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Committer: Package Import Robot
Author(s): Olivier Sallou
Date: 2011-12-14 11:21:56 UTC
Revision ID: package-import@ubuntu.com-20111214112156-y3chwm0t4yn2nevm

Tags: upstream-1.0.3

Import upstream version 1.0.3

files added:

AUTHORS

COPYING

ChangeLog

Doxyfile

Doxyfile.in

INSTALL

Makefile.am

Makefile.in

NEWS

README

TODO

aclocal.m4

clustalo.pc.in

config.guess

config.sub

configure

configure.ac

depcomp

install-sh

ltmain.sh

m4/ax_openmp.m4

m4/ax_prefix_config_h.m4

m4/libtool.m4

m4/ltoptions.m4

m4/ltsugar.m4

m4/ltversion.m4

m4/lt~obsolete.m4

missing

src/Makefile.am

src/Makefile.in

src/clustal

src/clustal-omega-config.h

src/clustal-omega.c

src/clustal-omega.h

src/clustal/Makefile.am

src/clustal/Makefile.in

src/clustal/hhalign_wrapper.c

src/clustal/hhalign_wrapper.h

src/clustal/ktuple_pair.c

src/clustal/ktuple_pair.h

src/clustal/list.c

src/clustal/list.h

src/clustal/log.c

src/clustal/log.h

src/clustal/mbed.c

src/clustal/mbed.h

src/clustal/muscle_tree.c

src/clustal/muscle_tree.h

src/clustal/muscle_upgma.c

src/clustal/muscle_upgma.h

src/clustal/pair_dist.c

src/clustal/pair_dist.h

src/clustal/progress.c

src/clustal/progress.h

src/clustal/queue.h

src/clustal/seq.c

src/clustal/seq.h

src/clustal/symmatrix.c

src/clustal/symmatrix.h

src/clustal/tree.c

src/clustal/tree.h

src/clustal/util.c

src/clustal/util.h

src/clustal/weights.c

src/clustal/weights.h

src/clustalo-api-test.c

src/config.h.in

src/hhalign

src/hhalign/Makefile.am

src/hhalign/Makefile.in

src/hhalign/general.h

src/hhalign/hash-C.h

src/hhalign/hash.h

src/hhalign/hhalign.cpp

src/hhalign/hhalign.h

src/hhalign/hhalignment-C.h

src/hhalign/hhalignment.h

src/hhalign/hhdecl-C.h

src/hhalign/hhfullalignment-C.h

src/hhalign/hhfullalignment.h

src/hhalign/hhfunc-C.h

src/hhalign/hhfunc.h

src/hhalign/hhhalfalignment-C.h

src/hhalign/hhhalfalignment.h

src/hhalign/hhhit-C.h

src/hhalign/hhhit.h

src/hhalign/hhhitlist-C.h

src/hhalign/hhhitlist.h

src/hhalign/hhhmm-C.h

src/hhalign/hhhmm.h

src/hhalign/hhmatrices-C.h

src/hhalign/hhutil-C.h

src/hhalign/list-C.h

src/hhalign/list.h

src/hhalign/util-C.h

src/kmpp

src/kmpp/KMeans.cpp

src/kmpp/KMeans.h

src/kmpp/KmTree.cpp

src/kmpp/KmTree.h

src/kmpp/KmUtils.cpp

src/kmpp/KmUtils.h

src/kmpp/Makefile.am

src/kmpp/Makefile.in

src/main.cpp

src/mymain.c

src/mymain.h

src/squid

src/squid/00README

src/squid/COPYRIGHT

src/squid/LICENSE

src/squid/Makefile.am

src/squid/Makefile.in

src/squid/a2m.c

src/squid/aligneval.c

src/squid/alignio.c

src/squid/clustal.c

src/squid/clustalo.README

src/squid/cluster.c

src/squid/dayhoff.c

src/squid/eps.c

src/squid/file.c

src/squid/getopt.c

src/squid/gki.c

src/squid/gki.h

src/squid/gsi.c

src/squid/gsi.h

src/squid/gsi64.c

src/squid/gsi64.h

src/squid/hsregex.c

src/squid/iupac.c

src/squid/msa.c

src/squid/msa.h

src/squid/msf.c

src/squid/phylip.c

src/squid/revcomp.c

src/squid/rk.c

src/squid/rk.h

src/squid/selex.c

src/squid/seqencode.c

src/squid/shuffle.c

src/squid/sqerror.c

src/squid/sqfuncs.h

src/squid/sqio.c

src/squid/squid-1.9g.tar.gz

src/squid/squid.h

src/squid/squidcore.c

src/squid/sre_ctype.c

src/squid/sre_math.c

src/squid/sre_random.c

src/squid/sre_random.h

src/squid/sre_string.c

src/squid/ssi.c

src/squid/ssi.h

src/squid/stack.c

src/squid/stockholm.c

src/squid/stockholm.h

src/squid/stopwatch.c

src/squid/stopwatch.h

src/squid/translate.c

src/squid/types.c

src/squid/vectorops.c

src/squid/vectorops.h

src/squid/version.h

src/squid/weight.c

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src/clustal/list.h

/*********************************************************************

* Clustal Omega - Multiple sequence alignment

* Clustal-Omega 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 2 of the

* License, or (at your option) any later version.

* This file is part of Clustal-Omega.

********************************************************************/

* RCS $Id: list.h 193 2011-02-07 15:45:21Z andreas $

* Generic single linked list storing pointers to data

#ifndef CLUSTALO_LIST_H

#define CLUSTALO_LIST_H

#include <stdlib.h>

typedef struct list_elem_s {

void *data;

struct list_elem_s *next;

} list_elem_t;

typedef struct {

/* size of list */

int size;

/* user defined function for freeing data */

void (*destroy)(void *data);

list_elem_t *head;

list_elem_t *tail;

} list_t;

void ListInit(list_t *prList, void (*destroy)(void *data));

void ListDestroy(list_t *prList);

int ListInsertNext(list_t *prList, list_elem_t *prElement, const void *data);

#define LIST_APPEND(prList, data) ListInsertNext((prList), LIST_TAIL(prList), (data))

#define LIST_PREPEND(prList, data) ListInsertNext((prList), CLUSTALO_LIST_HEAD(prList), (data))

int ListRemoveNext(list_t *prList, list_elem_t *prElement, void **data);

#define LIST_SIZE(prList) ((prList)->size)

#define CLUSTALO_LIST_HEAD(prList) ((prList)->head)

#define LIST_TAIL(prList) ((prList)->tail)

#define LIST_IS_HEAD(prList, prElement) ((prElement) == (prList)->head ? 1 : 0)

#define LIST_IS_TAIL(prElement) ((prElement)->next == NULL ? 1 : 0)

#define LIST_DATA(prElement) ((prElement)->data)

#define LIST_NEXT(prElement) ((prElement)->next)

/* special int list: stores ints by copying them (instead of storing

* pointers as generic list)

typedef list_t int_list_t;

#define INT_LIST_INIT(prList) ListInit((prList), free)

#define INT_LIST_DESTROY(prList) ListDestroy((prList));

int IntListInsertNext(list_t *prList, list_elem_t *prElement, const int data);

#define INT_LIST_APPEND(prList, data) IntListInsertNext((prList), LIST_TAIL(prList), (data))

#define INT_LIST_PREPEND(prList, data) IntListInsertNext((prList), CLUSTALO_LIST_HEAD(prList), (data))

int IntListRemoveNext(list_t *prList, list_elem_t *prElement, int *data);

#define INT_LIST_SIZE(prList) LIST_SIZE(prList)

#define INT_CLUSTALO_LIST_HEAD(prList) CLUSTALO_LIST_HEAD_INT((prList))

#define INT_LIST_TAIL(prList) LIST_TAIL_INT((prList) )

#define INT_LIST_IS_HEAD(prList, prElement) LIST_IS_HEAD(prList, prElement)

#define INT_LIST_IS_TAIL(prElement) LIST_IS_TAIL((prElement))

100

#define INT_LIST_DATA(prElement) LIST_DATA((prElement))

101

102

#define INT_LIST_NEXT(prElement) LIST_NEXT((prElement))

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#endif

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