double *compute_matrix_p ( double *n,int Nseq)
{
/*
reads in a frquency list of various amino acids:
sum freq(aa)=1 (gaps are ignored)
aa[1]=x1
aa[2]=x2
....
Outputs a similar list with frequencies 'Blurred' using a pam250 mt
*/
static int **matrix;
double *R;
int a, b;
double v,min, tot;
if ( !matrix)
{
matrix=read_matrice ( "pam250mt");
}
R=vcalloc ( 26, sizeof (double));
for ( a=0; a<26; a++)
{
if (!is_aa(a+'a'))continue;
if ( n[a]==0)continue;
for ( b=0; b< 26; b++)
{
if (!is_aa(b+'a'))continue;
v=n[a]*(matrix[a][b]);
if ( v>0)
{
R[b]+=v+(10*n[a]);
}
}
}
min=R[0];
for ( min=R[0],a=0; a< 26; a++)min=MIN(min,R[a]);
for ( tot=0, a=0; a< 26; a++) {R[a]-=min;tot+=R[a];}
for ( a=0; a< 26; a++)if ( is_aa(a+'a')){R[a]=R[a]*((float)(100)/(float)tot);}
return R;
}
int get_beta_sub_cost (Alignment *A, int**pos1, int ns1, int*list1, int col1, int**pos2, int ns2, int*list2, int col2, Constraint_list *CL)
{
static int **mat;
int s1, r1, s2, r2;
float score;
if (!mat && CL->matrices_list[1][0])mat=read_matrice (CL->matrices_list[1]);
else if ( !CL->matrices_list[1][0])return UNDEFINED;
s1=A->order[list1[0]][0];
r1=pos1[list1[0]][col1];
s2=A->order[list2[0]][0];
r2=pos1[list2[0]][col2];
if ( r1<0 || r2<0)return 0;
score=mat[(CL->S)->seq[s1][r1-1]-'A'][(CL->S)->seq[s2][r2-1]-'A']*SCORE_K;
return (int)score;
}
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 =(char*) vcalloc(200, sizeof (char));
char *hit_html_file =(char*) 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 = (char*) 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=(float**)vcalloc (nl, sizeof (float*));
for(i = 0; i < nl; i++)
ffpHitScoreMatrix[i]=(float*)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");
}
