void loadGappedBed(struct track *tg)
/* Convert bed info in window to linked feature. */
{
struct sqlResult *sr;
char **row;
int rowOffset;
struct bed *bed;
struct linkedFeatures *lfList = NULL, *lf;
struct trackDb *tdb = tg->tdb;
int scoreMin = atoi(trackDbSettingClosestToHomeOrDefault(tdb, "scoreMin", "0"));
int scoreMax = atoi(trackDbSettingClosestToHomeOrDefault(tdb, "scoreMax", "1000"));
boolean useItemRgb = FALSE;
useItemRgb = bedItemRgb(tdb);
if (tg->isBigBed)
{ // avoid opening an unneeded db connection for bigBed; required not to use mysql for parallel fetch tracks
bigBedAddLinkedFeaturesFrom(tg, chromName, winStart, winEnd,
scoreMin, scoreMax, useItemRgb, 12, &lfList);
}
else
{
/* Use tg->tdb->track because subtracks inherit composite track's tdb
* by default, and the variable is named after the composite track. */
struct sqlConnection *conn = hAllocConn(database);
char *scoreFilterClause = getScoreFilterClause(cart, tg->tdb,NULL);
if (scoreFilterClause != NULL)
{
sr = hRangeQuery(conn, tg->table, chromName, winStart, winEnd,scoreFilterClause, &rowOffset);
freeMem(scoreFilterClause);
}
else
{
sr = hRangeQuery(conn, tg->table, chromName, winStart, winEnd, NULL, &rowOffset);
}
while ((row = sqlNextRow(sr)) != NULL)
{
bed = bedLoad12(row+rowOffset);
adjustBedScoreGrayLevel(tdb, bed, scoreMin, scoreMax);
lf = lfFromBedExtra(bed, scoreMin, scoreMax);
if (useItemRgb)
{
lf->extra = (void *)USE_ITEM_RGB; /* signal for coloring */
lf->filterColor=bed->itemRgb;
}
slAddHead(&lfList, lf);
bedFree(&bed);
}
sqlFreeResult(&sr);
hFreeConn(&conn);
}
slReverse(&lfList);
if(tg->extraUiData)
filterBed(tg, &lfList);
slSort(&lfList, linkedFeaturesCmp);
tg->items = lfList;
}
static char *wigCheckBinaryOption(struct trackDb *tdb, char *Default,
char *notDefault, char *tdbString, char *secondTdbString)
/* A common operation for binary options (two values possible)
* check for trackDb.ra, then tdb->settings values
* return one of the two possibilities if found
* (the tdbString and secondTdbString are a result of
* early naming conventions changing over time resulting in
* two possible names for the same thing ...)
*/
{
char *tdbDefault = trackDbSettingClosestToHomeOrDefault(tdb, tdbString, "NONE");
char *ret;
ret = Default; /* the answer, unless found to be otherwise */
if (sameWord("NONE",tdbDefault) && (secondTdbString != (char *)NULL))
tdbDefault = trackDbSettingClosestToHomeOrDefault(tdb, secondTdbString, "NONE");
if (differentWord("NONE",tdbDefault))
{
if (differentWord(Default,tdbDefault))
ret = notDefault;
}
else
{
struct hashEl *hel;
/* no setting from trackDb, maybe it is in tdb->settings
* (custom tracks keep settings here)
*/
if ((tdb->settings != (char *)NULL) &&
(tdb->settingsHash != (struct hash *)NULL))
{
if ((hel = hashLookup(tdb->settingsHash, tdbString)) != NULL)
{
if (differentWord(Default,(char *)hel->val))
ret = notDefault;
}
else if (secondTdbString != (char *)NULL)
{
if ((hel = hashLookup(tdb->settingsHash, secondTdbString)) != NULL)
{
if (differentWord(Default,(char *)hel->val))
ret = notDefault;
}
}
}
}
return(cloneString(ret));
}
void loadBed8(struct track *tg)
/* Convert bed 8 info in window to linked feature. */
{
struct bed *bed;
struct linkedFeatures *lfList = NULL, *lf;
struct trackDb *tdb = tg->tdb;
int scoreMin = atoi(trackDbSettingClosestToHomeOrDefault(tdb, "scoreMin", "0"));
int scoreMax = atoi(trackDbSettingClosestToHomeOrDefault(tdb, "scoreMax", "1000"));
boolean useItemRgb = FALSE;
useItemRgb = bedItemRgb(tdb);
if (tg->isBigBed)
{ // avoid opening an unneeded db connection for bigBed; required not to use mysql for parallel fetch tracks
bigBedAddLinkedFeaturesFrom(tg, chromName, winStart, winEnd,
scoreMin, scoreMax, useItemRgb, 8, &lfList);
}
else
{
struct sqlConnection *conn = hAllocConn(database);
struct sqlResult *sr;
char **row;
int rowOffset;
char *scoreFilterClause = getScoreFilterClause(cart, tg->tdb,NULL);
if (scoreFilterClause != NULL)
{
sr = hRangeQuery(conn, tg->table, chromName, winStart, winEnd,scoreFilterClause, &rowOffset);
freeMem(scoreFilterClause);
}
else
{
sr = hRangeQuery(conn, tg->table, chromName, winStart, winEnd,
NULL, &rowOffset);
}
while ((row = sqlNextRow(sr)) != NULL)
{
bed = bedLoadN(row+rowOffset, 8);
lf = bedMungToLinkedFeatures(&bed, tdb, 8, scoreMin, scoreMax, useItemRgb);
slAddHead(&lfList, lf);
}
sqlFreeResult(&sr);
hFreeConn(&conn);
}
slReverse(&lfList);
slSort(&lfList, linkedFeaturesCmp);
tg->items = lfList;
}
enum netLevelEnum netFetchLevelOption(struct cart *cart, struct trackDb *tdb,
boolean compositeLevel)
/****** netLevelOption - net level 0 (All levels) by default ***********/
{
char *netLevel = NULL;
enum netLevelEnum ret;
netLevel = trackDbSettingClosestToHomeOrDefault(tdb, NET_LEVEL, "0");
/* trackDb can be netLevel=0 thru netLevel=1, need to translate that
number into enum strings */
/* assume "All levels" first */
ret = netLevelStringToEnum(NET_LEVEL_0);
switch(sqlUnsigned(netLevel))
{
case 0: break;
case 1: ret = netLevelStringToEnum(NET_LEVEL_1); break;
case 2: ret = netLevelStringToEnum(NET_LEVEL_2); break;
case 3: ret = netLevelStringToEnum(NET_LEVEL_3); break;
case 4: ret = netLevelStringToEnum(NET_LEVEL_4); break;
case 5: ret = netLevelStringToEnum(NET_LEVEL_5); break;
case 6: ret = netLevelStringToEnum(NET_LEVEL_6); break;
default: warn("trackDb setting %s=%s for track %s is unrecognized, should be in range [0-6]",
NET_LEVEL, netLevel, tdb->track);
break;
}
/* allow cart to override trackDb */
ret = netLevelStringToEnum(
cartUsualStringClosestToHome(cart, tdb, compositeLevel, NET_LEVEL,
netLevelEnumToString(ret)));
return(ret);
} /* enum netLevelEnum netFetchLevelOption() */
static void encodePeakLoadItemsBoth(struct track *tg, struct customTrack *ct)
/* Load up an encodePeak table from the regular database or the customTrash one. */
{
char *db, *table;
struct sqlConnection *conn;
struct sqlResult *sr = NULL;
char **row;
char *filterConstraints = NULL;
int rowOffset;
struct linkedFeatures *lfList = NULL;
enum encodePeakType pt = 0;
int scoreMin = atoi(trackDbSettingClosestToHomeOrDefault(tg->tdb, "scoreMin", "0"));
int scoreMax = atoi(trackDbSettingClosestToHomeOrDefault(tg->tdb, "scoreMax", "1000"));
if (ct)
{
db = CUSTOM_TRASH;
table = ct->dbTableName;
}
else
{
db = database;
table = tg->tdb->table;
}
conn = hAllocConn(db);
pt = encodePeakInferTypeFromTable(db, table, tg->tdb->type);
tg->customInt = pt;
filterConstraints = encodePeakFilter(tg->tdb->track, tg->tdb, (ct!=NULL));
sr = hRangeQuery(conn, table, chromName, winStart, winEnd, filterConstraints, &rowOffset);
while ((row = sqlNextRow(sr)) != NULL)
{
struct encodePeak *peak = encodePeakGeneralLoad(row + rowOffset, pt);
struct linkedFeatures *lf = lfFromEncodePeak((struct slList *)peak, tg->tdb, scoreMin, scoreMax);
if (lf)
slAddHead(&lfList, lf);
}
sqlFreeResult(&sr);
hFreeConn(&conn);
slReverse(&lfList);
slSort(&lfList, linkedFeaturesCmp);
tg->items = lfList;
}
enum wiggleAggregateFunctionEnum wigFetchAggregateFunctionWithCart(struct cart *theCart,
struct trackDb *tdb, char *name, char **optString)
/****** windowingFunction - Whiskers by default **************************/
{
char *Default = wiggleAggregateFunctionEnumToString(wiggleAggregateTransparent);
boolean parentLevel = isNameAtParentLevel(tdb,name);
char *aggregateFunction = NULL;
enum wiggleAggregateFunctionEnum ret;
aggregateFunction = cloneString(cartOptionalStringClosestToHome(theCart, tdb, parentLevel,
AGGREGATE));
/* If windowingFunction is a string, it came from the cart, otherwise
* see if it is specified in the trackDb option, finally
* return the default.
*/
if (!aggregateFunction)
{
char * tdbDefault =
trackDbSettingClosestToHomeOrDefault(tdb, AGGREGATE, Default);
freeMem(aggregateFunction);
if (differentWord(Default,tdbDefault))
aggregateFunction = cloneString(tdbDefault);
else
{
struct hashEl *hel;
/* no aggregateFunction from trackDb, maybe it is in tdb->settings
* (custom tracks keep settings here)
*/
aggregateFunction = cloneString(Default);
if ((tdb->settings != (char *)NULL) &&
(tdb->settingsHash != (struct hash *)NULL))
{
if ((hel =hashLookup(tdb->settingsHash, AGGREGATE)) !=NULL)
if (differentWord(Default,(char *)hel->val))
{
freeMem(aggregateFunction);
aggregateFunction = cloneString((char *)hel->val);
}
}
}
}
if (optString)
*optString = cloneString(aggregateFunction);
ret = wiggleAggregateFunctionStringToEnum(aggregateFunction);
freeMem(aggregateFunction);
return(ret);
} /* enum wiggleWindowingEnum wigFetchWindowingFunctionWithCart() */
void bedDrawSimpleAt(struct track *tg, void *item,
struct hvGfx *hvg, int xOff, int y,
double scale, MgFont *font, Color color, enum trackVisibility vis)
/* Draw a single simple bed item at position. */
{
struct bed *bed = item;
int heightPer = tg->heightPer;
int s = max(bed->chromStart, winStart), e = min(bed->chromEnd, winEnd);
if (s > e)
return;
int x1 = round((s-winStart)*scale) + xOff;
int x2 = round((e-winStart)*scale) + xOff;
int w = x2 - x1;
if (w < 1)
w = 1;
struct trackDb *tdb = tg->tdb;
int scoreMin = atoi(trackDbSettingClosestToHomeOrDefault(tdb, "scoreMin", "0"));
int scoreMax = atoi(trackDbSettingClosestToHomeOrDefault(tdb, "scoreMax", "1000"));
char *directUrl = trackDbSetting(tdb, "directUrl");
boolean withHgsid = (trackDbSetting(tdb, "hgsid") != NULL);
boolean thickDrawItem = (trackDbSetting(tdb, "thickDrawItem") != NULL);
if (tg->itemColor != NULL)
{
color = tg->itemColor(tg, bed, hvg);
}
else if (tg->colorShades)
{
adjustBedScoreGrayLevel(tdb, bed, scoreMin, scoreMax);
color = tg->colorShades[grayInRange(bed->score, scoreMin, scoreMax)];
}
/* Keep the item at least 4 pixels wide at all viewpoints */
if (thickDrawItem && (w < 4))
{
x1 -= ((5-w) >> 1);
w = 4;
x2 = x1 + w;
}
void wigFetchYLineMarkValueWithCart(struct cart *theCart,struct trackDb *tdb, char *name, double *tDbYMark )
/* y= marker line value
* User requested value is defined in the cart
* A Default value can be defined as
* yLineMark declaration from trackDb
*****************************************************************************/
{
boolean parentLevel = isNameAtParentLevel(tdb,name);
char *yLineMarkValue = NULL; /* string from cart */
double yLineValue; /* value from cart or trackDb */
char * tdbDefault = cloneString(
trackDbSettingClosestToHomeOrDefault(tdb, YLINEMARK, "NONE") );
if (sameWord("NONE",tdbDefault))
{
struct hashEl *hel;
/* no yLineMark from trackDb, maybe it is in tdb->settings
* (custom tracks keep settings here)
*/
if ((tdb->settings != (char *)NULL) &&
(tdb->settingsHash != (struct hash *)NULL))
{
if ((hel = hashLookup(tdb->settingsHash, YLINEMARK)) != NULL)
{
freeMem(tdbDefault);
tdbDefault = cloneString((char *)hel->val);
}
}
}
/* If nothing else, it is zero */
yLineValue = 0.0;
/* Let's see if a value is available in the cart */
yLineMarkValue = cartOptionalStringClosestToHome(theCart, tdb, parentLevel, YLINEMARK);
/* if yLineMarkValue is non-Null, it is the requested value */
if (yLineMarkValue)
yLineValue = atof(yLineMarkValue);
else /* See if a default line is specified in the trackDb.ra file */
if (differentWord("NONE",tdbDefault))
yLineValue = atof(tdbDefault);
/* If possible to return */
if (tDbYMark)
*tDbYMark = yLineValue;
freeMem(tdbDefault);
} /* void wigFetchYLineMarkValueWithCart() */
enum wiggleSmoothingEnum wigFetchSmoothingWindowWithCart(struct cart *theCart, struct trackDb *tdb,
char *name, char **optString)
/****** smoothingWindow - OFF by default **************************/
{
char * Default = wiggleSmoothingEnumToString(wiggleSmoothingOff);
boolean parentLevel = isNameAtParentLevel(tdb,name);
char * smoothingWindow = NULL;
enum wiggleSmoothingEnum ret;
smoothingWindow = cloneString(cartOptionalStringClosestToHome(theCart, tdb, parentLevel,
SMOOTHINGWINDOW));
if (!smoothingWindow) /* if nothing from the Cart, check trackDb/settings */
{
char * tdbDefault =
trackDbSettingClosestToHomeOrDefault(tdb, SMOOTHINGWINDOW, Default);
if (differentWord(Default,tdbDefault))
smoothingWindow = cloneString(tdbDefault);
else
{
struct hashEl *hel;
/* no smoothingWindow from trackDb, maybe it is in tdb->settings
* (custom tracks keep settings here)
*/
smoothingWindow = cloneString(Default);
if ((tdb->settings != (char *)NULL) &&
(tdb->settingsHash != (struct hash *)NULL))
{
if ((hel = hashLookup(tdb->settingsHash, SMOOTHINGWINDOW)) != NULL)
if (differentWord(Default,(char *)hel->val))
{
freeMem(smoothingWindow);
smoothingWindow = cloneString((char *)hel->val);
}
}
}
}
if (optString)
*optString = cloneString(smoothingWindow);
ret = wiggleSmoothingStringToEnum(smoothingWindow);
freeMem(smoothingWindow);
return(ret);
} /* enum wiggleSmoothingEnum wigFetchSmoothingWindowWithCart() */
enum netColorEnum netFetchColorOption(struct cart *cart, struct trackDb *tdb,
boolean parentLevel)
/****** netColorOption - Chrom colors by default **************************/
{
char *netColor = NULL;
enum netColorEnum ret;
netColor = trackDbSettingClosestToHomeOrDefault(tdb, NET_COLOR, CHROM_COLORS);
/* trackDb can be netColor=Chromosome or netColor=grayScale,
need to translate grayScale into "Gray scale" */
if (sameWord(TDB_GRAY_SCALE,netColor))
netColor = GRAY_SCALE;
/* and then, allow cart to override trackDb */
ret = netColorStringToEnum(
cartUsualStringClosestToHome(cart, tdb, parentLevel, NET_COLOR, netColor));
return(ret);
} /* enum netColorEnum netFetchColorOption() */
enum wiggleScaleOptEnum wigFetchAutoScaleWithCart(struct cart *theCart, struct trackDb *tdb,
char *name, char **optString)
/****** autoScale - off by default ***************************************/
{
char *autoString = wiggleScaleEnumToString(wiggleScaleAuto);
char *manualString = wiggleScaleEnumToString(wiggleScaleManual);
char *Default = manualString;
char *notDefault = autoString;
boolean parentLevel = isNameAtParentLevel(tdb,name);
char *autoScale = NULL;
enum wiggleScaleOptEnum ret;
autoScale = cloneString(cartOptionalStringClosestToHome(theCart, tdb, parentLevel, AUTOSCALE));
if (!autoScale) /* if nothing from the Cart, check trackDb/settings */
{
/* It may be the autoScale=on/off situation from custom tracks */
char * tdbDefault = trackDbSettingClosestToHomeOrDefault(tdb, AUTOSCALE, "NONE");
if (sameWord(tdbDefault,"on"))
autoScale = cloneString(autoString);
else if (sameWord(tdbDefault,"off"))
autoScale = cloneString(manualString);
else
{
if (isCustomTrack(tdb->track))
// backwards defaults for custom tracks, autoScale on
autoScale = wigCheckBinaryOption(tdb,notDefault,Default,
AUTOSCALEDEFAULT, AUTOSCALE);
else
autoScale = wigCheckBinaryOption(tdb,Default,notDefault,
AUTOSCALEDEFAULT, AUTOSCALE);
}
}
if (optString)
*optString = cloneString(autoScale);
ret = wiggleScaleStringToEnum(autoScale);
freeMem(autoScale);
return(ret);
} /* enum wiggleScaleOptEnum wigFetchAutoScaleWithCart() */
void wigFetchMinMaxYWithCart(struct cart *theCart, struct trackDb *tdb, char *name,
double *retMin, double *retMax, double *retAbsMin, double *retAbsMax,
int wordCount, char **words)
/*****************************************************************************
* Min, Max Y viewing limits
* Absolute limits are defined on the trackDb type line for wiggle,
* or MIN_LIMIT / MAX_LIMIT trackDb settings for bedGraph
* User requested limits are defined in the cart
* Default opening display limits are optionally defined with the
* defaultViewLimits or viewLimits declaration from trackDb
*****************************************************************************/
{
boolean isBedGraph = (wordCount == 0 || sameString(words[0],"bedGraph"));
// Determine absolute min and max. Someday hgTrackDb will enforce inclusion of data
// range settings, but until then, there is some circular logic where either one
// can provide a default for the other if the other is missing.
double absMax = 0.0, absMin = 0.0;
boolean missingAbsMin = FALSE, missingAbsMax = FALSE;
if (isBedGraph)
{
char *tdbMin = trackDbSettingClosestToHomeOrDefault(tdb, MIN_LIMIT, NULL);
char *tdbMax = trackDbSettingClosestToHomeOrDefault(tdb, MAX_LIMIT, NULL);
if (tdbMin == NULL)
missingAbsMin = TRUE;
else
absMin = sqlDouble(tdbMin);
if (tdbMax == NULL)
missingAbsMax = TRUE;
else
absMax = sqlDouble(tdbMax);
}
else
{
// Wiggle: get min and max from type setting, which has been chopped into words and wordCount:
// type wig <min> <max>
if (wordCount >= 3)
absMax = atof(words[2]);
else
missingAbsMax = TRUE;
if (wordCount >= 2)
absMin = atof(words[1]);
else
missingAbsMin = TRUE;
}
correctOrder(absMin, absMax);
// Determine current minY,maxY.
// Precedence: 1. cart; 2. defaultViewLimits; 3. viewLimits;
// 4. absolute [which may need to default to #2 or #3!]
boolean parentLevel = isNameAtParentLevel(tdb, name);
char *cartMinStr = cartOptionalStringClosestToHome(theCart, tdb, parentLevel, MIN_Y);
char *cartMaxStr = cartOptionalStringClosestToHome(theCart, tdb, parentLevel, MAX_Y);
double cartMin = 0.0, cartMax = 0.0;
if(cartMinStr)
*retMin = atof(cartMinStr);
if(cartMaxStr)
*retMax = atof(cartMaxStr);
if (cartMinStr && cartMaxStr)
correctOrder(*retMin, *retMax);
// If it weren't for the the allowance for missing data range values,
// we could set retAbs* and be done here.
if(cartMinStr)
cartMin = *retMin;
if(cartMaxStr)
cartMax = *retMax;
// Get trackDb defaults, and resolve missing wiggle data range if necessary.
char *defaultViewLimits = trackDbSettingClosestToHomeOrDefault(tdb, DEFAULTVIEWLIMITS, NULL);
if (defaultViewLimits == NULL)
defaultViewLimits = trackDbSettingClosestToHomeOrDefault(tdb, VIEWLIMITS, NULL);
if (defaultViewLimits != NULL)
{
double viewLimitMin = 0.0, viewLimitMax = 0.0;
parseColonRange(defaultViewLimits, &viewLimitMin, &viewLimitMax);
*retMin = viewLimitMin;
*retMax = viewLimitMax;
if (missingAbsMax)
absMax = viewLimitMax;
if (missingAbsMin)
absMin = viewLimitMin;
}
else if (missingAbsMin || missingAbsMax)
{
if (isBedGraph)
{
absMin = DEFAULT_MIN_BED_GRAPH;
absMax = DEFAULT_MAX_BED_GRAPH;
}
else
{
absMin = DEFAULT_MIN_Yv;
absMax = DEFAULT_MAX_Yv;
}
*retMin = absMin;
*retMax = absMax;
}
else
{
*retMin = absMin;
*retMax = absMax;
}
if (retAbsMin)
*retAbsMin = absMin;
if (retAbsMax)
*retAbsMax = absMax;
// After the dust settles from tdb's trackDb settings, now see if composite view
// settings from tdb's parents override that stuff anyway:
viewLimitsCompositeOverride(tdb, name, retMin, retMax, retAbsMin, retAbsMax);
// And as the final word after composite override, reset retMin and retMax if from cart:
if (cartMinStr)
*retMin = cartMin;
if (cartMaxStr)
*retMax = cartMax;
} /* void wigFetchMinMaxYWithCart() */
void bamDrawAt(struct track *tg, void *item,
struct hvGfx *hvg, int xOff, int y, double scale,
MgFont *font, Color color, enum trackVisibility vis)
/* Draw a single bam linkedFeatures item. Borrows a lot from linkedFeaturesDrawAt,
* but cuts a lot of unneeded features (like coding region) and adds a couple
* additional sources of color. */
{
struct linkedFeatures *lf = item;
struct simpleFeature *sf;
int heightPer = tg->heightPer;
int x1 = round((double)((int)lf->start-winStart)*scale) + xOff;
int x2 = round((double)((int)lf->end-winStart)*scale) + xOff;
int w = x2-x1;
int midY = y + (heightPer>>1);
char *exonArrowsDense = trackDbSettingClosestToHome(tg->tdb, "exonArrowsDense");
boolean exonArrowsEvenWhenDense = (exonArrowsDense != NULL && SETTING_IS_ON(exonArrowsDense));
boolean exonArrows = (tg->exonArrows &&
(vis != tvDense || exonArrowsEvenWhenDense));
struct dnaSeq *mrnaSeq = NULL;
enum baseColorDrawOpt drawOpt = baseColorDrawOff;
boolean indelShowDoubleInsert, indelShowQueryInsert, indelShowPolyA;
struct psl *psl = (struct psl *)(lf->original);
char *colorMode = cartOrTdbString(cart, tg->tdb, BAM_COLOR_MODE, BAM_COLOR_MODE_DEFAULT);
char *grayMode = cartOrTdbString(cart, tg->tdb, BAM_GRAY_MODE, BAM_GRAY_MODE_DEFAULT);
bool baseQualMode = (sameString(colorMode, BAM_COLOR_MODE_GRAY) &&
sameString(grayMode, BAM_GRAY_MODE_BASE_QUAL));
char *qSeq = lf->extra;
if (vis != tvDense && isNotEmpty(qSeq) && !sameString(qSeq, "*"))
{
drawOpt = baseColorDrawSetup(hvg, tg, lf, &mrnaSeq, &psl);
if (drawOpt > baseColorDrawOff)
exonArrows = FALSE;
}
static Color darkBlueColor = 0;
static Color darkRedColor = 0;
if (darkRedColor == 0)
{
darkRedColor = hvGfxFindColorIx(hvg, 100,0,0);
darkBlueColor = hvGfxFindColorIx(hvg, 0,0,100);
}
if (sameString(colorMode, BAM_COLOR_MODE_STRAND))
color = (lf->orientation < 0) ? darkRedColor : darkBlueColor;
else if (lf->filterColor != 0)
{
// In bamTrack, lf->filterColor is an RGBA value
color = lf->filterColor;
}
else if (tg->colorShades)
color = tg->colorShades[lf->grayIx];
else
color = tg->ixColor;
indelEnabled(cart, tg->tdb, basesPerPixel, &indelShowDoubleInsert, &indelShowQueryInsert,
&indelShowPolyA);
if (!indelShowDoubleInsert)
innerLine(hvg, x1, midY, w, color);
for (sf = lf->components; sf != NULL; sf = sf->next)
{
int s = sf->start, e = sf->end;
if (e <= s || e < winStart || s > winEnd)
continue;
if (baseQualMode)
color = tg->colorShades[sf->grayIx];
baseColorDrawItem(tg, lf, sf->grayIx, hvg, xOff, y, scale, font, s, e, heightPer,
zoomedToCodonLevel, mrnaSeq, sf, psl, drawOpt, MAXPIXELS, winStart, color);
if (tg->exonArrowsAlways ||
(exonArrows &&
(sf->start <= winStart || sf->start == lf->start) &&
(sf->end >= winEnd || sf->end == lf->end)))
{
Color barbColor = hvGfxContrastingColor(hvg, color);
x1 = round((double)((int)s-winStart)*scale) + xOff;
x2 = round((double)((int)e-winStart)*scale) + xOff;
w = x2-x1;
clippedBarbs(hvg, x1+1, midY, x2-x1-2, tl.barbHeight, tl.barbSpacing, lf->orientation,
barbColor, TRUE);
}
}
if (indelShowDoubleInsert && psl)
{
int intronGap = 0;
if (vis != tvDense)
intronGap = atoi(trackDbSettingClosestToHomeOrDefault(tg->tdb, "intronGap", "0"));
lfDrawSpecialGaps(lf, intronGap, TRUE, 0, tg, hvg, xOff, y, scale, color, color, vis);
}
if (vis != tvDense)
{
/* If highlighting differences between aligned sequence and genome when
* zoomed way out, this must be done in a separate pass after exons are
* drawn so that exons sharing the pixel don't overdraw differences. */
if ((indelShowQueryInsert || indelShowPolyA) && psl)
baseColorOverdrawQInsert(tg, lf, hvg, xOff, y, scale, heightPer, mrnaSeq, psl, winStart,
drawOpt, indelShowQueryInsert, indelShowPolyA);
baseColorOverdrawDiff(tg, lf, hvg, xOff, y, scale, heightPer, mrnaSeq, psl, winStart, drawOpt);
baseColorDrawCleanup(lf, &mrnaSeq, &psl);
}
}
void bamLoadItemsCore(struct track *tg, boolean isPaired)
/* Load BAM data into tg->items item list, unless zoomed out so far
* that the data would just end up in dense mode and be super-slow. */
{
/* protect against temporary network error */
struct errCatch *errCatch = errCatchNew();
if (errCatchStart(errCatch))
{
struct hash *pairHash = isPaired ? hashNew(18) : NULL;
int minAliQual = atoi(cartOrTdbString(cart, tg->tdb, BAM_MIN_ALI_QUAL, BAM_MIN_ALI_QUAL_DEFAULT));
char *colorMode = cartOrTdbString(cart, tg->tdb, BAM_COLOR_MODE, BAM_COLOR_MODE_DEFAULT);
char *grayMode = cartOrTdbString(cart, tg->tdb, BAM_GRAY_MODE, BAM_GRAY_MODE_DEFAULT);
char *userTag = cartOrTdbString(cart, tg->tdb, BAM_COLOR_TAG, BAM_COLOR_TAG_DEFAULT);
int aliQualShadeMin = 0, aliQualShadeMax = 99, baseQualShadeMin = 0, baseQualShadeMax = 40;
parseIntRangeSetting(tg->tdb, "aliQualRange", &aliQualShadeMin, &aliQualShadeMax);
parseIntRangeSetting(tg->tdb, "baseQualRange", &baseQualShadeMin, &baseQualShadeMax);
struct bamTrackData btd = {tg, pairHash, minAliQual, colorMode, grayMode, userTag,
aliQualShadeMin, aliQualShadeMax, baseQualShadeMin, baseQualShadeMax};
char *fileName = trackDbSetting(tg->tdb, "bigDataUrl");
if (fileName == NULL)
{
if (tg->customPt)
{
errAbort("bamLoadItemsCore: can't find bigDataUrl for custom track %s", tg->track);
}
else
{
struct sqlConnection *conn = hAllocConnTrack(database, tg->tdb);
fileName = bamFileNameFromTable(conn, tg->table, chromName);
hFreeConn(&conn);
}
}
char *fileName2 = hReplaceGbdb(fileName);
char posForBam[512];
safef(posForBam, sizeof(posForBam), "%s:%d-%d", chromName, winStart, winEnd);
char *cacheDir = cfgOption("cramRef");
char *refUrl = trackDbSetting(tg->tdb, "refUrl");
if (!isPaired)
bamFetchPlus(fileName2, posForBam, addBam, &btd, NULL, refUrl, cacheDir);
else
{
char *setting = trackDbSettingClosestToHomeOrDefault(tg->tdb, "pairSearchRange", "20000");
int pairSearchRange = atoi(setting);
if (pairSearchRange > 0)
safef(posForBam, sizeof(posForBam), "%s:%d-%d", chromName,
max(0, winStart-pairSearchRange), winEnd+pairSearchRange);
bamFetchPlus(fileName2, posForBam, addBamPaired, &btd, NULL, refUrl, cacheDir);
struct hashEl *hel;
struct hashCookie cookie = hashFirst(btd.pairHash);
while ((hel = hashNext(&cookie)) != NULL)
{
struct linkedFeatures *lf = hel->val;
if (lf->start < winEnd && lf->end > winStart)
slAddHead(&(tg->items), lfsFromLf(lf));
}
}
freez(&fileName2);
if (tg->visibility != tvDense)
{
slReverse(&(tg->items));
if (isPaired)
slSort(&(tg->items), linkedFeaturesSeriesCmp);
else if (sameString(colorMode, BAM_COLOR_MODE_STRAND))
slSort(&(tg->items), linkedFeaturesCmpOri);
else if (sameString(colorMode, BAM_COLOR_MODE_GRAY) &&
sameString(grayMode, BAM_GRAY_MODE_ALI_QUAL))
slSort(&(tg->items), linkedFeaturesCmpScore);
else
slSort(&(tg->items), linkedFeaturesCmpStart);
if (slCount(tg->items) > MAX_ITEMS_FOR_MAPBOX)
{
// flag drawItems to make a mapBox for the whole track
tg->customInt = 1;
tg->mapItem = dontMapItem;
}
}
}
errCatchEnd(errCatch);
if (errCatch->gotError)
{
tg->networkErrMsg = cloneString(errCatch->message->string);
tg->drawItems = bigDrawWarning;
tg->totalHeight = bigWarnTotalHeight;
}
errCatchFree(&errCatch);
}
static void pubsLoadKeywordYearItems(struct track *tg)
/* load items that fulfill keyword and year filter */
{
pubsParseClassColors();
struct sqlConnection *conn = hAllocConn(database);
char *keywords = cartOptionalStringClosestToHome(cart, tg->tdb, FALSE, "pubsFilterKeywords");
char *yearFilter = cartOptionalStringClosestToHome(cart, tg->tdb, FALSE, "pubsFilterYear");
char *publFilter = cartOptionalStringClosestToHome(cart, tg->tdb, FALSE, "pubsFilterPublisher");
char *articleTable = pubsArticleTable(tg);
if(sameOk(yearFilter, "anytime"))
yearFilter = NULL;
if(sameOk(publFilter, "all"))
publFilter = NULL;
if(isNotEmpty(keywords))
keywords = makeMysqlMatchStr(keywords);
if (isEmpty(yearFilter) && isEmpty(keywords) && isEmpty(publFilter))
{
loadGappedBed(tg);
}
else
{
// put together an "extra" query to hExtendedRangeQuery that removes articles
// without the keywords specified in hgTrackUi
char *oldLabel = tg->longLabel;
tg->longLabel = catTwoStrings(oldLabel, " (filter activated)");
freeMem(oldLabel);
char **row;
struct linkedFeatures *lfList = NULL;
struct trackDb *tdb = tg->tdb;
int scoreMin = atoi(trackDbSettingClosestToHomeOrDefault(tdb, "scoreMin", "0"));
int scoreMax = atoi(trackDbSettingClosestToHomeOrDefault(tdb, "scoreMax", "1000"));
boolean useItemRgb = bedItemRgb(tdb);
char *extra = NULL;
struct dyString *extraDy = dyStringNew(0);
struct hash *articleIds = searchForKeywords(conn, articleTable, keywords);
if (!sameWord(tg->table, "pubsBlat"))
// new table schema: filter fields are on main bed table
{
if (isNotEmpty(yearFilter))
sqlDyStringPrintfWithSep(extraDy, " AND ", " year >= '%s'", yearFilter);
if (isNotEmpty(publFilter))
sqlDyStringPrintfWithSep(extraDy, " AND ", " publisher = '%s'", publFilter);
}
else
// old table schema, filter by doing a join on article table
{
if(isNotEmpty(yearFilter))
sqlDyStringPrintfFrag(extraDy, "name IN (SELECT articleId FROM %s WHERE year>='%s')", articleTable, \
yearFilter);
}
if (extraDy->stringSize > 0)
extra = extraDy->string;
else
extra = NULL;
int rowOffset = 0;
struct sqlResult *sr = hExtendedRangeQuery(conn, tg->table, chromName, winStart, winEnd, extra,
FALSE, NULL, &rowOffset);
freeDyString(&extraDy);
while ((row = sqlNextRow(sr)) != NULL)
{
struct bed *bed = bedLoad12(row+rowOffset);
if (articleIds==NULL || hashFindVal(articleIds, bed->name))
slAddHead(&lfList, bedMungToLinkedFeatures(&bed, tdb, 12, scoreMin, scoreMax, useItemRgb));
}
sqlFreeResult(&sr);
slReverse(&lfList);
slSort(&lfList, linkedFeaturesCmp);
tg->items = lfList;
}
hFreeConn(&conn);
}
