// complement of sequence denoted 0, 1, 2, 3
char *compl_int_seq (char *seq, int len)
{
char *bal_seq = NULL, c, bal_c;
int i, index;
if (len < 1)
{
return bal_seq;
}
bal_seq = (char *) ckalloc (len * sizeof (char));
index = 0;
for (i = len - 1; i >= 0; i--)
{
c = seq[i];
if (c < 4)
{
bal_c = int_comp (c);
} //3-c;
else
{
bal_c = c;
}
bal_seq[index++] = bal_c;
}
return bal_seq;
}
// complement of sequence denoted 0, 1, 2, 3
void reverseComplementSeq (char *seq, int len, char *bal_seq)
{
int i, index = 0;
if (len < 1)
{
return;
}
for (i = len - 1; i >= 0; i--)
{
//mao 2011 10 8
// if(seq[i] >= 4)
// bal_seq[index++]=seq[i];
// else
bal_seq[index++] = int_comp (seq[i]);
}
return;
}
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;
}
//search linear structure starting with the root of a tree
static int startEdgeFromNode ( kmer_t * node1, FILE * fp )
{
int node_c, palindrome;
unsigned char flag;
KMER_PT * ite_pt, *temp_pt;
Kmer word1, bal_word1;
char ch1;
if ( node1->linear || node1->deleted )
{ return 0; }
// ignore floating loop
word1 = node1->seq;
bal_word1 = reverseComplement ( word1, overlaplen );
// linear structure
for ( ch1 = 0; ch1 < 4; ch1++ ) // for every node on outgoing list
{
flag = get_kmer_right_cov ( *node1, ch1 );
if ( !flag )
{ continue; }
emptyStack ( nodeStack );
temp_pt = ( KMER_PT * ) stackPush ( nodeStack );
temp_pt->node = node1;
temp_pt->isSmaller = 1;
temp_pt->kmer = word1;
stringBeads ( temp_pt, ch1, &node_c );
//printf("%d nodes\n",node_c);
if ( node_c < 2 )
{ printf ( "%d nodes in this line!!!!!!!!!!!\n", node_c ); }
else
{
//make a reverse complement node list
stackBackup ( nodeStack );
emptyStack ( bal_nodeStack );
while ( ( ite_pt = ( KMER_PT * ) stackPop ( nodeStack ) ) != NULL )
{
temp_pt = ( KMER_PT * ) stackPush ( bal_nodeStack );
temp_pt->kmer = reverseComplement ( ite_pt->kmer, overlaplen );
}
stackRecover ( nodeStack );
palindrome = check_iden_kmerList ( nodeStack, bal_nodeStack );
stackRecover ( nodeStack );
if ( palindrome )
{
merge_linearV2 ( 0, nodeStack, node_c, fp );
}
else
{ merge_linearV2 ( 1, nodeStack, node_c, fp ); }
}
} //every possible outgoing edges
for ( ch1 = 0; ch1 < 4; ch1++ ) // for every node on incoming list
{
flag = get_kmer_left_cov ( *node1, ch1 );
if ( !flag )
{ continue; }
emptyStack ( nodeStack );
temp_pt = ( KMER_PT * ) stackPush ( nodeStack );
temp_pt->node = node1;
temp_pt->isSmaller = 0;
temp_pt->kmer = bal_word1;
stringBeads ( temp_pt, int_comp ( ch1 ), &node_c );
if ( node_c < 2 )
{ printf ( "%d nodes in this line!!!!!!!!!!!\n", node_c ); }
else
{
//make a reverse complement node list
stackBackup ( nodeStack );
emptyStack ( bal_nodeStack );
while ( ( ite_pt = ( KMER_PT * ) stackPop ( nodeStack ) ) != NULL )
{
temp_pt = ( KMER_PT * ) stackPush ( bal_nodeStack );
temp_pt->kmer = reverseComplement ( ite_pt->kmer, overlaplen );
}
stackRecover ( nodeStack );
palindrome = check_iden_kmerList ( nodeStack, bal_nodeStack );
stackRecover ( nodeStack );
if ( palindrome )
{
merge_linearV2 ( 0, nodeStack, node_c, fp );
//printf("edge is palindrome with length %d\n",temp_edge.length);
}
else
{ merge_linearV2 ( 1, nodeStack, node_c, fp ); }
}
} //every possible incoming edges
return 0;
}
