void tigrOperonMethods(struct track *tg)
{
linkedFeaturesMethods(tg);
tg->loadItems = loadOperon;
tg->colorShades = shadesOfGray;
tg->drawItemAt = tigrOperonDrawAt;
}
void bamMethods(struct track *track)
/* Methods for BAM alignment files. */
{
knetUdcInstall();
boolean isBamWig = cartUsualBooleanClosestToHome(cart, track->tdb, FALSE,
BAMWIG_MODE, (trackDbSettingClosestToHome(track->tdb, BAMWIG_MODE) != NULL));
if (isBamWig)
{
bamWigMethods(track, track->tdb, 0, NULL);
return;
}
track->canPack = TRUE;
boolean isPaired = cartUsualBooleanClosestToHome(cart, track->tdb, FALSE,
BAM_PAIR_ENDS_BY_NAME,
(trackDbSettingClosestToHome(track->tdb, BAM_PAIR_ENDS_BY_NAME) != NULL));
char *tdbShowNames = trackDbSetting(track->tdb, BAM_SHOW_NAMES);
boolean showNames = cartUsualBooleanClosestToHome(cart, track->tdb, FALSE,
BAM_SHOW_NAMES, SETTING_IS_ON(tdbShowNames));
char *colorMode = cartOrTdbString(cart, track->tdb, BAM_COLOR_MODE, BAM_COLOR_MODE_DEFAULT);
char *userTag = cartOrTdbString(cart, track->tdb, BAM_COLOR_TAG, BAM_COLOR_TAG_DEFAULT);
if (sameString(colorMode, BAM_COLOR_MODE_TAG) && userTag != NULL)
{
if (! (isalpha(userTag[0]) && isalnum(userTag[1]) && userTag[2] == '\0'))
{
warn("%s: BAM tag '%s' is not valid -- must be a letter followed by a letter or number.",
track->tdb->shortLabel, htmlEncode(userTag));
cartRemoveVariableClosestToHome(cart, track->tdb, FALSE, BAM_COLOR_TAG);
}
}
addBamBaseAndIndelSettings(track->tdb);
if (isPaired)
{
linkedFeaturesSeriesMethods(track);
track->loadItems = bamPairedLoadItems;
track->drawItems = bamLinkedFeaturesSeriesDraw;
track->drawItemAt = bamPairedDrawAt;
}
else
{
linkedFeaturesMethods(track);
track->loadItems = bamLoadItems;
track->drawItems = bamLinkedFeaturesDraw;
track->drawItemAt = bamDrawAt;
}
if (!showNames)
{
track->drawName = TRUE; // ironic, but this is how to suppress item labels in pack mode.
track->drawLeftLabels = maybeDrawLeftLabels;
}
track->nextItemButtonable = track->nextExonButtonable = FALSE;
track->nextPrevItem = NULL;
track->nextPrevExon = NULL;
if (sameString(colorMode, BAM_COLOR_MODE_GRAY))
track->colorShades = shadesOfGray;
}
void sampleLinkedFeaturesMethods(struct track *tg)
/* Fill in track methods for 'sample' tracks. */
{
linkedFeaturesMethods(tg);
tg->drawItems = wiggleLinkedFeaturesDraw;
tg->totalHeight = sampleTotalHeight;
tg->itemHeight = tgFixedItemHeight;
}
void chainMethods(struct track *tg, struct trackDb *tdb,
int wordCount, char *words[])
/* Fill in custom parts of alignment chains. */
{
struct cartOptions *chainCart;
AllocVar(chainCart);
boolean normScoreAvailable = chainDbNormScoreAvailable(tdb);
/* what does the cart say about coloring option */
chainCart->chainColor = chainFetchColorOption(cart, tdb, FALSE);
chainCart->scoreFilter = cartUsualIntClosestToHome(cart, tdb,
FALSE, SCORE_FILTER, 0);
linkedFeaturesMethods(tg);
tg->itemColor = lfChromColor; /* default coloring option */
/* if normScore column is available, then allow coloring */
if (normScoreAvailable)
{
switch (chainCart->chainColor)
{
case (chainColorScoreColors):
tg->itemColor = chainScoreColor;
tg->colorShades = shadesOfGray;
break;
case (chainColorNoColors):
setNoColor(tg);
break;
default:
case (chainColorChromColors):
break;
}
}
else
{
char *optionStr; /* this old option was broken before */
optionStr = cartUsualStringClosestToHome(cart, tdb, FALSE, "color", "on");
if (differentWord("on",optionStr))
{
setNoColor(tg);
chainCart->chainColor = chainColorNoColors;
}
else
chainCart->chainColor = chainColorChromColors;
}
tg->loadItems = chainLoadItems;
tg->drawItems = chainDraw;
tg->mapItemName = lfMapNameFromExtra;
tg->subType = lfSubChain;
tg->extraUiData = (void *) chainCart;
}
void lrgMethods(struct track *tg)
/* Locus Reference Genomic (bigBed 12 +) handlers. */
{
linkedFeaturesMethods(tg);
tg->canPack = TRUE;
tg->isBigBed = TRUE;
tg->loadItems = lrgLoadItems;
tg->itemName = lrgItemName;
tg->nextPrevExon = simpleBedNextPrevEdge;
}
void cgapSageMethods(struct track *tg)
/* Make track for simple repeats. */
{
linkedFeaturesMethods(tg);
tg->loadItems = cgapSageLoadItems;
tg->itemColor = cgapSageItemColor;
tg->drawItems = cgapSageDrawItems;
tg->mapItemName = cgapSageMapItemName;
tg->mapItem = cgapSageMapItem;
}
void encodePeakMethods(struct track *tg)
/* Methods for ENCODE peak track uses mostly linkedFeatures. */
{
linkedFeaturesMethods(tg);
tg->loadItems = encodePeakLoadItemsNormal;
tg->drawItemAt = encodePeakDrawAt;
tg->nextPrevItem = linkedFeaturesLabelNextPrevItem;
tg->itemName = encodePeakItemName;
tg->canPack = TRUE;
}
void addWikiTrack(struct track **pGroupList)
/* Add wiki track and append to group list. */
{
if (wikiTrackEnabled(database, NULL))
{
struct track *tg = trackNew();
static char longLabel[80];
struct trackDb *tdb;
struct sqlConnection *wikiConn = wikiConnect();
if (! sqlTableExists(wikiConn,WIKI_TRACK_TABLE))
errAbort("loadWikiTrack configuration error, set wikiTrack.URL in hg.conf");
linkedFeaturesMethods(tg);
AllocVar(tdb);
tg->track = WIKI_TRACK_TABLE;
tg->table = WIKI_TRACK_TABLE;
tg->canPack = TRUE;
tg->visibility = tvHide;
tg->hasUi = TRUE;
tg->shortLabel = cloneString(WIKI_TRACK_LABEL);
safef(longLabel, sizeof(longLabel), WIKI_TRACK_LONGLABEL);
tg->longLabel = longLabel;
tg->loadItems = wikiTrackLoadItems;
tg->itemName = linkedFeaturesName;
tg->mapItemName = wikiTrackMapItemName;
tg->mapItem = wikiTrackMapItem;
tg->priority = WIKI_TRACK_PRIORITY;
tg->defaultPriority = WIKI_TRACK_PRIORITY;
tg->groupName = cloneString("map");
tg->defaultGroupName = cloneString("map");
tg->exonArrows = TRUE;
tg->nextItemButtonable = TRUE;
tdb->track = cloneString(tg->track);
tdb->canPack = tg->canPack;
tdb->table = cloneString(tg->table);
tdb->shortLabel = cloneString(tg->shortLabel);
tdb->longLabel = cloneString(tg->longLabel);
tdb->useScore = 1;
tdb->grp = cloneString(tg->groupName);
tdb->priority = tg->priority;
trackDbPolish(tdb);
tg->tdb = tdb;
slAddHead(pGroupList, tg);
wikiDisconnect(&wikiConn);
}
}