957e6639419c3faf3ca76d891903ea3023681555
kent
Tue Jun 28 18:02:27 2022 -0700
Making 'View details of parts of alignment within browser window.' link on bigPsl and psl work better when query sequence is big.
diff --git src/hg/hgc/hgc.c src/hg/hgc/hgc.c
index 0c22794..6dc9a51 100644
--- src/hg/hgc/hgc.c
+++ src/hg/hgc/hgc.c
@@ -6435,31 +6435,30 @@
/* Print list of mRNA alignments with special "in window" alignment function. */
{
if (pslList == NULL || tableName == NULL)
return;
printAlignmentsSimple(pslList, startFirst, hgcCommand, tableName, itemIn);
struct psl *psl = pslList;
for (psl = pslList; psl != NULL; psl = psl->next)
{
if ( pslTrimToTargetRange(psl, winStart, winEnd) != NULL
&&
!startsWith("xeno", tableName)
&& !(startsWith("user", tableName) && pslIsProtein(psl))
&& psl->tStart == startFirst
&& sameString(psl->tName, seqName)
- && psl->qSize <= MAX_DISPLAY_QUERY_SEQ_SIZE
)
{
char otherString[512];
safef(otherString, sizeof(otherString), "%d&aliTable=%s",
psl->tStart, tableName);
hgcAnchorSomewhere(hgcCommandInWindow, itemIn, otherString, psl->tName);
printf("
View details of parts of alignment within browser window.
\n");
}
}
}
void printAlignments(struct psl *pslList, int startFirst, char *hgcCommand,
char *tableName, char *itemIn)
/* Print list of mRNA alignments. */
{
@@ -7530,31 +7529,31 @@
fprintf(f, "Alignment of %s and %s:%d-%d
\n",
psl->qName, psl->tName, psl->tStart+1, psl->tEnd);
else
fprintf(f, "Alignment of %s and %s:%d-%d
\n",
qName, psl->tName, psl->tStart+1, psl->tEnd);
fputs("Click on links in the frame to the left to navigate through "
"the alignment.\n", f);
blockCount = pslShowAlignment(psl, qType == gftProt,
qName, qSeq, qStart, qEnd,
tName, tSeq, tStart, tEnd, f);
freeDnaSeq(&tSeq);
return blockCount;
}
-struct ffAli *pslToFfAliAndSequence(struct psl *psl, struct dnaSeq *qSeq,
+static struct ffAli *pslToFfAliAndSequence(struct psl *psl, struct dnaSeq *qSeq,
boolean *retIsRc, struct dnaSeq **retSeq,
int *retTStart)
/* Given psl, dig up target sequence and convert to ffAli.
* Note: if strand is -, this does a pslRc to psl! */
{
int tStart, tEnd, tRcAdjustedStart;
struct dnaSeq *dnaSeq;
tStart = psl->tStart - 100;
if (tStart < 0) tStart = 0;
if (retTStart)
*retTStart = tStart;
tEnd = psl->tEnd + 100;
if (tEnd > psl->tSize) tEnd = psl->tSize;
@@ -7569,75 +7568,101 @@
if (psl->strand[1] == '-')
pslRc(psl);
if (psl->strand[0] == '-')
{
if (retIsRc)
*retIsRc = TRUE;
reverseComplement(dnaSeq->dna, dnaSeq->size);
pslRc(psl);
tRcAdjustedStart = psl->tSize - tEnd;
}
return pslToFfAli(psl, qSeq, dnaSeq, tRcAdjustedStart);
}
+static void ffStartEndQ(char *qDna, struct ffAli *ff, int *retStartQ, int *retEndQ)
+/* Return query start and end */
+{
+if (ff == NULL)
+ *retStartQ = *retEndQ = 0;
+else
+ {
+ struct ffAli *right = ffRightmost(ff);
+ *retStartQ = ff->nStart - qDna;
+ *retEndQ = right->nEnd - qDna;
+ }
+}
+
int showPartialDnaAlignment(struct psl *wholePsl,
struct dnaSeq *rnaSeq, FILE *body,
int cdsS, int cdsE, boolean restrictToWindow)
/* Show (part of) alignment for accession. wholePsl is the whole alignment;
* if restrictToWindow then display the part of the alignment in the current
* browser window. */
{
+/* Do a consistency check between rnaSeq and psl*/
+int rnaSize = rnaSeq->size;
+if (rnaSize != wholePsl->qSize)
+ {
+ fprintf(body, "Cannot display alignment. Size of rna %s is %d has changed since alignment was performed when it was %d.\n",
+ wholePsl->qName, rnaSize, wholePsl->qSize);
+ return 0;
+ }
+
+/* Possibly just do smaller subset that is within window. */
+struct psl *psl = wholePsl;
+if (restrictToWindow)
+ {
+ psl = pslTrimToTargetRange(wholePsl, winStart, winEnd);
+ if (psl == NULL)
+ fprintf(body, "
No alignment of %s within browser window.", wholePsl->qName);
+ }
+
struct dnaSeq *dnaSeq;
int wholeTStart;
-int partTStart = wholePsl->tStart, partTEnd = wholePsl->tEnd;
-DNA *rna;
-int rnaSize;
+int partTStart = psl->tStart, partTEnd = psl->tEnd;
+DNA *rna = rnaSeq->dna;
boolean isRc = FALSE;
-struct ffAli *wholeFfAli;
+struct ffAli *ffAli;
int blockCount;
-/* Get RNA sequence and convert psl to ffAli. */
-rna = rnaSeq->dna;
-rnaSize = rnaSeq->size;
-
-/* Don't forget -- this may change wholePsl! */
-wholeFfAli = pslToFfAliAndSequence(wholePsl, rnaSeq, &isRc, &dnaSeq,
+/* Don't forget -- this may change psl if on reverse strand! */
+ffAli = pslToFfAliAndSequence(psl, rnaSeq, &isRc, &dnaSeq,
&wholeTStart);
+int rnaStart = 0;
+int rnaEnd = rnaSize;
+
if (restrictToWindow)
{
- partTStart = max(wholePsl->tStart, winStart);
- partTEnd = min(wholePsl->tEnd, winEnd);
+ /* Find start/end in ffAli, which is clipped to target from PSL and maybe RC'd */
+ ffStartEndQ(rna, ffAli, &rnaStart, &rnaEnd);
+
+ /* Add 100 bases either side if possible */
+ if (rnaStart >= 100) rnaStart -= 100;
+ if (rnaEnd + 100 <= rnaSize) rnaEnd += 100;
}
/* Write body heading info. */
fprintf(body, "
Alignment of %s and %s:%d-%d
\n",
- wholePsl->qName, wholePsl->tName, partTStart+1, partTEnd);
+ psl->qName, psl->tName, partTStart+1, partTEnd);
fprintf(body, "Click on links in the frame to the left to navigate through "
"the alignment.\n");
-if (rnaSize != wholePsl->qSize)
- {
- fprintf(body, "Cannot display alignment. Size of rna %s is %d has changed since alignment was performed when it was %d.\n",
- wholePsl->qName, rnaSize, wholePsl->qSize);
- return 0;
- }
-
-blockCount = ffShAliPart(body, wholeFfAli, wholePsl->qName,
- rna, rnaSize, 0,
+blockCount = ffShAliPart(body, ffAli, wholePsl->qName,
+ rna + rnaStart, rnaEnd - rnaStart, rnaStart,
dnaSeq->name, dnaSeq->dna, dnaSeq->size,
wholeTStart, 8, FALSE, isRc,
FALSE, TRUE, TRUE, TRUE, TRUE,
cdsS, cdsE, partTStart, partTEnd);
return blockCount;
}
void showSomeAlignment(struct psl *psl, bioSeq *oSeq,
enum gfType qType, int qStart, int qEnd,
char *qName, int cdsS, int cdsE)
/* Display protein or DNA alignment in a frame. */
{
int blockCount, i;
struct tempName indexTn, bodyTn;
FILE *index, *body;