+++ /dev/null
-#include <stdio.h>
-#include <stdlib.h>
-#include <math.h>
-#include <stdarg.h>
-#include <string.h>
-
-#include "io_lib_header.h"
-#include "util_lib_header.h"
-#include "define_header.h"
-#include "dp_lib_header.h"
-#include "dev1_lib_header.h"
-
-//Insert functions here
-void aln2hitMat_help()
-{
- fprintf ( stdout, "\n+aln2hitMat| _MODE_ : how to compare the two positions of the alignment (default:id)");
- fprintf ( stdout, "\n.................id : the sequence identity of those two positions");
- fprintf ( stdout, "\n.............pairscore : the pairwise score of the residues of those two positions");
- fprintf ( stdout, "\n+aln2hitMat| _MATRIX_ : matrix used for the comparison (idmat, blosum62mt, pam250mt.. default:blosum62mt)\n");
- exit (EXIT_SUCCESS);
-}
-
-void aln2hitMat (Alignment *A, char *phitmat)
-{
- float **ffpHitScoreMatrix;
- int i, j, k, l, s;
- int nl = A->len_aln;
- int inseq = A->nseq;
- int itmpScore;
- char matrix[100];
- char mode[100];
- int isim_count, itotal_count, r1, r2;
-
-//Initialization for files
- char *pcFileName = A->file[0];
- char prefix[200] ={0};
- char *hit_matrix_file = vcalloc(200, sizeof (char));
- char *hit_html_file = vcalloc(200, sizeof (char));
- int len = (strrchr(pcFileName,'.')?strrchr(pcFileName,'.')-pcFileName:strlen(pcFileName));
-
- strncpy(prefix, pcFileName, len);
- sprintf(hit_matrix_file, "%s%s", prefix, "_aln.hit_matrix");
- sprintf(hit_html_file, "%s%s", prefix, ".alnhit_html");
-
- if ( phitmat && strstr ( phitmat, "help"))
- aln2hitMat_help();
-
- if(phitmat == NULL) phitmat = vcalloc(1, sizeof(char)); //such that program could get default value
-
- strget_param (phitmat, "_MODE_", "id", "%s", mode);
- strget_param (phitmat, "_MATRIX_", "blosum62mt", "%s", matrix);
-
- fprintf ( stdout, "[START] aln to hit matrix\n");
- fprintf ( stdout, " Mode:%s\n", mode);
- fprintf ( stdout, " Matrix:%s\n", matrix);
-
- int **mat = read_matrice(matrix);
-
- ffpHitScoreMatrix=vcalloc (nl, sizeof (float*));
- for(i = 0; i < nl; i++)
- ffpHitScoreMatrix[i]=vcalloc (nl-i, sizeof (float));
-
- fprintf (stdout, "Process positions\n", i);
- for(i = 0; i < nl; i++)
- {
- fprintf (stdout, "%d, ", i);
- for(j = i; j < nl; j++)
- {
- if(strm (mode, "id"))
- ffpHitScoreMatrix[i][j-i]=generic_get_seq_sim (aln_column2string(A, i), aln_column2string(A, j), (A->cdna_cache)?A->cdna_cache[0]:NULL, matrix);
- else if(strm (mode, "pairscore"))
- {
- isim_count = itotal_count = 0;
- for (k=0; k< inseq; k++)
- {
- r1=tolower(A->seq_al[k][i]);
- if (is_gap(r1))continue;
- for (l=0; l< inseq; l++)
- {
- r2=tolower(A->seq_al[l][j]);
- if (is_gap (r2))continue;
- s=mat[r2-'A'][r1-'A'];
- s=(s<=0)?0:1;
- isim_count += s;
- itotal_count++;
- }
- }
- r1=(isim_count*100)/itotal_count;
- ffpHitScoreMatrix[i][j-i] = r1;
- }
- else
- aln2hitMat_help();
- }
- }
- fprintf (stdout, "\n");
- output_hit_matrix(hit_matrix_file, ffpHitScoreMatrix, nl);
-
-//Output Hit Score into color html
- output_hit_color_html (A, ffpHitScoreMatrix, nl, hit_html_file);
- vfree(ffpHitScoreMatrix);
- vfree(hit_matrix_file);
- vfree(hit_html_file);
- fprintf ( stdout, "[END] aln to hit matrix\n");
-}
-/*********************************COPYRIGHT NOTICE**********************************/
-/*© Centro de Regulacio Genomica */
-/*and */
-/*Cedric Notredame */
-/*Tue Oct 27 10:12:26 WEST 2009. */
-/*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**********************************/
git://source.jalview.org / jabaws.git / blobdiff