kalignP_input.h

/*
	kalignP_input.h 
	
    Copyright (C) 2010 Nanjiang Shu <nanjiang@sbc.su.se>
    Department of Biochemistry and Biophysics 
    Stockholm University

    Description: multiple sequence alignment supporting external supplied
    position specific gap penalties

    This software is derived from 
    Kalign version 2.03, Copyright (C) 2006 Timo Lassmann
    http://msa.cgb.ki.se/
    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

	A copy of this license is in the COPYING file.
*/


#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_new(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: kalignP   [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\
   -custom_matrix <FILE>  Supply the user defined substitution matrix\n\
    \n\
   -protein               Force the input type as protein sequences\n\
    \n\
   -q, -quiet             Print nothing to STDERR.\n\
                          Read nothing from STDIN\n\
      \n\
Examples:\n\n\
Using pipes:\n\
      kalignP [OPTIONS] < [INFILE]   > [OUTFILE]\n\
      more [INFILE] |  kalignP [OPTIONS] > [OUTFILE]\n\
\n\
Relaxed gap penalties:\n\
      kalignP -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\
      kalignP -in test.xml -distance pair -tree nj -sort gaps -feature STRUCT -format macsim -out test.macsim\n\
";