--- /dev/null
+/******************************COPYRIGHT NOTICE*******************************/
+/* (c) Centro de Regulacio Genomica */
+/* and */
+/* Cedric Notredame */
+/* 12 Aug 2014 - 22:07. */
+/*All rights reserved. */
+/*This file is part of T-COFFEE. */
+/* */
+/* T-COFFEE 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. */
+/* */
+/* T-COFFEE 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 Foobar; if not, write to the Free Software */
+/* Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA */
+/*............................................... */
+/* If you need some more information */
+/* cedric.notredame@europe.com */
+/*............................................... */
+/******************************COPYRIGHT NOTICE*******************************/
+
+#include "string.h"
+#include "stdio.h"
+#include "stdlib.h"
+#include "fastal_lib_header.h"
+
+
+void
+tree_parse(struct Fastal_arguments *arguments, char* param)
+{
+ char delims[] = "";
+ arguments->tree_method = strtok(param,delims);
+ if (arguments->tree_method == "parttree")
+ {
+ arguments->tree_param1 = 6;
+ arguments->tree_param2 = 150;
+ }
+ char *tmp = strtok(NULL,delims);
+ if (tmp != NULL)
+ {
+ arguments->tree_param1 = atoi(tmp);
+ arguments->tree_param2 = atoi(strtok(NULL,delims));
+ }
+// printf("A: %s %i %i", arguments->tree_method, arguments->tree_param1, arguments->tree_param2);
+}
+
+
+
+void
+arg_parse (int argc, char **argv, struct Fastal_arguments *arguments)
+{
+// default values
+
+ arguments->diag_method = "blast";
+ arguments->output_file = "out->aln";
+ arguments->tree_file = NULL;
+ arguments->gep = -1;
+ arguments->gop = -10;
+ arguments->method = "fast";
+ arguments->tree_method = "oligotree";
+ arguments->mat="dna_idmat";
+ arguments->tree_only = 0;
+ arguments->evaluate = 0;
+ arguments->score = 0;
+// arguments->retree = 0;
+ arguments->agreement_score = 0;
+ arguments->num_ref_aln = 0;
+ arguments->is_dna = 1;
+ arguments->aln_ref = NULL;
+ arguments->aln2test = NULL;
+ arguments->tree_out = 0;
+ arguments->gap_iterate = 0;
+
+
+ int i = 1;
+ char *param;
+
+ for (i = 0; i < argc; ++i)
+ {
+ param = argv[i];
+ if ( ( !strcmp(param, "-d" )) || ( !strcmp(param, "--is_dna")))
+ {
+ arguments->is_dna = 1;
+ arguments->mat = "dna_idmat";
+ }
+ else if ( ( !strcmp(param, "-a" )) || ( !strcmp(param, "--is_aa")))
+ {
+ arguments->is_dna = 0;
+ arguments->mat = "blosum62mt";
+
+ }
+// printf("%s\n", arguments->mat);
+ }
+ if (arguments->is_dna)
+ {
+ arguments->tree_param1 = 2;
+ arguments->tree_param2 = 5;
+ }
+ else
+ {
+ arguments->tree_param1 = 1;
+ arguments->tree_param2 = 10;
+ }
+
+
+ i = 1;
+ while (i < argc)
+ {
+ param = argv[i];
+ if ( ( !strcmp(param, "-i" )) || ( !strcmp(param, "--in")))
+ {
+ arguments->sequence_file = argv[++i];
+ }
+ else if ( ( !strcmp(param, "-t" )) || ( !strcmp(param, "--tree_file")))
+ {
+ arguments->tree_file = argv[++i];
+ }
+ else if ( !strcmp(param, "--mat"))
+ {
+ arguments->mat = argv[++i];
+ }
+ else if ( !strcmp(param, "--tree_method"))
+ {
+ tree_parse(arguments, argv[++i]);
+// arguments->tree_file = argv[++i];
+ }
+ else if ( ( !strcmp(param, "-o" )) || ( !strcmp(param, "--outfile")))
+ {
+ arguments->output_file = argv[++i];
+ }
+ else if ( ( !strcmp(param, "-m" )) || ( !strcmp(param, "--method")))
+ {
+ ++i;
+ if ( (!strcmp(argv[i], "fast")) || (!strcmp(argv[i], "nw")) || (!strcmp(argv[i], "gotoh")) || (!strcmp(argv[i], "udisc")) )
+ arguments->method = argv[i];
+ else
+ {
+ printf("Method %s unknown\n", argv[i]);
+ exit(1);
+ }
+ }
+ else if ( ( !strcmp(param, "-b" )) || ( !strcmp(param, "--diag_method")))
+ {
+ ++i;
+ if ( (!strcmp(argv[i], "blast")) || (!strcmp(argv[i], "blastz")) || (!strcmp(argv[i], "blat")) || (!strcmp(argv[i], "ktup")))
+ arguments->diag_method = argv[i];
+ else
+ {
+ printf("DIAG Method %s unknown\n", argv[i]);
+ exit(1);
+ }
+ }
+ else if ( ( !strcmp(param, "-d" )) || ( !strcmp(param, "--is_dna")))
+ {
+ arguments->is_dna = 1;
+ }
+ else if ( ( !strcmp(param, "-a" )) || ( !strcmp(param, "--is_aa")))
+ {
+ arguments->is_dna = 0;
+ }
+ else if ( ( !strcmp(param, "-g" )) || ( !strcmp(param, "--gop")))
+ {
+ arguments->gop = atof(argv[++i]);
+ }
+// else if ( ( !strcmp(param, "-r" )) || ( !strcmp(param, "--retree")))
+// {
+// arguments->retree = atoi(argv[++i]);
+// }
+ else if ( ( !strcmp(param, "-e" )) || ( !strcmp(param, "--gep")))
+ {
+ arguments->gep = atof(argv[++i]);
+ }
+ else if ( ( !strcmp(param, "-k" )) || ( !strcmp(param, "--p1")))
+ {
+ arguments->tree_param1 = atoi(argv[++i]);
+ }
+ else if ( ( !strcmp(param, "-c" )) || ( !strcmp(param, "--p2")))
+ {
+ arguments->tree_param2 = atoi(argv[++i]);
+ }
+ else if ( !strcmp(param, "--eval_aln"))
+ {
+ arguments->evaluate = 1;
+ }
+ else if ( ( !strcmp(param, "-s" )) || ( !strcmp(param, "--score")))
+ {
+ arguments->score = 1;
+ }
+ else if ( !strcmp(param, "--tree_out"))
+ {
+ arguments->tree_out = 1;
+ }
+ else if ( !strcmp(param, "--tree_only"))
+ {
+ arguments->tree_only = 1;
+ }
+ else if ( !strcmp(param, "--agreement_score"))
+ {
+ arguments->agreement_score = 1;
+ }
+ else if ( !strcmp(param, "--make_ref_aln"))
+ {
+ arguments->num_ref_aln = atoi(argv[++i]);
+ arguments->num_seq_in_ref = atoi(argv[++i]);
+ }
+ else if ( !strcmp(param, "--aln_ref"))
+ {
+ arguments->aln_ref = argv[++i];
+ }
+ else if ( !strcmp(param, "--gap_iterate"))
+ {
+ arguments->gap_iterate = atoi(argv[++i]);
+ }
+ else if ( !strcmp(param, "--aln2test"))
+ {
+ arguments->aln2test = argv[++i];
+ }
+ else if ( ( !strcmp(param, "-h" )) || ( !strcmp(param, "--help")) || ( !strcmp(param, "-?" )))
+ {
+ printf("Fastal - a fast alignment tool\n");
+ printf("-i --in The sequence_file\n");
+ printf("-t --tree_file The treefile\n");
+ printf(" --tree_method The method to produce the tree:\n");
+ printf(" oligo - very fast method\n");
+ printf(" parttree - method like in mafft\n");
+ printf("-o --outfile The output file\n");
+ printf("-m --method The method to use:\n");
+ printf(" fast - fast approximate algorithm [default]\n");
+ printf(" nw - needleman-wunsch\n");
+ printf(" gotoh - gotoh\n");
+ printf("-d --is_dna Sequence are DNA\n");
+ printf("-a --is_aa Sequences are amino acids\n");
+ printf("-g --gop Gap opening costs\n");
+ printf("-e --gep Gap extension costs\n");
+ printf("-r --retree Number of reconstructions [default=0]\n");
+ printf(" --tree_only only tree is produced\n");
+ printf(" --eval_aln calculates only the sum-of-pairs-score of a given alignment\n");
+ printf("-s --score calculates the sum of paris score after construction of an alignment. Can take a long time. [default: off]\n");
+// printf(" --make_ref_aln calculates the sum of paris score after construction of an alignment. Can take a long time. [default: off]\n");
+ exit(0);
+ }
+ else
+ {
+ printf("Argument %s unknown\n", param);
+ exit(1);
+ }
+ ++i;
+ }
+}
git://source.jalview.org / jabaws.git / blobdiff