enum wiggleGridOptEnum wigFetchTransformFuncWithCart(struct cart *theCart,
struct trackDb *tdb, char *name,char **optString)
/* transformFunc - none by default **********************************/
{
boolean parentLevel = isNameAtParentLevel(tdb,name);
char *transformFunc;
enum wiggleTransformFuncEnum ret = wiggleTransformFuncNone;
char * tdbDefault = trackDbSettingClosestToHome(tdb, TRANSFORMFUNC);
transformFunc = cloneString(cartOptionalStringClosestToHome(theCart, tdb, parentLevel,
TRANSFORMFUNC));
if ((transformFunc == NULL) && (tdbDefault != NULL))
transformFunc = cloneString(tdbDefault);
if (optString && transformFunc)
*optString = cloneString(transformFunc);
if (transformFunc)
{
ret = wiggleTransformFuncToEnum(transformFunc);
freeMem(transformFunc);
}
return((enum wiggleGridOptEnum)ret);
}
void snakeCfgUi(struct cart *cart, struct trackDb *tdb, char *name, char *title, boolean boxed)
{
boolean parentLevel = isNameAtParentLevel(tdb, name);
showSnpWidthCfg(cart, tdb, name, parentLevel);
colorByCfg(cart, tdb, name, parentLevel);
}
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 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() */
boolean wigFetchDoNegativeWithCart(struct cart *theCart, struct trackDb *tdb, char *name,char **optString)
/* doNegative - false by default **********************************/
{
boolean parentLevel = isNameAtParentLevel(tdb,name);
char *doNegativeDefault = trackDbSettingClosestToHome(tdb, DONEGATIVEMODE);
char *doNegative = cloneString(cartOptionalStringClosestToHome(theCart, tdb, parentLevel, DONEGATIVEMODE));
if ((doNegative == NULL) && (doNegativeDefault != NULL))
doNegative = cloneString(doNegativeDefault);
if (doNegative == NULL)
return FALSE;
return sameString(doNegative, "1") || sameString(doNegative, "on");
}
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 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() */
static void viewLimitsCompositeOverride(struct trackDb *tdb,char *name, double *retMin,
double *retMax,double *absMin, double *absMax)
/* If aquiring min/max for composite level wig cfg. Look in parents as well as self. */
{
if (isNameAtParentLevel(tdb,name))
{
char *setting = NULL;
if (absMin != NULL && absMax != NULL)
{
setting = trackDbSettingByView(tdb,MIN_LIMIT);
if (setting != NULL)
{
if (setting[0] != '\0')
*absMin = sqlDouble(setting);
}
setting = trackDbSettingByView(tdb,MAX_LIMIT);
if (setting != NULL)
{
if (setting[0] != '\0')
*absMax = sqlDouble(setting);
}
else
{
setting = trackDbSettingByView(tdb,VIEWLIMITSMAX); // Legacy
if (setting != NULL)
{
parseColonRange(setting, absMin, absMax);
}
}
}
setting = trackDbSettingByView(tdb, VIEWLIMITS);
if (setting != NULL)
{
parseColonRange(setting, retMin, retMax);
}
}
}
enum wiggleYLineMarkEnum wigFetchYLineMarkWithCart(struct cart *theCart, struct trackDb *tdb,
char *name, char **optString)
/* yLineMark - off by default **********************************/
{
char *Default = wiggleYLineMarkEnumToString(wiggleYLineMarkOff);
char *notDefault = wiggleYLineMarkEnumToString(wiggleYLineMarkOn);
boolean parentLevel = isNameAtParentLevel(tdb,name);
char *yLineMark = NULL;
enum wiggleYLineMarkEnum ret;
yLineMark = cloneString(cartOptionalStringClosestToHome(theCart, tdb, parentLevel, YLINEONOFF));
if (!yLineMark) /* if nothing from the Cart, check trackDb/settings */
yLineMark = wigCheckBinaryOption(tdb,Default,notDefault,YLINEONOFF,
(char *)NULL);
if (optString)
*optString = cloneString(yLineMark);
ret = wiggleYLineMarkStringToEnum(yLineMark);
freeMem(yLineMark);
return(ret);
} /* enum wiggleYLineMarkEnum wigFetchYLineMarkWithCart() */
enum wiggleGraphOptEnum wigFetchGraphTypeWithCart(struct cart *theCart, struct trackDb *tdb,
char *name, char **optString)
/****** graphType - line(points) or bar graph *****************************/
{
char *Default = wiggleGraphEnumToString(wiggleGraphBar);
char *notDefault = wiggleGraphEnumToString(wiggleGraphPoints);
boolean parentLevel = isNameAtParentLevel(tdb,name);
char *graphType = NULL;
enum wiggleGraphOptEnum ret;
graphType = cloneString(cartOptionalStringClosestToHome(theCart, tdb, parentLevel, LINEBAR));
if (!graphType) /* if nothing from the Cart, check trackDb/settings */
graphType = wigCheckBinaryOption(tdb,Default,notDefault,GRAPHTYPEDEFAULT,
GRAPHTYPE);
if (optString)
*optString = cloneString(graphType);
ret = wiggleGraphStringToEnum(graphType);
freeMem(graphType);
return(ret);
} /* enum wiggleGraphOptEnum wigFetchGraphTypeWithCart() */
enum wiggleGridOptEnum wigFetchHorizontalGridWithCart(struct cart *theCart, struct trackDb *tdb,
char *name,char **optString)
/* horizontalGrid - off by default **********************************/
{
char *Default = wiggleGridEnumToString(wiggleHorizontalGridOff);
char *notDefault = wiggleGridEnumToString(wiggleHorizontalGridOn);
boolean parentLevel = isNameAtParentLevel(tdb,name);
char *horizontalGrid = NULL;
enum wiggleGridOptEnum ret;
horizontalGrid = cloneString(cartOptionalStringClosestToHome(theCart, tdb, parentLevel, HORIZGRID));
if (!horizontalGrid) /* if it is NULL */
horizontalGrid = wigCheckBinaryOption(tdb,Default,notDefault,GRIDDEFAULT,
HORIZGRID);
if (optString)
*optString = cloneString(horizontalGrid);
ret = wiggleGridStringToEnum(horizontalGrid);
freeMem(horizontalGrid);
return(ret);
} /* enum wiggleGridOptEnum wigFetchHorizontalGridWithCart() */
enum wiggleGridOptEnum wigFetchAlwaysZeroWithCart(struct cart *theCart,
struct trackDb *tdb, char *name,char **optString)
/* alwaysZero - off by default **********************************/
{
boolean parentLevel = isNameAtParentLevel(tdb,name);
char *alwaysZero;
enum wiggleAlwaysZeroEnum ret = wiggleAlwaysZeroOff;
char * tdbDefault = trackDbSettingClosestToHome(tdb, ALWAYSZERO);
alwaysZero = cloneString(cartOptionalStringClosestToHome(theCart, tdb, parentLevel, ALWAYSZERO));
if ((alwaysZero == NULL) && (tdbDefault != NULL))
alwaysZero = cloneString(tdbDefault);
if (optString && alwaysZero)
*optString = cloneString(alwaysZero);
if (alwaysZero)
{
ret = wiggleAlwaysZeroToEnum(alwaysZero);
freeMem(alwaysZero);
}
return((enum wiggleGridOptEnum)ret);
}
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() */
