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/*
* segemehl - a read aligner
* Copyright (C) 2008-2017 Steve Hoffmann and Christian Otto
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
#ifndef ALURUSORT_H
#define ALURUSORT_H
/*
*
* aluruSort.h
* declarations for aluruSort.c
*
* @author Steve Hoffmann, steve@bioinf.uni-leipzig.de
* @company Bioinformatics, University of Leipzig
* @date 07/11/2007 07:06:04 PM CEST
*
* SVN
* Revision of last commit: $Rev: 31 $
* Author: $Author: steve $
* Date: $Date: 2008-05-16 14:11:09 +0200 (Fri, 16 May 2008) $
*
* Id: $Id: aluruSort.h 31 2008-05-16 12:11:09Z steve $
* Url: $URL: file:///homes/bierdepot/steve/svn/segemehl/trunk/libs/aluruSort.h $
*/
#include "mathematics.h"
#include "bitArray.h"
#define BUCKETRET(X, N, I, B) for(B=0; B < (N); B++) { \
if(X[B].id == (I)) break; \
}
#define BUCKETINIT(X,I) (X).id = (I);\
(X).elems=NULL; \
(X).noofelems=0;\
(X).allocsize=0
#define BUCKETSWAP(X,A,B) {\
Uint resc = (X)->elems[(A)]; \
(X)->elems[(A)] = (X)->elems[(B)];\
(X)->elems[(B)] = resc;\
}
#define BUCKETINC 1000
#define BUCKETADD(S,X,E) {\
if((X).allocsize <= (X).noofelems) {\
(X).elems = ALLOCMEMORY((S), (X).elems, Uint, ((X).allocsize+=BUCKETINC)); \
}\
(X).elems[(X).noofelems++] = (E);\
}
#define BUCKETFRONT(X) (X)->front++
#define SUFA(X, N, I) {\
Uint ITER;\
Uint CUMSUM=0;\
for(ITER=0; ITER < N; ITER++) {\
if(CUMSUM+X[ITER].noofelems > I) {\
break;\
}\
CUMSUM+=X[ITER].noofelems;\
}\
} X[ITER].elems[I-CUMSUM]
typedef struct {
Uint id;
Uint *elems;
Uint noofelems;
Uint front;
Uint allocsize;
} Alurubucket;
Alurubucket* getAluruBuckets(void *, char *, Uint, Uint *, Uint **);
Uint* Qdist(void *, bitarray, Uint, unsigned char);
bitarray classify(void *, char* s, Uint, Uint*, Uint*);
Uint* getAluruArray(void *space, char *s, Uint len, char delim);
vector_t** getQdistList(void *space, Alurubucket*, Uint, Uint *, Uint);
void showAluruBuckets(Alurubucket *bckts, Uint*, Uint n);
void sortAluruSubstrings (void *space,
vector_t** qdlist,
Uint nooflists,
Alurubucket *bckts,
Uint noofbckts,
Uint *R,
char *cl,
Uint len,
char Q);
Uint* alurusortint(void *space, Uint *s, Uint *l);
Uint* alurusort(void *space, char *s, Uint *l);
extern void getinterval(Uint *s, Uint len, Uint *min, Uint *max);
#endif
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