Exemplo n.º 1
0
static void addTablesAccordingToTrackType(char *db, struct slName **pList, struct hash *uniqHash,
                                          struct trackDb *track)
/* Parse out track->type and if necessary add some tables from it. */
{
struct slName *name;
char *trackDupe = cloneString(track->type);
if (trackDupe != NULL && trackDupe[0] != 0)
    {
    char *s = trackDupe;
    char *type = nextWord(&s);
    if (sameString(type, "wigMaf"))
        {
	static char *wigMafAssociates[] = {"frames", "summary"};
	int i;
	for (i=0; i<ArraySize(wigMafAssociates); ++i)
	    {
	    char *setting = wigMafAssociates[i];
	    char *table = trackDbSetting(track, setting);
            if (table != NULL)
                {
                name = slNameNew(table);
                slAddHead(pList, name);
                hashAdd(uniqHash, table, NULL);
                }
	    }
        /* include conservation wiggle tables */
        struct consWiggle *wig, *wiggles = wigMafWiggles(db, track);
        slReverse(&wiggles);
        for (wig = wiggles; wig != NULL; wig = wig->next)
            {
            name = slNameNew(wig->table);
            slAddHead(pList, name);
            hashAdd(uniqHash, wig->table, NULL);
            }
	}
    if (track->subtracks)
        {
        struct slName *subList = NULL;
	struct slRef *tdbRefList = trackDbListGetRefsToDescendantLeaves(track->subtracks);
	slSort(&tdbRefList, trackDbRefCmp);
	struct slRef *tdbRef;
	for (tdbRef = tdbRefList; tdbRef != NULL; tdbRef = tdbRef->next)
            {
	    struct trackDb *subTdb = tdbRef->val;
	    name = slNameNew(subTdb->table);
	    slAddTail(&subList, name);
	    hashAdd(uniqHash, subTdb->table, NULL);
            }
        pList = slCat(pList, subList);
        }
    }
freez(&trackDupe);
}
struct consWiggle *consWiggleFind(char *db,struct trackDb *parent,char *table)
/* Return conservation wig if it is found in the parent. */
{
if(parent == NULL || !startsWith("wigMaf", parent->type))
    return NULL;

struct consWiggle *wig, *wiggles = wigMafWiggles(db, parent);
for (wig = wiggles;
     wig != NULL && differentString(wig->table,table);
     wig = wig->next) {}
return wig;
}
Exemplo n.º 3
0
static void mafOrAxtClick2(struct sqlConnection *conn, struct sqlConnection *conn2, struct trackDb *tdb, char *axtOtherDb, char *fileName)
/* Display details for MAF or AXT tracks. */
{
hgBotDelay();
if (winEnd - winStart > 30000)
    {
    printf("Zoom so that window is 30,000 bases or less to see alignments and conservation statistics\n");
    }
else
    {
    struct mafAli *mafList = NULL, *maf, *subList = NULL;
    int aliIx = 0, realCount = 0;
    char dbChrom[64];
    char option[128];
    char *capTrack;
    struct consWiggle *consWig, *consWiggles;
    struct hash *speciesOffHash = NULL;
    char *speciesOrder = NULL;
    char *speciesTarget = trackDbSetting(tdb, SPECIES_TARGET_VAR);
    char buffer[1024];
    int useTarg = FALSE;
    int useIrowChains = FALSE;

    safef(option, sizeof(option), "%s.%s", tdb->track, MAF_CHAIN_VAR);
    if (cartCgiUsualBoolean(cart, option, FALSE) &&
	trackDbSetting(tdb, "irows") != NULL)
	    useIrowChains = TRUE;

    safef(buffer, sizeof(buffer), "%s.vis",tdb->track);
    if (useIrowChains)
	{
	if (!cartVarExists(cart, buffer) && (speciesTarget != NULL))
	    useTarg = TRUE;
	else
	    {
	    char *val;

	    val = cartUsualString(cart, buffer, "useCheck");
            useTarg = sameString("useTarg",val);
            }
        }

    if (sameString(tdb->type, "bigMaf"))
        {
        char *fileName = trackDbSetting(tdb, "bigDataUrl");
        struct bbiFile *bbi = bigBedFileOpen(fileName);
        mafList = bigMafLoadInRegion(bbi, seqName, winStart, winEnd);
        }
    else
        mafList = mafOrAxtLoadInRegion2(conn,conn2, tdb, seqName, winStart, winEnd,
                                        axtOtherDb, fileName);
    safef(dbChrom, sizeof(dbChrom), "%s.%s", hubConnectSkipHubPrefix(database), seqName);

    safef(option, sizeof(option), "%s.speciesOrder", tdb->track);
    speciesOrder = cartUsualString(cart, option, NULL);
    if (speciesOrder == NULL)
	speciesOrder = trackDbSetting(tdb, "speciesOrder");

    for (maf = mafList; maf != NULL; maf = maf->next)
        {
        int mcCount = 0;
        struct mafComp *mc;
        struct mafAli *subset;
        struct mafComp *nextMc;

        /* remove empty components and configured off components
         * from MAF, and ignore
         * the entire MAF if all components are empty
         * (solely for gap annotation) */

        if (!useTarg)
            {
            for (mc = maf->components->next; mc != NULL; mc = nextMc)
		{
		char buf[64];
                char *organism;
		mafSrcDb(mc->src, buf, sizeof buf);
                organism = hOrganism(buf);
                if (!organism)
                    organism = buf;
		nextMc = mc->next;
		safef(option, sizeof(option), "%s.%s", tdb->track, buf);
		if (!cartUsualBoolean(cart, option, TRUE))
		    {
		    if (speciesOffHash == NULL)
			speciesOffHash = newHash(4);
		    hashStoreName(speciesOffHash, organism);
		    }
		if (!cartUsualBoolean(cart, option, TRUE))
		    slRemoveEl(&maf->components, mc);
		else
		    mcCount++;
		}
	    }
        if (mcCount == 0)
            continue;

	if (speciesOrder)
	    {
	    int speciesCt;
	    char *species[2048];
	    struct mafComp **newOrder, *mcThis;
	    int i;

	    mcCount = 0;
	    speciesCt = chopLine(cloneString(speciesOrder), species);
	    newOrder = needMem((speciesCt + 1) * sizeof (struct mafComp *));
	    newOrder[mcCount++] = maf->components;

	    for (i = 0; i < speciesCt; i++)
		{
		if ((mcThis = mafMayFindCompSpecies(maf, species[i], '.')) == NULL)
		    continue;
		newOrder[mcCount++] = mcThis;
		}

	    maf->components = NULL;
	    for (i = 0; i < mcCount; i++)
		{
		newOrder[i]->next = 0;
		slAddHead(&maf->components, newOrder[i]);
		}

	    slReverse(&maf->components);
	    }
	subset = mafSubsetE(maf, dbChrom, winStart, winEnd, TRUE);
	if (subset != NULL)
	    {
	    /* Reformat MAF if needed so that sequence from current
	     * database is the first component and on the
	     * plus strand. */
	    mafMoveComponentToTop(subset, dbChrom);
	    if (subset->components->strand == '-')
		mafFlipStrand(subset);
	    subset->score = mafScoreMultiz(subset);
	    slAddHead(&subList, subset);
	    ++realCount;
	    }
	}
    slReverse(&subList);
    mafAliFreeList(&mafList);
    if (subList != NULL)
	{
	char *showVarName = "hgc.showMultiBase";
	char *showVarVal = cartUsualString(cart, showVarName, "all");
	boolean onlyDiff = sameWord(showVarVal, "diff");
#ifdef ADDEXONCAPITAL
	char *codeVarName = "hgc.multiCapCoding";
	char *codeVarVal = cartUsualString(cart, codeVarName, "coding");
	boolean onlyCds = sameWord(codeVarVal, "coding");
#endif
        /* add links for conservation score statistics */
        consWiggles = wigMafWiggles(database, tdb);
        int wigCount = slCount(consWiggles);
        if (wigCount == 1)
            {
            conservationStatsLink(tdb, "Conservation score statistics", consWiggles->table);
            }
        else if (wigCount > 1)
            {
            /* multiple wiggles. List all that have been turned on with
             * checkboxes */

            /* Scan for cart variables -- do any exist, are any turned on ? */
            boolean wigSet = FALSE;
            boolean wigOn = FALSE;
            for (consWig = consWiggles; consWig != NULL;
                        consWig = consWig->next)
                {
                char *wigVarSuffix = NULL;
                (void)wigMafWiggleVar(tdb->track, consWig, &wigVarSuffix);
                if (cartVarExistsAnyLevel(cart, tdb, FALSE, wigVarSuffix))
                    {
                    wigSet = TRUE;
                    if (cartBooleanClosestToHome(cart, tdb, FALSE, wigVarSuffix))
                        wigOn = TRUE;
                    }
                }
            /* If there are no cart vars, turn on the first (default) wig */
            if (!wigSet)
                {
                char *prefix = tdb->track; // use when setting things to the cart
                if (tdbIsContainerChild(tdb))
                    prefix = tdbGetContainer(tdb)->track;

                cartSetBoolean(cart, wigMafWiggleVar(prefix, consWiggles, NULL), TRUE);
                wigOn = TRUE;
                }
            if (wigOn)
                {
                boolean first = TRUE;
                for (consWig = consWiggles; consWig != NULL;
                            consWig = consWig->next)
                    {
                    if (first)
                        {
                        printf("Conservation score statistics:");
                        first = FALSE;
                        }
                    char *wigVarSuffix = NULL;
                    (void)wigMafWiggleVar(tdb->track, consWig, &wigVarSuffix);
                    if (cartUsualBooleanClosestToHome(cart, tdb, FALSE, wigVarSuffix,FALSE))
                        {
                        printf("&nbsp;&nbsp;");
                        subChar(consWig->uiLabel, '_', ' ');
                        conservationStatsLink(tdb,
                            consWig->uiLabel, consWig->table);
                        }
                    }
                }
            }
        puts("</P>\n");

        /* no alignment to display when in visibilities where only wiggle is shown */
        char *vis = cartOptionalString(cart, tdb->track);
        if (vis)
            {
            enum trackVisibility tv = hTvFromStringNoAbort(vis);
            if (tv == tvSquish || tv == tvDense)
                return;
            }

#ifdef ADDEXONCAPITAL
	puts("<FORM ACTION=\"../cgi-bin/hgc\" NAME=\"gpForm\" METHOD=\"GET\">");
	cartSaveSession(cart);
	cgiContinueHiddenVar("g");
	cgiContinueHiddenVar("c");
	cgiContinueHiddenVar("i");
	printf("Capitalize ");
        cgiMakeDropListFull(codeVarName, codeAll, codeAll,
	    ArraySize(codeAll), codeVarVal, autoSubmit);
	printf("exons based on ");
        capTrack = genePredDropDown(cart, trackHash,
                                       "gpForm", "hgc.multiCapTrack");
#endif
	printf("show ");
        cgiMakeDropListFull(showVarName, showAll, showAll,
	    ArraySize(showAll), showVarVal, autoSubmit);
	printf("bases");
	printf("<BR>\n");
	printf("</FORM>\n");

#ifdef REVERSESTRAND
        /* notify if bases are complemented (hgTracks is on reverse strand) */
        if (cartCgiUsualBoolean(cart, COMPLEMENT_BASES_VAR, FALSE))
            puts("<EM>Alignment displayed on reverse strand</EM><BR>");
#endif
	puts("Place cursor over species for alignment detail. Click on 'B' to link to browser ");
	puts("for aligned species, click on 'D' to get DNA for aligned species.<BR>");

	printf("<TT><PRE>");

        /* notify if species removed from alignment */
        if (speciesOffHash) 
            {
            char *species;
            struct hashCookie hc = hashFirst(speciesOffHash);
            puts("<B>Components not displayed:</B> ");
            while ((species = hashNextName(&hc)) != NULL)
                printf("%s ", species);
            puts("<BR>");
            }


	for (maf = subList; maf != NULL; maf = maf->next)
	    {
	    mafLowerCase(maf);
#ifdef ADDEXONCAPITAL
	    if (capTrack != NULL)
                capMafOnTrack(maf, capTrack, onlyCds);
#endif
            printf("<B>Alignment block %d of %d in window, %d - %d, %d bps </B>\n",
                   ++aliIx,realCount,maf->components->start + 1,
                   maf->components->start + maf->components->size, maf->components->size);
            mafPrettyOut(stdout, maf, 70,onlyDiff, aliIx);
            }
	mafAliFreeList(&subList);
	}
    else
	{
        printf("No multiple alignment in browser window");
	}
    printf("</PRE></TT>");
    }
}