static int cmp_seq ( const void * a, const void * b )
{
EDGE * A, *B;
A = ( EDGE * ) a;
B = ( EDGE * ) b;
if ( KmerLarger ( vt_array[A->from_vt].kmer, vt_array[B->from_vt].kmer ) )
{
return 1;
}
else if ( KmerSmaller ( vt_array[A->from_vt].kmer , vt_array[B->from_vt].kmer ) )
{
return -1;
}
else
{
if ( A->seq[0] > B->seq[0] )
{
return 1;
}
else if ( A->seq[0] == B->seq[0] )
{
int i = 0;
for ( i = 1; i < A->length && i < B->length; i++ )
{
if ( getCharInTightString ( A->seq, i ) > getCharInTightString ( B->seq, i ) )
{ return 1; }
else if ( getCharInTightString ( A->seq, i ) < getCharInTightString ( B->seq, i ) )
{ return -1; }
}
if ( i == A->length && i < B->length )
{ return -1; }
else if ( i < A->length && i == B->length )
{ return 1; }
else
{
printKmerSeq ( stderr , vt_array[A->from_vt].kmer );
fprintf ( stderr , "\n" );
printKmerSeq ( stderr , vt_array[B->from_vt].kmer );
fprintf ( stderr , "\n" );
for ( i = 0; i < A->length; i++ )
{
printf( "%c", int2base ( ( int ) getCharInTightString ( A->seq, i ) ) );
}
printf( "\n" );
for ( i = 0; i < B->length; i++ )
{
printf( "%c", int2base ( ( int ) getCharInTightString ( B->seq, i ) ) );
}
printf( "\n" );
printf( "cmp_seq:\terr\n" );
exit ( 0 );
return 0;
}
}
else
{
return -1;
}
}
};
static void stringBeads ( KMER_PT * firstBead, char nextch, int * node_c )
{
boolean smaller, found;
Kmer tempKmer, bal_word;
Kmer word = firstBead->kmer;
ubyte8 hash_ban;
kmer_t * outgoing_node;
int nodeCounter = 1, setPicker;
char ch;
unsigned char flag;
KMER_PT * temp_pt, *prev_pt = firstBead;
word = prev_pt->kmer;
nodeCounter = 1;
word = nextKmer ( word, nextch );
bal_word = reverseComplement ( word, overlaplen );
if ( KmerLarger ( word, bal_word ) )
{
tempKmer = bal_word;
bal_word = word;
word = tempKmer;
smaller = 0;
}
else
{ smaller = 1; }
hash_ban = hash_kmer ( word );
setPicker = hash_ban % thrd_num;
found = search_kmerset ( KmerSets[setPicker], word, &outgoing_node );
while ( found && ( outgoing_node->linear ) ) // for every node in this line
{
nodeCounter++;
temp_pt = ( KMER_PT * ) stackPush ( nodeStack );
temp_pt->node = outgoing_node;
temp_pt->isSmaller = smaller;
if ( smaller )
{ temp_pt->kmer = word; }
else
{ temp_pt->kmer = bal_word; }
prev_pt = temp_pt;
if ( smaller )
{
for ( ch = 0; ch < 4; ch++ )
{
flag = get_kmer_right_cov ( *outgoing_node, ch );
if ( flag )
{ break; }
}
word = nextKmer ( prev_pt->kmer, ch );
bal_word = reverseComplement ( word, overlaplen );
if ( KmerLarger ( word, bal_word ) )
{
tempKmer = bal_word;
bal_word = word;
word = tempKmer;
smaller = 0;
}
else
{ smaller = 1; }
hash_ban = hash_kmer ( word );
setPicker = hash_ban % thrd_num;
found = search_kmerset ( KmerSets[setPicker], word, &outgoing_node );
}
else
{
for ( ch = 0; ch < 4; ch++ )
{
flag = get_kmer_left_cov ( *outgoing_node, ch );
if ( flag )
{ break; }
}
word = nextKmer ( prev_pt->kmer, int_comp ( ch ) );
bal_word = reverseComplement ( word, overlaplen );
if ( KmerLarger ( word, bal_word ) )
{
tempKmer = bal_word;
bal_word = word;
word = tempKmer;
smaller = 0;
}
else
{ smaller = 1; }
hash_ban = hash_kmer ( word );
setPicker = hash_ban % thrd_num;
found = search_kmerset ( KmerSets[setPicker], word, &outgoing_node );
}
}
if ( outgoing_node ) //this is always true
{
nodeCounter++;
temp_pt = ( KMER_PT * ) stackPush ( nodeStack );
temp_pt->node = outgoing_node;
temp_pt->isSmaller = smaller;
if ( smaller )
{ temp_pt->kmer = word; }
else
{ temp_pt->kmer = bal_word; }
}
*node_c = nodeCounter;
}
void swapedge()
{
unsigned int i;
ARC * arc, *bal_arc, *temp_arc;
int count_swap = 0, count_equal = 0;
for ( i = 1; i <= num_ed; ++i )
{
if ( edge_array[i].deleted || EdSameAsTwin ( i ) )
{ continue; }
if ( EdSmallerThanTwin ( i ) )
{
if ( KmerLarger ( vt_array[edge_array[i].from_vt].kmer, vt_array[edge_array[i + 1].from_vt].kmer ) )
{
count_swap++;
copyEdge ( i, num_ed + 1 + 1 );
copyEdge ( i + 1, num_ed + 1 );
copyEdge ( num_ed + 1, i );
copyEdge ( num_ed + 1 + 1, i + 1 );
edge_array[i].bal_edge = 2;
edge_array[i + 1].bal_edge = 0;
//take care of the arcs
arc = edge_array[i].arcs;
while ( arc )
{
arc->bal_arc->to_ed = i + 1;
arc = arc->next;
}
arc = edge_array[i + 1].arcs;
while ( arc )
{
arc->bal_arc->to_ed = i;
arc = arc->next;
}
}
else if ( KmerEqual ( vt_array[edge_array[i].from_vt].kmer, vt_array[edge_array[i + 1].from_vt].kmer ) )
{
int temp = EdgeEqual ( i, i + 1 );
if ( temp == 0 )
{
count_equal++;
edge_array[i].bal_edge = 1;
delete1Edge ( i + 1 );
//take care of the arcs
arc = edge_array[i].arcs;
while ( arc )
{
arc->bal_arc->to_ed = i;
arc = arc->next;
}
bal_arc = edge_array[i + 1].arcs;
edge_array[i + 1].arcs = NULL;
while ( bal_arc )
{
temp_arc = bal_arc;
bal_arc = bal_arc->next;
if ( edge_array[i].arcs )
{ edge_array[i].arcs->prev = temp_arc; }
temp_arc->next = edge_array[i].arcs;
edge_array[i].arcs = temp_arc;
}
}
else if ( temp > 0 )
{
count_swap++;
copyEdge ( i, num_ed + 1 + 1 );
copyEdge ( i + 1, num_ed + 1 );
copyEdge ( num_ed + 1, i );
copyEdge ( num_ed + 1 + 1, i + 1 );
edge_array[i].bal_edge = 2;
edge_array[i + 1].bal_edge = 0;
//take care of the arcs
arc = edge_array[i].arcs;
while ( arc )
{
arc->bal_arc->to_ed = i + 1;
arc = arc->next;
}
arc = edge_array[i + 1].arcs;
while ( arc )
{
arc->bal_arc->to_ed = i;
arc = arc->next;
}
}
}
++i;
}
else
{
delete1Edge ( i );
printf( "Warning : Front edge %d is larger than %d.\n", i, i + 1 );
}
}
printf( "%d none-palindrome edge(s) swapped, %d palindrome edge(s) processed.\n", count_swap, count_equal );
};
