static void sim4QueryOut(struct gfOutput *out, FILE *f)
/* Do sim4-like output - at end of processing query. */
{
struct axtData *aod = out->data;
struct axtBundle *gab;
for (gab = aod->bundleList; gab != NULL; gab = gab->next)
{
struct axt *axt = gab->axtList;
fprintf(f, "\n");
fprintf(f, "seq1 = %s, %d bp\n", axt->qName, gab->qSize);
fprintf(f, "seq2 = %s, %d bp\n", axt->tName, gab->tSize);
fprintf(f, "\n");
if (axt->qStrand == '-')
fprintf(f, "(complement)\n");
for (axt = gab->axtList; axt != NULL; axt = axt->next)
{
fprintf(f, "%d-%d ", axt->qStart+1, axt->qEnd);
fprintf(f, "(%d-%d) ", axt->tStart+1, axt->tEnd);
fprintf(f, "%1.0f%% ", 100.0 * axtIdRatio(axt));
if (axt->qStrand == '-')
fprintf(f, "<-\n");
else
fprintf(f, "->\n");
}
}
axtBundleFreeList(&aod->bundleList);
}
static void sim4QueryOut(struct gfOutput *out, FILE *f)
/* Do sim4-like output - at end of processing query. */
{
struct axtData *aod = out->data;
struct axtBundle *gab;
slReverse(&aod->bundleList);
for (gab = aod->bundleList; gab != NULL; gab = gab->next)
{
struct axt *axt = gab->axtList;
// check minIdentity of the entire alignment
int goodPpt = 1000 * axtListRatio(axt);
if (!(goodPpt >= out->minGood))
continue;
fprintf(f, "\n");
fprintf(f, "seq1 = %s, %d bp\n", axt->qName, gab->qSize);
fprintf(f, "seq2 = %s, %d bp\n", axt->tName, gab->tSize);
fprintf(f, "\n");
if (axt->qStrand == '-')
fprintf(f, "(complement)\n");
for (; axt != NULL; axt = axt->next)
{
fprintf(f, "%d-%d ", axt->qStart+1, axt->qEnd);
fprintf(f, "(%d-%d) ", axt->tStart+1, axt->tEnd);
fprintf(f, "%1.0f%% ", 100.0 * axtIdRatio(axt));
if (axt->qStrand == '-')
fprintf(f, "<-\n");
else
fprintf(f, "->\n");
}
}
axtBundleFreeList(&aod->bundleList);
}
static void blastQueryOut(struct gfOutput *out, FILE *f)
/* Output blast on query. */
{
struct axtData *aod = out->data;
axtBlastOut(aod->bundleList, out->queryIx, out->qIsProt, f,
aod->databaseName, aod->databaseSeqCount, aod->databaseLetters,
aod->blastType, "blat", aod->minIdentity);
axtBundleFreeList(&aod->bundleList);
}
static void axtQueryOut(struct gfOutput *out, FILE *f)
/* Do axt oriented output - at end of processing query. */
{
struct axtData *aod = out->data;
struct axtBundle *gab;
for (gab = aod->bundleList; gab != NULL; gab = gab->next)
{
struct axt *axt;
for (axt = gab->axtList; axt != NULL; axt = axt->next)
axtWrite(axt, f);
}
axtBundleFreeList(&aod->bundleList);
}
static void mafQueryOut(struct gfOutput *out, FILE *f)
/* Do axt oriented output - at end of processing query. */
{
struct axtData *aod = out->data;
struct axtBundle *gab;
for (gab = aod->bundleList; gab != NULL; gab = gab->next)
{
struct axt *axt;
for (axt = gab->axtList; axt != NULL; axt = axt->next)
{
struct mafAli temp;
mafFromAxtTemp(axt, gab->tSize, gab->qSize, &temp);
mafWrite(f, &temp);
}
}
axtBundleFreeList(&aod->bundleList);
}
