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kalign2_input.h

/*
      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\
            \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\
        -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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