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/*
kalign2_input.h
Released under GPL - see the 'COPYING' file
Copyright (C) 2006 Timo Lassmann <timolassmann@gmail.com>
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 2 of the License, or
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, write to the Free Software
Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
Please send bug reports, comments etc. to:
timolassmann@gmail.com
*/
#include <unistd.h>
#include <string.h>
#include <ctype.h>
#define SEEK_START 0
#define SEEK_END 2
struct alignment* read_sequences(struct alignment* aln,char* string);
struct alignment* read_sequences_from_swissprot(struct alignment* aln,char* string);
struct alignment* read_sequences_uniprot_xml(struct alignment* aln,char* string);
struct alignment* read_sequences_macsim_xml(struct alignment* aln,char* string);
struct feature* read_ft(struct feature* ft,char* p);
struct alignment* read_sequences_clustal(struct alignment* aln,char* string);
struct alignment* read_sequences_stockholm(struct alignment* aln,char* string);
struct alignment* read_alignment(struct alignment* aln,char* string);
struct alignment* read_alignment_from_swissprot(struct alignment* aln,char* string);
struct alignment* read_alignment_uniprot_xml(struct alignment* aln,char* string);
struct alignment* read_alignment_macsim_xml(struct alignment* aln,char* string);
struct feature* read_ft(struct feature* ft,char* p);
struct alignment* read_alignment_clustal(struct alignment* aln,char* string);
struct alignment* read_alignment_stockholm(struct alignment* aln,char* string);
char* get_input_into_string(char* string,char* infile);
int count_sequences_macsim(char* string);
int count_sequences_swissprot(char* string);
int count_sequences_uniprot(char* string);
int count_sequences_stockholm(char* string);
int count_sequences_clustalw(char* string);
int count_sequences_fasta(char* string);
static char usage[] = "\n\
Usage: kalign2 [INFILE] [OUTFILE] [OPTIONS]\n\
\n\
Options:\n\n\
-s, -gapopen Gap open penalty\n\
-gap_open\n\
-gpo\n\
\n\
-e, -gapextension Gap extension penalty\n\
-gap_ext\n\
-gpe\n\
\n\
-t, -terminal_gap_extension_penalty Terminal gap penalties\n\
-tgpe\n\
\n\
-m, -matrix_bonus A constant added to the substitution matrix.\n\
-bonus\n\
\n\
-c, -sort The order in which the sequences appear in the output alignment.\n\
<input, tree, gaps.>\n\
\n\
-g, -feature Selects feature mode and specifies which features are to be used:\n\
e.g. all, maxplp, STRUCT, PFAM-A....\n\
-same_feature_score Score for aligning same features\n\
-diff_feature_score Penalty for aligning different features\n\
\n\
-d, -distance Distance method.\n\
<wu,pair>\n\
\n\
-b, -guide-tree Guide tree method.\n\
-tree <nj,upgma>\n\
\n\
-z, -zcutoff Parameter used in the wu-manber based distance calculation\n\
\n\
-i, -input The input file.\n\
-infile\n\
-in\n\
\n\
-o, -output The output file.\n\
-outfile\n\
-out\n\
\n\
-a, -gap_inc Parameter increases gap penalties depending on the number of existing gaps\n\
\n\
-f, -format The output format:\n\
<fasta, msf, aln, clu, macsim>\n\
\n\
-q, -quiet Print nothing to STDERR.\n\
Read nothing from STDIN\n\
\n\
Examples:\n\n\
Using pipes:\n\
kalign2 [OPTIONS] < [INFILE] > [OUTFILE]\n\
more [INFILE] | kalign2 [OPTIONS] > [OUTFILE]\n\
\n\
Relaxed gap penalties:\n\
kalign2 -gpo 60 -gpe 9 -tgpe 0 -bonus 0 < [INFILE] > [OUTFILE]\n\
\n\
Feature alignment with pairwise alignment based distance method and NJ guide tree:\n\
kalign2 -in test.xml -distance pair -tree nj -sort gaps -feature STRUCT -format macsim -out test.macsim\n\
";
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