static void printGenomicAnchor(char *table, char *itemName,
char *chrom, int start, int end)
/* Print genomic sequence anchor. */
{
hPrintf("<A HREF=\"%s?%s", hgcName(),
cartSidUrlString(cart));
hPrintf("&g=htcGeneInGenome&i=%s", itemName);
hPrintf("&c=%s&l=%d&r=%d", chrom, start, end);
hPrintf("&o=%s&table=%s", table, table);
hPrintf("\" class=\"toc\">");
}
void showAliPlaces(char *pslName, char *faName, char *database,
enum gfType qType, enum gfType tType,
char *organism, boolean feelingLucky)
/* Show all the places that align. */
{
struct lineFile *lf = pslFileOpen(pslName);
struct psl *pslList = NULL, *psl;
char *browserUrl = hgTracksName();
char *hgcUrl = hgcName();
char uiState[64];
char *vis;
char unhideTrack[64];
char *sort = cartUsualString(cart, "sort", sortList[0]);
char *output = cartUsualString(cart, "output", outputList[0]);
boolean pslOut = startsWith("psl", output);
boolean isStraightNuc = (qType == gftRna || qType == gftDna);
int minThreshold = (isStraightNuc ? minMatchShown : 0);
sprintf(uiState, "%s=%s", cartSessionVarName(), cartSessionId(cart));
/* If user has hidden BLAT track, add a setting that will unhide the
track if user clicks on a browser link. */
vis = cartOptionalString(cart, "hgUserPsl");
if (vis != NULL && sameString(vis, "hide"))
snprintf(unhideTrack, sizeof(unhideTrack), "&hgUserPsl=dense");
else
unhideTrack[0] = 0;
while ((psl = pslNext(lf)) != NULL)
{
if (psl->match >= minThreshold)
slAddHead(&pslList, psl);
}
lineFileClose(&lf);
if (pslList == NULL)
{
puts("<table><tr><td><hr>Sorry, no matches found<hr><td></tr></table>");
return;
}
if (sameString(sort, "query,start"))
{
slSort(&pslList, pslCmpQuery);
}
else if (sameString(sort, "query,score"))
{
slSort(&pslList, pslCmpQueryScore);
}
else if (sameString(sort, "score"))
{
slSort(&pslList, pslCmpScore);
}
else if (sameString(sort, "chrom,start"))
{
slSort(&pslList, pslCmpTargetStart);
}
else if (sameString(sort, "chrom,score"))
{
slSort(&pslList, pslCmpTargetScore);
}
else
{
slSort(&pslList, pslCmpQueryScore);
}
if(feelingLucky)
{
/* If we found something jump browser to there. */
if(slCount(pslList) > 0)
printLuckyRedirect(browserUrl, pslList, database, pslName, faName, uiState, unhideTrack);
/* Otherwise call ourselves again not feeling lucky to print empty
results. */
else
{
cartWebStart(cart, database, "%s BLAT Results", trackHubSkipHubName(organism));
showAliPlaces(pslName, faName, database, qType, tType, organism, FALSE);
cartWebEnd();
}
}
else if (pslOut)
{
printf("<TT><PRE>");
if (!sameString(output, "psl no header"))
pslxWriteHead(stdout, qType, tType);
for (psl = pslList; psl != NULL; psl = psl->next)
pslTabOut(psl, stdout);
printf("</PRE></TT>");
}
else
{
printf("<H2>BLAT Search Results</H2>");
printf("<TT><PRE>");
printf(" ACTIONS QUERY SCORE START END QSIZE IDENTITY CHRO STRAND START END SPAN\n");
printf("---------------------------------------------------------------------------------------------------\n");
for (psl = pslList; psl != NULL; psl = psl->next)
{
printf("<A HREF=\"%s?position=%s:%d-%d&db=%s&ss=%s+%s&%s%s\">",
browserUrl, psl->tName, psl->tStart + 1, psl->tEnd, database,
pslName, faName, uiState, unhideTrack);
printf("browser</A> ");
printf("<A HREF=\"%s?o=%d&g=htcUserAli&i=%s+%s+%s&c=%s&l=%d&r=%d&db=%s&%s\">",
hgcUrl, psl->tStart, pslName, cgiEncode(faName), psl->qName, psl->tName,
psl->tStart, psl->tEnd, database, uiState);
printf("details</A> ");
printf("%-14s %5d %5d %5d %5d %5.1f%% %4s %2s %9d %9d %6d\n",
psl->qName, pslScore(psl), psl->qStart+1, psl->qEnd, psl->qSize,
100.0 - pslCalcMilliBad(psl, TRUE) * 0.1,
skipChr(psl->tName), psl->strand, psl->tStart+1, psl->tEnd,
psl->tEnd - psl->tStart);
}
printf("</PRE></TT>");
}
pslFreeList(&pslList);
}
void mafPrettyOut(FILE *f, struct mafAli *maf, int lineSize,
boolean onlyDiff, int blockNo)
{
int ii, ch;
int srcChars = 0;
struct mafComp *mc;
int lineStart, lineEnd;
char *summaryLine = needMem(lineSize+1);
char *referenceText;
int startChars, sizeChars, srcSizeChars;
boolean haveInserts = FALSE;
struct mafComp *masterMc = maf->components;
startChars = sizeChars = srcSizeChars = 0;
for (mc = maf->components; mc != NULL; mc = mc->next)
{
/* Figure out length of source (species) field. */
/*if (mc->size != 0)*/
{
char dbOnly[128];
int len;
char *org;
memset(dbOnly, 0, sizeof(dbOnly));
safef(dbOnly, sizeof(dbOnly), "%s", mc->src);
chopPrefix(dbOnly);
if ((org = hOrganism(dbOnly)) == NULL)
len = strlen(dbOnly);
else
len = strlen(org);
if (srcChars < len)
srcChars = len;
len = digitsBaseTen(mc->start);
if (startChars < len)
startChars = len;
len = digitsBaseTen(mc->size);
if (sizeChars < len)
sizeChars = len;
len = digitsBaseTen(mc->srcSize);
if (srcSizeChars < len)
srcSizeChars = len;
if (mc->text && (mc->rightStatus == MAF_INSERT_STATUS) && (masterMc->start + masterMc->size < winEnd))
haveInserts = TRUE;
#ifdef REVERSESTRAND
/* complement bases if hgTracks is on reverse strand */
if (mc->size && cartCgiUsualBoolean(cart, COMPLEMENT_BASES_VAR, FALSE))
complement(mc->text, maf->textSize);
#endif
}
}
/* first sequence in the alignment */
referenceText = maf->components->text;
for (lineStart = 0; lineStart < maf->textSize; lineStart = lineEnd)
{
int size;
lineEnd = lineStart + lineSize;
if (lineEnd >= maf->textSize)
lineEnd = maf->textSize;
size = lineEnd - lineStart;
initSummaryLine(summaryLine, size, '*');
for (mc = maf->components; mc != NULL; mc = mc->next)
{
char dbOnly[128], *chrom;
int s = mc->start;
int e = s + mc->size;
char *org;
char *revComp = "";
char strand = mc->strand;
struct dyString *dy = newDyString(512);
#ifdef REVERSESTRAND
if (cartCgiUsualBoolean(cart, COMPLEMENT_BASES_VAR, FALSE))
strand = (strand == '+') ? '-' : '+';
#endif
if (strand == '-') revComp = "&hgSeq.revComp=on";
dyStringClear(dy);
safef(dbOnly, sizeof(dbOnly), "%s", mc->src);
chrom = chopPrefix(dbOnly);
if ((org = hOrganism(dbOnly)) == NULL)
org = dbOnly;
if (mc->strand == '-')
reverseIntRange(&s, &e, mc->srcSize);
if (mc->text != NULL)
{
if (lineStart == 0)
{
if (hDbIsActive(dbOnly))
{
dyStringPrintf(dy, "%s Browser %s:%d-%d %c %*dbps",hOrganism(dbOnly),chrom, s+1, e, mc->strand,sizeChars, mc->size);
linkToOtherBrowserTitle(dbOnly, chrom, s, e, dy->string);
dyStringClear(dy);
fprintf(f, "B</A> ");
}
else
fprintf(f, " ");
if (hDbExists(dbOnly))
{
dyStringPrintf(dy, "Get %s DNA %s:%d-%d %c %*dbps",hOrganism(dbOnly),chrom, s+1, e, mc->strand,sizeChars, mc->size);
printf("<A TITLE=\"%s\" TARGET=\"_blank\" HREF=\"%s?o=%d&g=getDna&i=%s&c=%s&l=%d&r=%d&db=%s%s\">D</A> ", dy->string,hgcName(),
s, cgiEncode(chrom),
chrom, s, e, dbOnly, revComp);
}
else
fprintf(f, " ");
}
else
{
fprintf(f, " ");
}
dyStringClear(dy);
dyStringPrintf(dy, "%s:%d-%d %c %*dbps",chrom, s+1, e, mc->strand,sizeChars, mc->size);
fprintf(f, "<A TITLE=\"%s\"> %*s </A> ", dy->string, srcChars, org);
updateSummaryLine(summaryLine, referenceText + lineStart, mc->text + lineStart, size);
blueCapWrite(f, mc->text + lineStart, size,
(onlyDiff && mc != maf->components) ? referenceText + lineStart : NULL);
fprintf(f, "\n");
}
else
{
if (((mc->leftStatus == MAF_CONTIG_STATUS) && (mc->rightStatus == MAF_CONTIG_STATUS) )
|| ((mc->leftStatus == MAF_TANDEM_STATUS) && (mc->rightStatus == MAF_TANDEM_STATUS) )
|| ((mc->leftStatus == MAF_INSERT_STATUS) && (mc->rightStatus == MAF_INSERT_STATUS) )
|| ((mc->leftStatus == MAF_MISSING_STATUS) && (mc->rightStatus == MAF_MISSING_STATUS) ))
{
if (lineStart == 0)
{
int s = mc->start;
int e = s + mc->rightLen;
struct dyString *dy = newDyString(512);
if (mc->strand == '-')
reverseIntRange(&s, &e, mc->srcSize);
if ( hDbIsActive(dbOnly))
{
dyStringPrintf(dy, "%s Browser %s:%d-%d %c %d bps Unaligned",hOrganism(dbOnly),chrom, s+1, e, mc->strand, e-s);
linkToOtherBrowserTitle(dbOnly, chrom, s, e, dy->string);
fprintf(f,"B</A> ");
dyStringClear(dy);
}
else
fprintf(f," ");
if (hDbExists(dbOnly))
{
dyStringPrintf(dy, "Get %s DNA %s:%d-%d %c %d bps Unaligned",hOrganism(dbOnly),chrom, s+1, e, mc->strand, e-s);
printf("<A TITLE=\"%s\" TARGET=\"_blank\" HREF=\"%s?o=%d&g=getDna&i=%s&c=%s&l=%d&r=%d&db=%s%s\">D</A> ", dy->string, hgcName(),
s, cgiEncode(chrom),
chrom, s, e, dbOnly,revComp);
}
else
fprintf(f, " ");
}
else
fprintf(f, " ");
initSummaryLine(summaryLine, size, ' ');
dyStringClear(dy);
dyStringPrintf(dy, "%s:%d-%d %c %*dbps",chrom, s+1, e, mc->strand,sizeChars, mc->size);
fprintf(f, "<A TITLE=\"%s\">%*s</A> ", dy->string, srcChars, org);
ch = '-';
switch(mc->rightStatus)
{
case MAF_INSERT_STATUS:
ch = '=';
break;
case MAF_MISSING_STATUS:
ch = 'N';
break;
case MAF_TANDEM_STATUS:
case MAF_CONTIG_STATUS:
ch = '-';
break;
}
for(ii=lineStart; ii < lineEnd ; ii++)
fputc(ch,f);
fprintf(f,"\n");
}
}
}
#ifdef ADDMATCHLINE
if (lineStart == 0)
fprintf(f, " %-*s %s\n", srcChars, "", summaryLine);
else
fprintf(f, "%-*s %s\n", srcChars, "", summaryLine);
#else
fprintf(f, "\n");
#endif
}
if (haveInserts)
{
fprintf(f, "<B>Inserts between block %d and %d in window</B>\n",blockNo, blockNo+1);
for (mc = maf->components; mc != NULL; mc = mc->next)
{
char dbOnly[128], *chrom;
int s = mc->start + mc->size;
int e = s + mc->rightLen;
char *org;
if (mc->text == NULL)
continue;
if (mc->strand == '-')
reverseIntRange(&s, &e, mc->srcSize);
safef(dbOnly, sizeof(dbOnly), "%s", mc->src);
chrom = chopPrefix(dbOnly);
if ((org = hOrganism(dbOnly)) == NULL)
org = dbOnly;
if (mc->rightStatus == MAF_INSERT_STATUS)
{
char *revComp = "";
if (hDbIsActive(dbOnly))
{
char strand = mc->strand;
#ifdef REVERSESTRAND
if (cartCgiUsualBoolean(cart, COMPLEMENT_BASES_VAR, FALSE))
strand = (strand == '+') ? '-' : '+';
#endif
if (strand == '-') revComp = "&hgSeq.revComp=on";
linkToOtherBrowser(dbOnly, chrom, s, e);
fprintf(f,"B");
fprintf(f, "</A>");
fprintf(f, " ");
}
else
fprintf(f, " ");
if (hDbExists(dbOnly))
{
printf("<A TARGET=\"_blank\" HREF=\"%s?o=%d&g=getDna&i=%s&c=%s&l=%d&r=%d"
"&db=%s%s\">D</A> ", hgcName(), s, cgiEncode(chrom), chrom, s,
e, dbOnly,revComp);
}
else
fprintf(f, " ");
fprintf(f, "%*s %dbp\n", srcChars, org,mc->rightLen);
}
}
fprintf(f, "\n");
}
freeMem(summaryLine);
}