int main() {
int evalcost;
char *align = "R7I2R2D1R3I1R3";
char *seq1 = "acgtagatatatagat";
char *seq2 = "agaaagaggtaagaggga";
alignment alg = alignment_new(seq1, seq2, align);
alignment_show(alg);
evalcost = alignment_evalcost(alg);
printf("\tCosts: %d\n\n", evalcost);
printf("\tadding one deletion...\n");
alignment_add_operation(&alg, 1, 'D');
alignment_show(alg);
printf("\tadding one insertion...\n");
alignment_add_operation(&alg, 1, 'I');
alignment_show(alg);
printf("\tadding one replacement...\n");
alignment_add_operation(&alg, 1, 'R');
alignment_show(alg);
return(EXIT_SUCCESS);
}
int main(int argc, char* argv[])
{
// check argument count
if (argc < 5)
{
printf("usage: %s seq1 seq2 scorematrix indelcosts\n!", argv[0]);
return 1;
}
// read sequences and m (cost function) from command line
char* s1 = argv[1];
int len1 = strlen(s1);
char* s2 = argv[2];
int len2 = strlen(s2);
char* filename = argv[3];
int indel;
sscanf(argv[4], "%d", &indel);
printf("Sequenz 1: %s\n", s1);
printf("Sequenz 2: %s\n", s2);
scorematrix* sm = read_scorematrix(filename,indel);
if (sm == NULL)
return 1;
// reserve memory for dynamic programing table
alignentry*** table = initializeDP (len1+1, len2+1);
// calculate costs for optimal alignment of s1 and s2
int imax,jmax;
int score = align (table, s1, len1, s2, len2, sm, &imax, &jmax);
// print dynamic programing table
show_DPtable(s1,len1,s2,len2,table);
printf("Alignment: %d\n", score);
alignment* align = alignment_new(s1,len1,s2,len2);
traceback(table,align,imax,jmax);
if (alignment_show(align))
{
puts("FEHLER: inkonsistentes Alignment!");
}
alignment_delete(align);
deleteDP (table, len1+1, len2+1);
return 0;
}
int main(int argc, char * ARGV[])
{
if (argc < 5 || argc%2 == 0)
{
printf("FEHLER: falsche Anzahl Argumente!\n");
return 1;
}
char * s1 = ARGV[1];
int len1 = strlen(s1);
char * s2 = ARGV[2];
int len2 = strlen(s2);
int ops = 0;
int i;
alignment *al = alignment_new (s1, len1, s2, len2);
for (i = 3; i < argc; i+=2)
{
ops |= alignment_add_operations (al, ARGV[i][0], atoi(ARGV[i+1]));
}
if (ops)
{
printf ("Fehler beim Einfuegen einer Operation (Ueberlauf)!\n");
}
int show = alignment_show (al);
if (show)
{
printf ("Fehler beim Ausgeben des Alignments (Alignment inkonsistent)!\n");
}
printf ("Länge des Alignments (Länge der Multiedit-Liste): %d (%d)\n", \
al->length, al->editlength);
int costs = alignment_evalcost (al, unit_cost);
printf ("Kosten des Alignments: %d\n", costs);
alignment_delete (al);
al = NULL;
return 0;
}
int main(int argc, char* argv[])
{
// check argument count
if (argc < 3)
{
printf("usage: %s seq1 seq2\n!", argv[0]);
return 0;
}
int costs;
alignment* a = optimal_alignment(argv[1], argv[2], unity, &costs);
printf("Alignment: %d\n", costs);
if (alignment_show(a))
{
puts("FEHLER: inkonsistentes Alignment!");
}
alignment_delete(a);
return 0;
}
int main(int argc, char* argv[])
{
// check argument count
if (argc < 4)
{
printf("FEHLER: zu wenig Argumente angegeben\n!");
return 1;
}
// read sequences and m (cost function) from command line
char* s1 = argv[1];
int len1 = strlen(s1);
char* s2 = argv[2];
int len2 = strlen(s2);
int m = atoi(argv[3]);
// determine function-pointer for cost function
int (*costFunc)(char,char);
if (m == 0)
costFunc = unity;
else if (m == 1)
costFunc = hamming;
else
costFunc = otherCosts;
printf("Sequenz 1: %s\n", s1);
printf("Sequenz 2: %s\n", s2);
// reserve memory for dynamic programing table
alignentry*** table = initializeDP (len1+1, len2+1);
// calculate costs for optimal alignment of s1 and s2
int costs = align (table, s1, len1, s2, len2, costFunc);
// print dynamic programing table
printf("------------------------------------------------------\n");
int i,j;
int c;
for (i = -1; i <= len1; i++)
{
for (j = -1; j <= len2; j++)
{
if (i == -1 && j != -1)
{
if (j == 0)
printf("%3c ", '-');
else
printf("%3c ", s2[j-1]);
}
else if (j == -1 && i != -1)
{
if (i == 0)
printf("%3c ", '-');
else
printf("%3c ", s1[i-1]);
}
else if (i == -1 && j == -1)
{
printf("%3c ", ' ');
}
else
{
c = table[i][j]->value;
if (c == INF)
printf("%3c ", 'I');
else
printf("%3d ", c);
}
}
printf("\n");
}
printf("------------------------------------------------------\n");
printf("Alignment: %d\n", costs);
alignment* align = alignment_new(s1,len1,s2,len2);
traceback(table,align,len1,len2);
if (alignment_show(align))
{
puts("FEHLER: inkonsistentes Alignment!");
}
alignment_delete(align);
deleteDP (table, len1+1, len2+1);
return 0;
}
