コード例 #1
0
ファイル: wiggle.c プロジェクト: ucscGenomeBrowser/kent
struct dataVector *bedGraphDataVector(char *table,
	struct sqlConnection *conn, struct region *region)
/* Read in bedGraph as dataVector and return it.  Filtering, subtrack merge
 * and intersection are handled. */
{
struct dataVector *dv = NULL;

if (anySubtrackMerge(database, table))
    dv = mergedWigDataVector(table, conn, region);
else
    {
    struct trackDb *tdb;
    if (isCustomTrack(table))
        {
        struct customTrack *ct = ctLookupName(table);
        tdb = ct->tdb;
        conn = hAllocConn(CUSTOM_TRASH);
        }
    else
        {
        tdb = hTrackDbForTrack(database, table);
        }
    struct trackTable *tt1 = trackTableNew(tdb, table, conn);
    dv = dataVectorFetchOneRegion(tt1, region, conn);
    intersectDataVector(table, dv, region, conn);
    if (isCustomTrack(table))
        hFreeConn(&conn);
    }
return dv;
}
コード例 #2
0
ファイル: bigWig.c プロジェクト: davidhoover/kent
struct dataVector *bigWigDataVector(char *table,
	struct sqlConnection *conn, struct region *region)
/* Read in bigWig as dataVector and return it.  Filtering, subtrack merge
 * and intersection are handled. */
{
if (anySubtrackMerge(database, table))
    return mergedWigDataVector(table, conn, region);
else
    {
    struct dataVector *dv = dataVectorNew(region->chrom, region->end - region->start);
    bigWigFillDataVector(table, region, conn, dv);
    return dv;
    }
}
コード例 #3
0
ファイル: wiggle.c プロジェクト: ucscGenomeBrowser/kent
struct dataVector *wiggleDataVector(struct trackDb *tdb, char *table,
	struct sqlConnection *conn, struct region *region)
/* Read in wiggle as dataVector and return it.  Filtering, subtrack merge
 * and intersection are handled. */
{
struct dataVector *dv = NULL;

if (anySubtrackMerge(database, table))
    dv = mergedWigDataVector(table, conn, region);
else
    {
    struct trackTable *tt1 = trackTableNew(tdb, table, conn);
    dv = dataVectorFetchOneRegion(tt1, region, conn);
    }
return dv;
}
コード例 #4
0
ファイル: bigWig.c プロジェクト: davidhoover/kent
int bigWigOutRegion(char *table, struct sqlConnection *conn,
			     struct region *region, int maxOut,
			     enum wigOutputType wigOutType)
/* Write out bigWig for region, doing intersecting and filtering as need be. */
{
boolean isMerged = anySubtrackMerge(table, database);
int resultCount = 0;
char *wigFileName = bigWigFileName(table, conn);
if (wigFileName)
    {
    struct bbiFile *bwf = bigWigFileOpen(wigFileName);
    if (bwf)
	{
	/* Easy case, just dump out data. */
	if (!anyFilter() && !anyIntersection() && !isMerged && wigOutType == wigOutData)
	    resultCount = bigWigIntervalDump(bwf, region->chrom, region->start, region->end,
		    maxOut, stdout);
	/* Pretty easy case, still do it ourselves. */
	else if (!isMerged && wigOutType == wigOutData)
	    {
	    double ll, ul;
	    enum wigCompare cmp;
	    getWigFilter(database, curTable, &cmp, &ll, &ul);
	    struct lm *lm = lmInit(0);
	    struct bbiInterval *ivList, *iv;
	    ivList = intersectedFilteredBbiIntervalsOnRegion(conn, bwf, region, cmp, ll, ul, lm);
	    for (iv=ivList; iv != NULL && resultCount < maxOut; iv = iv->next, ++resultCount)
	        {
		fprintf(stdout, "%s\t%d\t%d\t%g\n", region->chrom, iv->start, iv->end, iv->val);
		}
	    lmCleanup(&lm);
	    }
	/* Harder cases - resort to making a data vector and letting that machinery handle it. */
	else
	    {
	    struct dataVector *dv = bigWigDataVector(table, conn, region);
	    resultCount = wigPrintDataVectorOut(dv, wigOutType, maxOut, NULL);
	    dataVectorFree(&dv);
	    }
	}
    bbiFileClose(&bwf);
    }
freeMem(wigFileName);
return resultCount;
}
コード例 #5
0
ファイル: filterFields.c プロジェクト: noelnamai/kent
void doOutSelectedFields(char *table, struct sqlConnection *conn)
/* Put up select fields (for tab-separated output) page. */
{
if (anySubtrackMerge(database, curTable))
    errAbort("Can't do selected fields output when subtrack merge is on. "
    "Please go back and select another output type, or clear the subtrack merge.");
else if (anyIntersection())
    errAbort("Can't do selected fields output when intersection is on. "
    "Please go back and select another output type, or clear the intersection.");
else
    {
    char *fsTable = cartOptionalString(cart, hgtaFieldSelectTable);
    char *dbTable = NULL;
    table = connectingTableForTrack(table);
    dbTable = getDbTable(database, table);
    /* Remove cart state if table has been changed: */
    if (fsTable && ! sameString(fsTable, dbTable))
	{
	cartRemovePrefix(cart, hgtaFieldSelectPrefix);
	cartRemove(cart, hgtaFieldSelectTable);
	}
    doBigSelectPage(database, table);
    }
}
コード例 #6
0
ファイル: bedList.c プロジェクト: Nicholas-NVS/kentUtils
boolean doGetBedOrCt(struct sqlConnection *conn, boolean doCt,
                     boolean doCtFile, boolean redirectToGb)
/* Actually output bed or custom track. Return TRUE unless no results. */
{
char *db = cloneString(database);
char *table = curTable;
struct hTableInfo *hti = getHti(db, table, conn);
struct featureBits *fbList = NULL, *fbPtr;
struct customTrack *ctNew = NULL;
boolean doCtHdr = (cartUsualBoolean(cart, hgtaPrintCustomTrackHeaders, FALSE)
	|| doCt || doCtFile);
char *ctWigOutType = cartCgiUsualString(cart, hgtaCtWigOutType, outWigData);
char *fbQual = fbOptionsToQualifier();
char fbTQ[128];
int fields = hTableInfoBedFieldCount(hti);
boolean gotResults = FALSE;
struct region *region, *regionList = getRegions();
boolean isBedGr = isBedGraph(curTable);
boolean isBgWg = isBigWigTable(curTable);
boolean needSubtrackMerge = anySubtrackMerge(database, curTable);
boolean doDataPoints = FALSE;
boolean isWig = isWiggle(database, table);
struct wigAsciiData *wigDataList = NULL;
struct dataVector *dataVectorList = NULL;
boolean doRgb = bedItemRgb(hTrackDbForTrack(db, curTable));

if (!cartUsualBoolean(cart, hgtaDoGreatOutput, FALSE) && !doCt)
    {
    textOpen();
    }

if (cartUsualBoolean(cart, hgtaDoGreatOutput, FALSE))
    fputs("#", stdout);

if ((isWig || isBedGr || isBgWg) && sameString(outWigData, ctWigOutType))
    doDataPoints = TRUE;

for (region = regionList; region != NULL; region = region->next)
    {
    struct bed *bedList = NULL, *bed;
    struct lm *lm = lmInit(64*1024);
    struct dataVector *dv = NULL;

    if (isWig && doDataPoints)
        {
        if (needSubtrackMerge)
            {
            dv = wiggleDataVector(curTrack, curTable, conn, region);
            if (dv != NULL)
                slAddHead(&dataVectorList, dv);
            }
        else
            {
            int count = 0;
            struct wigAsciiData *wigData = NULL;
            struct wigAsciiData *asciiData;
            struct wigAsciiData *next;

            wigData = getWiggleAsData(conn, curTable, region);
            for (asciiData = wigData; asciiData; asciiData = next)
                {
                next = asciiData->next;
                if (asciiData->count)
                    {
                    slAddHead(&wigDataList, asciiData);
                    ++count;
                    }
                }
            slReverse(&wigDataList);
            }
        }
    else if (isBedGr && doDataPoints)
        {
        dv = bedGraphDataVector(curTable, conn, region);
        if (dv != NULL)
            slAddHead(&dataVectorList, dv);
        }
    else if (isBgWg && doDataPoints)
        {
        dv = bigWigDataVector(curTable, conn, region);
        if (dv != NULL)
            slAddHead(&dataVectorList, dv);
        }
    else if (isWig || isBgWg)
        {
        dv = wiggleDataVector(curTrack, curTable, conn, region);
        bedList = dataVectorToBedList(dv);
        dataVectorFree(&dv);
        }
    else if (isBedGr)
        {
        bedList = getBedGraphAsBed(conn, curTable, region);
        }
    else
        {
        bedList = cookedBedList(conn, curTable, region, lm, &fields);
        }

    /*  this is a one-time only initial creation of the custom track
     *  structure to receive the results.  gotResults turns it off after
     *  the first time.
     */
    if (doCtHdr && !gotResults &&
	((bedList != NULL) || (wigDataList != NULL) ||
         (dataVectorList != NULL)))
        {
        ctNew = beginCustomTrack(table, fields,
                                 doCt, (isWig || isBedGr || isBgWg), doDataPoints);
        }

    if (doDataPoints && (wigDataList || dataVectorList))
        gotResults = TRUE;
    else
        {
        if ((fbQual == NULL) || (fbQual[0] == 0))
            {
            for (bed = bedList;  bed != NULL;  bed = bed->next)
                {
                if (bed->name != NULL)
                    {
                    subChar(bed->name, ' ', '_');
                    }
                if (doCt)
                    {
                    struct bed *dupe = cloneBed(bed); /* Out of local memory. */
                    slAddHead(&ctNew->bedList, dupe);
                    }
                else
                    {
                    if (doRgb)
                        bedTabOutNitemRgb(bed, fields, stdout);
                    else
                        bedTabOutN(bed, fields, stdout);
                    }

                gotResults = TRUE;
                }
            }
        else
            {
            safef(fbTQ, sizeof(fbTQ), "%s:%s", hti->rootName, fbQual);
            fbList = fbFromBed(db, fbTQ, hti, bedList, 0, 0, FALSE, FALSE);
            if (fields >= 6)
                fields = 6;
            else if (fields >= 4)
                fields = 4;
            else
                fields = 3;
            if (doCt && ctNew)
                {
                ctNew->fieldCount = fields;
                safef(ctNew->tdb->type, strlen(ctNew->tdb->type)+1,
                      "bed %d", fields);
                }
            for (fbPtr=fbList;  fbPtr != NULL;  fbPtr=fbPtr->next)
                {
                if (fbPtr->name != NULL)
                    {
                    char *ptr = strchr(fbPtr->name, ' ');
                    if (ptr != NULL)
                        *ptr = 0;
                    }
                if (doCt)
                    {
                    struct bed *fbBed = fbToBedOne(fbPtr);
                    slAddHead(&ctNew->bedList, fbBed );
                    }
                else
                    {
                    if (fields >= 6)
                        hPrintf("%s\t%d\t%d\t%s\t%d\t%c\n",
                                fbPtr->chrom, fbPtr->start, fbPtr->end, fbPtr->name,
                                0, fbPtr->strand);
                    else if (fields >= 4)
                        hPrintf("%s\t%d\t%d\t%s\n",
                                fbPtr->chrom, fbPtr->start, fbPtr->end, fbPtr->name);
                    else
                        hPrintf("%s\t%d\t%d\n",
                                fbPtr->chrom, fbPtr->start, fbPtr->end);
                    }
                gotResults = TRUE;
                }
            featureBitsFreeList(&fbList);
            }
        }
    bedList = NULL;
    lmCleanup(&lm);
    }
if (!gotResults)
    {
    hPrintf(NO_RESULTS);
    }
else if (doCt)
    {
    int wigDataSize = 0;
    /* Load existing custom tracks and add this new one: */
    struct customTrack *ctList = getCustomTracks();
    removeNamedCustom(&ctList, ctNew->tdb->table);
    if (doDataPoints)
        {
        if (needSubtrackMerge || isBedGr || isBgWg)
            {
            slReverse(&dataVectorList);
            wigDataSize = dataVectorWriteWigAscii(dataVectorList, ctNew->wigAscii, 0, NULL);
            // TODO: see if can make prettier wig output here that
            // doesn't necessarily have one value per base
            }
        else
            {
            struct wiggleDataStream *wds = NULL;
            /* create an otherwise empty wds so we can print out the list */
            wds = wiggleDataStreamNew();
            wds->ascii = wigDataList;
            wigDataSize = wds->asciiOut(wds, db, ctNew->wigAscii, TRUE, FALSE);
#if defined(DEBUG)    /*      dbg     */
            /* allow file readability for debug */
            chmod(ctNew->wigAscii, 0666);
#endif
            wiggleDataStreamFree(&wds);
            }
        }
    else
        slReverse(&ctNew->bedList);

    slAddHead(&ctList, ctNew);
    /* Save the custom tracks out to file (overwrite the old file): */
    customTracksSaveCart(db, cart, ctList);
    /*  Put up redirect-to-browser page. */
    if (redirectToGb)
        {
        char browserUrl[256];
        char headerText[512];
        int redirDelay = 3;
        safef(browserUrl, sizeof(browserUrl),
              "%s?%s&db=%s", hgTracksName(), cartSidUrlString(cart), database);
        safef(headerText, sizeof(headerText),
              "<META HTTP-EQUIV=\"REFRESH\" CONTENT=\"%d;URL=%s\">",
              redirDelay, browserUrl);
        webStartHeader(cart, database, headerText,
                       "Table Browser: %s %s: %s", hOrganism(database),
                       freezeName, "get custom track");
        if (doDataPoints)
            {
            hPrintf("There are %d data points in custom track. ", wigDataSize);
            }
        else
            {
            hPrintf("There are %d items in custom track. ",
                    slCount(ctNew->bedList));
            }
        hPrintf("You will be automatically redirected to the genome browser in\n"
                "%d seconds, or you can \n"
                "<A HREF=\"%s\">click here to continue</A>.\n",
                redirDelay, browserUrl);
        }
    }
else if (doDataPoints)
    {
    if (needSubtrackMerge || isBedGr || isBgWg)
        {
        slReverse(&dataVectorList);
        dataVectorWriteWigAscii(dataVectorList, "stdout", 0, NULL);
        }
    else
        {
        /*	create an otherwise empty wds so we can print out the list */
        struct wiggleDataStream *wds = NULL;
        wds = wiggleDataStreamNew();
        wds->ascii = wigDataList;
        wds->asciiOut(wds, db, "stdout", TRUE, FALSE);
        wiggleDataStreamFree(&wds);
        }
    }
return gotResults;
}
コード例 #7
0
ファイル: bedList.c プロジェクト: Nicholas-NVS/kentUtils
void doBedOrCtOptions(char *table, struct sqlConnection *conn,
                      boolean doCt)
/* Put up form to get options on BED or custom track output. */
/* (Taken from hgText.c/doBedCtOptions) */
{
char *table2 = NULL;	/* For now... */
struct hTableInfo *hti = getHti(database, table, conn);
char buf[256];
char *setting;
htmlOpen("Output %s as %s", table, (doCt ? "Custom Track" : "BED"));
if (doGalaxy())
    startGalaxyForm();
else if (doGreat())
    {
    verifyGreatAssemblies();
    startGreatForm();
    }
else
    hPrintf("<FORM ACTION=\"%s\" METHOD=GET>\n", getScriptName());
cartSaveSession(cart);
if (!doGreat())
{
    hPrintf("%s\n", "<TABLE><TR><TD>");
    if (doCt)
        {
        hPrintf("%s\n", "</TD><TD>"
                "<A HREF=\"../goldenPath/help/customTrack.html\" TARGET=_blank>"
                "Custom track</A> header: </B>");
        }
    else
        {
        cgiMakeCheckBox(hgtaPrintCustomTrackHeaders,
                        cartCgiUsualBoolean(cart, hgtaPrintCustomTrackHeaders, FALSE));
        hPrintf("%s\n", "</TD><TD> <B> Include "
                        "<A HREF=\"../goldenPath/help/customTrack.html\" TARGET=_blank>"
                        "custom track</A> header: </B>");
        }
    hPrintf("%s\n", "</TD></TR><TR><TD></TD><TD>name=");
    safef(buf, sizeof(buf), "tb_%s", hti->rootName);
    setting = cgiUsualString(hgtaCtName, buf);
    cgiMakeTextVar(hgtaCtName, setting, 16);
    hPrintf("%s\n", "</TD></TR><TR><TD></TD><TD>description=");
    safef(buf, sizeof(buf), "table browser query on %s%s%s",
          table, (table2 ? ", " : ""), (table2 ? table2 : ""));
    setting = cgiUsualString(hgtaCtDesc, buf);
    cgiMakeTextVar(hgtaCtDesc, setting, 50);
    hPrintf("%s\n", "</TD></TR><TR><TD></TD><TD>visibility=");
    if (isWiggle(database, table) || isBigWigTable(table))
        {
        setting = cartCgiUsualString(cart, hgtaCtVis, ctVisWigMenu[2]);
        cgiMakeDropList(hgtaCtVis, ctVisWigMenu, ctVisWigMenuSize, setting);
        }
    else
        {
        setting = cartCgiUsualString(cart, hgtaCtVis, ctVisMenu[3]);
        cgiMakeDropList(hgtaCtVis, ctVisMenu, ctVisMenuSize, setting);
        }
    hPrintf("%s\n", "</TD></TR><TR><TD></TD><TD>url=");
    setting = cartCgiUsualString(cart, hgtaCtUrl, "");
    cgiMakeTextVar(hgtaCtUrl, setting, 50);
    hPrintf("%s\n", "</TD></TR><TR><TD></TD><TD>");
    hPrintf("%s\n", "</TD></TR></TABLE>");
}
if (isWiggle(database, table) || isBedGraph(table) || isBigWigTable(table) )
    {
    char *setting = NULL;
    hPrintf("<P> <B> Select type of data output: </B> <BR>\n");
    setting = cartCgiUsualString(cart, hgtaCtWigOutType, outWigData);
    cgiMakeRadioButton(hgtaCtWigOutType, outWigBed, sameString(setting, outWigBed));
    hPrintf("BED format (no data value information, only position)<BR>\n");
    cgiMakeRadioButton(hgtaCtWigOutType, outWigData, sameString(setting, outWigData));
    hPrintf("DATA VALUE format (position and real valued data)</P>\n");
    }
else
    {
    cgiDown(0.9);
    hPrintf("<B> Create one BED record per: </B>\n");
    if ((anyIntersection() && intersectionIsBpWise()) ||
	(anySubtrackMerge(database, table) && subtrackMergeIsBpWise()))
	{
        /* The original table may have blocks/CDS, described in hti, but
         * that info will be lost after base pair-wise operations.  So make
         * a temporary copy of hti with its flags tweaked: */
	struct hTableInfo simplifiedHti;
	memcpy(&simplifiedHti, hti, sizeof(simplifiedHti));
	simplifiedHti.hasBlocks = FALSE;
	simplifiedHti.hasCDS = FALSE;
	fbOptionsHtiCart(&simplifiedHti, cart);
	}
    else
	fbOptionsHtiCart(hti, cart);
    }
if (doCt)
    {
    if (doGalaxy())
        {
        /* send the action parameter with the form as well */
        cgiMakeHiddenVar(hgtaDoGetCustomTrackFile, "get custom track in file");
        printGalaxySubmitButtons();
        }
    else
        {
        cgiMakeButton(hgtaDoGetCustomTrackTb, "get custom track in table browser");
        hPrintf(" ");
        cgiMakeButton(hgtaDoGetCustomTrackFile, "get custom track in file");
        hPrintf("<BR>\n");
        cgiMakeButton(hgtaDoGetCustomTrackGb, "get custom track in genome browser");
        }
    }
else
    {
    if (doGalaxy())
        {
        cgiMakeHiddenVar(hgtaDoGetBed, "get BED");
        printGalaxySubmitButtons();
        }
    else if (doGreat())
        {
        cgiMakeHiddenVar(hgtaDoGetBed, "get BED");
        printGreatSubmitButtons();
        }
    else
        cgiMakeButton(hgtaDoGetBed, "get BED");
    }
if (!doGalaxy() && !doGreat())
    {
    hPrintf(" ");
    cgiMakeButton(hgtaDoMainPage, "cancel");
    hPrintf("</FORM>\n");
    }
cgiDown(0.9);
htmlClose();
}
コード例 #8
0
ファイル: wiggle.c プロジェクト: ucscGenomeBrowser/kent
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> &nbsp; </TD>\n");	/*	chromStart	*/
    hPrintf("\t<TD> &nbsp; </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("&nbsp;(%.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)	*/
コード例 #9
0
ファイル: wiggle.c プロジェクト: ucscGenomeBrowser/kent
static void doOutWig(struct trackDb *track, char *table, struct sqlConnection *conn,
	enum wigOutputType wigOutType)
{
struct region *regionList = getRegions(), *region;
int maxOut = 0, outCount, curOut = 0;
char *shortLabel = table, *longLabel = table;

if (track == NULL)
    errAbort("Sorry, can't find necessary track information for %s.  "
	     "If you reached this page by selecting \"All tables\" as the "
	     "group, please go back and select the same table via a regular "
	     "track group if possible.",
	     table);

maxOut = bigFileMaxOutput();

if (cartUsualBoolean(cart, hgtaDoGreatOutput, FALSE))
    fputs("#", stdout);
else
    textOpen();

if (track != NULL)
    {
    if (!sameString(track->table, table) && track->subtracks != NULL)
	{
	struct slRef *tdbRefList = trackDbListGetRefsToDescendantLeaves(track->subtracks);
	struct slRef *tdbRef;
	for (tdbRef = tdbRefList; tdbRef != NULL; tdbRef = tdbRef->next)
	    {
	    struct trackDb *tdb = tdbRef->val;
	    if (sameString(tdb->table, table))
		{
		track = tdb;
		break;
		}
	    }
	slFreeList(&tdbRefList);
	}
    shortLabel = track->shortLabel;
    longLabel = track->longLabel;
    }
wigDataHeader(shortLabel, longLabel, NULL, wigOutType);

for (region = regionList; region != NULL; region = region->next)
    {
    int curMaxOut = maxOut - curOut;
    if (anySubtrackMerge(database, table))
	outCount = mergedWigOutRegion(table, conn, region, curMaxOut,
				      wigOutType);
    else if (startsWithWord("bedGraph", track->type))
	outCount = bedGraphOutRegion(table, conn, region, curMaxOut,
				     wigOutType);
    else if (startsWithWord("mathWig", track->type))
        outCount = mathWigOutRegion(track, table, conn, region, curMaxOut, wigOutType);
    else if (startsWithWord("bigWig", track->type))
        outCount = bigWigOutRegion(table, conn, region, curMaxOut, wigOutType);
    else
	outCount = wigOutRegion(table, conn, region, curMaxOut,
				wigOutType, NULL, 0);
    curOut += outCount;
    if (curOut >= maxOut)
        break;
    }
if (curOut >= maxOut)
    errAbort("Reached output limit of %d data values, please make region smaller,\n\tor set a higher output line limit with the filter settings.", curOut);
}
コード例 #10
0
ファイル: intersect.c プロジェクト: Nicholas-NVS/kentUtils
struct bed *getRegionAsMergedBed(
	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. */
	int *retFieldCount)	/* Number of fields. */
/* Return a bed list of all items in the given range in subtrack-merged table.
 * Cleanup result via lmCleanup(&lm) rather than bedFreeList.  */
{
if (! anySubtrackMerge(db, table))
    return getRegionAsBed(db, table, region, filter, idHash, lm, retFieldCount);
else
    {
    struct hTableInfo *hti = getHtiOnDb(database, table);
    int chromSize = hChromSize(database, region->chrom);
    Bits *bits1 = NULL;
    Bits *bits2 = NULL;
    struct bed *bedMerged = NULL;
    struct trackDb *subtrack = NULL;
    char *primaryType = findTypeForTable(database,curTrack,table, ctLookupName);
    char *op = cartString(cart, hgtaSubtrackMergeOp);
    boolean isBpWise = (sameString(op, "and") || sameString(op, "or"));
    double moreThresh = cartDouble(cart, hgtaSubtrackMergeMoreThreshold);
    double lessThresh = cartDouble(cart, hgtaSubtrackMergeLessThreshold);
    boolean firstTime = TRUE;
    if (sameString(op, "cat"))
	{
	struct bed *bedList = getRegionAsBed(db, table, region, filter,
					     idHash, lm, retFieldCount);
	struct slRef *tdbRefList = trackDbListGetRefsToDescendantLeaves(curTrack->subtracks);
	struct slRef *tdbRef;
	for (tdbRef = tdbRefList; tdbRef != NULL; tdbRef = tdbRef->next)
	    {
	    subtrack = tdbRef->val;
	    if (! sameString(curTable, subtrack->table) &&
		isSubtrackMerged(subtrack->table) &&
		sameString(subtrack->type, primaryType))
		{
		struct bed *bedList2 =
		    getRegionAsBed(db, subtrack->table, region, NULL,
				   idHash, lm, retFieldCount);
		bedList = slCat(bedList, bedList2);
		}
	    }
	slFreeList(&tdbRefList);
	return bedList;
	}
    bits1 = bitAlloc(chromSize+8);
    bits2 = bitAlloc(chromSize+8);
    /* If doing a base-pair-wise operation, then start with the primary
     * subtrack's ranges in bits1, and AND/OR all the selected subtracks'
     * ranges into bits1.  If doing a non-bp-wise intersection, then
     * start with all bits clear in bits1, and then OR selected subtracks'
     * ranges into bits1.  */
    if (isBpWise)
	{
	struct lm *lm2 = lmInit(64*1024);
	struct bed *bedList1 = getRegionAsBed(db, table, region, filter,
					      idHash, lm2, retFieldCount);
	bedOrBits(bits1, chromSize, bedList1, hti->hasBlocks, 0);
	lmCleanup(&lm2);
	}
    struct slRef *tdbRefList = trackDbListGetRefsToDescendantLeaves(curTrack->subtracks);
    struct slRef *tdbRef;
    for (tdbRef = tdbRefList; tdbRef != NULL; tdbRef = tdbRef->next)
	{
	subtrack = tdbRef->val;
	if (! sameString(curTable, subtrack->table) &&
	    isSubtrackMerged(subtrack->table) &&
	    sameString(subtrack->type, primaryType))
	    {
	    struct hTableInfo *hti2 = getHtiOnDb(database, subtrack->table);
	    struct lm *lm2 = lmInit(64*1024);
	    struct bed *bedList2 =
		getRegionAsBed(db, subtrack->table, region, NULL, idHash,
			       lm2, NULL);
	    if (firstTime)
		firstTime = FALSE;
	    else
		bitClear(bits2, chromSize);
	    bedOrBits(bits2, chromSize, bedList2, hti2->hasBlocks, 0);
	    if (sameString(op, "and"))
		bitAnd(bits1, bits2, chromSize);
	    else
		bitOr(bits1, bits2, chromSize);
	    lmCleanup(&lm2);
	    }
	}
    slFreeList(&tdbRefList);
    if (isBpWise)
	{
	bedMerged = bitsToBed4List(bits1, chromSize, region->chrom, 1,
				   region->start, region->end, lm);
	if (retFieldCount != NULL)
	    *retFieldCount = 4;
	}
    else
	{
	struct bed *bedList1 = getRegionAsBed(db, table, region, filter,
					      idHash, lm, retFieldCount);
	bedMerged = filterBedByOverlap(bedList1, hti->hasBlocks, op,
				       moreThresh, lessThresh, bits1,
				       chromSize);
	}
    bitFree(&bits1);
    bitFree(&bits2);
    return bedMerged;
    }
}
コード例 #11
0
ファイル: mainPage.c プロジェクト: davidhoover/kent
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("&nbsp;<span"NO_GENOME_CLASS">genome (unavailable for selected track)</span>"
                "&nbsp;");
        }
    else
        {
        makeRegionButton(hgtaRegionTypeGenome, regionType);
        hPrintf("&nbsp;genome&nbsp;");
        }
    if (doEncode)
        {
	makeRegionButton(hgtaRegionTypeEncode, regionType);
	hPrintf("&nbsp;ENCODE Pilot regions&nbsp;");
	}
    makeRegionButton(hgtaRegionTypeRange, regionType);
    hPrintf("&nbsp;position&nbsp;");
    hPrintf("<INPUT TYPE=TEXT NAME=\"%s\" SIZE=26 VALUE=\"%s\" onFocus=\"%s\">\n",
    	hgtaRange, range, jsRadioUpdate(hgtaRegionType, "regionType", "range"));
    cgiMakeButton(hgtaDoLookupPosition, "lookup");
    hPrintf("&nbsp;");
    if (userRegionsFileName() != NULL)
	{
	makeRegionButton(hgtaRegionTypeUserRegions, regionType);
	hPrintf("&nbsp;defined regions&nbsp;");
	cgiMakeButton(hgtaDoSetUserRegions, "change");
	hPrintf("&nbsp;");
	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("&nbsp;");
	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("&nbsp;(with:&nbsp;&nbsp;%s)", tdb2->shortLabel);

#ifdef NOT_YET
        /* debugging 	dbg	vvvvv	*/
        if (curTrack && curTrack->type)		/*	dbg	*/
            {
            hPrintf("<BR>&nbsp;(debug:&nbsp;'%s',&nbsp;'%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>&nbsp;");
    cgiMakeTextVar(hgtaOutFileName, fileName, 29);
    hPrintf("&nbsp;(leave blank to keep output in browser)</TD></TR>\n");
    hPrintf("<TR><TD>\n");
    hPrintf("<B>file type returned:&nbsp;</B>");
    cgiMakeRadioButton(hgtaCompressType, textOutCompressNone,
	sameWord(textOutCompressNone, compressType));
    hPrintf("&nbsp;plain text&nbsp&nbsp");
    cgiMakeRadioButton(hgtaCompressType, textOutCompressGzip,
	sameWord(textOutCompressGzip, compressType));
    hPrintf("&nbsp;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());

}
コード例 #12
0
ファイル: mainPage.c プロジェクト: davidhoover/kent
static void showOutputTypeRow(boolean isWig, boolean isBedGr,
    boolean isPositional, boolean isMaf, boolean isChromGraphCt,
    boolean isPal, boolean isMicroarray, boolean isHalSnake)
/* Print output line. */
{
struct outputType *otList = NULL, *otDefault = NULL;
boolean bedifiedOnly = (anySubtrackMerge(database, curTable) || anyIntersection());

hPrintf("<TR><TD><B>output format:</B>\n");

if (isBedGr)
    {
    if (! bedifiedOnly)
	{
	slAddTail(&otList, &otAllFields);
	slAddTail(&otList, &otSelected);
	}
    slAddTail(&otList, &otWigData);
    slAddTail(&otList, &otWigBed);
    slAddTail(&otList, &otCustomTrack);
    slAddTail(&otList, &otHyperlinks);
    }
else if (isWig)
    {
    slAddTail(&otList, &otWigData);
    slAddTail(&otList, &otWigBed);
    slAddTail(&otList, &otCustomTrack);
    // hyperlinks output works for db-wiggle but not for bigWig
    }
else if (isHalSnake)
    {
    slAddTail(&otList, &otMaf);
    }
else if (isMaf)
    {
    slAddTail(&otList, &otMaf);
    if (! bedifiedOnly)
	slAddTail(&otList, &otAllFields);
    }
else if (isChromGraphCt)
    {
    slAddTail(&otList, &otChromGraphData);
    }
else if (isMicroarray)
    {
    slAddTail(&otList, &otMicroarrayNames);
    slAddTail(&otList, &otAllFields);
    slAddTail(&otList, &otSelected);
    slAddTail(&otList, &otHyperlinks);
    }
else if (isPositional)
    {
    if (! bedifiedOnly)
	{
	slAddTail(&otList, &otAllFields);
	slAddTail(&otList, &otSelected);
	}
    else
	otDefault = &otBed;
    slAddTail(&otList, &otSequence);
    slAddTail(&otList, &otGff);
    if (isPal)
	slAddTail(&otList, &otPal);
    slAddTail(&otList, &otBed);
    slAddTail(&otList, &otCustomTrack);
    slAddTail(&otList, &otHyperlinks);
    }
else
    {
    slAddTail(&otList, &otAllFields);
    slAddTail(&otList, &otSelected);
    }
showOutDropDown(otList, otDefault);
}
コード例 #13
0
ファイル: bigWig.c プロジェクト: davidhoover/kent
void doSummaryStatsBigWig(struct sqlConnection *conn)
/* Put up page showing summary stats for bigWig track. */
{
struct trackDb *track = curTrack;
char *table = curTable;
char *shortLabel = (track == NULL ? table : track->shortLabel);
char *fileName = bigWigFileName(table, conn);
long startTime = clock1000();

htmlOpen("%s (%s) Big Wig 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);

struct bbiFile *bwf = bigWigFileOpen(fileName);
struct region *region, *regionList = getRegions();
double sumData = 0, sumSquares = 0, minVal = 0, maxVal = 0;
bits64 validCount = 0;

if (!anyFilter() && !anyIntersection())
    {
    for (region = regionList; region != NULL; region = region->next)
	{
	struct bbiSummaryElement sum;
	if (bbiSummaryArrayExtended(bwf, region->chrom, region->start, region->end,
		bigWigIntervalQuery, 1, &sum))
	    {
	    if (validCount == 0)
		{
		minVal = sum.minVal;
		maxVal = sum.maxVal;
		}
	    else
	        {
		if (sum.minVal < minVal)
		    minVal = sum.minVal;
		if (sum.maxVal > maxVal)
		    maxVal = sum.maxVal;
		}
	    sumData += sum.sumData;
	    sumSquares += sum.sumSquares;
	    validCount += sum.validCount;
	    }
	}
    }
else
    {
    double ll, ul;
    enum wigCompare cmp;
    getWigFilter(database, curTable, &cmp, &ll, &ul);
    for (region = regionList; region != NULL; region = region->next)
        {
	struct lm *lm = lmInit(0);
	struct bbiInterval *iv, *ivList;
	ivList = intersectedFilteredBbiIntervalsOnRegion(conn, bwf, region, cmp, ll, ul, lm);
	for (iv = ivList; iv != NULL; iv = iv->next)
	    {
	    double val = iv->val;
	    double size = iv->end - iv->start;
	    if (validCount == 0)
		minVal = maxVal = val;
	    else
	        {
		if (val < minVal)
		    minVal = val;
		if (val > maxVal)
		    maxVal = val;
		}
	    sumData += size*val;
	    sumSquares += size*val*val;
	    validCount += size;
	    }
	lmCleanup(&lm);
	}
    }

hTableStart();
floatStatRow("mean", sumData/validCount);
floatStatRow("min", minVal);
floatStatRow("max", maxVal);
floatStatRow("standard deviation", calcStdFromSums(sumData, sumSquares, validCount));
numberStatRow("bases with data", validCount);
long long regionSize = basesInRegion(regionList,0);
long long gapTotal = gapsInRegion(conn, regionList,0);
numberStatRow("bases with sequence", regionSize - gapTotal);
numberStatRow("bases in region", regionSize);
wigFilterStatRow(conn);
stringStatRow("intersection", cartUsualString(cart, hgtaIntersectTable, "off"));
long wigFetchTime = clock1000() - startTime;
floatStatRow("load and calc time", 0.001*wigFetchTime);
hTableEnd();

bbiFileClose(&bwf);
htmlClose();
}