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); }