static void showTableFieldsDb(char *db, char *rootTable, boolean withGetButton)
/* Put up a little html table with a check box, name, and hopefully
* a description for each field in SQL rootTable. */
{
struct sqlConnection *conn = NULL;
if (!trackHubDatabase(database))
conn = hAllocConn(db);
struct trackDb *tdb = findTdbForTable(db, curTrack, rootTable, ctLookupName);
struct asObject *asObj = asForTable(conn, rootTable);
boolean showItemRgb = FALSE;
showItemRgb=bedItemRgb(tdb); /* should we expect itemRgb instead of "reserved" */
struct slName *fieldList;
if (isBigBed(database, rootTable, curTrack, ctLookupName))
fieldList = bigBedGetFields(rootTable, conn);
else if (isBamTable(rootTable))
fieldList = bamGetFields();
else if (isVcfTable(rootTable, NULL))
fieldList = vcfGetFields();
else
{
char *table = chromTable(conn, rootTable);
fieldList = sqlListFields(conn, table);
freez(&table);
}
showTableFieldsOnList(db, rootTable, asObj, fieldList, showItemRgb, withGetButton);
hFreeConn(&conn);
}
static void printSampleRows(int sampleCount, struct sqlConnection *conn, char *table)
/* Put up sample values. */
{
char query[256];
struct sqlResult *sr;
char **row;
int i, columnCount = 0;
int itemRgbCol = -1;
boolean showItemRgb = FALSE;
showItemRgb=bedItemRgb(findTdbForTable(database, curTrack, table, ctLookupName));
// should we expect itemRgb instead of "reserved"
/* Make table with header row containing name of fields. */
sqlSafef(query, sizeof(query), "describe %s", table);
sr = sqlGetResult(conn, query);
hTableStart();
hPrintf("<TR>");
while ((row = sqlNextRow(sr)) != NULL)
{
if (showItemRgb && sameWord(row[0],"reserved"))
{
hPrintf("<TH>itemRgb</TH>");
itemRgbCol = columnCount;
}
else
hPrintf("<TH>%s</TH>", row[0]);
++columnCount;
}
hPrintf("</TR>");
sqlFreeResult(&sr);
/* Get some sample fields. */
sqlSafef(query, sizeof(query), "select * from %s limit %d", table, sampleCount);
sr = sqlGetResult(conn, query);
while ((row = sqlNextRow(sr)) != NULL)
{
hPrintf("<TR>");
for (i=0; i<columnCount; ++i)
{
if (showItemRgb && (i == itemRgbCol))
{
int rgb = atoi(row[i]);
hPrintf("<TD>%d,%d,%d</TD>", (rgb & 0xff0000) >> 16,
(rgb & 0xff00) >> 8, (rgb & 0xff));
}
else
{
if (row[i] == NULL)
{
hPrintf("<TD></TD>");
}
else
{
writeHtmlCell(row[i]);
}
}
}
char *showTableField(struct trackDb *track, char *varName, boolean useJoiner)
/* Show table control and label. */
{
struct slName *name, *nameList = NULL;
char *selTable;
if (track == NULL)
nameList = tablesForDb(findSelDb());
else
nameList = cartTrackDbTablesForTrack(database, track, useJoiner);
/* Get currently selected table. If it isn't in our list
* then revert to first in list. */
selTable = cartUsualString(cart, varName, nameList->name);
if (!slNameInListUseCase(nameList, selTable))
selTable = nameList->name;
/* Print out label and drop-down list. */
hPrintf("<B>table: </B>");
hPrintf("<SELECT NAME=\"%s\" %s>\n", varName, onChangeTable());
struct trackDb *selTdb = NULL;
for (name = nameList; name != NULL; name = name->next)
{
struct trackDb *tdb = NULL;
if (track != NULL)
tdb = findTdbForTable(database,track,name->name, ctLookupName);
hPrintf("<OPTION VALUE=\"%s\"", name->name);
// Disable options for related tables that are noGenome -- if a non-positional table
// is selected then we output its entire contents.
if (cartTrackDbIsNoGenome(database, name->name) &&
(track == NULL || differentString(track->table, name->name)))
hPrintf(" DISABLED"NO_GENOME_CLASS);
else if (sameString(selTable, name->name))
{
hPrintf(" SELECTED");
selTdb = tdb;
}
if (tdb != NULL)
if ((curTrack == NULL) || differentWord(tdb->shortLabel, curTrack->shortLabel))
hPrintf(">%s (%s)\n", tdb->shortLabel, name->name);
else
hPrintf(">%s\n", name->name);
else
hPrintf(">%s\n", name->name);
}
hPrintf("</SELECT>\n");
if (!trackHubDatabase(database))
{
char *restrictDate = encodeRestrictionDateDisplay(database,selTdb);
if (restrictDate)
{
hPrintf("<A HREF=\'%s\' TARGET=BLANK>restricted until:</A> %s",
ENCODE_DATA_RELEASE_POLICY, restrictDate);
freeMem(restrictDate);
}
}
return selTable;
}
void doOutSequence(struct sqlConnection *conn)
/* Output sequence page. */
{
struct trackDb *tdb = findTdbForTable(database, curTrack, curTable, ctLookupName);
if (tdb != NULL && startsWith("genePred", tdb->type))
genePredOptions(tdb, curTrack->type, conn);
else
genomicFormatPage(conn);
}
void doSummaryStats(struct sqlConnection *conn)
/* Put up page showing summary stats for track. */
{
if (isWiggle(database, curTable))
doSummaryStatsWiggle(conn);
else if (isBigWigTable(curTable))
doSummaryStatsBigWig(conn);
else if (isChromGraph(findTdbForTable(database, curTrack, curTable, ctLookupName)))
doSummaryStatsChromGraph(conn);
else if (sameWord(curTable,WIKI_TRACK_TABLE))
doSummaryStatsWikiTrack(conn);
else
doSummaryStatsBed(conn);
}
void doValueRange(char *field)
/* Put up value histogram. */
{
char *db = cartString(cart, hgtaDatabase);
char *table = cartString(cart, hgtaHistoTable);
boolean showItemRgb = FALSE;
showItemRgb=bedItemRgb(findTdbForTable(db, curTrack, table, ctLookupName));
// should we expect itemRgb instead of "reserved"
if (showItemRgb && sameWord(field, "reserved"))
htmlOpen("Value range for %s.%s.itemRgb", db, table);
else
htmlOpen("Value range for %s.%s.%s", db, table, field);
printValueRange(db, table, field);
htmlClose();
}
void describeFields(char *db, char *table,
struct asObject *asObj, struct sqlConnection *conn)
/* Print out an HTML table showing table fields and types, and optionally
* offering histograms for the text/enum fields. */
{
struct sqlResult *sr;
char **row;
#define TOO_BIG_FOR_HISTO 500000
boolean tooBig = (sqlTableSize(conn, table) > TOO_BIG_FOR_HISTO);
char query[256];
struct slName *exampleList, *example;
boolean showItemRgb = FALSE;
showItemRgb=bedItemRgb(findTdbForTable(db, curTrack, table, ctLookupName));
// should we expect itemRgb instead of "reserved"
sqlSafef(query, sizeof(query), "select * from %s limit 1", table);
exampleList = storeRow(conn, query);
sqlSafef(query, sizeof(query), "describe %s", table);
sr = sqlGetResult(conn, query);
hTableStart();
hPrintf("<TR><TH>field</TH>");
if (exampleList != NULL)
hPrintf("<TH>example</TH>");
hPrintf("<TH>SQL type</TH> ");
if (!tooBig)
hPrintf("<TH>info</TH> ");
if (asObj != NULL)
hPrintf("<TH>description</TH> ");
puts("</TR>\n");
example = exampleList;
while ((row = sqlNextRow(sr)) != NULL)
{
if (showItemRgb && (sameWord(row[0],"reserved")))
hPrintf("<TR><TD><TT>itemRgb</TT></TD> ");
else
hPrintf("<TR><TD><TT>%s</TT></TD> ", row[0]);
if (exampleList != NULL)
{
hPrintf("<TD>");
if (example != NULL)
hPrintf("%s", cleanExample(example->name));
else
hPrintf("n/a");
hPrintf("</TD>");
}
// enums/sets with many items can make for painfully wide rows in the table --
// add spaces between quoted list values:
if (stringIn("','", row[1]))
{
struct dyString *spaced = dyStringSub(row[1], "','", "', '");
hPrintf("<TD><TT>%s</TT></TD>", spaced->string);
}
else
hPrintf("<TD><TT>%s</TT></TD>", row[1]);
if (!tooBig)
{
hPrintf(" <TD>");
if ((isSqlStringType(row[1]) && !sameString(row[1], "longblob")) ||
isSqlEnumType(row[1]) || isSqlSetType(row[1]))
{
hPrintf("<A HREF=\"%s", getScriptName());
hPrintf("?%s", cartSidUrlString(cart));
hPrintf("&%s=%s", hgtaDatabase, db);
hPrintf("&%s=%s", hgtaHistoTable, table);
hPrintf("&%s=%s", hgtaDoValueHistogram, row[0]);
hPrintf("\">");
hPrintf("values");
hPrintf("</A>");
}
else if (isSqlNumType(row[1]))
{
hPrintf("<A HREF=\"%s", getScriptName());
hPrintf("?%s", cartSidUrlString(cart));
hPrintf("&%s=%s", hgtaDatabase, db);
hPrintf("&%s=%s", hgtaHistoTable, table);
hPrintf("&%s=%s", hgtaDoValueRange, row[0]);
hPrintf("\">");
hPrintf("range");
hPrintf("</A>");
}
else
{
hPrintf(" ");
}
hPrintf("</TD>");
}
if (asObj != NULL)
{
struct asColumn *asCol = asColumnFind(asObj, row[0]);
hPrintf(" <TD>");
if (asCol != NULL)
hPrintf("%s", asCol->comment);
else
{
if (sameString("bin", row[0]))
hPrintf("Indexing field to speed chromosome range queries.");
else
hPrintf(" ");
}
hPrintf("</TD>");
}
puts("</TR>");
if (example != NULL)
example = example->next;
}
hTableEnd();
sqlFreeResult(&sr);
}
void doSummaryStatsWiggle(struct sqlConnection *conn)
/* Put up page showing summary stats for wiggle track. */
{
// grab the right trackDb for the current table. The curTrack variable
// has the composite trackDb in it
struct trackDb *track = hTrackDbForTrack(database, curTable);
char *table = curTable;
struct region *region, *regionList = getRegions();
char *regionName = getRegionName();
long long regionSize = 0;
long long gapTotal = 0;
long startTime = 0, wigFetchTime = 0;
char splitTableOrFileName[HDB_MAX_TABLE_STRING];
struct customTrack *ct = NULL;
boolean isCustom = FALSE;
struct wiggleDataStream *wds = NULL;
unsigned long long valuesMatched = 0;
int regionCount = 0;
int regionsDone = 0;
unsigned span = 0;
char *dataConstraint;
double ll = 0.0;
double ul = 0.0;
boolean hasConstraint = FALSE;
char *table2 = NULL;
boolean fullGenome = FALSE;
boolean statsHeaderDone = FALSE;
boolean gotSome = FALSE;
char *shortLabel = table;
long long statsItemCount = 0; /* global accumulators for overall */
int statsSpan = 0; /* stats summary on a multiple region */
double statsSumData = 0.0; /* output */
double statsSumSquares = 0.0; /* " " */
double lowerLimit = INFINITY; /* " " */
double upperLimit = -1.0 * INFINITY; /* " " */
startTime = clock1000();
if (track != NULL)
shortLabel = track->shortLabel;
/* Count the regions, when only one, we can do more stats */
for (region = regionList; region != NULL; region = region->next)
++regionCount;
htmlOpen("%s (%s) Wiggle Summary Statistics", shortLabel, table);
if (anySubtrackMerge(database, curTable))
hPrintf("<P><EM><B>Note:</B> subtrack merge is currently ignored on this "
"page (not implemented yet). Statistics shown here are only for "
"the primary table %s (%s).</EM>", shortLabel, table);
fullGenome = fullGenomeRegion();
WIG_INIT; /* ct, isCustom, hasConstraint, wds and table2 are set here */
for (region = regionList; region != NULL; region = region->next)
{
struct bed *intersectBedList = NULL;
int operations;
++regionsDone;
if (table2)
intersectBedList = bedTable2(conn, region, table2);
operations = wigFetchStats;
#if defined(NOT)
/* can't do the histogram now, that operation times out */
if (1 == regionCount)
operations |= wigFetchAscii;
#endif
wds->setChromConstraint(wds, region->chrom);
if (fullGenome)
wds->setPositionConstraint(wds, 0, 0);
else
wds->setPositionConstraint(wds, region->start, region->end);
if (hasConstraint)
wds->setDataConstraint(wds, dataConstraint, ll, ul);
/* depending on what is coming in on regionList, we may need to be
* smart about how often we call getData for these custom tracks
* since that is potentially a large file read each time.
*/
if (isCustom)
{
if (ct->dbTrack)
{
struct sqlConnection *trashConn = hAllocConn(CUSTOM_TRASH);
struct trackDb *tdb = findTdbForTable(database, curTrack, table, ctLookupName);
span = minSpan(trashConn, splitTableOrFileName, region->chrom,
region->start, region->end, cart, tdb);
wds->setSpanConstraint(wds, span);
valuesMatched = getWigglePossibleIntersection(wds, region,
CUSTOM_TRASH, table2, &intersectBedList,
splitTableOrFileName, operations);
hFreeConn(&trashConn);
}
else
{
valuesMatched = getWigglePossibleIntersection(wds, region, NULL,
table2, &intersectBedList, splitTableOrFileName, operations);
/* XXX We need to properly get the smallest span for custom tracks */
/* This is not necessarily the correct answer here */
if (wds->stats)
span = wds->stats->span;
else
span = 1;
}
}
else
{
if (hFindSplitTable(database, region->chrom, table, splitTableOrFileName, sizeof splitTableOrFileName, NULL))
{
span = minSpan(conn, splitTableOrFileName, region->chrom,
region->start, region->end, cart, track);
wds->setSpanConstraint(wds, span);
valuesMatched = getWigglePossibleIntersection(wds, region,
database, table2, &intersectBedList, splitTableOrFileName,
operations);
if (intersectBedList)
span = 1;
}
}
/* when doing multiple regions, we need to print out each result as
* it happens to keep the connection open to the browser and
* prevent any timeout since this could take a while.
* (worst case test is quality track on panTro1)
*/
if (wds->stats)
statsItemCount += wds->stats->count;
if (wds->stats && (regionCount > 1) && (valuesMatched > 0))
{
double sumData = wds->stats->mean * wds->stats->count;
double sumSquares;
if (wds->stats->count > 1)
sumSquares = (wds->stats->variance * (wds->stats->count - 1)) +
((sumData * sumData)/wds->stats->count);
else
sumSquares = sumData * sumData;
/* global accumulators for overall summary */
statsSpan = wds->stats->span;
statsSumData += sumData;
statsSumSquares += sumSquares;
if (wds->stats->lowerLimit < lowerLimit)
lowerLimit = wds->stats->lowerLimit;
if ((wds->stats->lowerLimit + wds->stats->dataRange) > upperLimit)
upperLimit = wds->stats->lowerLimit + wds->stats->dataRange;
if (statsHeaderDone)
wds->statsOut(wds, database, "stdout", TRUE, TRUE, FALSE, TRUE);
else
{
wds->statsOut(wds, database, "stdout", TRUE, TRUE, TRUE, TRUE);
statsHeaderDone = TRUE;
}
wds->freeStats(wds);
gotSome = TRUE;
}
if ((regionCount > MAX_REGION_DISPLAY) &&
(regionsDone >= MAX_REGION_DISPLAY))
{
hPrintf("<TR><TH ALIGN=CENTER COLSPAN=12> Can not display more "
"than %d regions, <BR> would take too much time </TH></TR>\n",
MAX_REGION_DISPLAY);
break; /* exit this for loop */
}
} /*for (region = regionList; region != NULL; region = region->next) */
if (hasConstraint)
freeMem(dataConstraint); /* been cloned into wds */
if (1 == regionCount)
{
statsPreamble(wds, regionList->chrom, regionList->start, regionList->end,
span, valuesMatched, table2);
/* 3 X TRUE = sort results, html table output, with header,
* the FALSE means close the table after printing, no more rows to
* come. The case in the if() statement was already taken care of
* in the statsPreamble() printout. No need to do that again.
*/
if ( ! ((valuesMatched == 0) && table2) )
wds->statsOut(wds, database, "stdout", TRUE, TRUE, TRUE, FALSE);
regionSize = basesInRegion(regionList,0);
gapTotal = gapsInRegion(conn, regionList,0);
}
else
{ /* this is a bit of a kludge here since these printouts are done in the
* library source wigDataStream.c statsOut() function and
* this is a clean up of that. That function should be
* pulled out of there and made independent and more
* versatile.
*/
long long realSize;
double variance;
double stddev;
/* Too expensive to lookup the numbers for thousands of regions */
regionSize = basesInRegion(regionList,MAX_REGION_DISPLAY);
gapTotal = gapsInRegion(conn, regionList,MAX_REGION_DISPLAY);
realSize = regionSize - gapTotal;
/* close the table which was left open in the loop above */
if (!gotSome)
hPrintf("<TR><TH ALIGN=CENTER COLSPAN=12> No data found matching this request </TH></TR>\n");
hPrintf("<TR><TH ALIGN=LEFT> SUMMARY: </TH>\n");
hPrintf("\t<TD> </TD>\n"); /* chromStart */
hPrintf("\t<TD> </TD>\n"); /* chromEnd */
hPrintf("\t<TD ALIGN=RIGHT> ");
printLongWithCommas(stdout, statsItemCount);
hPrintf(" </TD>\n" );
hPrintf("\t<TD ALIGN=RIGHT> %d </TD>\n", statsSpan);
hPrintf("\t<TD ALIGN=RIGHT> ");
printLongWithCommas(stdout, statsItemCount*statsSpan);
hPrintf(" (%.2f%%) </TD>\n",
100.0*(double)(statsItemCount*statsSpan)/(double)realSize);
hPrintf("\t<TD ALIGN=RIGHT> %g </TD>\n", lowerLimit);
hPrintf("\t<TD ALIGN=RIGHT> %g </TD>\n", upperLimit);
hPrintf("\t<TD ALIGN=RIGHT> %g </TD>\n", upperLimit - lowerLimit);
if (statsItemCount > 0)
hPrintf("\t<TD ALIGN=RIGHT> %g </TD>\n", statsSumData/statsItemCount);
else
hPrintf("\t<TD ALIGN=RIGHT> 0.0 </TD>\n");
stddev = 0.0;
variance = 0.0;
if (statsItemCount > 1)
{
variance = (statsSumSquares -
((statsSumData * statsSumData)/(double) statsItemCount)) /
(double) (statsItemCount - 1);
if (variance > 0.0)
stddev = sqrt(variance);
}
hPrintf("\t<TD ALIGN=RIGHT> %g </TD>\n", variance);
hPrintf("\t<TD ALIGN=RIGHT> %g </TD>\n", stddev);
hPrintf("</TR>\n");
wigStatsTableHeading(stdout, TRUE);
hPrintf("</TABLE></TD></TR></TABLE></P>\n");
}
#if defined(NOT)
/* can't do the histogram now, that operation times out */
/* Single region, we can do the histogram */
if ((valuesMatched > 1) && (1 == regionCount))
{
float *valuesArray = NULL;
size_t valueCount = 0;
struct histoResult *histoGramResult;
/* convert the ascii data listings to one giant float array */
valuesArray = wds->asciiToDataArray(wds, valuesMatched, &valueCount);
/* histoGram() may return NULL if it doesn't work */
histoGramResult = histoGram(valuesArray, valueCount,
NAN, (unsigned) 0, NAN, (float) wds->stats->lowerLimit,
(float) (wds->stats->lowerLimit + wds->stats->dataRange),
(struct histoResult *)NULL);
printHistoGram(histoGramResult, TRUE); /* TRUE == html output */
freeHistoGram(&histoGramResult);
wds->freeAscii(wds);
wds->freeArray(wds);
}
#endif
wds->freeStats(wds);
wiggleDataStreamFree(&wds);
wigFetchTime = clock1000() - startTime;
webNewSection("Region and Timing Statistics");
hTableStart();
stringStatRow("region", regionName);
numberStatRow("bases in region", regionSize);
numberStatRow("bases in gaps", gapTotal);
floatStatRow("load and calc time", 0.001*wigFetchTime);
wigFilterStatRow(conn);
stringStatRow("intersection", cartUsualString(cart, hgtaIntersectTable, "off"));
hTableEnd();
htmlClose();
} /* void doSummaryStatsWiggle(struct sqlConnection *conn) */
struct bed *getWiggleAsBed(
char *db, char *table, /* Database and table. */
struct region *region, /* Region to get data for. */
char *filter, /* Filter to add to SQL where clause if any. */
struct hash *idHash, /* Restrict to id's in this hash if non-NULL. */
struct lm *lm, /* Where to allocate memory. */
struct sqlConnection *conn) /* SQL connection to work with */
/* Return a bed list of all items in the given range in table.
* Cleanup result via lmCleanup(&lm) rather than bedFreeList. */
/* filter, idHash and lm are currently unused, perhaps future use */
{
struct bed *bedList=NULL;
char splitTableOrFileName[HDB_MAX_TABLE_STRING];
struct customTrack *ct = NULL;
boolean isCustom = FALSE;
boolean hasConstraint = FALSE;
struct wiggleDataStream *wds = NULL;
unsigned long long valuesMatched = 0;
int operations = wigFetchBed;
char *dataConstraint;
double ll = 0.0;
double ul = 0.0;
char *table2 = NULL;
struct bed *intersectBedList = NULL;
int maxOut;
WIG_INIT; /* ct, isCustom, hasConstraint, wds and table2 are set here */
if (hasConstraint)
freeMem(dataConstraint); /* been cloned into wds */
maxOut = bigFileMaxOutput();
wds->setMaxOutput(wds, maxOut);
wds->setChromConstraint(wds, region->chrom);
wds->setPositionConstraint(wds, region->start, region->end);
if (table2)
intersectBedList = bedTable2(conn, region, table2);
if (isCustom)
{
if (ct->dbTrack)
{
unsigned span = 0;
struct sqlConnection *trashConn = hAllocConn(CUSTOM_TRASH);
struct trackDb *tdb = findTdbForTable(database, curTrack, table, ctLookupName);
valuesMatched = getWigglePossibleIntersection(wds, region,
CUSTOM_TRASH, table2, &intersectBedList,
splitTableOrFileName, operations);
span = minSpan(trashConn, splitTableOrFileName, region->chrom,
region->start, region->end, cart, tdb);
wds->setSpanConstraint(wds, span);
hFreeConn(&trashConn);
}
else
valuesMatched = getWigglePossibleIntersection(wds, region, NULL, table2,
&intersectBedList, splitTableOrFileName, operations);
}
else
{
if (conn == NULL)
errAbort( "getWiggleAsBed: NULL conn given for database table");
if (hFindSplitTable(database, region->chrom, table, splitTableOrFileName, sizeof splitTableOrFileName, NULL))
{
struct trackDb *tdb = findTdbForTable(database, curTrack, table, ctLookupName);
unsigned span = 0;
/* XXX TBD, watch for a span limit coming in as an SQL filter */
span = minSpan(conn, splitTableOrFileName, region->chrom,
region->start, region->end, cart, tdb);
wds->setSpanConstraint(wds, span);
valuesMatched = getWigglePossibleIntersection(wds, region, database,
table2, &intersectBedList, splitTableOrFileName, operations);
}
}
if (valuesMatched > 0)
{
struct bed *bed;
wds->sortResults(wds);
for (bed = wds->bed; bed != NULL; bed = bed->next)
{
struct bed *copy = lmCloneBed(bed, lm);
slAddHead(&bedList, copy);
}
slReverse(&bedList);
}
wiggleDataStreamFree(&wds);
return bedList;
} /* struct bed *getWiggleAsBed() */
static int wigOutRegion(char *table, struct sqlConnection *conn,
struct region *region, int maxOut, enum wigOutputType wigOutType,
struct wigAsciiData **data, int spanConstraint)
/* Write out wig data in region. Write up to maxOut elements.
* Returns number of elements written. */
{
int linesOut = 0;
char splitTableOrFileName[HDB_MAX_TABLE_STRING];
struct customTrack *ct = NULL;
boolean isCustom = FALSE;
boolean hasConstraint = FALSE;
struct wiggleDataStream *wds = NULL;
unsigned long long valuesMatched = 0;
int operations = wigFetchAscii;
char *dataConstraint;
double ll = 0.0;
double ul = 0.0;
char *table2 = NULL;
struct bed *intersectBedList = NULL;
switch (wigOutType)
{
case wigOutBed:
operations = wigFetchBed;
break;
default:
case wigDataNoPrint:
case wigOutData:
operations = wigFetchAscii;
break;
};
WIG_INIT; /* ct, isCustom, hasConstraint, wds and table2 are set here */
if (hasConstraint)
freeMem(dataConstraint); /* been cloned into wds */
wds->setMaxOutput(wds, maxOut);
wds->setChromConstraint(wds, region->chrom);
wds->setPositionConstraint(wds, region->start, region->end);
if (table2)
intersectBedList = bedTable2(conn, region, table2);
if (isCustom)
{
if (ct->dbTrack)
{
if (spanConstraint)
wds->setSpanConstraint(wds,spanConstraint);
else
{
struct sqlConnection *trashConn = hAllocConn(CUSTOM_TRASH);
struct trackDb *tdb = findTdbForTable(database, curTrack, table, ctLookupName);
unsigned span = minSpan(trashConn, splitTableOrFileName,
region->chrom, region->start, region->end, cart, tdb);
wds->setSpanConstraint(wds, span);
hFreeConn(&trashConn);
}
valuesMatched = getWigglePossibleIntersection(wds, region,
CUSTOM_TRASH, table2, &intersectBedList,
splitTableOrFileName, operations);
}
else
valuesMatched = getWigglePossibleIntersection(wds, region, NULL, table2,
&intersectBedList, splitTableOrFileName, operations);
}
else
{
if (hFindSplitTable(database, region->chrom, table, splitTableOrFileName, sizeof splitTableOrFileName, NULL))
{
/* XXX TBD, watch for a span limit coming in as an SQL filter */
if (intersectBedList)
{
struct trackDb *tdb = findTdbForTable(database, curTrack, table, ctLookupName);
unsigned span;
span = minSpan(conn, splitTableOrFileName, region->chrom,
region->start, region->end, cart, tdb);
wds->setSpanConstraint(wds, span);
}
else if (spanConstraint)
wds->setSpanConstraint(wds,spanConstraint);
valuesMatched = getWigglePossibleIntersection(wds, region, database,
table2, &intersectBedList, splitTableOrFileName, operations);
}
}
switch (wigOutType)
{
case wigDataNoPrint:
if (data)
{
if (*data != NULL) /* no exercise of this function yet */
{ /* data not null, add to existing list */
struct wigAsciiData *asciiData;
struct wigAsciiData *next;
for (asciiData = *data; asciiData; asciiData = next)
{
next = asciiData->next;
slAddHead(&wds->ascii, asciiData);
}
}
wds->sortResults(wds);
*data = wds->ascii; /* moving the list to *data */
wds->ascii = NULL; /* gone as far as wds is concerned */
}
linesOut = valuesMatched;
break;
case wigOutBed:
linesOut = wds->bedOut(wds, "stdout", TRUE);/* TRUE == sort output */
break;
default:
case wigOutData:
linesOut = wds->asciiOut(wds, database, "stdout", TRUE, FALSE);
break; /* TRUE == sort output, FALSE == not raw data out */
};
wiggleDataStreamFree(&wds);
return linesOut;
} /* static int wigOutRegion() */
static void filterControlsForTableDb(char *db, char *rootTable)
/* Put up filter controls for a single database table. */
{
struct sqlConnection *conn = NULL;
if (!trackHubDatabase(db))
conn = hAllocConn(db);
char *table = chromTable(conn, rootTable);
struct trackDb *tdb = findTdbForTable(db, curTrack, rootTable, ctLookupName);
boolean isSmallWig = isWiggle(db, table);
boolean isBigWig = tdb ? tdbIsBigWig(tdb) : isBigWigTable(table);
boolean isWig = isSmallWig || isBigWig;
boolean isBedGr = tdb ? tdbIsBedGraph(tdb) : isBedGraph(rootTable);
boolean isBb = tdb ? tdbIsBigBed(tdb) : isBigBed(database, table, curTrack, ctLookupName);
boolean isBam = tdb ? tdbIsBam(tdb) : isBamTable(rootTable);
boolean isVcf = tdb ? tdbIsVcf(tdb) : isVcfTable(rootTable, NULL);
int bedGraphColumn = 5; /* default score column */
if (isBedGr)
{
int wordCount;
char *words[8];
char *typeLine = cloneString(tdb->type);
wordCount = chopLine(typeLine,words);
if (wordCount > 1)
bedGraphColumn = sqlUnsigned(words[1]);
freez(&typeLine);
}
if (isWig)
{
hPrintf("<TABLE BORDER=0>\n");
if ((tdb != NULL) && (tdb->type != NULL))
{
double min, max;
wiggleMinMax(tdb,&min,&max);
numericFilterWithLimits(db, rootTable, filterDataValueVar,filterDataValueVar,min,max,"");
hPrintf("<TR><TD COLSPAN=3 ALIGN=RIGHT> (dataValue range: [%g:%g]) "
"</TD></TR></TABLE>\n", min, max);
}
else
{
numericFilter(db, rootTable, filterDataValueVar,filterDataValueVar, "");
hPrintf("</TABLE>\n");
}
}
else
{
struct sqlFieldType *ftList;
if (isBb)
ftList = bigBedListFieldsAndTypes(tdb, conn);
else if (isBam)
ftList = bamListFieldsAndTypes();
else if (isVcf)
ftList = vcfListFieldsAndTypes();
else
ftList = sqlListFieldsAndTypes(conn, table);
printSqlFieldListAsControlTable(ftList, db, rootTable, tdb, isBedGr);
}
/* Printf free-form query row. */
if (!(isWig||isBedGr||isBam||isVcf))
{
char *name;
hPrintf("<TABLE BORDER=0><TR><TD>\n");
name = filterFieldVarName(db, rootTable, "", filterRawLogicVar);
cgiMakeDropList(name, logOpMenu, logOpMenuSize,
cartUsualString(cart, name, logOpMenu[0]));
hPrintf(" Free-form query: ");
name = filterFieldVarName(db, rootTable, "", filterRawQueryVar);
char *val = cartUsualString(cart, name, "");
// escape double quotes to avoid HTML parse trouble in the text input.
val = htmlEncodeText(val, FALSE);
cgiMakeTextVar(name, val, 50);
hPrintf("</TD></TR></TABLE>\n");
}
if (isWig||isBedGr||isBam||isVcf)
{
char *name;
hPrintf("<TABLE BORDER=0><TR><TD> Limit data output to: \n");
name = filterFieldVarName(db, rootTable, "_", filterMaxOutputVar);
cgiMakeDropList(name, maxOutMenu, maxOutMenuSize,
cartUsualString(cart, name, maxOutMenu[0]));
hPrintf(" lines</TD></TR></TABLE>\n");
}
freez(&table);
hFreeConn(&conn);
hPrintf("<BR>\n");
cgiMakeButton(hgtaDoFilterSubmit, "submit");
hPrintf(" ");
cgiMakeButton(hgtaDoMainPage, "cancel");
}
void showMainControlTable(struct sqlConnection *conn)
/* Put up table with main controls for main page. */
{
struct grp *selGroup;
boolean isWig = FALSE, isPositional = FALSE, isMaf = FALSE, isBedGr = FALSE,
isChromGraphCt = FALSE, isPal = FALSE, isArray = FALSE, isBam = FALSE, isVcf = FALSE, isHalSnake = FALSE, isLongTabix = FALSE;
boolean gotClade = hGotClade();
struct hTableInfo *hti = NULL;
hPrintf("<TABLE BORDER=0>\n");
/* Print clade, genome and assembly line. */
{
if (gotClade)
{
hPrintf("<TR><TD><B>clade:</B>\n");
printCladeListHtml(hGenome(database), onChangeClade());
nbSpaces(3);
hPrintf("<B>genome:</B>\n");
printGenomeListForCladeHtml(database, onChangeOrg());
}
else
{
hPrintf("<TR><TD><B>genome:</B>\n");
printGenomeListHtml(database, onChangeOrg());
}
nbSpaces(3);
hPrintf("<B>assembly:</B>\n");
printAssemblyListHtml(database, onChangeDb());
hPrintf("</TD></TR>\n");
}
/* Print group and track line. */
{
hPrintf("<TR><TD>");
selGroup = showGroupField(hgtaGroup, onChangeGroupOrTrack(), conn, hAllowAllTables());
nbSpaces(3);
curTrack = showTrackField(selGroup, hgtaTrack, onChangeGroupOrTrack(), FALSE);
nbSpaces(3);
boolean hasCustomTracks = FALSE;
struct trackDb *t;
for (t = fullTrackList; t != NULL; t = t->next)
{
if (isCustomTrack(t->table))
{
hasCustomTracks = TRUE;
break;
}
}
hOnClickButton("document.customTrackForm.submit();return false;",
hasCustomTracks ? CT_MANAGE_BUTTON_LABEL : CT_ADD_BUTTON_LABEL);
hPrintf(" ");
if (hubConnectTableExists())
hOnClickButton("document.trackHubForm.submit();return false;", "track hubs");
hPrintf("</TD></TR>\n");
}
/* Print table line. */
{
hPrintf("<TR><TD>");
curTable = showTableField(curTrack, hgtaTable, TRUE);
if (isHubTrack(curTable) || (strchr(curTable, '.') == NULL)) /* In same database */
{
hti = getHti(database, curTable, conn);
isPositional = htiIsPositional(hti);
}
isLongTabix = isLongTabixTable( curTable);
isBam = isBamTable( curTable);
isVcf = isVcfTable(curTable, NULL);
isWig = isWiggle(database, curTable);
if (isBigWigTable(curTable))
{
isPositional = TRUE;
isWig = TRUE;
}
isHalSnake = isHalTable( curTable);
isMaf = isMafTable(database, curTrack, curTable);
isBedGr = isBedGraph(curTable);
isArray = isMicroarray(curTrack, curTable);
struct trackDb *tdb = findTdbForTable(database, curTrack, curTable, ctLookupName);
isPal = isPalCompatible(conn, tdb, curTable);
nbSpaces(1);
if (isCustomTrack(curTable))
{
isChromGraphCt = isChromGraph(tdb);
}
cgiMakeButton(hgtaDoSchema, "describe table schema");
hPrintf("</TD></TR>\n");
}
if (curTrack == NULL)
{
struct trackDb *tdb = hTrackDbForTrack(database, curTable);
struct trackDb *cTdb = hCompositeTrackDbForSubtrack(database, tdb);
if (cTdb)
curTrack = cTdb;
else
curTrack = tdb;
isMaf = isMafTable(database, curTrack, curTable);
}
/* Region line */
{
char *regionType = cartUsualString(cart, hgtaRegionType, hgtaRegionTypeGenome);
char *range = cartUsualString(cart, hgtaRange, "");
if (isPositional)
{
boolean doEncode = FALSE;
if (!trackHubDatabase(database))
doEncode = sqlTableExists(conn, "encodeRegions");
hPrintf("<TR><TD><B>region:</B>\n");
/* If regionType not allowed force it to "genome". */
if ((sameString(regionType, hgtaRegionTypeUserRegions) &&
userRegionsFileName() == NULL) ||
(sameString(regionType, hgtaRegionTypeEncode) && !doEncode))
regionType = hgtaRegionTypeGenome;
// Is "genome" is not allowed because of tdb 'tableBrowser noGenome'?
boolean disableGenome = ((curTrack && cartTrackDbIsNoGenome(database, curTrack->table)) ||
(curTable && cartTrackDbIsNoGenome(database, curTable)));
// If "genome" is selected but not allowed, force it to "range":
if (sameString(regionType, hgtaRegionTypeGenome) && disableGenome)
regionType = hgtaRegionTypeRange;
jsTrackingVar("regionType", regionType);
if (disableGenome)
{
makeRegionButtonExtraHtml(hgtaRegionTypeGenome, regionType, "DISABLED");
hPrintf(" <span"NO_GENOME_CLASS">genome (unavailable for selected track)</span>"
" ");
}
else
{
makeRegionButton(hgtaRegionTypeGenome, regionType);
hPrintf(" genome ");
}
if (doEncode)
{
makeRegionButton(hgtaRegionTypeEncode, regionType);
hPrintf(" ENCODE Pilot regions ");
}
makeRegionButton(hgtaRegionTypeRange, regionType);
hPrintf(" position ");
hPrintf("<INPUT TYPE=TEXT NAME=\"%s\" SIZE=26 VALUE=\"%s\" onFocus=\"%s\">\n",
hgtaRange, range, jsRadioUpdate(hgtaRegionType, "regionType", "range"));
cgiMakeButton(hgtaDoLookupPosition, "lookup");
hPrintf(" ");
if (userRegionsFileName() != NULL)
{
makeRegionButton(hgtaRegionTypeUserRegions, regionType);
hPrintf(" defined regions ");
cgiMakeButton(hgtaDoSetUserRegions, "change");
hPrintf(" ");
cgiMakeButton(hgtaDoClearUserRegions, "clear");
}
else
cgiMakeButton(hgtaDoSetUserRegions, "define regions");
hPrintf("</TD></TR>\n");
}
else
{
/* Need to put at least stubs of cgi variables in for JavaScript to work. */
jsTrackingVar("regionType", regionType);
cgiMakeHiddenVar(hgtaRange, range);
cgiMakeHiddenVar(hgtaRegionType, regionType);
}
/* Select identifiers line (if applicable). */
if (!isWig && getIdField(database, curTrack, curTable, hti) != NULL)
{
hPrintf("<TR><TD><B>identifiers (names/accessions):</B>\n");
cgiMakeButton(hgtaDoPasteIdentifiers, "paste list");
hPrintf(" ");
cgiMakeButton(hgtaDoUploadIdentifiers, "upload list");
if (identifierFileName() != NULL)
{
hPrintf(" ");
cgiMakeButton(hgtaDoClearIdentifiers, "clear list");
}
hPrintf("</TD></TR>\n");
}
}
/* microarray options */
/* button for option page here (median/log-ratio, etc) */
/* Filter line. */
{
hPrintf("<TR><TD><B>filter:</B>\n");
if (anyFilter())
{
cgiMakeButton(hgtaDoFilterPage, "edit");
hPrintf(" ");
cgiMakeButton(hgtaDoClearFilter, "clear");
if (isWig || isBedGr)
wigShowFilter(conn);
}
else
{
cgiMakeButton(hgtaDoFilterPage, "create");
}
hPrintf("</TD></TR>\n");
}
/* Composite track subtrack merge line. */
boolean canSubtrackMerge = (curTrack && tdbIsComposite(curTrack) && !isBam && !isVcf && !isLongTabix);
if (canSubtrackMerge)
{
hPrintf("<TR><TD><B>subtrack merge:</B>\n");
if (anySubtrackMerge(database, curTable))
{
cgiMakeButton(hgtaDoSubtrackMergePage, "edit");
hPrintf(" ");
cgiMakeButton(hgtaDoClearSubtrackMerge, "clear");
}
else
{
cgiMakeButton(hgtaDoSubtrackMergePage, "create");
}
hPrintf("</TD></TR>\n");
}
/* Intersection line. */
if (isPositional)
{
if (anyIntersection())
{
hPrintf("<TR><TD><B>intersection with %s:</B>\n",
cartString(cart, hgtaIntersectTable));
cgiMakeButton(hgtaDoIntersectPage, "edit");
hPrintf(" ");
cgiMakeButton(hgtaDoClearIntersect, "clear");
hPrintf("</TD></TR>\n");
}
else if (canIntersect(database, curTable))
{
hPrintf("<TR><TD><B>intersection:</B>\n");
cgiMakeButton(hgtaDoIntersectPage, "create");
hPrintf("</TD></TR>\n");
}
}
/* Correlation line. */
struct trackDb *tdb = findTdbForTable(database, curTrack, curTable, ctLookupName);
if (correlateTrackTableOK(tdb, curTable))
{
char *table2 = cartUsualString(cart, hgtaCorrelateTable, "none");
hPrintf("<TR><TD><B>correlation:</B>\n");
if (differentWord(table2, "none") && strlen(table2) && ! isNoGenomeDisabled(database, table2))
{
struct grp *groupList = fullGroupList;
struct grp *selGroup = findSelectedGroup(groupList, hgtaCorrelateGroup);
struct trackDb *tdb2 = findSelectedTrack(fullTrackList, selGroup,hgtaCorrelateTrack);
if (tdbIsComposite(tdb2))
{
struct slRef *tdbRefList = trackDbListGetRefsToDescendantLeaves(tdb2->subtracks);
struct slRef *tdbRef;
for (tdbRef = tdbRefList; tdbRef != NULL; tdbRef = tdbRef->next)
{
struct trackDb *subTdb = tdbRef->val;
if (sameString(table2, subTdb->table))
{
tdb2 = subTdb;
break;
}
}
slFreeList(&tdbRefList);
}
cgiMakeButton(hgtaDoCorrelatePage, "calculate");
cgiMakeButton(hgtaDoClearCorrelate, "clear");
if (tdb2 && tdb2->shortLabel)
hPrintf(" (with: %s)", tdb2->shortLabel);
#ifdef NOT_YET
/* debugging dbg vvvvv */
if (curTrack && curTrack->type) /* dbg */
{
hPrintf("<BR> (debug: '%s', '%s(%s)')",
curTrack->type, tdb2->type, table2);
}
/* debugging debug ^^^^^ */
#endif
}
else
cgiMakeButton(hgtaDoCorrelatePage, "create");
hPrintf("</TD></TR>\n");
}
/* Print output type line. */
showOutputTypeRow(isWig, isBedGr, isPositional, isMaf, isChromGraphCt, isPal, isArray, isHalSnake);
/* Print output destination line. */
{
char *compressType =
cartUsualString(cart, hgtaCompressType, textOutCompressNone);
char *fileName = cartUsualString(cart, hgtaOutFileName, "");
hPrintf("<TR><TD>\n");
hPrintf("<B>output file:</B> ");
cgiMakeTextVar(hgtaOutFileName, fileName, 29);
hPrintf(" (leave blank to keep output in browser)</TD></TR>\n");
hPrintf("<TR><TD>\n");
hPrintf("<B>file type returned: </B>");
cgiMakeRadioButton(hgtaCompressType, textOutCompressNone,
sameWord(textOutCompressNone, compressType));
hPrintf(" plain text  ");
cgiMakeRadioButton(hgtaCompressType, textOutCompressGzip,
sameWord(textOutCompressGzip, compressType));
hPrintf(" gzip compressed");
hPrintf("</TD></TR>\n");
}
hPrintf("</TABLE>\n");
/* Submit buttons. */
{
hPrintf("<BR>\n");
if (isWig || isBam || isVcf || isLongTabix)
{
char *name;
extern char *maxOutMenu[];
char *maxOutput = maxOutMenu[0];
if (isCustomTrack(curTable))
name=filterFieldVarName("ct", curTable, "_", filterMaxOutputVar);
else
name=filterFieldVarName(database,curTable, "_",filterMaxOutputVar);
maxOutput = cartUsualString(cart, name, maxOutMenu[0]);
if (isWig)
hPrintf(
"<I>Note: to return more than %s lines, change the filter setting"
" (above). The entire data set may be available for download as"
" a very large file that contains the original data values (not"
" compressed into the wiggle format) -- see the Downloads page."
"</I><BR>", maxOutput);
else if (isBam || isVcf || isLongTabix)
hPrintf(
"<I>Note: to return more than %s lines, change the filter setting"
" (above). Please consider downloading the entire data from our Download pages."
"</I><BR>", maxOutput);
}
else if (anySubtrackMerge(database, curTable) || anyIntersection())
{
hPrintf("<I>Note: The all fields and selected fields output formats "
"are not available when a%s has been specified.</I><BR>",
canSubtrackMerge ? " subtrack merge or intersection" : "n intersection");
}
cgiMakeButton(hgtaDoTopSubmit, "get output");
hPrintf(" ");
if (isPositional || isWig)
{
cgiMakeButton(hgtaDoSummaryStats, "summary/statistics");
hPrintf(" ");
}
#ifdef SOMETIMES
hPrintf(" ");
cgiMakeButton(hgtaDoTest, "test");
#endif /* SOMETIMES */
}
hPrintf("<P>"
"To reset <B>all</B> user cart settings (including custom tracks), \n"
"<A HREF=\"/cgi-bin/cartReset?destination=%s\">click here</A>.\n",
getScriptName());
}
