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MIN12352
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codeparrot

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#define SAVE_EXONSCORE_ALLOWED_DIFFERENCE 30
typedef enum
{
MERGEABLE_LEFTSIDE_A_BEFORE_B = 0,
MERGEABLE_LEFTSIDE_A_EQUALS_B,
MERGEABLE_LEFTSIDE_A_AFTER_B,
NON_MERGEABLE_LEFTSIDE,
} Leftsidestatus;
typedef enum
{
MERGEABLE_RIGHTSIDE_A_BEFORE_B = 0,
MERGEABLE_RIGHTSIDE_A_EQUALS_B,
MERGEABLE_RIGHTSIDE_A_AFTER_B,
NON_MERGEABLE_RIGHTSIDE,
} Rightsidestatus;
/*
The following function returns the core of an Exonnode.
That is, the node without the pointers to the successors of this node.
The input is the spliced alignment \textit{sa}, and the index <exonindex>
of the exon to be processed.
*/
Exonnode getcoreExonnodefromSA(GthSA *sa, unsigned long exonindex)
{
Exonnode node;
Exonscoreinfo scoreinfo;
/* alignment contains at least one exon */
gt_assert(gth_sa_num_of_exons(sa));
/* number of exons minus 1 equals number of introns */
gt_assert(gth_sa_num_of_exons(sa) - 1 ==
gth_sa_num_of_introns(sa));
/* exonindex is valid */
gt_assert(exonindex < gth_sa_num_of_exons(sa));
node.exonscores = gt_array_new(sizeof (Exonscoreinfo));
node.range.start = gth_sa_get_exon(sa, exonindex)->leftgenomicexonborder;
node.range.end = gth_sa_get_exon(sa, exonindex)->rightgenomicexonborder;
if (exonindex == 0) /* this is the first exon */
node.leftmergeable = true;
else
node.leftmergeable = false;
if (exonindex == gth_sa_num_of_exons(sa) - 1) {
/* this is the last exon */
node.rightmergeable = true;
}
else
node.rightmergeable = false;
/* save successor intron */
if (exonindex < gth_sa_num_of_exons(sa) - 1) {
/* exon has successor intron */
node.successorintron = gth_sa_get_intron(sa, exonindex);
}
else {
/* exon has no successor intron */
node.successorintron = NULL;
}
/* save exonscore */
scoreinfo.exonscore = gth_sa_get_exon(sa, exonindex)->exonscore;
scoreinfo.lengthofscoringexon = node.range.end - node.range.start + 1;
gt_array_add(node.exonscores, scoreinfo);
return node;
}
static void freecoreExonnode(Exonnode *node)
{
if (!node) return;
gt_array_delete(node->exonscores);
}
static Leftsidestatus getleftsidestatus(Exonnode *nodeA, Exonnode *nodeB)
{
/* -------...
]-----... */
if (nodeA->range.start < nodeB->range.start && nodeB->leftmergeable)
return MERGEABLE_LEFTSIDE_A_BEFORE_B;
/* -------...
-------... */
if (nodeA->range.start == nodeB->range.start)
return MERGEABLE_LEFTSIDE_A_EQUALS_B;
/* ]-----...
-------... */
if (nodeA->range.start > nodeB->range.start && nodeA->leftmergeable)
return MERGEABLE_LEFTSIDE_A_AFTER_B;
return NON_MERGEABLE_LEFTSIDE;
}