllRepeats;
}
void free_Repeats(Repeats AllRep)
{
if(AllRep.nDirRep)
MyFree(AllRep.DirRep, AllRep.nDirRep*sizeof(Rep));
if(AllRep.nInvRep)
MyFree(AllRep.InvRep, AllRep.nInvRep*sizeof(Rep));
}

105
src/libKMRK/memory.h
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@ -1,105 +0,0 @@
/**
* @file memory.h
* @author Achaz G
* @date April 2004
*
* @brief header for memory alloc/dealloc
* modif : Dec 2004 <EC> ; Corrected Memory declaration
*
*
*/
#ifndef _MEMORY_H_
#define _MEMORY_H_
#include "repseek_types.h"
typedef struct { /********** Memory Usage structure **************/
int32_t Max;
int32_t Current;
} MemUsage;
#include <stdint.h>
/********** **********
Global Variable(s)
********** **********/
extern MemUsage Memory; /* Instance of the global variable for memory tracking */
/*
Follow memory usage
*/
void PrintMem(char *Comment);
void PrintMaxMem( void );
void Update_Mem(int32_t Value);
void Init_Mem(int32_t Value);
/*
All Alloc/Free to follow of memory usage
*/
void *MyMalloc( int32_t size , char *Error );
void *MyCalloc( int32_t number, int32_t TypeSize , char *Error );
void MyFree( void *Pointer, int32_t size);
void *MyRealloc( void *Pointer, int32_t newsize, int32_t oldsize, char *Error);
/*
For Stacks
void MallocStack(Stacks *s, int32_t number, int32_t *histo, int32_t AllValues);
void FreeStack( Stacks *p);
For Seeds
void free_Seeds(Seeds AllSeeds);
void AllocSeeds(Seeds *AllSeeds, int32_t size, int32_t old_size, int8_t opt_dir, int8_t opt_inv);
*/
/*
For Repeats
*/
Repeats mem_Repeats(int32_t Ndir, int32_t Ninv);
void free_Repeats(Repeats AllRep);
/*
Not used anymore, but just in case
*/
#include <stdio.h>
#include <stdlib.h>
#define KMRK_MALLOC(var,type,size,message) { \
var = (type*) malloc(size); \
if (!var) \
{ \
fprintf(stderr,"%s\n",message); \
exit(4); \
} \
}
#define KMRK_CALLOC(var,type,length,message) { \
var = (type*) calloc(length,sizeof(type)); \
if (!var) \
{ \
fprintf(stderr,"%s\n",message); \
exit(4); \
} \
}
#define KMRK_REALLOC(var,type,size,message) { \
var = (type*) realloc(var,size); \
if (!var) \
{ \
fprintf(stderr,"%s\n",message); \
exit(4); \
} \
}
#endif /* _MEMORY_H_*/

197
src/libKMRK/repseek_types.h
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@ -1,197 +0,0 @@
/**
* @file repseek_types.h
* @author Guillaume Achaz <gachaz@oeb.harvard.edu>
* @date April 2004
* @modif July 2004 turn scores into doubles
* @brief definition of general types and macros for repseek
*
*
*/
#ifndef _REPSEEK_TYPES_
#define _REPSEEK_TYPES_
/*
Version of the program
*/
#define REPSEEK_VERSION "4.2"
#define REPSEEK_DATE "Nov 2004"
/********** **********
General Macros
********** **********/
/*
Macros to compare 2 or three values
*/
#define MAX2( A, B ) ( ((A)>(B))?(A):(B) )
#define MAX3( A, B, C ) ( ((MAX2(A,B))>(C))?(MAX2(A,B)):(C) )
#define MIN2( A, B ) ( ((A)<(B))?(A):(B) )
#define MAX( A, B ) MAX2( A, B )
#define MIN( A, B ) MIN2( A, B )
/*
Absolute values
*/
#define ABS(x) (( (x)>=0 )? (x) : -(x))
/********** **********
All types used in repseek
********** **********/
#include <stdio.h> /* The type FILE * is defined here */
#include <stdint.h> /* all, the int??_t are defined in there */
/**
* Store informations about one STRICT repeat (seeds)
*
*/
typedef struct { /* the complete seed structure */
int32_t pos1; /**< position of the first copy */
int32_t pos2; /**< position of the second copy */
int32_t length; /**< length of the strict repeats */
float rmean; /**< mean repeat leavel */
} Seed_type;
typedef struct { /* Just after a KMRK length X, only the 2 pos matter */
int32_t pos1; /**< postion of the first copy */
int32_t pos2; /**< postion of the second copy */
} SmallSeed_type;
/**
* Store informations about all strict repeat (seeds)
*
*/
typedef struct {
int32_t cDirSeeds; /**< currently allocated space in dirSeeds array */
int32_t nDirSeeds; /**< count of direct strict repeats */
int32_t nFilteredDirSeeds; /**< ??? */
Seed_type* dirSeeds; /**< array of direct repeats */
int32_t cInvSeeds; /**< currently allocated space in invSeeds array */
int32_t nInvSeeds; /**< count of inverted strict repeats */
int32_t nFilteredInvSeeds; /**< ??? */
Seed_type* invSeeds; /**< array of inverted repeats */
} AllSeeds_type;
/**
* Store informations about one GENERIC repeat
*
*/
typedef struct{
char type[20]; /* its name; i.e. Tandem, Palindrome, etc... */
int32_t pos1, pos2, /* both copies postions */
len1, len2, /* both copies length */
seed_pos1,seed_pos2, /* pos1 and pos2 of the originate seed */
seed_len, /* len of the seed */
match, align_len; /* number of match and length of alignment */
double score; /* the alignment score */
float seed_meanR; /* the seed meanR */
float meanR; /* The mean R-level of the repeat */
int32_t mainR; /* its Mode R */
float fraction_mainR; /* the fraction of length containing the Mode R */
} Rep;
/**
* Store informations about All GENERIC repeats
*
*/
typedef struct {
int32_t nDirRep; /* Total Number of Direct Repats in Mem */
int32_t nDirBadRep; /* Direct repeats set to -1 -- filtered out and co. */
Rep *DirRep; /* The array of Dir Rep */
int32_t nInvRep; /* Total Number of Inverted Repats in Mem */
int32_t nInvBadRep; /* Inverted Repeats set to -1 -- filtered out and co. */
Rep *InvRep; /* The array of Inverted Rep */
} Repeats;
#define MATRIX_SIZE 26
typedef struct { /******* The scoring Matrix ************/
double matrix[MATRIX_SIZE][MATRIX_SIZE]; /* the matrix of match/missmatch */
double gap_open; /* value of gap-open */
double gap_ext; /* value of gap_ext */
double expect;
} SCORING;
typedef struct { /******* The Results of Alignement by Dynamik programming ************/
double *scores; /* the score strings (+/- 'matrix') */
double *pscore; /* pointer to the current score */
char *traces; /* the path matrix - could take values 'l'eft, 'd'iagonal, or 'a'bove or 'u'nknown */
double *F; /* *Above -- needed for memorizing deletion in seq2 */
double *pBestScore; /* pointer to it */
int32_t BestScore_row; /* its row and col */
int32_t BestScore_col;
char *traceback; /* all you need for bactracking */
char *traceback_f; /* memory for forward traceback and then check other seeds */
char *traceback_b; /* memory needed for backward traceback - to avoid erasing the forward one */
int32_t alignment_len; /* guess ?? */
int32_t matches; /* number of match (score>0 in scoring matrix) */
int32_t nSegment; /* number of segment */
int32_t *Segment_begin; /* begin and end of each segment */
int32_t *Segment_end;
int32_t max_scores; /* size of the matrices only for memory purposes */
int32_t max_col;
int32_t max_row;
int32_t max_alignlen;
} RESULTS;
#endif /* _REPSEEK_TYPES_ */

25
src/libKMRK/sequence.h
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@ -1,25 +0,0 @@
/**
* @file KMRK_sequence.h
* @author Eric Coissac <coissac@inrialpes.fr>
* @date Tue Feb 24 22:22:57 2004
*
* @brief Header file for sequence utilities
*
*
*/
#ifndef KMRK_sequence_h
#define KMRK_sequence_h
#include <stdint.h>
int8_t CheckSeq(char *seq, char *alpha);
void nonACGTXtoN(char *seq);
void UpperSequence(char *seq);
void invseq(char *seqsrc, char *seqdest);
#endif /* KMRK_sequence_h */

14
src/libapat/CODES/dft_code.h
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@ -1,14 +0,0 @@
/* ----------------------------------------------- */
/* dft_pat_seq_code.h */
/* default alphabet encoding for alpha */
/* ----------------------------------------------- */
0x00000001 /* A */, 0x00000002 /* B */, 0x00000004 /* C */,
0x00000008 /* D */, 0x00000010 /* E */, 0x00000020 /* F */,
0x00000040 /* G */, 0x00000080 /* H */, 0x00000100 /* I */,
0x00000200 /* J */, 0x00000400 /* K */, 0x00000800 /* L */,
0x00001000 /* M */, 0x00002000 /* N */, 0x00004000 /* O */,
0x00008000 /* P */, 0x00010000 /* Q */, 0x00020000 /* R */,
0x00040000 /* S */, 0x00080000 /* T */, 0x00100000 /* U */,
0x00200000 /* V */, 0x00400000 /* W */, 0x00800000 /* X */,
0x01000000 /* Y */, 0x02000000 /* Z */

71
src/libapat/CODES/dna_code.h
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@ -1,71 +0,0 @@
/* ----------------------------------------------- */
/* dna_code.h */
/* alphabet encoding for dna/rna */
/* ----------------------------------------- */
/* IUPAC encoding */
/* ----------------------------------------- */
/* G/A/T/C */
/* U=T */
/* R=AG */
/* Y=CT */
/* M=AC */
/* K=GT */
/* S=CG */
/* W=AT */
/* H=ACT */
/* B=CGT */
/* V=ACG */
/* D=AGT */
/* N=ACGT */
/* X=ACGT */
/* EFIJLOPQZ not recognized */
/* ----------------------------------------- */
/* dual encoding */
/* ----------------------------------------- */
/* A=ADHMNRVW */
/* B=BCDGHKMNRSTUVWY */
/* C=BCHMNSVY */
/* D=ABDGHKMNRSTUVWY */
/* G=BDGKNRSV */
/* H=ABCDHKMNRSTUVWY */
/* K=BDGHKNRSTUVWY */
/* M=ABCDHMNRSVWY */
/* N=ABCDGHKMNRSTUVWY */
/* R=ABDGHKMNRSVW */
/* S=BCDGHKMNRSVY */
/* T=BDHKNTUWY */
/* U=BDHKNTUWY */
/* V=ABCDGHKMNRSVWY */
/* W=ABDHKMNRTUVWY */
/* X=ABCDGHKMNRSTUVWY */
/* Y=BCDHKMNSTUVWY */
/* EFIJLOPQZ not recognized */
/* ----------------------------------------------- */
#ifndef USE_DUAL
/* IUPAC */
0x00000001 /* A */, 0x00080044 /* B */, 0x00000004 /* C */,
0x00080041 /* D */, 0x00000000 /* E */, 0x00000000 /* F */,
0x00000040 /* G */, 0x00080005 /* H */, 0x00000000 /* I */,
0x00000000 /* J */, 0x00080040 /* K */, 0x00000000 /* L */,
0x00000005 /* M */, 0x00080045 /* N */, 0x00000000 /* O */,
0x00000000 /* P */, 0x00000000 /* Q */, 0x00000041 /* R */,
0x00000044 /* S */, 0x00080000 /* T */, 0x00080000 /* U */,
0x00000045 /* V */, 0x00080001 /* W */, 0x00080045 /* X */,
0x00080004 /* Y */, 0x00000000 /* Z */
#else
/* DUAL */
0x00623089 /* A */, 0x017e34ce /* B */, 0x01243086 /* C */,
0x017e34cb /* D */, 0x00000000 /* E */, 0x00000000 /* F */,
0x0026244a /* G */, 0x017e348f /* H */, 0x00000000 /* I */,
0x00000000 /* J */, 0x017e24ca /* K */, 0x00000000 /* L */,
0x0166308f /* M */, 0x017e34cf /* N */, 0x00000000 /* O */,
0x00000000 /* P */, 0x00000000 /* Q */, 0x006634cb /* R */,
0x012634ce /* S */, 0x0158248a /* T */, 0x0158248a /* U */,
0x016634cf /* V */, 0x017a348b /* W */, 0x017e34cf /* X */,
0x017c348e /* Y */, 0x00000000 /* Z */
#endif

51
src/libapat/CODES/prot_code.h
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@ -1,51 +0,0 @@
/* ----------------------------------------------- */
/* prot_code.h */
/* alphabet encoding for proteins */
/* ----------------------------------------- */
/* IUPAC encoding */
/* ----------------------------------------- */
/* B=DN */
/* Z=EQ */
/* X=any - {X} */
/* JOU not recognized */
/* ----------------------------------------- */
/* dual encoding */
/* ----------------------------------------- */
/* B=BDN */
/* D=BD */
/* E=EZ */
/* N=BN */
/* Q=QZ */
/* X=any - {X} */
/* Z=EQZ */
/* JOU not recognized */
/* ----------------------------------------------- */
#ifndef USE_DUAL
/* IUPAC */
0x00000001 /* A */, 0x00002008 /* B */, 0x00000004 /* C */,
0x00000008 /* D */, 0x00000010 /* E */, 0x00000020 /* F */,
0x00000040 /* G */, 0x00000080 /* H */, 0x00000100 /* I */,
0x00000000 /* J */, 0x00000400 /* K */, 0x00000800 /* L */,
0x00001000 /* M */, 0x00002000 /* N */, 0x00000000 /* O */,
0x00008000 /* P */, 0x00010000 /* Q */, 0x00020000 /* R */,
0x00040000 /* S */, 0x00080000 /* T */, 0x00000000 /* U */,
0x00200000 /* V */, 0x00400000 /* W */, 0x037fffff /* X */,
0x01000000 /* Y */, 0x00010010 /* Z */
#else
/* DUAL */
0x00000001 /* A */, 0x0000200a /* B */, 0x00000004 /* C */,
0x0000000a /* D */, 0x02000010 /* E */, 0x00000020 /* F */,
0x00000040 /* G */, 0x00000080 /* H */, 0x00000100 /* I */,
0x00000000 /* J */, 0x00000400 /* K */, 0x00000800 /* L */,
0x00001000 /* M */, 0x00002002 /* N */, 0x00000000 /* O */,
0x00008000 /* P */, 0x02010000 /* Q */, 0x00020000 /* R */,
0x00040000 /* S */, 0x00080000 /* T */, 0x00000000 /* U */,
0x00200000 /* V */, 0x00400000 /* W */, 0x037fffff /* X */,
0x01000000 /* Y */, 0x02010010 /* Z */
#endif

97
src/libapat/Gmach.h
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@ -1,97 +0,0 @@
/* ---------------------------------------------------------------- */
/* Copyright (c) Atelier de BioInformatique */
/* @file: Gmach.h */
/* @desc: machine dependant setup */
/* @+ *should* be included in all ABI softs */
/* */
/* @history: */
/* @+ <Gloup> : Jul 95 : MWC first draft */
/* @+ <Gloup> : Jan 96 : adapted to Pwg */
/* @+ <Gloup> : Nov 00 : adapted to Mac_OS_X */
/* ---------------------------------------------------------------- */
#ifndef _H_Gmach
/* OS names */
#define _H_Gmach
/* Macintosh Classic */
/* Think C environment */
#ifdef THINK_C
#define MACINTOSH
#define MAC_OS_C
#endif
/* Macintosh Classic */
/* Code-Warrior */
#ifdef __MWERKS__
#define MACINTOSH
#define MAC_OS_C
#endif
/* Macintosh OS-X */
#ifdef MAC_OS_X
#define MACINTOSH
#define UNIX
#define UNIX_BSD
#endif
/* LINUX */
#ifdef LINUX
#define UNIX
#define UNIX_BSD
#endif
/* other Unix Boxes */
/* SunOS / Solaris */
#ifdef SUN
#define UNIX
#ifdef SOLARIS
#define UNIX_S7
#else
#define UNIX_BSD
#endif
#endif
/* SGI Irix */
#ifdef SGI
#define UNIX
#define UNIX_S7
#endif
/* ansi setup */
/* for unix machines see makefile */
#ifndef PROTO
#define PROTO 1
#endif
#ifndef ANSI_PROTO
#define ANSI_PROTO PROTO
#endif
#ifndef ANSI_STR
#define ANSI_STR 1
#endif
/* unistd.h header file */
#ifdef UNIX
#define HAS_UNISTD_H <unistd.h>
#endif
/* getopt.h header file */
#ifdef MAC_OS_C
#define HAS_GETOPT_H "getopt.h"
#endif
#ifdef SGI
#define HAS_GETOPT_H <getopt.h>
#endif
#endif

104
src/libapat/Gtypes.h
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@ -1,104 +0,0 @@
/* ---------------------------------------------------------------- */
/* Copyright (c) Atelier de BioInformatique */
/* @file: Gtypes.h */
/* @desc: general & machine dependant types */
/* @+ *should* be included in all ABI softs */
/* */
/* @history: */
/* @+ <Gloup> : Jan 91 : MWC first draft */
/* @+ <Gloup> : Jul 95 : Gmach addition */
/* ---------------------------------------------------------------- */
#define _H_Gtypes
#ifndef _H_Gmach
#include "Gmach.h"
#endif
#ifndef NULL
#include <stdio.h> /* is the official NULL here ? */
#endif
/* ==================================================== */
/* constantes */
/* ==================================================== */
#ifndef PROTO
#define PROTO 1 /* prototypes flag */
#endif
#ifdef MAC_OS_C
#define Vrai true /* TC boolean values */
#define Faux false /* */
#else
#define Vrai 0x1 /* bool values = TRUE */
#define Faux 0x0 /* = FALSE */
#endif
#define Nil NULL /* nil pointer */
#define kBigInt16 0x7fff /* plus grand 16 bits signe */
#define kBigInt32 0x7fffffff /* plus grand 32 bits signe */
#define kBigUInt16 0xffff /* plus grand 16 bits ~signe */
#define kBigUInt32 0xffffffff /* plus grand 32 bits ~signe */
#ifdef MAC_OS_C
/* ==================================================== */
/* Types (for Macintosh ThinK C || MWerks) */
/* ==================================================== */
/* --- specific sizes --------- */
typedef long Int32; /* Int32 = 32 bits signe */
typedef unsigned long UInt32; /* UInt32 = 32 bits ~signe */
typedef short Int16; /* Int16 = 16 bits signe */
typedef unsigned short UInt16; /* UInt32 = 16 bits ~signe */
typedef char Int8; /* Int8 = 8 bits signe */
typedef unsigned char UInt8; /* UInt8 = 8 bits ~signe */
/* --- default types ---------- */
typedef Boolean Bool; /* booleen */
typedef long Int; /* 'natural' int (>= 32 bits) */
typedef void *Ptr; /* pointeur */
#elif ((defined SUN) || (defined SGI) || (defined UNIX))
/* ==================================================== */
/* Types (for Sun & Iris - 32 bits machines) */
/* ==================================================== */
/* --- specific sizes --------- */
typedef int Int32; /* Int32 = 32 bits signe */
typedef unsigned int UInt32; /* UInt32 = 32 bits ~signe */
typedef short Int16; /* Int16 = 16 bits signe */
typedef unsigned short UInt16; /* UInt32 = 16 bits ~signe */
typedef char Int8; /* Int8 = 8 bits signe */
typedef unsigned char UInt8; /* UInt8 = 8 bits ~signe */
/* --- default types ---------- */
typedef int Bool; /* booleen (int for ANSI) */
typedef int Int; /* 'natural' int (>= 32 bits) */
typedef void *Ptr; /* pointeur */
#else
/* ==================================================== */
/* Types (for undefined machines) */
/* ==================================================== */
#error undefined MACHINE <please edit Gmach.h>
#endif
/* ==================================================== */
/* special macro for prototypes */
/* ==================================================== */
#if PROTO
#define P(s) s
#else
#define P(s) ()
#endif

24
src/libapat/Makefile
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@ -1,24 +0,0 @@
SOURCES = apat_parse.c \
apat_search.c \
libstki.c
SRCS=$(SOURCES)
OBJECTS= $(patsubst %.c,%.o,$(SOURCES))
LIBFILE= libapat.a
RANLIB=ranlib
include ../global.mk
all: $(LIBFILE)
clean:
rm -rf $(OBJECTS) $(LIBFILE)
$(LIBFILE): $(OBJECTS)
ar -cr $@ $?
$(RANLIB) $@

173
src/libapat/apat.h
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/* ==================================================== */
/* Copyright (c) Atelier de BioInformatique */
/* Dec. 94 */
/* File: apat.h */
/* Purpose: pattern scan */
/* History: */
/* 28/12/94 : <Gloup> ascan first version */
/* 14/05/99 : <Gloup> last revision */
/* ==================================================== */
#ifndef _H_Gtypes
#include "Gtypes.h"
#endif
#ifndef _H_libstki
#include "libstki.h"
#endif
#define H_apat
/* ----------------------------------------------- */
/* constantes */
/* ----------------------------------------------- */
#ifndef BUFSIZ
#define BUFSIZ 1024 /* io buffer size */
#endif
#define MAX_NAME_LEN BUFSIZ /* max length of sequence name */
#define ALPHA_LEN 26 /* alphabet length */
/* *DO NOT* modify */
#define MAX_PATTERN 4 /* max # of patterns */
/* *DO NOT* modify */
#define MAX_PAT_LEN 32 /* max pattern length */
/* *DO NOT* modify */
#define MAX_PAT_ERR 32 /* max # of errors */
/* *DO NOT* modify */
#define PATMASK 0x3ffffff /* mask for 26 symbols */
/* *DO NOT* modify */
#define OBLIBIT 0x4000000 /* bit 27 to 1 -> oblig. pos */
/* *DO NOT* modify */
/* mask for position */
#define ONEMASK 0x80000000 /* mask for highest position */
/* masks for Levenhstein edit */
#define OPER_IDT 0x00000000 /* identity */
#define OPER_INS 0x40000000 /* insertion */
#define OPER_DEL 0x80000000 /* deletion */
#define OPER_SUB 0xc0000000 /* substitution */
#define OPER_SHFT 30 /* <unused> shift */
/* Levenhstein Opcodes */
#define SOPER_IDT 0x0 /* identity */
#define SOPER_INS 0x1 /* insertion */
#define SOPER_DEL 0x2 /* deletion */
#define SOPER_SUB 0x3 /* substitution */
/* Levenhstein Opcodes masks */
#define OPERMASK 0xc0000000 /* mask for Opcodes */
#define NOPERMASK 0x3fffffff /* negate of previous */
/* special chars in pattern */
#define PATCHARS "[]!#"
/* 26 letter alphabet */
/* in alphabetical order */
#define ORD_ALPHA "ABCDEFGHIJKLMNOPQRSTUVWXYZ"
/* protein alphabet */
#define PROT_ALPHA "ACDEFGHIKLMNPQRSTVWY"
/* dna/rna alphabet */
#define DNA_ALPHA "ABCDGHKMNRSTUVWXY"
/* ----------------------------------------------- */
/* data structures */
/* ----------------------------------------------- */
/* -------------------- */
typedef enum { /* data encoding */
/* -------------------- */
alpha = 0, /* [A-Z] */
dna, /* IUPAC DNA */
protein /* IUPAC proteins */
} CodType;
/* -------------------- */
typedef struct { /* sequence */
/* -------------------- */
char *name; /* sequence name */
Int32 seqlen; /* sequence length */
Int32 seqsiz; /* sequence buffer size */
Int32 datsiz; /* data buffer size */
Int32 circular;
UInt8 *data; /* data buffer */
char *cseq; /* sequence buffer */
StackiPtr hitpos[MAX_PATTERN]; /* stack of hit pos. */
StackiPtr hiterr[MAX_PATTERN]; /* stack of errors */
} Seq, *SeqPtr;
/* -------------------- */
typedef struct { /* pattern */
/* -------------------- */
int patlen; /* pattern length */
int maxerr; /* max # of errors */
char *cpat; /* pattern string */
Int32 *patcode; /* encoded pattern */
UInt32 *smat; /* S matrix */
UInt32 omask; /* oblig. bits mask */
Bool hasIndel; /* are indels allowed */
Bool ok; /* is pattern ok */
} Pattern, *PatternPtr;
/* ----------------------------------------------- */
/* macros */
/* ----------------------------------------------- */
#ifndef NEW
#define NEW(typ) (typ*)malloc(sizeof(typ))
#define NEWN(typ, dim) (typ*)malloc((unsigned long)(dim) * sizeof(typ))
#define REALLOC(typ, ptr, dim) (typ*)realloc((void *) (ptr), (unsigned long)(dim) * sizeof(typ))
#define FREE(ptr) free((void *) ptr)
#endif
/* ----------------------------------------------- */
/* prototypes */
/* ----------------------------------------------- */
/* apat_seq.c */
SeqPtr FreeSequence (SeqPtr pseq);
SeqPtr NewSequence (void);
int ReadNextSequence (SeqPtr pseq);
int WriteSequence (FILE *filou , SeqPtr pseq);
/* apat_parse.c */
Int32 *GetCode (CodType ctype);
int CheckPattern (Pattern *ppat);
int EncodePattern (Pattern *ppat, CodType ctype);
int ReadPattern (Pattern *ppat);
void PrintDebugPattern (Pattern *ppat);
/* apat_search.c */
int CreateS (Pattern *ppat, Int32 lalpha);
Int32 ManberNoErr (Seq *pseq , Pattern *ppat, int patnum,int begin,int length);
Int32 ManberSub (Seq *pseq , Pattern *ppat, int patnum,int begin,int length);
Int32 ManberIndel (Seq *pseq , Pattern *ppat, int patnum,int begin,int length);
Int32 ManberAll (Seq *pseq , Pattern *ppat, int patnum,int begin,int length);
Int32 NwsPatAlign (Seq *pseq , Pattern *ppat, Int32 nerr ,
Int32 *reslen , Int32 *reserr);
/* apat_sys.c */
float UserCpuTime (int reset);
float SysCpuTime (int reset);
char *StrCpuTime (int reset);
void Erreur (char *msg , int stat);
int AccessFile (char *path, char *mode);

369
src/libapat/apat_parse.c
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/* ==================================================== */
/* Copyright (c) Atelier de BioInformatique */
/* Mar. 92 */
/* File: apat_parse.c */
/* Purpose: Codage du pattern */
/* History: */
/* 00/07/94 : <Gloup> first version (stanford) */
/* 00/11/94 : <Gloup> revised for DNA/PROTEIN */
/* 30/12/94 : <Gloup> modified EncodePattern */
/* for manber search */
/* 14/05/99 : <Gloup> indels added */
/* ==================================================== */
#include <ctype.h>
#include <stdlib.h>
#include <stdio.h>
#include <string.h>
#include "Gtypes.h"
#include "apat.h"
/* -------------------- */
/* default char */
/* encodings */
/* -------------------- */
static Int32 sDftCode[] = {
#include "CODES/dft_code.h"
};
/* -------------------- */
/* char encodings */
/* IUPAC */
/* -------------------- */
/* IUPAC Proteins */
static Int32 sProtCode[] = {
#include "CODES/prot_code.h"
};
/* IUPAC Dna/Rna */
static Int32 sDnaCode[] = {
#include "CODES/dna_code.h"
};
/* -------------------------------------------- */
/* internal replacement of gets */
/* -------------------------------------------- */
static char *sGets(char *buffer, int size) {
char *ebuf;
if (! fgets(buffer, size-1, stdin))
return NULL;
/* remove trailing line feed */
ebuf = buffer + strlen(buffer);
while (--ebuf >= buffer) {
if ((*ebuf == '\n') || (*ebuf == '\r'))
*ebuf = '\000';
else
break;
}
return buffer;
}
/* -------------------------------------------- */
/* returns actual code associated to type */
/* -------------------------------------------- */
Int32 *GetCode(CodType ctype)
{
Int32 *code = sDftCode;
switch (ctype) {
case dna : code = sDnaCode ; break;
case protein : code = sProtCode ; break;
default : code = sDftCode ; break;
}
return code;
}
/* -------------------------------------------- */
#define BAD_IF(tst) if (tst) return 0
int CheckPattern(Pattern *ppat)
{
int lev;
char *pat;
pat = ppat->cpat;
BAD_IF (*pat == '#');
for (lev = 0; *pat ; pat++)
switch (*pat) {
case '[' :
BAD_IF (lev);
BAD_IF (*(pat+1) == ']');
lev++;
break;
case ']' :
lev--;
BAD_IF (lev);
break;
case '!' :
BAD_IF (lev);
BAD_IF (! *(pat+1));
BAD_IF (*(pat+1) == ']');
break;
case '#' :
BAD_IF (lev);
BAD_IF (*(pat-1) == '[');
break;
default :
if (! isupper(*pat))
return 0;
break;
}
return (lev ? 0 : 1);
}
#undef BAD_IF
/* -------------------------------------------- */
static char *skipOblig(char *pat)
{
return (*(pat+1) == '#' ? pat+1 : pat);
}
/* -------------------------------------------- */
static char *splitPattern(char *pat)
{
switch (*pat) {
case '[' :
for (; *pat; pat++)
if (*pat == ']')
return skipOblig(pat);
return NULL;
break;
case '!' :
return splitPattern(pat+1);
break;
}
return skipOblig(pat);
}
/* -------------------------------------------- */
static Int32 valPattern(char *pat, Int32 *code)
{
Int32 val;
switch (*pat) {
case '[' :
return valPattern(pat+1, code);
break;
case '!' :
val = valPattern(pat+1, code);
return (~val & PATMASK);
break;
default :
val = 0x0;
while (isupper(*pat)) {
val |= code[*pat - 'A'];
pat++;
}
return val;
}
return 0x0;
}
/* -------------------------------------------- */
static Int32 obliBitPattern(char *pat)
{
return (*(pat + strlen(pat) - 1) == '#' ? OBLIBIT : 0x0);
}
/* -------------------------------------------- */
static int lenPattern(char *pat)
{
int lpat;
lpat = 0;
while (*pat) {
if (! (pat = splitPattern(pat)))
return 0;
pat++;
lpat++;
}
return lpat;
}
/* -------------------------------------------- */
/* Interface */
/* -------------------------------------------- */
/* -------------------------------------------- */
/* encode un pattern */
/* -------------------------------------------- */
int EncodePattern(Pattern *ppat, CodType ctype)
{
int pos, lpat;
Int32 *code;
char *pp, *pa, c;
ppat->ok = Faux;
code = GetCode(ctype);
ppat->patlen = lpat = lenPattern(ppat->cpat);
if (lpat <= 0)
return 0;
if (! (ppat->patcode = NEWN(Int32, lpat)))
return 0;
pa = pp = ppat->cpat;
pos = 0;
while (*pa) {
pp = splitPattern(pa);
c = *++pp;
*pp = '\000';
ppat->patcode[pos++] = valPattern(pa, code) | obliBitPattern(pa);
*pp = c;
pa = pp;
}
ppat->ok = Vrai;
return lpat;
}
/* -------------------------------------------- */
/* remove blanks */
/* -------------------------------------------- */
static char *RemBlanks(char *s)
{
char *sb, *sc;
for (sb = sc = s ; *sb ; sb++)
if (! isspace(*sb))
*sc++ = *sb;
return s;
}
/* -------------------------------------------- */
/* count non blanks */
/* -------------------------------------------- */
static Int32 CountAlpha(char *s)
{
Int32 n;
for (n = 0 ; *s ; s++)
if (! isspace(*s))
n++;
return n;
}
/* -------------------------------------------- */
/* lit un pattern */
/* <pattern> #mis */
/* ligne starting with '/' are comments */
/* -------------------------------------------- */
int ReadPattern(Pattern *ppat)
{
int val;
char *spac;
char buffer[BUFSIZ];
ppat->ok = Vrai;
if (! sGets(buffer, sizeof(buffer)))
return 0;
if (*buffer == '/')
return ReadPattern(ppat);
if (! CountAlpha(buffer))
return ReadPattern(ppat);
for (spac = buffer ; *spac ; spac++)
if ((*spac == ' ') || (*spac == '\t'))
break;
ppat->ok = Faux;
if (! *spac)
return 0;
if (sscanf(spac, "%d", &val) != 1)
return 0;
ppat->hasIndel = (val < 0);
ppat->maxerr = ((val >= 0) ? val : -val);
*spac = '\000';
(void) RemBlanks(buffer);
if ((ppat->cpat = NEWN(char, strlen(buffer)+1)))
strcpy(ppat->cpat, buffer);
ppat->ok = (ppat->cpat != NULL);
return (ppat->ok ? 1 : 0);
}
/* -------------------------------------------- */
/* ecrit un pattern - Debug - */
/* -------------------------------------------- */
void PrintDebugPattern(Pattern *ppat)
{
int i;
printf("Pattern : %s\n", ppat->cpat);
printf("Encoding : \n\t");
for (i = 0 ; i < ppat->patlen ; i++) {
printf("0x%8.8x ", ppat->patcode[i]);
if (i%4 == 3)
printf("\n\t");
}
printf("\n");
}

339
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/* ==================================================== */
/* Copyright (c) Atelier de BioInformatique */
/* Dec. 94 */
/* File: apat_search.c */
/* Purpose: recherche du pattern */
/* algorithme de Baeza-Yates/Gonnet */
/* Manber (agrep) */
/* History: */
/* 07/12/94 : <MFS> first version */
/* 28/12/94 : <Gloup> revised version */
/* 14/05/99 : <Gloup> last revision */
/* ==================================================== */
#if 0
#ifndef THINK_C
#include <sys/types.h>
#endif
#endif
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include "Gtypes.h"
#include "libstki.h"
#include "apat.h"
#define POP PopiOut
#define PUSH PushiIn
#define TOPCURS CursiToTop
#define DOWNREAD ReadiDown
#define KRONECK(x, msk) ((~x & msk) ? 0 : 1)
#define MIN(x, y) ((x) < (y) ? (x) : (y))
/* -------------------------------------------- */
/* Construction de la matrice S */
/* -------------------------------------------- */
int CreateS(Pattern *ppat, Int32 lalpha)
{
Int32 i, j, indx;
UInt32 pindx, amask, omask, *smat;
ppat->ok = Faux;
omask = 0x0L;
if (! (smat = NEWN(UInt32, lalpha)))
return 0;
for (i = 0 ; i < lalpha ; i++)
smat[i] = 0x0;
for (i = ppat->patlen - 1, amask = 0x1L ; i >= 0 ; i--, amask <<= 1) {
indx = ppat->patcode[i];
if (ppat->patcode[i] & OBLIBIT)
omask |= amask;
for (j = 0, pindx = 0x1L ; j < lalpha ; j++, pindx <<= 1)
if (indx & pindx)
smat[j] |= amask;
}
ppat->smat = smat;
ppat->omask = omask;
ppat->ok = Vrai;
return 1;
}
/* -------------------------------------------- */
/* Baeza-Yates/Manber algorithm */
/* NoError */
/* -------------------------------------------- */
Int32 ManberNoErr(Seq *pseq, Pattern *ppat, int patnum,int begin,int length)
{
UInt32 pos;
UInt32 smask, r;
UInt8 *data;
StackiPtr *stkpos, *stkerr;
UInt32 end;
end = begin + length;
end = (end <= (size_t)(pseq->seqlen+pseq->circular)) ? end:(size_t)(pseq->seqlen+pseq->circular);
/* create local masks */
smask = r = 0x1L << ppat->patlen;
/* init. scan */
data = pseq->data + begin;
stkpos = pseq->hitpos + patnum;
stkerr = pseq->hiterr + patnum;
/* loop on text data */
for (pos = begin ; pos < end ; pos++) {
r = (r >> 1) & ppat->smat[*data++];
if (r & 0x1L) {
PUSH(stkpos, pos - ppat->patlen + 1);
PUSH(stkerr, 0);
}
r |= smask;
}
return (*stkpos)->top; /* aka # of hits */
}
/* -------------------------------------------- */
/* Baeza-Yates/Manber algorithm */
/* Substitution only */
/* */
/* Note : r array is stored as : */
/* 0 0 r(0,j) r(0,j+1) r(1,j) r(1,j+1) ... */
/* */
/* -------------------------------------------- */
Int32 ManberSub(Seq *pseq, Pattern *ppat, int patnum,int begin,int length)
{
int e, emax, found;
UInt32 pos;
UInt32 smask, cmask, sindx;
UInt32 *pr, r[2 * MAX_PAT_ERR + 2];
UInt8 *data;
StackiPtr *stkpos, *stkerr;
UInt32 end;
end = begin + length;
end = (end <= (size_t)(pseq->seqlen+pseq->circular)) ? end:(size_t)(pseq->seqlen+pseq->circular);
/* create local masks */
emax = ppat->maxerr;
r[0] = r[1] = 0x0;
cmask = smask = 0x1L << ppat->patlen;
for (e = 0, pr = r + 3 ; e <= emax ; e++, pr += 2)
*pr = cmask;
cmask = ~ ppat->omask;
/* init. scan */
data = pseq->data + begin;
stkpos = pseq->hitpos + patnum;
stkerr = pseq->hiterr + patnum;
/* loop on text data */
for (pos = begin ; pos < end ; pos++) {
sindx = ppat->smat[*data++];
for (e = found = 0, pr = r ; e <= emax ; e++, pr += 2) {
pr[2] = pr[3] | smask;
pr[3] = ((pr[0] >> 1) & cmask) /* sub */
| ((pr[2] >> 1) & sindx); /* ident */
if (pr[3] & 0x1L) { /* found */
if (! found) {
PUSH(stkpos, pos - ppat->patlen + 1);
PUSH(stkerr, e);
}
found++;
}
}
}
return (*stkpos)->top; /* aka # of hits */
}
/* -------------------------------------------- */
/* Baeza-Yates/Manber algorithm */
/* Substitution + Indels */
/* */
/* Note : r array is stored as : */
/* 0 0 r(0,j) r(0,j+1) r(1,j) r(1,j+1) ... */
/* */
/* Warning: may return shifted pos. */
/* */
/* -------------------------------------------- */
Int32 ManberIndel(Seq *pseq, Pattern *ppat, int patnum,int begin,int length)
{
int e, emax, found;
UInt32 pos;
UInt32 smask, cmask, sindx;
UInt32 *pr, r[2 * MAX_PAT_ERR + 2];
UInt8 *data;
StackiPtr *stkpos, *stkerr;
UInt32 end;
end = begin + length;
end = (end <= (size_t)(pseq->seqlen+pseq->circular)) ? end:(size_t)(pseq->seqlen+pseq->circular);
/* create local masks */
emax = ppat->maxerr;
r[0] = r[1] = 0x0;
cmask = smask = 0x1L << ppat->patlen;
for (e = 0, pr = r + 3 ; e <= emax ; e++, pr += 2) {
*pr = cmask;
cmask = (cmask >> 1) | smask;
}
cmask = ~ ppat->omask;
/* init. scan */
data = pseq->data + begin;
stkpos = pseq->hitpos + patnum;
stkerr = pseq->hiterr + patnum;
/* loop on text data */
for (pos = begin ; pos < end ; pos++) {
sindx = ppat->smat[*data++];
for (e = found = 0, pr = r ; e <= emax ; e++, pr += 2) {
pr[2] = pr[3] | smask;
pr[3] = (( pr[0] /* ins */
| (pr[0] >> 1) /* sub */
| (pr[1] >> 1)) /* del */
& cmask)
| ((pr[2] >> 1) & sindx); /* ident */
if (pr[3] & 0x1L) { /* found */
if (! found) {
PUSH(stkpos, pos - ppat->patlen + 1);
PUSH(stkerr, e);
}
found++;
}
}
}
return (*stkpos)->top; /* aka # of hits */
}
/* -------------------------------------------- */
/* Baeza-Yates/Manber algorithm */
/* API call to previous functions */
/* -------------------------------------------- */
Int32 ManberAll(Seq *pseq, Pattern *ppat, int patnum,int begin,int length)
{
if (ppat->maxerr == 0)
return ManberNoErr(pseq, ppat, patnum, begin, length);
else if (ppat->hasIndel)
return ManberIndel(pseq, ppat, patnum, begin, length);
else
return ManberSub(pseq, ppat, patnum, begin, length);
}
/* -------------------------------------------- */
/* Alignement NWS */
/* pour edition des hits */
/* (avec substitution obligatoire aux bords) */
/* -------------------------------------------- */
Int32 NwsPatAlign(pseq, ppat, nerr, reslen, reserr)
Seq *pseq;
Pattern *ppat;
Int32 nerr, *reslen, *reserr;
{
UInt8 *sseq, *px;
Int32 i, j, lseq, lpat, npos, dindel, dsub,
*pc, *pi, *pd, *ps;
UInt32 amask;
static Int32 sTab[(MAX_PAT_LEN+MAX_PAT_ERR+1) * (MAX_PAT_LEN+1)];
lseq = pseq->seqlen;
pc = sTab; /* |----|----| --> i */
pi = pc - 1; /* | ps | pd | | */
pd = pi - lseq; /* |----|----| | */
ps = pd - 1; /* | pi | pc | v j */
/* |---------| */
lseq = pseq->seqlen;
lpat = ppat->patlen;
sseq = pseq->data - 1;
amask = ONEMASK >> lpat;
for (j = 0 ; j <= lpat ; j++) {
for (i = 0 , px = sseq ; i <= lseq ; i++, px++) {
if (i && j) {
dindel = MIN(*pi, *pd) + 1;
dsub = *ps + KRONECK(ppat->smat[*px], amask);
*pc = MIN(dindel, dsub);
}
else if (i) /* j == 0 */
*pc = *pi + 1;
else if (j) /* i == 0 */
*pc = *pd + 1;
else /* root */
*pc = 0;
pc++;
pi++;
pd++;
ps++;
}
amask <<= 1;
}
pc--;
for (i = lseq, npos = 0 ; i >= 0 ; i--, pc--) {
if (*pc <= nerr) {
*reslen++ = i;
*reserr++ = *pc;
npos++;
}
}
return npos;
}

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/* ==================================================== */
/* Copyright (c) Atelier de BioInformatique */
/* Mar. 92 */
/* File: libstki.c */
/* Purpose: A library to deal with 'stacks' of */
/* integers */
/* Note: 'stacks' are dynamic (i.e. size is */
/* automatically readjusted when needed) */
/* History: */
/* 00/03/92 : <Gloup> first draft */
/* 15/08/93 : <Gloup> revised version */
/* 14/05/99 : <Gloup> last revision */
/* ==================================================== */
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include "Gtypes.h"
#include "libstki.h"
/* ============================ */
/* Constantes et Macros locales */
/* ============================ */
#define ExpandStack(stkh) ResizeStacki((stkh), (*stkh)->size << 1)
#define ShrinkStack(stkh) ResizeStacki((stkh), (*stkh)->size >> 1)
static Int16 sStkiLastError = kStkiNoErr;
/* -------------------------------------------- */
/* gestion des erreurs */
/* get/reset erreur flag */
/* */
/* @function: StkiError */
/* -------------------------------------------- */
Int16 StkiError(Bool reset)
{
Int16 err;
err = sStkiLastError;
if (reset)
sStkiLastError = kStkiNoErr;
return err;
} /* end of StkiError */
/* -------------------------------------------- */
/* creation d'un stack */
/* */
/* @function: NewStacki */
/* -------------------------------------------- */
StackiPtr NewStacki(Int32 size)
{
StackiPtr stki;
if (! (stki = NEW(Stacki)))
return NULL;
stki->size = size;
stki->top = 0;
stki->cursor = 0;
if ( ! (stki->val = NEWN(Int32, size))) {
sStkiLastError = kStkiMemErr;
return FreeStacki(stki);
}
return stki;
} /* end of NewStacki */
/* -------------------------------------------- */
/* liberation d'un stack */
/* */
/* @function: FreeStacki */
/* -------------------------------------------- */
StackiPtr FreeStacki(StackiPtr stki)
{
if (stki) {
if (stki->val)
FREE(stki->val);
FREE(stki);
}
return NULL;
} /* end of FreeStacki */
/* -------------------------------------------- */
/* creation d'un vecteur de stacks */
/* */
/* @function: NewStackiVector */
/* -------------------------------------------- */
StackiHdle NewStackiVector(Int32 vectSize, Int32 stackSize)
{
Int32 i;
StackiHdle stkh;
if (! (stkh = NEWN(StackiPtr, vectSize))) {
sStkiLastError = kStkiMemErr;
return NULL;
}
for (i = 0 ; i < vectSize ; i++)
if (! (stkh[i] = NewStacki(stackSize)))
return FreeStackiVector(stkh, i);
return stkh;
} /* end of NewStackiVector */
/* -------------------------------------------- */
/* liberation d'un vecteur de stacks */
/* */
/* @function: FreeStackiVector */
/* -------------------------------------------- */
StackiHdle FreeStackiVector(StackiHdle stkh, Int32 vectSize)
{
Int32 i;
if (stkh) {
for (i = 0 ; i < vectSize ; i++)
(void) FreeStacki(stkh[i]);
FREE(stkh);
}
return NULL;
} /* end of FreeStackiVector */
/* -------------------------------------------- */
/* resize d'un stack */
/* */
/* @function: ResizeStacki */
/* -------------------------------------------- */
Int32 ResizeStacki(StackiHdle stkh, Int32 size)
{
Int32 resize = 0; /* assume error */
Int32 *val;
if ((val = REALLOC(Int32, (*stkh)->val, size))) {
(*stkh)->size = resize = size;
(*stkh)->val = val;
}
if (! resize)
sStkiLastError = kStkiMemErr;
return resize;
} /* end of ResizeStacki */
/* -------------------------------------------- */
/* empilage(/lement) */
/* */
/* @function: PushiIn */
/* -------------------------------------------- */
Bool PushiIn(StackiHdle stkh, Int32 val)
{
if (((*stkh)->top >= (*stkh)->size) && (! ExpandStack(stkh)))
return Faux;
(*stkh)->val[((*stkh)->top)++] = val;
return Vrai;
} /* end of PushiIn */
/* -------------------------------------------- */
/* depilage(/lement) */
/* */
/* @function: PopiOut */
/* -------------------------------------------- */
Bool PopiOut(StackiHdle stkh, Int32 *val)
{
if ((*stkh)->top <= 0)
return Faux;
*val = (*stkh)->val[--((*stkh)->top)];
if ( ((*stkh)->top < ((*stkh)->size >> 1))
&& ((*stkh)->top > kMinStackiSize))
(void) ShrinkStack(stkh);
return Vrai;
} /* end of PopiOut */
/* -------------------------------------------- */
/* lecture descendante */
/* */
/* @function: ReadiDown */
/* -------------------------------------------- */
Bool ReadiDown(StackiPtr stki, Int32 *val)
{
if (stki->cursor <= 0)
return Faux;
*val = stki->val[--(stki->cursor)];
return Vrai;
} /* end of ReadiDown */
/* -------------------------------------------- */
/* lecture ascendante */
/* */
/* @function: ReadiUp */
/* -------------------------------------------- */
Bool ReadiUp(StackiPtr stki, Int32 *val)
{
if (stki->cursor >= stki->top)
return Faux;
*val = stki->val[(stki->cursor)++];
return Vrai;
} /* end of ReadiUp */
/* -------------------------------------------- */
/* remontee/descente du curseur */
/* */
/* @function: CursiToTop */
/* @function: CursiToBottom */
/* -------------------------------------------- */
void CursiToTop(StackiPtr stki)
{
stki->cursor = stki->top;
} /* end of CursiToTop */
void CursiToBottom(stki)
StackiPtr stki;
{
stki->cursor = 0;
} /* end of CursiToBottom */
/* -------------------------------------------- */
/* echange des valeurs cursor <-> (top - 1) */
/* */
/* @function: CursiSwap */
/* -------------------------------------------- */
void CursiSwap(StackiPtr stki)
{
Int32 tmp;
if ((stki->top <= 0) || (stki->cursor < 0))
return;
tmp = stki->val[stki->cursor];
stki->val[stki->cursor] = stki->val[stki->top - 1];
stki->val[stki->top - 1] = tmp;
} /* end of CursiSwap */
/* -------------------------------------------- */
/* Recherche d'une valeur en stack a partir du */
/* curseur courant en descendant. */
/* on laisse le curseur a l'endroit trouve */
/* */
/* @function: SearchDownStacki */
/* -------------------------------------------- */
Bool SearchDownStacki(StackiPtr stki, Int32 sval)
{
Int32 val;
Bool more;
while ((more = ReadiDown(stki, &val)))
if (val == sval)
break;
return more;
} /* end of SearchDownStacki */
/* -------------------------------------------- */
/* Recherche dichotomique d'une valeur en stack */
/* le stack est suppose trie par valeurs */
/* croissantes. */
/* on place le curseur a l'endroit trouve */
/* */
/* @function: BinSearchStacki */
/* -------------------------------------------- */
Bool BinSearchStacki(StackiPtr stki, Int32 sval)
{
Int32 midd, low, high, span;
low = 0;
high = stki->top - 1;
while (high >= low) {
midd = (high + low) / 2;
span = stki->val[midd] - sval;
if (span == 0) {
stki->cursor = midd;
return Vrai;
}
if (span > 0)
high = midd - 1;
else
low = midd + 1;
}
return Faux;
} /* end of BinSearchStacki */
/* -------------------------------------------- */
/* teste l'egalite *physique* de deux stacks */
/* */
/* @function: SameStacki */
/* -------------------------------------------- */
Bool SameStacki(StackiPtr stki1, StackiPtr stki2)
{
if (stki1->top != stki2->top)
return Faux;
return ((memcmp(stki1->val, stki2->val,
stki1->top * sizeof(Int32)) == 0) ? Vrai : Faux);
} /* end of SameStacki */
/* -------------------------------------------- */
/* inverse l'ordre des elements dans un stack */
/* */
/* @function: ReverseStacki */
/* -------------------------------------------- */
Bool ReverseStacki(StackiPtr stki)
{
Int32 *t, *b, swp;
if (stki->top <= 0)
return Faux;
b = stki->val;
t = b + stki->top - 1;
while (t > b) {
swp = *t;
*t-- = *b;
*b++ = swp;
}
return Vrai;
} /* end of ReverseStacki */

87
src/libapat/libstki.h
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/* ==================================================== */
/* Copyright (c) Atelier de BioInformatique */
/* Mar. 92 */
/* File: libstki.h */
/* Purpose: library of dynamic stacks holding */
/* integer values */
/* History: */
/* 00/03/92 : <Gloup> first draft */
/* 07/07/93 : <Gloup> complete revision */
/* 10/03/94 : <Gloup> added xxxVector funcs */
/* 14/05/99 : <Gloup> last revision */
/* ==================================================== */
#ifndef _H_Gtypes
#include "Gtypes.h"
#endif
#define _H_libstki
/* ==================================================== */
/* Constantes de dimensionnement */
/* ==================================================== */
#ifndef kMinStackiSize
#define kMinStackiSize 2 /* taille mini stack */
#endif
#define kStkiNoErr 0 /* ok */
#define kStkiMemErr 1 /* not enough memory */
#define kStkiReset Vrai
#define kStkiGet Faux
/* ==================================================== */
/* Macros standards */
/* ==================================================== */
#ifndef NEW
#define NEW(typ) (typ*)malloc(sizeof(typ))
#define NEWN(typ, dim) (typ*)malloc((unsigned long)(dim) * sizeof(typ))
#define REALLOC(typ, ptr, dim) (typ*)realloc((void *) (ptr), (unsigned long)(dim) * sizeof(typ))
#define FREE(ptr) free((Ptr) ptr)
#endif
/* ==================================================== */
/* Types & Structures de donnees */
/* ==================================================== */
/* -------------------- */
/* structure : pile */
/* -------------------- */
typedef struct Stacki {
/* ---------------------*/
Int32 size; /* stack size */
Int32 top; /* current free pos. */
Int32 cursor; /* current cursor */
Int32 *val; /* values */
/* ---------------------*/
} Stacki, *StackiPtr, **StackiHdle;
/* ==================================================== */
/* Prototypes (generated by mproto) */
/* ==================================================== */
/* libstki.c */
Int16 StkiError (Bool reset );
StackiPtr NewStacki (Int32 size );
StackiPtr FreeStacki (StackiPtr stki );
StackiHdle NewStackiVector (Int32 vectSize, Int32 stackSize );
StackiHdle FreeStackiVector (StackiHdle stkh, Int32 vectSize );
Int32 ResizeStacki (StackiHdle stkh , Int32 size );
Bool PushiIn (StackiHdle stkh , Int32 val );
Bool PopiOut (StackiHdle stkh , Int32 *val );
Bool ReadiDown (StackiPtr stki , Int32 *val );
Bool ReadiUp (StackiPtr stki , Int32 *val );
void CursiToTop (StackiPtr stki );
void CursiToBottom (StackiPtr stki );
void CursiSwap (StackiPtr stki );
Bool SearchDownStacki (StackiPtr stki , Int32 sval );
Bool BinSearchStacki (StackiPtr stki , Int32 sval );
Bool SameStacki (StackiPtr stki1 , StackiPtr stki2 );
Bool ReverseStacki (StackiPtr stki );

31
src/libecoPCR/Makefile
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@ -1,31 +0,0 @@
SOURCES = ecoapat.c \
ecodna.c \
ecoError.c \
ecoIOUtils.c \
ecoMalloc.c \
ecorank.c \
ecoseq.c \
ecotax.c \
ecofilter.c \
econame.c
SRCS=$(SOURCES)
OBJECTS= $(patsubst %.c,%.o,$(SOURCES))
LIBFILE= libecoPCR.a
RANLIB= ranlib
include ../global.mk
all: $(LIBFILE)
clean:
rm -rf $(OBJECTS) $(LIBFILE)
$(LIBFILE): $(OBJECTS)
ar -cr $@ $?
$(RANLIB) $@

26
src/libecoPCR/ecoError.c
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@ -1,26 +0,0 @@
#include "ecoPCR.h"
#include <stdio.h>
#include <stdlib.h>
/*
* print the message given as argument and exit the program
* @param error error number
* @param message the text explaining what's going on
* @param filename the file source where the program failed
* @param linenumber the line where it has failed
* filename and linenumber are written at pre-processing
* time by a macro
*/
void ecoError(int32_t error,
const char* message,
const char * filename,
int linenumber)
{
fprintf(stderr,"Error %d in file %s line %d : %s\n",
error,
filename,
linenumber,
message);
abort();
}

122
src/libecoPCR/ecoIOUtils.c
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#include "ecoPCR.h"
#include <stdio.h>
#include <stdlib.h>
#define SWAPINT32(x) ((((x) << 24) & 0xFF000000) | (((x) << 8) & 0xFF0000) | \
(((x) >> 8) & 0xFF00) | (((x) >> 24) & 0xFF))
int32_t is_big_endian()
{
int32_t i=1;
return (int32_t)((char*)&i)[0];
}
int32_t swap_int32_t(int32_t i)
{
return SWAPINT32(i);
}
/**
* Read part of the file
* @param *f the database
* @param recordSize the size to be read
*
* @return buffer
*/
void *read_ecorecord(FILE *f,int32_t *recordSize)
{
static void *buffer =NULL;
int32_t buffersize=0;
int32_t read;
if (!recordSize)
ECOERROR(ECO_ASSERT_ERROR,
"recordSize cannot be NULL");
read = fread(recordSize,
1,
sizeof(int32_t),
f);
if (feof(f))
return NULL;
if (read != sizeof(int32_t))
ECOERROR(ECO_IO_ERROR,"Reading record size error");
if (is_big_endian())
*recordSize=swap_int32_t(*recordSize);
if (buffersize < *recordSize)
{
if (buffer)
buffer = ECOREALLOC(buffer,*recordSize,
"Increase size of record buffer");
else
buffer = ECOMALLOC(*recordSize,
"Allocate record buffer");
}
read = fread(buffer,
1,
*recordSize,
f);
if (read != *recordSize)
ECOERROR(ECO_IO_ERROR,"Reading record data error");
return buffer;
};
/**
* Open the database and check it's readable
* @param filename name of the database (.sdx, .rdx, .tbx)
* @param sequencecount buffer - pointer to variable storing the number of occurence
* @param abort_on_open_error boolean to define the behaviour in case of error
* while opening the database
* @return FILE type
**/
FILE *open_ecorecorddb(const char *filename,
int32_t *sequencecount,
int32_t abort_on_open_error)
{
FILE *f;
int32_t read;
f = fopen(filename,"rb");
if (!f)
{
if (abort_on_open_error)
ECOERROR(ECO_IO_ERROR,"Cannot open file");
else
{
*sequencecount=0;
return NULL;
}
}
read = fread(sequencecount,
1,
sizeof(int32_t),
f);
if (read != sizeof(int32_t))
ECOERROR(ECO_IO_ERROR,"Reading record size error");
if (is_big_endian())
*sequencecount=swap_int32_t(*sequencecount);
return f;
}

79
src/libecoPCR/ecoMalloc.c
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@ -1,79 +0,0 @@
#include "ecoPCR.h"
#include <stdlib.h>
static int eco_log_malloc = 0;
void eco_trace_memory_allocation()
{
eco_log_malloc=1;
}
void eco_untrace_memory_allocation()
{
eco_log_malloc=0;
}
void *eco_malloc(int32_t chunksize,
const char *error_message,
const char *filename,
int32_t line)
{
void * chunk;
chunk = calloc(1,chunksize);
if (!chunk)
ecoError(ECO_MEM_ERROR,error_message,filename,line);
if (eco_log_malloc)
fprintf(stderr,
"Memory segment located at %p of size %d is allocated (file : %s [%d])",
chunk,
chunksize,
filename,
line);
return chunk;
}
void *eco_realloc(void *chunk,
int32_t newsize,
const char *error_message,
const char *filename,
int32_t line)
{
void *newchunk;
newchunk = realloc(chunk,newsize);
if (!newchunk)
ecoError(ECO_MEM_ERROR,error_message,filename,line);
if (eco_log_malloc)
fprintf(stderr,
"Old memory segment %p is reallocated at %p with a size of %d (file : %s [%d])",
chunk,
newchunk,
newsize,
filename,
line);
return newchunk;
}
void eco_free(void *chunk,
const char *error_message,
const char *filename,
int32_t line)
{
free(chunk);
if (eco_log_malloc)
fprintf(stderr,
"Memory segment %p is released => %s (file : %s [%d])",
chunk,
error_message,
filename,
line);
}

269
src/libecoPCR/ecoPCR.h
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@ -1,269 +0,0 @@
#ifndef ECOPCR_H_
#define ECOPCR_H_
#include <stdio.h>
#include <inttypes.h>
#ifndef H_apat
#include "../libapat/apat.h"
#endif
/*****************************************************
*
* Data type declarations
*
*****************************************************/
/*
*
* Sequence types
*
*/
typedef struct {
int32_t taxid;
char AC[20];
int32_t DE_length;
int32_t SQ_length;
int32_t CSQ_length;
char data[1];
} ecoseqformat_t;
typedef struct {
int32_t taxid;
int32_t SQ_length;
char *AC;
char *DE;
char *SQ;
} ecoseq_t;
/*
*
* Taxonomy taxon types
*
*/
typedef struct {
int32_t taxid;
int32_t rank;
int32_t parent;
int32_t namelength;
char name[1];
} ecotxformat_t;
typedef struct ecotxnode {
int32_t taxid;
int32_t rank;
struct ecotxnode *parent;
char *name;
} ecotx_t;
typedef struct {
int32_t count;
ecotx_t taxon[1];
} ecotxidx_t;
/*
*
* Taxonomy rank types
*
*/
typedef struct {
int32_t count;
char* label[1];
} ecorankidx_t;
/*
*
* Taxonomy name types
*
*/
typedef struct {
int32_t is_scientificname;
int32_t namelength;
int32_t classlength;
int32_t taxid;
char names[1];
} econameformat_t;
typedef struct {
char *name;
char *classname;
int32_t is_scientificname;
struct ecotxnode *taxon;
} econame_t;
typedef struct {
int32_t count;
econame_t names[1];
} econameidx_t;
typedef struct {
ecorankidx_t *ranks;
econameidx_t *names;
ecotxidx_t *taxons;
} ecotaxonomy_t;
/*****************************************************
*
* Function declarations
*
*****************************************************/
/*
*
* Low level system functions
*
*/
int32_t is_big_endian();
int32_t swap_int32_t(int32_t);
void *eco_malloc(int32_t chunksize,
const char *error_message,
const char *filename,
int32_t line);
void *eco_realloc(void *chunk,
int32_t chunksize,
const char *error_message,
const char *filename,
int32_t line);
void eco_free(void *chunk,
const char *error_message,
const char *filename,
int32_t line);
void eco_trace_memory_allocation();
void eco_untrace_memory_allocation();
#define ECOMALLOC(size,error_message) \
eco_malloc((size),(error_message),__FILE__,__LINE__)
#define ECOREALLOC(chunk,size,error_message) \
eco_realloc((chunk),(size),(error_message),__FILE__,__LINE__)
#define ECOFREE(chunk,error_message) \
eco_free((chunk),(error_message),__FILE__,__LINE__)
/*
*
* Error managment
*
*/
void ecoError(int32_t,const char*,const char *,int);
#define ECOERROR(code,message) ecoError((code),(message),__FILE__,__LINE__)
#define ECO_IO_ERROR (1)
#define ECO_MEM_ERROR (2)
#define ECO_ASSERT_ERROR (3)
#define ECO_NOTFOUND_ERROR (4)
/*
*
* Low level Disk access functions
*
*/
FILE *open_ecorecorddb(const char *filename,
int32_t *sequencecount,
int32_t abort_on_open_error);
void *read_ecorecord(FILE *,int32_t *recordSize);
/*
* Read function in internal binary format
*/
FILE *open_ecoseqdb(const char *filename,
int32_t *sequencecount);
ecoseq_t *readnext_ecoseq(FILE *);
ecorankidx_t *read_rankidx(const char *filename);
econameidx_t *read_nameidx(const char *filename,ecotaxonomy_t *taxonomy);
/**
* Read taxonomy data as formated by the ecoPCRFormat.py script.
*
* This function is normaly uses internaly by the read_taxonomy
* function and should not be called directly.
*
* @arg filename path to the *.tdx file of the reformated db
*
* @return pointer to a taxonomy index structure
*/
ecotxidx_t *read_taxonomyidx(const char *filename);
ecotaxonomy_t *read_taxonomy(const char *prefix,int32_t readAlternativeName);
ecotx_t *eco_findtaxonbytaxid(ecotaxonomy_t *taxonomy, int32_t taxid);
int eco_isundertaxon(ecotx_t *taxon, int other_taxid);
ecoseq_t *ecoseq_iterator(const char *prefix);
ecoseq_t *new_ecoseq();
int32_t delete_ecoseq(ecoseq_t *);
ecoseq_t *new_ecoseq_with_data( char *AC,
char *DE,
char *SQ,
int32_t taxid
);
int32_t delete_taxon(ecotx_t *taxon);
int32_t delete_taxonomy(ecotxidx_t *index);
int32_t rank_index(const char* label,ecorankidx_t* ranks);
int32_t delete_apatseq(SeqPtr pseq);
PatternPtr buildPattern(const char *pat, int32_t error_max);
PatternPtr complementPattern(PatternPtr pat);
SeqPtr ecoseq2apatseq(ecoseq_t *in,SeqPtr out,int32_t circular);
char *ecoComplementPattern(char *nucAcSeq);
char *ecoComplementSequence(char *nucAcSeq);
char *getSubSequence(char* nucAcSeq,int32_t begin,int32_t end);
ecotx_t *eco_getspecies(ecotx_t *taxon,ecotaxonomy_t *taxonomy);
ecotx_t *eco_getgenus(ecotx_t *taxon,ecotaxonomy_t *taxonomy);
ecotx_t *eco_getfamily(ecotx_t *taxon,ecotaxonomy_t *taxonomy);
ecotx_t *eco_getkingdom(ecotx_t *taxon,ecotaxonomy_t *taxonomy);
ecotx_t *eco_getsuperkingdom(ecotx_t *taxon,ecotaxonomy_t *taxonomy);
int eco_is_taxid_ignored(int32_t *ignored_taxid, int32_t tab_len, int32_t taxid);
int eco_is_taxid_included(ecotaxonomy_t *taxonomy, int32_t *included_taxid, int32_t tab_len, int32_t taxid);
#endif /*ECOPCR_H_*/

199
src/libecoPCR/ecoapat.c
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#include "../libapat/libstki.h"
#include "../libapat/apat.h"
#include "ecoPCR.h"
#include <string.h>
static void EncodeSequence(SeqPtr seq);
static void UpperSequence(char *seq);
/* -------------------------------------------- */
/* uppercase sequence */
/* -------------------------------------------- */
#define IS_LOWER(c) (((c) >= 'a') && ((c) <= 'z'))
#define TO_UPPER(c) ((c) - 'a' + 'A')
void UpperSequence(char *seq)
{
char *cseq;
for (cseq = seq ; *cseq ; cseq++)
if (IS_LOWER(*cseq))
*cseq = TO_UPPER(*cseq);
}
#undef IS_LOWER
#undef TO_UPPER
/* -------------------------------------------- */
/* encode sequence */
/* IS_UPPER is slightly faster than isupper */
/* -------------------------------------------- */
#define IS_UPPER(c) (((c) >= 'A') && ((c) <= 'Z'))
void EncodeSequence(SeqPtr seq)
{
int i;
UInt8 *data;
char *cseq;
data = seq->data;
cseq = seq->cseq;
while (*cseq) {
*data = (IS_UPPER(*cseq) ? *cseq - 'A' : 0x0);
data++;
cseq++;
}
for (i=0,cseq=seq->cseq;i < seq->circular; i++,cseq++,data++)
*data = (IS_UPPER(*cseq) ? *cseq - 'A' : 0x0);
for (i = 0 ; i < MAX_PATTERN ; i++)
seq->hitpos[i]->top = seq->hiterr[i]->top = 0;
}
#undef IS_UPPER
SeqPtr ecoseq2apatseq(ecoseq_t *in,SeqPtr out,int32_t circular)
{
int i;
if (!out)
{
out = ECOMALLOC(sizeof(Seq),
"Error in Allocation of a new Seq structure");
for (i = 0 ; i < MAX_PATTERN ; i++)
{
if (! (out->hitpos[i] = NewStacki(kMinStackiSize)))
ECOERROR(ECO_MEM_ERROR,"Error in hit stack Allocation");
if (! (out->hiterr[i] = NewStacki(kMinStackiSize)))
ECOERROR(ECO_MEM_ERROR,"Error in error stack Allocation");
}
}
out->name = in->AC;
out->seqsiz = out->seqlen = in->SQ_length;
out->circular = circular;
if (!out->data)
{
out->data = ECOMALLOC((out->seqlen+circular) *sizeof(UInt8),
"Error in Allocation of a new Seq data member");
out->datsiz= out->seqlen+circular;
}
else if ((out->seqlen +circular) >= out->datsiz)
{
out->data = ECOREALLOC(out->data,(out->seqlen+circular),
"Error during Seq data buffer realloc");
out->datsiz= out->seqlen+circular;
}
out->cseq = in->SQ;
EncodeSequence(out);
return out;
}
int32_t delete_apatseq(SeqPtr pseq)
{
int i;
if (pseq) {
if (pseq->data)
ECOFREE(pseq->data,"Freeing sequence data buffer");
for (i = 0 ; i < MAX_PATTERN ; i++) {
if (pseq->hitpos[i]) FreeStacki(pseq->hitpos[i]);
if (pseq->hiterr[i]) FreeStacki(pseq->hiterr[i]);
}
ECOFREE(pseq,"Freeing apat sequence structure");
return 0;
}
return 1;
}
PatternPtr buildPattern(const char *pat, int32_t error_max)
{
PatternPtr pattern;
int32_t patlen;
pattern = ECOMALLOC(sizeof(Pattern),
"Error in pattern allocation");
pattern->ok = Vrai;
pattern->hasIndel= Faux;
pattern->maxerr = error_max;
patlen = strlen(pat);
pattern->cpat = ECOMALLOC(sizeof(char)*patlen+1,
"Error in sequence pattern allocation");
strncpy(pattern->cpat,pat,patlen);
pattern->cpat[patlen]=0;
UpperSequence(pattern->cpat);
if (!CheckPattern(pattern))
ECOERROR(ECO_ASSERT_ERROR,"Error in pattern checking");
if (! EncodePattern(pattern, dna))
ECOERROR(ECO_ASSERT_ERROR,"Error in pattern encoding");
if (! CreateS(pattern, ALPHA_LEN))
ECOERROR(ECO_ASSERT_ERROR,"Error in pattern compiling");
return pattern;
}
PatternPtr complementPattern(PatternPtr pat)
{
PatternPtr pattern;
pattern = ECOMALLOC(sizeof(Pattern),
"Error in pattern allocation");
pattern->ok = Vrai;
pattern->hasIndel= pat->hasIndel;
pattern->maxerr = pat->maxerr;
pattern->patlen = pat->patlen;
pattern->cpat = ECOMALLOC(sizeof(char)*(strlen(pat->cpat)+1),
"Error in sequence pattern allocation");
strcpy(pattern->cpat,pat->cpat);
ecoComplementPattern(pattern->cpat);
if (!CheckPattern(pattern))
ECOERROR(ECO_ASSERT_ERROR,"Error in pattern checking");
if (! EncodePattern(pattern, dna))
ECOERROR(ECO_ASSERT_ERROR,"Error in pattern encoding");
if (! CreateS(pattern, ALPHA_LEN))
ECOERROR(ECO_ASSERT_ERROR,"Error in pattern compiling");
return pattern;
}

153
src/libecoPCR/ecodna.c
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@ -1,153 +0,0 @@
#include <string.h>
#include "ecoPCR.h"
/*
* @doc: DNA alphabet (IUPAC)
*/
#define LX_BIO_DNA_ALPHA "ABCDEFGHIJKLMNOPQRSTUVWXYZ#![]"
/*
* @doc: complementary DNA alphabet (IUPAC)
*/
#define LX_BIO_CDNA_ALPHA "TVGHEFCDIJMLKNOPQYSAABWXRZ#!]["
static char sNuc[] = LX_BIO_DNA_ALPHA;
static char sAnuc[] = LX_BIO_CDNA_ALPHA;
static char LXBioBaseComplement(char nucAc);
static char *LXBioSeqComplement(char *nucAcSeq);
static char *reverseSequence(char *str,char isPattern);
/* ---------------------------- */
char LXBioBaseComplement(char nucAc)
{
char *c;
if ((c = strchr(sNuc, nucAc)))
return sAnuc[(c - sNuc)];
else
return nucAc;
}
/* ---------------------------- */
char *LXBioSeqComplement(char *nucAcSeq)
{
char *s;
for (s = nucAcSeq ; *s ; s++)
*s = LXBioBaseComplement(*s);
return nucAcSeq;
}
char *reverseSequence(char *str,char isPattern)
{
char *sb, *se, c;
if (! str)
return str;
sb = str;
se = str + strlen(str) - 1;
while(sb <= se) {
c = *sb;
*sb++ = *se;
*se-- = c;
}
sb = str;
se = str + strlen(str) - 1;
if (isPattern)
for (;sb < se; sb++)
{
if (*sb=='#')
{
if (((se - sb) > 2) && (*(sb+2)=='!'))
{
*sb='!';
sb+=2;
*sb='#';
}
else
{
*sb=*(sb+1);
sb++;
*sb='#';
}
}
else if (*sb=='!')
{
*sb=*(sb-1);
*(sb-1)='!';
}
}
return str;
}
char *ecoComplementPattern(char *nucAcSeq)
{
return reverseSequence(LXBioSeqComplement(nucAcSeq),1);
}
char *ecoComplementSequence(char *nucAcSeq)
{
return reverseSequence(LXBioSeqComplement(nucAcSeq),0);
}
char *getSubSequence(char* nucAcSeq,int32_t begin,int32_t end)
{
static char *buffer = NULL;
static int32_t buffSize= 0;
int32_t length;
if (begin < end)
{
length = end - begin;
if (length >= buffSize)
{
buffSize = length+1;
if (buffer)
buffer=ECOREALLOC(buffer,buffSize,
"Error in reallocating sub sequence buffer");
else
buffer=ECOMALLOC(buffSize,
"Error in allocating sub sequence buffer");
}
strncpy(buffer,nucAcSeq + begin,length);
buffer[length]=0;
}
else
{
length = end + strlen(nucAcSeq) - begin;
if (length >= buffSize)
{
buffSize = length+1;
if (buffer)
buffer=ECOREALLOC(buffer,buffSize,
"Error in reallocating sub sequence buffer");
else
buffer=ECOMALLOC(buffSize,
"Error in allocating sub sequence buffer");
}
strncpy(buffer,nucAcSeq+begin,length - end);
strncpy(buffer+(length-end),nucAcSeq ,end);
buffer[length]=0;
}
return buffer;
}

19
src/libecoPCR/ecofilter.c
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@ -1,19 +0,0 @@
#include "ecoPCR.h"
int eco_is_taxid_included( ecotaxonomy_t *taxonomy,
int32_t *restricted_taxid,
int32_t tab_len,
int32_t taxid)
{
int i;
ecotx_t *taxon;
taxon = eco_findtaxonbytaxid(taxonomy, taxid);
for (i=0; i < tab_len; i++)
if ( (taxon->taxid == restricted_taxid[i]) ||
(eco_isundertaxon(taxon, restricted_taxid[i])) )
return 1;
return 0;
}

61
src/libecoPCR/econame.c
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#include "ecoPCR.h"
#include <string.h>
#include <stdlib.h>
static econame_t *readnext_econame(FILE *f,econame_t *name,ecotaxonomy_t *taxonomy);
econameidx_t *read_nameidx(const char *filename,ecotaxonomy_t *taxonomy)
{
int32_t count;
FILE *f;
econameidx_t *indexname;
int32_t i;
f = open_ecorecorddb(filename,&count,1);
indexname = (econameidx_t*) ECOMALLOC(sizeof(econameidx_t) + sizeof(econame_t) * (count-1),"Allocate names");
indexname->count=count;
for (i=0; i < count; i++){
readnext_econame(f,(indexname->names)+i,taxonomy);
}
return indexname;
}
econame_t *readnext_econame(FILE *f,econame_t *name,ecotaxonomy_t *taxonomy)
{
econameformat_t *raw;
int32_t rs;
raw = read_ecorecord(f,&rs);
if (!raw)
return NULL;
if (is_big_endian())
{
raw->is_scientificname = swap_int32_t(raw->is_scientificname);
raw->namelength = swap_int32_t(raw->namelength);
raw->classlength = swap_int32_t(raw->classlength);
raw->taxid = swap_int32_t(raw->taxid);
}
name->is_scientificname=raw->is_scientificname;
name->name = ECOMALLOC((raw->namelength+1) * sizeof(char),"Allocate name");
strncpy(name->name,raw->names,raw->namelength);
name->name[raw->namelength]=0;
name->classname = ECOMALLOC((raw->classlength+1) * sizeof(char),"Allocate classname");
strncpy(name->classname,(raw->names+raw->namelength),raw->classlength);
name->classname[raw->classlength]=0;
name->taxon = taxonomy->taxons->taxon + raw->taxid;
return name;
}

52
src/libecoPCR/ecorank.c
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@ -1,52 +0,0 @@
#include "ecoPCR.h"
#include <string.h>
#include <stdlib.h>
static int compareRankLabel(const void *label1, const void *label2);
ecorankidx_t *read_rankidx(const char *filename)
{
int32_t count;
FILE *f;
ecorankidx_t *index;
int32_t i;
int32_t rs;
char *buffer;
f = open_ecorecorddb(filename,&count,1);
index = (ecorankidx_t*) ECOMALLOC(sizeof(ecorankidx_t) + sizeof(char*) * (count-1),
"Allocate rank index");
index->count=count;
for (i=0; i < count; i++)
{
buffer = read_ecorecord(f,&rs);
index->label[i]=(char*) ECOMALLOC(rs+1,
"Allocate rank label");
strncpy(index->label[i],buffer,rs);
}
return index;
}
int32_t rank_index(const char* label,ecorankidx_t* ranks)
{
char **rep;
rep = bsearch(label,ranks->label,ranks->count,sizeof(char*),compareRankLabel);
if (rep)
return rep-ranks->label;
else
ECOERROR(ECO_NOTFOUND_ERROR,"Rank label not found");
return -1;
}
int compareRankLabel(const void *label1, const void *label2)
{
return strcmp((const char*)label1,*(const char**)label2);
}

223
src/libecoPCR/ecoseq.c
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@ -1,223 +0,0 @@
#include "ecoPCR.h"
#include <stdlib.h>
#include <string.h>
#include <zlib.h>
#include <string.h>
#include <stdio.h>
static FILE *open_seqfile(const char *prefix,int32_t index);
ecoseq_t *new_ecoseq()
{
void *tmp;
tmp = ECOMALLOC(sizeof(ecoseq_t),"Allocate new ecoseq structure");
return tmp;
}
int32_t delete_ecoseq(ecoseq_t * seq)
{
if (seq)
{
if (seq->AC)
ECOFREE(seq->AC,"Free sequence AC");
if (seq->DE)
ECOFREE(seq->DE,"Free sequence DE");
if (seq->SQ)
ECOFREE(seq->SQ,"Free sequence SQ");
ECOFREE(seq,"Free sequence structure");
return 0;
}
return 1;
}
ecoseq_t *new_ecoseq_with_data( char *AC,
char *DE,
char *SQ,
int32_t taxid_idx
)
{
ecoseq_t *tmp;
int32_t lstr;
tmp = new_ecoseq();
tmp->taxid=taxid_idx;
if (AC)
{
lstr =strlen(AC);
tmp->AC=ECOMALLOC((lstr+1) * sizeof(char),
"Allocate sequence accession");
strcpy(tmp->AC,AC);
}
if (DE)
{
lstr =strlen(DE);
tmp->DE=ECOMALLOC((lstr+1) * sizeof(char),
"Allocate sequence definition");
strcpy(tmp->DE,DE);
}
if (SQ)
{
lstr =strlen(SQ);
tmp->SQ=ECOMALLOC((lstr+1) * sizeof(char),
"Allocate sequence data");
strcpy(tmp->SQ,SQ);
}
return tmp;
}
/**
* ?? used ??
**/
FILE *open_ecoseqdb(const char *filename,
int32_t *sequencecount)
{
return open_ecorecorddb(filename,sequencecount,1);
}
ecoseq_t *readnext_ecoseq(FILE *f)
{
char *compressed=NULL;
ecoseqformat_t *raw;
ecoseq_t *seq;
int32_t comp_status;
unsigned long int seqlength;
int32_t rs;
raw = read_ecorecord(f,&rs);
if (!raw)
return NULL;
if (is_big_endian())
{
raw->CSQ_length = swap_int32_t(raw->CSQ_length);
raw->DE_length = swap_int32_t(raw->DE_length);
raw->SQ_length = swap_int32_t(raw->SQ_length);
raw->taxid = swap_int32_t(raw->taxid);
}
seq = new_ecoseq();
seq->taxid = raw->taxid;
seq->AC = ECOMALLOC(strlen(raw->AC) +1,
"Allocate Sequence Accesion number");
strncpy(seq->AC,raw->AC,strlen(raw->AC));
seq->DE = ECOMALLOC(raw->DE_length+1,
"Allocate Sequence definition");
strncpy(seq->DE,raw->data,raw->DE_length);
seqlength = seq->SQ_length = raw->SQ_length;
compressed = raw->data + raw->DE_length;
seq->SQ = ECOMALLOC(seqlength+1,
"Allocate sequence buffer");
comp_status = uncompress((unsigned char*)seq->SQ,
&seqlength,
(unsigned char*)compressed,
raw->CSQ_length);
if (comp_status != Z_OK)
ECOERROR(ECO_IO_ERROR,"I cannot uncompress sequence data");
return seq;
}
/**
* Open the sequences database (.sdx file)
* @param prefix name of the database (radical without extension)
* @param index integer
*
* @return file object
*/
FILE *open_seqfile(const char *prefix,int32_t index)
{
char filename_buffer[1024];
int32_t filename_length;
FILE *input;
int32_t seqcount;
filename_length = snprintf(filename_buffer,
1023,
"%s_%03d.sdx",
prefix,
index);
fprintf(stderr,"# Coucou %s\n",filename_buffer);
if (filename_length >= 1024)
ECOERROR(ECO_ASSERT_ERROR,"file name is too long");
filename_buffer[filename_length]=0;
input=open_ecorecorddb(filename_buffer,&seqcount,0);
if (input)
fprintf(stderr,"# Reading file %s containing %d sequences...\n",
filename_buffer,
seqcount);
return input;
}
ecoseq_t *ecoseq_iterator(const char *prefix)
{
static FILE *current_seq_file= NULL;
static int32_t current_file_idx = 1;
static char current_prefix[1024];
ecoseq_t *seq;
if (prefix)
{
current_file_idx = 1;
if (current_seq_file)
fclose(current_seq_file);
strncpy(current_prefix,prefix,1023);
current_prefix[1024]=0;
current_seq_file = open_seqfile(current_prefix,
current_file_idx);
if (!current_seq_file)
return NULL;
}
seq = readnext_ecoseq(current_seq_file);
if (!seq && feof(current_seq_file))
{
current_file_idx++;
fclose(current_seq_file);
current_seq_file = open_seqfile(current_prefix,
current_file_idx);
if (current_seq_file)
seq = readnext_ecoseq(current_seq_file);
}
return seq;
}

329
src/libecoPCR/ecotax.c
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@ -1,329 +0,0 @@
#include "ecoPCR.h"
#include <string.h>
#include <stdlib.h>
#include <stdio.h>
static ecotx_t *readnext_ecotaxon(FILE *f,ecotx_t *taxon);
/**
* Open the taxonomy database
* @param pointer to the database (.tdx file)
* @return a ecotxidx_t structure
*/
ecotxidx_t *read_taxonomyidx(const char *filename)
{
int32_t count;
FILE *f;
ecotxidx_t *index;
int32_t i;
f = open_ecorecorddb(filename,&count,1);
index = (ecotxidx_t*) ECOMALLOC(sizeof(ecotxidx_t) + sizeof(ecotx_t) * (count-1),
"Allocate taxonomy");
index->count=count;
for (i=0; i < count; i++){
readnext_ecotaxon(f,&(index->taxon[i]));
index->taxon[i].parent=index->taxon + (int32_t)index->taxon[i].parent;
}
return index;
}
int32_t delete_taxonomy(ecotxidx_t *index)
{
int32_t i;
if (index)
{
for (i=0; i< index->count; i++)
if (index->taxon[i].name)
ECOFREE(index->taxon[i].name,"Free scientific name");
ECOFREE(index,"Free Taxonomy");
return 0;
}
return 1;
}
int32_t delete_taxon(ecotx_t *taxon)
{
if (taxon)
{
if (taxon->name)
ECOFREE(taxon->name,"Free scientific name");
ECOFREE(taxon,"Free Taxon");
return 0;
}
return 1;
}
/**
* Read the database for a given taxon a save the data
* into the taxon structure(if any found)
* @param *f pointer to FILE type returned by fopen
* @param *taxon pointer to the structure
*
* @return a ecotx_t structure if any taxon found else NULL
*/
ecotx_t *readnext_ecotaxon(FILE *f,ecotx_t *taxon)
{
ecotxformat_t *raw;
int32_t rs;
raw = read_ecorecord(f,&rs);
if (!raw)
return NULL;
if (is_big_endian())
{
raw->namelength = swap_int32_t(raw->namelength);
raw->parent = swap_int32_t(raw->parent);
raw->rank = swap_int32_t(raw->rank);
raw->taxid = swap_int32_t(raw->taxid);
}
taxon->parent = (ecotx_t*)raw->parent;
taxon->taxid = raw->taxid;
taxon->rank = raw->rank;
taxon->name = ECOMALLOC((raw->namelength+1) * sizeof(char),
"Allocate taxon scientific name");
strncpy(taxon->name,raw->name,raw->namelength);
return taxon;
}
ecotaxonomy_t *read_taxonomy(const char *prefix,int32_t readAlternativeName)
{
ecotaxonomy_t *tax;
char *filename;
int buffsize;
tax = ECOMALLOC(sizeof(ecotaxonomy_t),
"Allocate taxonomy structure");
buffsize = strlen(prefix)+10;
filename = ECOMALLOC(buffsize,
"Allocate filename");
snprintf(filename,buffsize,"%s.rdx",prefix);
tax->ranks = read_rankidx(filename);
snprintf(filename,buffsize,"%s.tdx",prefix);
tax->taxons = read_taxonomyidx(filename);
if (readAlternativeName)
{
snprintf(filename,buffsize,"%s.ndx",prefix);
tax->names=read_nameidx(filename,tax);
}
else
tax->names=NULL;
return tax;
}
int32_t delete_ecotaxonomy(ecotaxonomy_t *taxonomy)
{
if (taxonomy)
{
if (taxonomy->ranks)
ECOFREE(taxonomy->ranks,"Free rank index");
if (taxonomy->taxons)
ECOFREE(taxonomy->taxons,"Free taxon index");
ECOFREE(taxonomy,"Free taxonomy structure");
return 0;
}
return 1;
}
ecotx_t *eco_findtaxonatrank(ecotx_t *taxon,
int32_t rankidx)
{
ecotx_t *current_taxon;
ecotx_t *next_taxon;
current_taxon = taxon;
next_taxon = current_taxon->parent;
while ((current_taxon!=next_taxon) && // I' am the root node
(current_taxon->rank!=rankidx))
{
current_taxon = next_taxon;
next_taxon = current_taxon->parent;
}
if (current_taxon->rank==rankidx)
return current_taxon;
else
return NULL;
}
/**
* Get back information concerning a taxon from a taxonomic id
* @param *taxonomy the taxonomy database
* @param taxid the taxonomic id
*
* @result a ecotx_t structure containing the taxonimic information
**/
ecotx_t *eco_findtaxonbytaxid(ecotaxonomy_t *taxonomy,
int32_t taxid)
{
ecotx_t *current_taxon;
int32_t taxoncount;
int32_t i;
taxoncount=taxonomy->taxons->count;
for (current_taxon=taxonomy->taxons->taxon,
i=0;
i < taxoncount;
i++,
current_taxon++){
if (current_taxon->taxid==taxid){
return current_taxon;
}
}
return (ecotx_t*)NULL;
}
/**
* Find out if taxon is son of other taxon (identified by its taxid)
* @param *taxon son taxon
* @param parent_taxid taxonomic id of the other taxon
*
* @return 1 is the other taxid math a parent taxid, else 0
**/
int eco_isundertaxon(ecotx_t *taxon,
int other_taxid)
{
ecotx_t *next_parent;
next_parent = taxon->parent;
while ( (other_taxid != next_parent->taxid) &&
(strcmp(next_parent->name, "root")) )
{
next_parent = next_parent->parent;
}
if (other_taxid == next_parent->taxid)
return 1;
else
return 0;
}
ecotx_t *eco_getspecies(ecotx_t *taxon,
ecotaxonomy_t *taxonomy)
{
static ecotaxonomy_t *tax=NULL;
static int32_t rankindex=-1;
if (taxonomy && tax!=taxonomy)
{
rankindex = rank_index("species",taxonomy->ranks);
tax=taxonomy;
}
if (!tax || rankindex < 0)
ECOERROR(ECO_ASSERT_ERROR,"No taxonomy defined");
return eco_findtaxonatrank(taxon,rankindex);
}
ecotx_t *eco_getgenus(ecotx_t *taxon,
ecotaxonomy_t *taxonomy)
{
static ecotaxonomy_t *tax=NULL;
static int32_t rankindex=-1;
if (taxonomy && tax!=taxonomy)
{
rankindex = rank_index("genus",taxonomy->ranks);
tax=taxonomy;
}
if (!tax || rankindex < 0)
ECOERROR(ECO_ASSERT_ERROR,"No taxonomy defined");
return eco_findtaxonatrank(taxon,rankindex);
}
ecotx_t *eco_getfamily(ecotx_t *taxon,
ecotaxonomy_t *taxonomy)
{
static ecotaxonomy_t *tax=NULL;
static int32_t rankindex=-1;
if (taxonomy && tax!=taxonomy)
{
rankindex = rank_index("family",taxonomy->ranks);
tax=taxonomy;
}
if (!tax || rankindex < 0)
ECOERROR(ECO_ASSERT_ERROR,"No taxonomy defined");
return eco_findtaxonatrank(taxon,rankindex);
}
ecotx_t *eco_getkingdom(ecotx_t *taxon,
ecotaxonomy_t *taxonomy)
{
static ecotaxonomy_t *tax=NULL;
static int32_t rankindex=-1;
if (taxonomy && tax!=taxonomy)
{
rankindex = rank_index("kingdom",taxonomy->ranks);
tax=taxonomy;
}
if (!tax || rankindex < 0)
ECOERROR(ECO_ASSERT_ERROR,"No taxonomy defined");
return eco_findtaxonatrank(taxon,rankindex);
}
ecotx_t *eco_getsuperkingdom(ecotx_t *taxon,
ecotaxonomy_t *taxonomy)
{
static ecotaxonomy_t *tax=NULL;
static int32_t rankindex=-1;
if (taxonomy && tax!=taxonomy)
{
rankindex = rank_index("superkingdom",taxonomy->ranks);
tax=taxonomy;
}
if (!tax || rankindex < 0)
ECOERROR(ECO_ASSERT_ERROR,"No taxonomy defined");
return eco_findtaxonatrank(taxon,rankindex);
}

31
src/libtm/tm.c
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@ -1,31 +0,0 @@
/**
*
* J Jr SantaLucia.
* A uni<6E>ed view of polymer, dumbbell, and oligonucleotide
* dna nearest-neighbor thermodynamics.
* Proc Natl Acad Sci U S A, 95(4):1460<36>1465, 1998 Feb 17.
*/
//Nearest-neighbor sequence
//(5'-3'/5'-3') deltaH deltaS
// kcal/mol cal/(mol<6F>K)
//AA/TT -7.9 -22.2
//AG/CT -7.8 -21.0
//AT/AT -7.2 -20.4
//AC/GT -8.4 -22.4
//GA/TC -8.2 -22.2
//GG/CC -8.0 -19.9
//GC/GC -9.8 -24.4
//TA/TA -7.2 -21.3
//TG/CA -8.5 -22.7
//CG/CG -10.6 -27.2
//Terminal A-T base pair 2.3 4.1
//Terminal G-C base pair 0.1 -2.8
float nearestNeighborTm(const char *oligo,float probe,float target)
{
}