--- /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 */
+/*Fri Feb 18 08:27:45 CET 2011 - Revision 596. */
+/*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