");
puts("");
}
char *hUserCookie()
/* Return our cookie name. */
{
return cfgOptionDefault("central.cookie", "hguid");
}
char *hDownloadsServer()
/* get the downloads server from hg.conf or the default */
{
return cfgOptionDefault("downloads.server", "hgdownload.cse.ucsc.edu");
}
void setUdcCacheDir()
/* set the path to the udc cache dir */
{
udcSetDefaultDir(cfgOptionDefault("udc.cacheDir", udcDefaultDir()));
}
char *wrapWhiteFont(char *s)
/* Write white font around s */
{
static char buf[256];
safef(buf, sizeof(buf), "%s", s);
return buf;
}
char *hDocumentRoot()
/* get the path to the DocumentRoot, or the default */
{
return cfgOptionDefault("browser.documentRoot", DOCUMENT_ROOT);
}
char *hHelpFile(char *fileRoot)
/* Given a help file root name (e.g. "hgPcrResult" or "cutters"),
* prepend the complete help directory path and add .html suffix.
* Do not free the statically allocated result. */
{
static char helpName[PATH_LEN];
/* This cfgOption comes from Todd Lowe's hgTrackUi.c addition (r1.230): */
char *helpDir = cfgOption("help.html");
if (helpDir != NULL)
safef(helpName, sizeof(helpName), "%s/%s.html", helpDir, fileRoot);
else
safef(helpName, sizeof(helpName), "%s%s/%s.html", hDocumentRoot(),
HELP_DIR, fileRoot);
return helpName;
}
char *hFileContentsOrWarning(char *file)
/* Return the contents of the html file, or a warning message.
* The file path may begin with hDocumentRoot(); if it doesn't, it is
* assumed to be relative and hDocumentRoot() will be prepended. */
{
if (isEmpty(file))
return cloneString(" Program Error: Empty file name for include file"
" \n");
char path[PATH_LEN];
char *docRoot = hDocumentRoot();
if (startsWith(docRoot, file))
safecpy(path, sizeof path, file);
else
safef(path, sizeof path, "%s/%s", docRoot, file);
if (! fileExists(path))
{
char message[1024];
safef(message, sizeof(message), " Program Error: Missing file %s",
path);
return cloneString(message);
}
/* If the file is there but not readable, readInGulp will errAbort,
* but I think that is serious enough that errAbort is OK. */
char *result;
readInGulp(path, &result, NULL);
return result;
}
char *hCgiRoot()
/* get the path to the CGI directory.
* Returns NULL when not running as a CGI (unless specified by browser.cgiRoot) */
{
static char defaultDir[PATH_LEN];
char *scriptFilename = getenv("SCRIPT_FILENAME");
if(scriptFilename)
{
char dir[PATH_LEN], name[FILENAME_LEN], extension[FILEEXT_LEN];
dir[0] = 0;
splitPath(scriptFilename, dir, name, extension);
safef(defaultDir, sizeof(defaultDir), "%s", dir);
int len = strlen(defaultDir);
// Get rid of trailing slash to be consistent with hDocumentRoot
if(defaultDir[len-1] == '/')
defaultDir[len-1] = 0;
}
else
{
defaultDir[0] = 0;
}
return cfgOptionDefault("browser.cgiRoot", defaultDir);
}
char *hBackgroundImage()
/* get the path to the configured background image to use, or the default */
{
return cfgOptionDefault("browser.background", DEFAULT_BACKGROUND);
}
/****** Some stuff for tables of controls ******/
struct controlGrid *startControlGrid(int columns, char *align)
/* Start up a control grid. */
{
struct controlGrid *cg;
AllocVar(cg);
cg->columns = columns;
cg->align = cloneString(align);
cg->rowOpen = FALSE;
return cg;
}
void controlGridEndRow(struct controlGrid *cg)
/* Force end of row. */
{
printf("");
cg->rowOpen = FALSE;
cg->columnIx = 0;
}
void controlGridStartCell(struct controlGrid *cg)
/* Start a new cell in control grid. */
{
if (cg->columnIx == cg->columns)
controlGridEndRow(cg);
if (!cg->rowOpen)
{
printf("
");
cg->rowOpen = TRUE;
}
if (cg->align)
printf("
", cg->align);
else
printf("
");
}
void controlGridEndCell(struct controlGrid *cg)
/* End cell in control grid. */
{
printf("
");
++cg->columnIx;
}
void endControlGrid(struct controlGrid **pCg)
/* Finish up a control grid. */
{
struct controlGrid *cg = *pCg;
if (cg != NULL)
{
int i;
if (cg->columnIx != 0 && cg->columnIx < cg->columns)
for( i = cg->columnIx; i <= cg->columns; i++)
printf("
\n");
if (cg->rowOpen)
printf("
\n");
printf("\n");
freeMem(cg->align);
freez(pCg);
}
}
/****** Some stuff for hide/dense/full controls ******/
static char *hTvStrings[] =
/* User interface strings for track visibility controls. */
{
"hide",
"dense",
"full",
"pack",
"squish"
};
enum trackVisibility hTvFromStringNoAbort(char *s)
/* Given a string representation of track visibility, return as
* equivalent enum. */
{
int vis = stringArrayIx(s, hTvStrings, ArraySize(hTvStrings));
if (vis < 0)
vis = 0; // don't generate bogus value on invalid input
return vis;
}
enum trackVisibility hTvFromString(char *s)
/* Given a string representation of track visibility, return as
* equivalent enum. */
{
enum trackVisibility vis = hTvFromStringNoAbort(s);
if ((int)vis < 0)
errAbort("Unknown visibility %s", s);
return vis;
}
char *hStringFromTv(enum trackVisibility vis)
/* Given enum representation convert to string. */
{
return hTvStrings[vis];
}
void hTvDropDownClassWithJavascript(char *varName, enum trackVisibility vis, boolean canPack, char *class,char * javascript)
/* Make track visibility drop down for varName with style class */
{
static char *noPack[] =
{
"hide",
"dense",
"full",
};
static char *pack[] =
{
"hide",
"dense",
"squish",
"pack",
"full",
};
static int packIx[] = {tvHide,tvDense,tvSquish,tvPack,tvFull};
if (canPack)
cgiMakeDropListClassWithStyleAndJavascript(varName, pack, ArraySize(pack),
pack[packIx[vis]], class, TV_DROPDOWN_STYLE,javascript);
else
cgiMakeDropListClassWithStyleAndJavascript(varName, noPack, ArraySize(noPack),
noPack[vis], class, TV_DROPDOWN_STYLE,javascript);
}
void hTvDropDownClassVisOnly(char *varName, enum trackVisibility vis,
boolean canPack, char *class, char *visOnly)
/* Make track visibility drop down for varName with style class,
and potentially limited to visOnly */
{
static char *denseOnly[] =
{
"hide",
"dense",
};
static char *squishOnly[] =
{
"hide",
"squish",
};
static char *packOnly[] =
{
"hide",
"pack",
};
static char *fullOnly[] =
{
"hide",
"full",
};
static char *noPack[] =
{
"hide",
"dense",
"full",
};
static char *pack[] =
{
"hide",
"dense",
"squish",
"pack",
"full",
};
static int packIx[] = {tvHide,tvDense,tvSquish,tvPack,tvFull};
if (visOnly != NULL)
{
int visIx = (vis > 0) ? 1 : 0;
if (sameWord(visOnly,"dense"))
cgiMakeDropListClassWithStyle(varName, denseOnly, ArraySize(denseOnly),
denseOnly[visIx], class, TV_DROPDOWN_STYLE);
else if (sameWord(visOnly,"squish"))
cgiMakeDropListClassWithStyle(varName, squishOnly,
ArraySize(squishOnly), squishOnly[visIx],
class, TV_DROPDOWN_STYLE);
else if (sameWord(visOnly,"pack"))
cgiMakeDropListClassWithStyle(varName, packOnly, ArraySize(packOnly),
packOnly[visIx], class, TV_DROPDOWN_STYLE);
else if (sameWord(visOnly,"full"))
cgiMakeDropListClassWithStyle(varName, fullOnly, ArraySize(fullOnly),
fullOnly[visIx], class, TV_DROPDOWN_STYLE);
else /* default when not recognized */
cgiMakeDropListClassWithStyle(varName, denseOnly, ArraySize(denseOnly),
denseOnly[visIx], class, TV_DROPDOWN_STYLE);
}
else
{
if (canPack)
cgiMakeDropListClassWithStyle(varName, pack, ArraySize(pack),
pack[packIx[vis]], class, TV_DROPDOWN_STYLE);
else
cgiMakeDropListClassWithStyle(varName, noPack, ArraySize(noPack),
noPack[vis], class, TV_DROPDOWN_STYLE);
}
}
void hideShowDropDown(char *varName, boolean show, char *class)
/* Make hide/show dropdown for varName */
{
static char *hideShow[] =
{
"hide",
"show"
};
cgiMakeDropListClassWithStyle(varName, hideShow, ArraySize(hideShow),
hideShow[show], class, TV_DROPDOWN_STYLE);
}
/****** Some stuff for stsMap related controls *******/
static char *stsMapOptions[] = {
"All Genetic",
"Genethon",
"Marshfield",
"deCODE",
"GeneMap 99",
"Whitehead YAC",
"Whitehead RH",
"Stanford TNG",
};
enum stsMapOptEnum smoeStringToEnum(char *string)
/* Convert from string to enum representation. */
{
int x = stringIx(string, stsMapOptions);
if (x < 0)
errAbort("Unknown option %s", string);
return x;
}
char *smoeEnumToString(enum stsMapOptEnum x)
/* Convert from enum to string representation. */
{
return stsMapOptions[x];
}
void smoeDropDown(char *var, char *curVal)
/* Make drop down of options. */
{
cgiMakeDropList(var, stsMapOptions, ArraySize(stsMapOptions),
curVal);
}
/****** Some stuff for stsMapMouseNew related controls *******/
static char *stsMapMouseOptions[] = {
"All Genetic",
"WICGR Genetic Map",
"MGD Genetic Map",
"RH",
};
enum stsMapMouseOptEnum smmoeStringToEnum(char *string)
/* Convert from string to enum representation. */
{
int x = stringIx(string, stsMapMouseOptions);
if (x < 0)
errAbort("Unknown option %s", string);
return x;
}
char *smmoeEnumToString(enum stsMapMouseOptEnum x)
/* Convert from enum to string representation. */
{
return stsMapMouseOptions[x];
}
void smmoeDropDown(char *var, char *curVal)
/* Make drop down of options. */
{
cgiMakeDropList(var, stsMapMouseOptions, ArraySize(stsMapMouseOptions),
curVal);
}
/****** Some stuff for stsMapRat related controls *******/
static char *stsMapRatOptions[] = {
"All Genetic",
"FHHxACI",
"SHRSPxBN",
"RH",
};
enum stsMapRatOptEnum smroeStringToEnum(char *string)
/* Convert from string to enum representation. */
{
int x = stringIx(string, stsMapRatOptions);
if (x < 0)
errAbort("Unknown option %s", string);
return x;
}
char *smroeEnumToString(enum stsMapRatOptEnum x)
/* Convert from enum to string representation. */
{
return stsMapRatOptions[x];
}
void smroeDropDown(char *var, char *curVal)
/* Make drop down of options. */
{
cgiMakeDropList(var, stsMapRatOptions, ArraySize(stsMapRatOptions),
curVal);
}
/****** Some stuff for fishClones related controls *******/
static char *fishClonesOptions[] = {
"Fred Hutchinson CRC",
"National Cancer Institute",
"Sanger Centre",
"Roswell Park Cancer Institute",
"Cedars-Sinai Medical Center",
"Los Alamos National Lab",
"UC San Francisco",
};
enum fishClonesOptEnum fcoeStringToEnum(char *string)
/* Convert from string to enum representation. */
{
int x = stringIx(string, fishClonesOptions);
if (x < 0)
errAbort("Unknown option %s", string);
return x;
}
char *fcoeEnumToString(enum fishClonesOptEnum x)
/* Convert from enum to string representation. */
{
return fishClonesOptions[x];
}
void fcoeDropDown(char *var, char *curVal)
/* Make drop down of options. */
{
cgiMakeDropList(var, fishClonesOptions, ArraySize(fishClonesOptions),
curVal);
}
/****** Some stuff for recombRate related controls *******/
static char *recombRateOptions[] = {
"deCODE Sex Averaged Distances",
"deCODE Female Distances",
"deCODE Male Distances",
"Marshfield Sex Averaged Distances",
"Marshfield Female Distances",
"Marshfield Male Distances",
"Genethon Sex Averaged Distances",
"Genethon Female Distances",
"Genethon Male Distances",
};
enum recombRateOptEnum rroeStringToEnum(char *string)
/* Convert from string to enum representation. */
{
int x = stringIx(string, recombRateOptions);
if (x < 0)
errAbort("Unknown option %s", string);
return x;
}
char *rroeEnumToString(enum recombRateOptEnum x)
/* Convert from enum to string representation. */
{
return recombRateOptions[x];
}
void rroeDropDown(char *var, char *curVal)
/* Make drop down of options. */
{
cgiMakeDropList(var, recombRateOptions, ArraySize(recombRateOptions),
curVal);
}
/****** Some stuff for recombRateRat related controls *******/
static char *recombRateRatOptions[] = {
"SHRSPxBN Sex Averaged Distances",
"FHHxACI Sex Averaged Distances",
};
enum recombRateRatOptEnum rrroeStringToEnum(char *string)
/* Convert from string to enum representation. */
{
int x = stringIx(string, recombRateRatOptions);
if (x < 0)
errAbort("Unknown option %s", string);
return x;
}
char *rrroeEnumToString(enum recombRateRatOptEnum x)
/* Convert from enum to string representation. */
{
return recombRateRatOptions[x];
}
void rrroeDropDown(char *var, char *curVal)
/* Make drop down of options. */
{
cgiMakeDropList(var, recombRateRatOptions, ArraySize(recombRateRatOptions),
curVal);
}
/****** Some stuff for recombRateMouse related controls *******/
static char *recombRateMouseOptions[] = {
"WI Genetic Map Sex Averaged Distances",
"MGD Genetic Map Sex Averaged Distances",
};
enum recombRateMouseOptEnum rrmoeStringToEnum(char *string)
/* Convert from string to enum representation. */
{
int x = stringIx(string, recombRateMouseOptions);
if (x < 0)
errAbort("Unknown option %s", string);
return x;
}
char *rrmoeEnumToString(enum recombRateMouseOptEnum x)
/* Convert from enum to string representation. */
{
return recombRateMouseOptions[x];
}
void rrmoeDropDown(char *var, char *curVal)
/* Make drop down of options. */
{
cgiMakeDropList(var, recombRateMouseOptions, ArraySize(recombRateMouseOptions),
curVal);
}
/****** Some stuff for CGH NCI60 related controls *******/
static char *cghNci60Options[] = {
"Tissue Averages",
"BREAST",
"CNS",
"COLON",
"LEUKEMIA",
"LUNG",
"MELANOMA",
"OVARY",
"PROSTATE",
"RENAL",
"All Cell Lines",
};
enum cghNci60OptEnum cghoeStringToEnum(char *string)
/* Convert from string to enum representation. */
{
int x = stringIx(string, cghNci60Options);
if (x < 0)
errAbort("Unknown option %s", string);
return x;
}
char *cghoeEnumToString(enum cghNci60OptEnum x)
/* Convert from enum to string representation. */
{
return cghNci60Options[x];
}
void cghoeDropDown(char *var, char *curVal)
/* Make drop down of options. */
{
cgiMakeDropList(var, cghNci60Options, ArraySize(cghNci60Options),
curVal);
}
/****** Some stuff for nci60 related controls *******/
static char *nci60Options[] = {
"Tissue Averages",
"All Cell Lines",
"BREAST",
"CNS",
"COLON",
"LEUKEMIA",
"MELANOMA",
"OVARIAN",
"PROSTATE",
"RENAL",
"NSCLC",
"DUPLICATE",
"UNKNOWN"
};
enum nci60OptEnum nci60StringToEnum(char *string)
/* Convert from string to enum representation. */
{
int x = stringIx(string, nci60Options);
if (x < 0)
errAbort("hui::nci60StringToEnum() - Unknown option %s", string);
return x;
}
char *nci60EnumToString(enum nci60OptEnum x)
/* Convert from enum to string representation. */
{
return nci60Options[x];
}
void nci60DropDown(char *var, char *curVal)
/* Make drop down of options. */
{
cgiMakeDropList(var, nci60Options, ArraySize(nci60Options),
curVal);
}
/*** Control of base/codon coloring code: ***/
/* All options (parallel to enum baseColorDrawOpt): */
static char *baseColorDrawAllOptionLabels[] =
{
BASE_COLOR_DRAW_OFF_LABEL,
BASE_COLOR_DRAW_GENOMIC_CODONS_LABEL,
BASE_COLOR_DRAW_ITEM_CODONS_LABEL,
BASE_COLOR_DRAW_DIFF_CODONS_LABEL,
BASE_COLOR_DRAW_ITEM_BASES_CDS_LABEL,
BASE_COLOR_DRAW_DIFF_BASES_CDS_LABEL,
};
static char *baseColorDrawAllOptionValues[] =
{
BASE_COLOR_DRAW_OFF,
BASE_COLOR_DRAW_GENOMIC_CODONS,
BASE_COLOR_DRAW_ITEM_CODONS,
BASE_COLOR_DRAW_DIFF_CODONS,
BASE_COLOR_DRAW_ITEM_BASES,
BASE_COLOR_DRAW_DIFF_BASES,
};
/* Subset of options for tracks with CDS info but not item sequence: */
static char *baseColorDrawGenomicOptionLabels[] =
{
BASE_COLOR_DRAW_OFF_LABEL,
BASE_COLOR_DRAW_GENOMIC_CODONS_LABEL,
};
static char *baseColorDrawGenomicOptionValues[] =
{
BASE_COLOR_DRAW_OFF,
BASE_COLOR_DRAW_GENOMIC_CODONS,
};
/* Subset of options for tracks with aligned item sequence but not CDS: */
static char *baseColorDrawItemOptionLabels[] =
{
BASE_COLOR_DRAW_OFF_LABEL,
BASE_COLOR_DRAW_ITEM_BASES_NC_LABEL,
BASE_COLOR_DRAW_DIFF_BASES_NC_LABEL,
};
static char *baseColorDrawItemOptionValues[] =
{
BASE_COLOR_DRAW_OFF,
BASE_COLOR_DRAW_ITEM_BASES,
BASE_COLOR_DRAW_DIFF_BASES,
};
enum baseColorDrawOpt baseColorDrawOptStringToEnum(char *string)
/* Convert from string to enum representation. */
{
int x = stringIx(string, baseColorDrawAllOptionValues);
if (x < 0)
errAbort("hui::baseColorDrawOptStringToEnum() - Unknown option %s", string);
return x;
}
static boolean baseColorGotCds(struct trackDb *tdb)
/* Return true if this track has CDS info according to tdb (or is genePred). */
{
boolean gotIt = FALSE;
char *setting = trackDbSetting(tdb, BASE_COLOR_USE_CDS);
if (isNotEmpty(setting))
{
if (sameString(setting, "all") || sameString(setting, "given") ||
sameString(setting, "genbank") || startsWith("table", setting))
gotIt = TRUE;
else if (! sameString(setting, "none"))
errAbort("trackDb for %s, setting %s: unrecognized value \"%s\". "
"must be one of {none,all,given,genbank,table}.",
tdb->track, BASE_COLOR_USE_CDS, setting);
}
else if (startsWith("genePred", tdb->type))
gotIt = TRUE;
return gotIt;
}
static boolean baseColorGotSequence(struct trackDb *tdb)
/* Return true if this track has aligned sequence according to tdb. */
{
boolean gotIt = FALSE;
char *setting = trackDbSetting(tdb, BASE_COLOR_USE_SEQUENCE);
if (isNotEmpty(setting))
{
if (sameString(setting, "genbank") || sameString(setting, "seq") ||
sameString(setting, "ss") || startsWith("extFile", setting) ||
sameString(setting, "hgPcrResult") || sameString(setting, "nameIsSequence") ||
sameString(setting, "seq1Seq2") || sameString(setting, "lfExtra"))
gotIt = TRUE;
else if (differentString(setting, "none"))
errAbort("trackDb for %s, setting %s: unrecognized value \"%s\". "
"must be one of {none,genbank,seq,ss,extFile,nameIsSequence,seq1Seq2,"
"hgPcrResult,lfExtra}.",
tdb->track, BASE_COLOR_USE_SEQUENCE, setting);
}
return gotIt;
}
void baseColorDrawOptDropDown(struct cart *cart, struct trackDb *tdb)
/* Make appropriately labeled drop down of options if any are applicable.*/
{
enum baseColorDrawOpt curOpt = baseColorDrawOptEnabled(cart, tdb);
char *curValue = baseColorDrawAllOptionValues[curOpt];
char var[512];
boolean gotCds = baseColorGotCds(tdb);
boolean gotSeq = baseColorGotSequence(tdb);
safef(var, sizeof(var), "%s." BASE_COLOR_VAR_SUFFIX, tdb->track);
if (gotCds && gotSeq)
{
puts("
Color track by codons or bases:");
cgiMakeDropListFull(var, baseColorDrawAllOptionLabels,
baseColorDrawAllOptionValues,
ArraySize(baseColorDrawAllOptionLabels),
curValue, NULL);
printf(" Help on mRNA coloring ",
CDS_MRNA_HELP_PAGE);
}
else if (gotCds)
{
puts("
Color track by codons:");
cgiMakeDropListFull(var, baseColorDrawGenomicOptionLabels,
baseColorDrawGenomicOptionValues,
ArraySize(baseColorDrawGenomicOptionLabels),
curValue, NULL);
printf(" Help on codon coloring ",
CDS_HELP_PAGE);
}
else if (gotSeq)
{
puts("
Color track by bases:");
cgiMakeDropListFull(var, baseColorDrawItemOptionLabels,
baseColorDrawItemOptionValues,
ArraySize(baseColorDrawItemOptionLabels),
curValue, NULL);
printf(" Help on base coloring ",
CDS_BASE_HELP_PAGE);
}
}
enum baseColorDrawOpt baseColorDrawOptEnabled(struct cart *cart,
struct trackDb *tdb)
/* Query cart & trackDb to determine what drawing mode (if any) is enabled. */
{
char *stringVal = NULL;
assert(cart);
assert(tdb);
/* trackDb can override default of OFF; cart can override trackDb. */
stringVal = trackDbSettingOrDefault(tdb, BASE_COLOR_DEFAULT,
BASE_COLOR_DRAW_OFF);
stringVal = cartUsualStringClosestToHome(cart, tdb, FALSE, BASE_COLOR_VAR_SUFFIX,stringVal);
return baseColorDrawOptStringToEnum(stringVal);
}
/*** Control of fancy indel display code: ***/
static boolean indelAppropriate(struct trackDb *tdb)
/* Return true if it makes sense to offer indel display options for tdb. */
{
return (tdb && (startsWith("psl", tdb->type) || sameString("bam", tdb->type)) &&
(cfgOptionDefault("browser.indelOptions", NULL) != NULL));
}
void indelShowOptions(struct cart *cart, struct trackDb *tdb)
/* Make HTML inputs for indel display options if any are applicable. */
{
if (indelAppropriate(tdb))
{
boolean showDoubleInsert, showQueryInsert, showPolyA;
char var[512];
indelEnabled(cart, tdb, 0.0, &showDoubleInsert, &showQueryInsert, &showPolyA);
printf("
Alignment Gap/Insertion Display Options \n");
safef(var, sizeof(var), "%s_%s", INDEL_DOUBLE_INSERT, tdb->track);
cgiMakeCheckBox(var, showDoubleInsert);
printf("Draw double horizontal lines when both genome and query have "
"an insertion "
" \n");
safef(var, sizeof(var), "%s_%s", INDEL_QUERY_INSERT, tdb->track);
cgiMakeCheckBox(var, showQueryInsert);
printf("Draw a vertical purple line for an insertion at the beginning or "
"end of the query, orange for insertion in the middle of the query"
" \n");
safef(var, sizeof(var), "%s_%s", INDEL_POLY_A, tdb->track);
/* We can highlight valid polyA's only if we have query sequence --
* so indelPolyA code piggiebacks on baseColor code: */
if (baseColorGotSequence(tdb))
{
cgiMakeCheckBox(var, showPolyA);
printf("Draw a vertical green line where query has a polyA tail "
"insertion"
" \n");
}
printf("Help on alignment gap/insertion display options"
" \n",
INDEL_HELP_PAGE);
}
}
static boolean tdbOrCartBoolean(struct cart *cart, struct trackDb *tdb,
char *settingName, char *defaultOnOff)
/* Query cart & trackDb to determine if a boolean variable is set. */
{
boolean alreadySet;
char optionStr[512];
alreadySet = !sameString("off",
trackDbSettingOrDefault(tdb, settingName, defaultOnOff));
safef(optionStr, sizeof(optionStr), "%s_%s",
settingName, tdb->track);
alreadySet = cartUsualBoolean(cart, optionStr, alreadySet);
return alreadySet;
}
void indelEnabled(struct cart *cart, struct trackDb *tdb, float basesPerPixel,
boolean *retDoubleInsert, boolean *retQueryInsert,
boolean *retPolyA)
/* Query cart & trackDb to determine what indel display (if any) is enabled. Set
* basesPerPixel to 0.0 to disable check for zoom level. */
{
boolean apropos = indelAppropriate(tdb);
if (apropos && (basesPerPixel > 0.0))
{
// check indel max zoom
float showIndelMaxZoom = trackDbFloatSettingOrDefault(tdb, "showIndelMaxZoom", -1.0);
if ((showIndelMaxZoom >= 0)
&& ((basesPerPixel > showIndelMaxZoom) || (showIndelMaxZoom == 0.0)))
apropos = FALSE;
}
if (retDoubleInsert)
*retDoubleInsert = apropos &&
tdbOrCartBoolean(cart, tdb, INDEL_DOUBLE_INSERT, "off");
if (retQueryInsert)
*retQueryInsert = apropos &&
tdbOrCartBoolean(cart, tdb, INDEL_QUERY_INSERT, "off");
if (retPolyA)
*retPolyA = apropos &&
tdbOrCartBoolean(cart, tdb, INDEL_POLY_A, "off");
}
/****** base position (ruler) controls *******/
static char *zoomOptions[] = {
ZOOM_1PT5X,
ZOOM_3X,
ZOOM_10X,
ZOOM_BASE
};
void zoomRadioButtons(char *var, char *curVal)
/* Make a list of radio buttons for all zoom options */
{
int i;
int size = ArraySize(zoomOptions);
for (i = 0; i < size; i++)
{
char *s = zoomOptions[i];
cgiMakeRadioButton(var, s, sameString(s, curVal));
printf(" %s ", s);
}
}
/****** Some stuff for affy related controls *******/
static char *affyOptions[] = {
"Chip Type",
"Chip ID",
"Tissue Averages"
};
enum affyOptEnum affyStringToEnum(char *string)
/* Convert from string to enum representation. */
{
int x = stringIx(string, affyOptions);
if (x < 0)
errAbort("hui::affyStringToEnum() - Unknown option %s", string);
return x;
}
char *affyEnumToString(enum affyOptEnum x)
/* Convert from enum to string representation. */
{
return affyOptions[x];
}
void affyDropDown(char *var, char *curVal)
/* Make drop down of options. */
{
cgiMakeDropList(var, affyOptions, ArraySize(affyOptions),
curVal);
}
/****** Some stuff for affy all exon related controls *******/
static char *affyAllExonOptions[] = {
"Chip",
"Tissue Averages"
};
enum affyAllExonOptEnum affyAllExonStringToEnum(char *string)
/* Convert from string to enum representation. */
{
int x = stringIx(string, affyAllExonOptions);
if (x < 0)
errAbort("hui::affyAllExonStringToEnum() - Unknown option %s", string);
return x;
}
char *affyAllExonEnumToString(enum affyAllExonOptEnum x)
/* Convert from enum to string representation. */
{
return affyAllExonOptions[x];
}
void affyAllExonDropDown(char *var, char *curVal)
/* Make drop down of options. */
{
cgiMakeDropList(var, affyAllExonOptions, ArraySize(affyAllExonOptions),
curVal);
}
/****** Some stuff for Rosetta related controls *******/
static char *rosettaOptions[] = {
"All Experiments",
"Common Reference and Other",
"Common Reference",
"Other Exps"
};
static char *rosettaExonOptions[] = {
"Confirmed Only",
"Predicted Only",
"All",
};
enum rosettaOptEnum rosettaStringToEnum(char *string)
/* Convert from string to enum representation. */
{
int x = stringIx(string, rosettaOptions);
if (x < 0)
errAbort("hui::rosettaStringToEnum() - Unknown option %s", string);
return x;
}
char *rosettaEnumToString(enum rosettaOptEnum x)
/* Convert from enum to string representation. */
{
return rosettaOptions[x];
}
void rosettaDropDown(char *var, char *curVal)
/* Make drop down of options. */
{
cgiMakeDropList(var, rosettaOptions, ArraySize(rosettaOptions),
curVal);
}
enum rosettaExonOptEnum rosettaStringToExonEnum(char *string)
/* Convert from string to enum representation of exon types. */
{
int x = stringIx(string, rosettaExonOptions);
if (x < 0)
errAbort("hui::rosettaStringToExonEnum() - Unknown option %s", string);
return x;
}
char *rosettaExonEnumToString(enum rosettaExonOptEnum x)
/* Convert from enum to string representation of exon types. */
{
return rosettaExonOptions[x];
}
void rosettaExonDropDown(char *var, char *curVal)
/* Make drop down of exon type options. */
{
cgiMakeDropList(var, rosettaExonOptions, ArraySize(rosettaExonOptions), curVal);
}
/****** Options for the net track level display options *******/
static char *netLevelOptions[] = {
NET_LEVEL_0,
NET_LEVEL_1,
NET_LEVEL_2,
NET_LEVEL_3,
NET_LEVEL_4,
NET_LEVEL_5,
NET_LEVEL_6
};
enum netLevelEnum netLevelStringToEnum(char *string)
/* Convert from string to enum representation. */
{
int x = stringIx(string, netLevelOptions);
if (x < 0)
errAbort("hui::netLevelStringToEnum() - Unknown option %s", string);
return x;
}
char *netLevelEnumToString(enum netLevelEnum x)
/* Convert from enum to string representation. */
{
return netLevelOptions[x];
}
void netLevelDropDown(char *var, char *curVal)
/* Make drop down of options. */
{
cgiMakeDropList(var, netLevelOptions, ArraySize(netLevelOptions), curVal);
}
/****** Options for the net track color options *******/
static char *netColorOptions[] = {
CHROM_COLORS,
GRAY_SCALE
};
enum netColorEnum netColorStringToEnum(char *string)
/* Convert from string to enum representation. */
{
int x = stringIx(string, netColorOptions);
if (x < 0)
errAbort("hui::netColorStringToEnum() - Unknown option %s", string);
return x;
}
char *netColorEnumToString(enum netColorEnum x)
/* Convert from enum to string representation. */
{
return netColorOptions[x];
}
void netColorDropDown(char *var, char *curVal)
/* Make drop down of options. */
{
cgiMakeDropList(var, netColorOptions, ArraySize(netColorOptions), curVal);
}
/****** Options for the chain track color options *******/
static char *chainColorOptions[] = {
CHROM_COLORS,
SCORE_COLORS,
NO_COLORS
};
enum chainColorEnum chainColorStringToEnum(char *string)
/* Convert from string to enum representation. */
{
int x = stringIx(string, chainColorOptions);
if (x < 0)
errAbort("hui::chainColorStringToEnum() - Unknown option %s", string);
return x;
}
char *chainColorEnumToString(enum chainColorEnum x)
/* Convert from enum to string representation. */
{
return chainColorOptions[x];
}
void chainColorDropDown(char *var, char *curVal)
/* Make drop down of options. */
{
cgiMakeDropList(var, chainColorOptions, ArraySize(chainColorOptions), curVal);
}
/****** Options for the wiggle track Windowing *******/
static char *wiggleWindowingOptions[] = {
"mean+whiskers",
"maximum",
"mean",
"minimum",
};
enum wiggleWindowingEnum wiggleWindowingStringToEnum(char *string)
/* Convert from string to enum representation. */
{
int x = stringIx(string, wiggleWindowingOptions);
if (x < 0)
errAbort("hui::wiggleWindowingStringToEnum() - Unknown option %s", string);
return x;
}
char *wiggleWindowingEnumToString(enum wiggleWindowingEnum x)
/* Convert from enum to string representation. */
{
return wiggleWindowingOptions[x];
}
void wiggleWindowingDropDown(char *var, char *curVal)
/* Make drop down of options. */
{
cgiMakeDropList(var, wiggleWindowingOptions, ArraySize(wiggleWindowingOptions),
curVal);
}
/****** Options for the wiggle track Smoothing *******/
static char *wiggleSmoothingOptions[] = {
"OFF", "2", "3", "4", "5", "6", "7", "8", "9", "10", "11",
"12", "13", "14", "15", "16"
};
enum wiggleSmoothingEnum wiggleSmoothingStringToEnum(char *string)
/* Convert from string to enum representation. */
{
int x = stringIx(string, wiggleSmoothingOptions);
if (x < 0)
errAbort("hui::wiggleSmoothingStringToEnum() - Unknown option %s", string);
return x;
}
char *wiggleSmoothingEnumToString(enum wiggleSmoothingEnum x)
/* Convert from enum to string representation. */
{
return wiggleSmoothingOptions[x];
}
void wiggleSmoothingDropDown(char *var, char *curVal)
/* Make drop down of options. */
{
cgiMakeDropList(var, wiggleSmoothingOptions, ArraySize(wiggleSmoothingOptions),
curVal);
}
/****** Options for the wiggle track y Line Mark On/Off *******/
static char *wiggleYLineMarkOptions[] = {
"OFF",
"ON"
};
enum wiggleYLineMarkEnum wiggleYLineMarkStringToEnum(char *string)
/* Convert from string to enum representation. */
{
int x = stringIx(string, wiggleYLineMarkOptions);
if (x < 0)
errAbort("hui::wiggleYLineMarkStringToEnum() - Unknown option %s", string);
return x;
}
char *wiggleYLineMarkEnumToString(enum wiggleYLineMarkEnum x)
/* Convert from enum to string representation. */
{
return wiggleYLineMarkOptions[x];
}
void wiggleYLineMarkDropDown(char *var, char *curVal)
/* Make drop down of options. */
{
cgiMakeDropList(var, wiggleYLineMarkOptions, ArraySize(wiggleYLineMarkOptions),
curVal);
}
/****** Options for the wiggle track AutoScale *******/
static char *wiggleScaleOptions[] = {
"use vertical viewing range setting",
"auto-scale to data view"
};
enum wiggleScaleOptEnum wiggleScaleStringToEnum(char *string)
/* Convert from string to enum representation. */
{
int x = stringIx(string, wiggleScaleOptions);
if (x < 0)
errAbort("hui::wiggleScaleStringToEnum() - Unknown option %s", string);
return x;
}
char *wiggleScaleEnumToString(enum wiggleScaleOptEnum x)
/* Convert from enum to string representation. */
{
return wiggleScaleOptions[x];
}
void wiggleScaleDropDown(char *var, char *curVal)
/* Make drop down of options. */
{
cgiMakeDropList(var, wiggleScaleOptions, ArraySize(wiggleScaleOptions),
curVal);
}
/****** Options for the wiggle track type of graph *******/
static char *wiggleGraphOptions[] = {
"points",
"bar",
};
enum wiggleGraphOptEnum wiggleGraphStringToEnum(char *string)
/* Convert from string to enum representation. */
{
int x = stringIx(string, wiggleGraphOptions);
if (x < 0)
errAbort("hui::wiggleGraphStringToEnum() - Unknown option %s", string);
return x;
}
char *wiggleGraphEnumToString(enum wiggleGraphOptEnum x)
/* Convert from enum to string representation. */
{
return wiggleGraphOptions[x];
}
void wiggleGraphDropDown(char *var, char *curVal)
/* Make drop down of options. */
{
cgiMakeDropList(var, wiggleGraphOptions, ArraySize(wiggleGraphOptions),
curVal);
}
static char *aggregateLabels[] =
{
"none",
"transparent",
"solid",
};
static char *aggregateValues[] =
{
WIG_AGGREGATE_NONE,
WIG_AGGREGATE_TRANSPARENT,
WIG_AGGREGATE_SOLID,
};
void aggregateDropDown(char *var, char *curVal)
/* Make drop down menu for aggregate strategy */
{
cgiMakeDropListFull(var, aggregateLabels, aggregateValues,
ArraySize(aggregateValues), curVal, NULL);
}
static char *wiggleTransformFuncOptions[] = {
"NONE",
"LOG"
};
+static char *wiggleTransformFuncLabels[] = {
+ "NONE",
+ "LOG (ln(1+x))"
+ };
+
enum wiggleTransformFuncEnum wiggleTransformFuncToEnum(char *string)
/* Convert from string to enum representation. */
{
int x = stringIx(string, wiggleTransformFuncOptions);
if (x < 0)
errAbort("hui::wiggleTransformFuncToEnum() - Unknown option %s", string);
return x;
}
void wiggleTransformFuncDropDown(char *var, char *curVal)
/* Make drop down of options. */
{
-cgiMakeDropList(var, wiggleTransformFuncOptions,
- ArraySize(wiggleTransformFuncOptions), curVal);
+cgiMakeDropListFull(var, wiggleTransformFuncLabels, wiggleTransformFuncOptions,
+ ArraySize(wiggleTransformFuncOptions), curVal, NULL);
}
static char *wiggleAlwaysZeroOptions[] = {
"OFF",
"ON"
};
enum wiggleAlwaysZeroEnum wiggleAlwaysZeroToEnum(char *string)
/* Convert from string to enum representation. */
{
int x = stringIx(string, wiggleAlwaysZeroOptions);
if (x < 0)
errAbort("hui::wiggleAlwaysZeroToEnum() - Unknown option %s", string);
return x;
}
void wiggleAlwaysZeroDropDown(char *var, char *curVal)
/* Make drop down of options. */
{
cgiMakeDropList(var, wiggleAlwaysZeroOptions,
ArraySize(wiggleAlwaysZeroOptions), curVal);
}
/****** Options for the wiggle track horizontal grid lines *******/
static char *wiggleGridOptions[] = {
"ON",
"OFF"
};
enum wiggleGridOptEnum wiggleGridStringToEnum(char *string)
/* Convert from string to enum representation. */
{
int x = stringIx(string, wiggleGridOptions);
if (x < 0)
errAbort("hui::wiggleGridStringToEnum() - Unknown option %s", string);
return x;
}
char *wiggleGridEnumToString(enum wiggleGridOptEnum x)
/* Convert from enum to string representation. */
{
return wiggleGridOptions[x];
}
void wiggleGridDropDown(char *var, char *curVal)
/* Make drop down of options. */
{
cgiMakeDropList(var, wiggleGridOptions, ArraySize(wiggleGridOptions),
curVal);
}
/****** Some stuff for wiggle track related controls *******/
static char *wiggleOptions[] = {
"samples only",
"linear interpolation"
};
enum wiggleOptEnum wiggleStringToEnum(char *string)
/* Convert from string to enum representation. */
{
int x = stringIx(string, wiggleOptions);
if (x < 0)
errAbort("hui::wiggleStringToEnum() - Unknown option %s", string);
return x;
}
char *wiggleEnumToString(enum wiggleOptEnum x)
/* Convert from enum to string representation. */
{
return wiggleOptions[x];
}
void wiggleDropDown(char *var, char *curVal)
/* Make drop down of options. */
{
cgiMakeDropList(var, wiggleOptions, ArraySize(wiggleOptions),
curVal);
}
/****** Some stuff for GCwiggle track related controls *******/
static char *GCwiggleOptions[] = {
"samples only",
"linear interpolation"
};
enum GCwiggleOptEnum GCwiggleStringToEnum(char *string)
/* Convert from string to enum representation. */
{
int x = stringIx(string, GCwiggleOptions);
if (x < 0)
errAbort("hui::GCwiggleStringToEnum() - Unknown option %s", string);
return x;
}
char *GCwiggleEnumToString(enum GCwiggleOptEnum x)
/* Convert from enum to string representation. */
{
return GCwiggleOptions[x];
}
void GCwiggleDropDown(char *var, char *curVal)
/* Make drop down of options. */
{
cgiMakeDropList(var, GCwiggleOptions, ArraySize(GCwiggleOptions),
curVal);
}
/****** Some stuff for chimp track related controls *******/
static char *chimpOptions[] = {
"samples only",
"linear interpolation"
};
enum chimpOptEnum chimpStringToEnum(char *string)
/* Convert from string to enum representation. */
{
int x = stringIx(string, chimpOptions);
if (x < 0)
errAbort("hui::chimpStringToEnum() - Unknown option %s", string);
return x;
}
char *chimpEnumToString(enum chimpOptEnum x)
/* Convert from enum to string representation. */
{
return chimpOptions[x];
}
void chimpDropDown(char *var, char *curVal)
/* Make drop down of options. */
{
cgiMakeDropList(var, chimpOptions, ArraySize(chimpOptions),
curVal);
}
/****** Some stuff for mRNA and EST related controls *******/
static void addMrnaFilter(struct mrnaUiData *mud, char *track, char *label, char *key, char *table)
/* Add an mrna filter */
{
struct mrnaFilter *fil;
char buf[128];
AllocVar(fil);
fil->label = label;
safef(buf, sizeof(buf), "%s_%s", track, key);
fil->key = cloneString(buf);
fil->table = table;
slAddTail(&mud->filterList, fil);
}
struct mrnaUiData *newBedUiData(char *track)
/* Make a new in extra-ui data structure for a bed. */
{
struct mrnaUiData *mud;
char buf[128]; /* Expand me here */
AllocVar(mud);
safef(buf, sizeof(buf), "%sFt", track);
mud->filterTypeVar = cloneString(buf);
safef(buf, sizeof(buf), "%sLt", track);
mud->logicTypeVar = cloneString(buf);
addMrnaFilter(mud, track, "name", "name",track);
return mud;
}
struct mrnaUiData *newMrnaUiData(char *track, boolean isXeno)
/* Make a new in extra-ui data structure for mRNA. */
{
struct mrnaUiData *mud;
char buf[128];
AllocVar(mud);
safef(buf, sizeof(buf), "%sFt", track);
mud->filterTypeVar = cloneString(buf);
safef(buf, sizeof(buf), "%sLt", track);
mud->logicTypeVar = cloneString(buf);
if (isXeno)
addMrnaFilter(mud, track, "organism", "org", "organism");
addMrnaFilter(mud, track, "accession", "acc", "acc");
addMrnaFilter(mud, track, "author", "aut", "author");
addMrnaFilter(mud, track, "library", "lib", "library");
addMrnaFilter(mud, track, "tissue", "tis", "tissue");
addMrnaFilter(mud, track, "cell", "cel", "cell");
addMrnaFilter(mud, track, "keyword", "key", "keyword");
addMrnaFilter(mud, track, "gene", "gen", "geneName");
addMrnaFilter(mud, track, "product", "pro", "productName");
addMrnaFilter(mud, track, "description", "des", "description");
return mud;
}
int trackNameAndLabelCmp(const void *va, const void *vb)
/* Compare to sort on label. */
{
const struct trackNameAndLabel *a = *((struct trackNameAndLabel **)va);
const struct trackNameAndLabel *b = *((struct trackNameAndLabel **)vb);
return strcmp(a->label, b->label);
}
char *trackFindLabel(struct trackNameAndLabel *list, char *label)
/* Try to find label in list. Return NULL if it's
* not there. */
{
struct trackNameAndLabel *el;
for (el = list; el != NULL; el = el->next)
{
if (sameString(el->label, label))
return label;
}
return NULL;
}
char *genePredDropDown(struct cart *cart, struct hash *trackHash,
char *formName, char *varName)
/* Make gene-prediction drop-down(). Return track name of
* currently selected one. Return NULL if no gene tracks.
* If formName isn't NULL, it's the form for auto submit (onchange attr).
* If formName is NULL, no submit occurs when menu is changed */
{
char *cartTrack = cartOptionalString(cart, varName);
struct hashEl *trackList, *trackEl;
char *selectedName = NULL;
struct trackNameAndLabel *nameList = NULL, *name;
char *trackName = NULL;
/* Make alphabetized list of all genePred track names. */
trackList = hashElListHash(trackHash);
for (trackEl = trackList; trackEl != NULL; trackEl = trackEl->next)
{
struct trackDb *tdb = trackEl->val;
char *dupe = cloneString(tdb->type);
char *type = firstWordInLine(dupe);
if ((sameString(type, "genePred")) && (!sameString(tdb->table, "tigrGeneIndex") && !tdbIsComposite(tdb)))
{
AllocVar(name);
name->name = tdb->track;
name->label = tdb->shortLabel;
slAddHead(&nameList, name);
}
freez(&dupe);
}
slSort(&nameList, trackNameAndLabelCmp);
/* No gene tracks - not much we can do. */
if (nameList == NULL)
{
slFreeList(&trackList);
return NULL;
}
/* Try to find current track - from cart first, then
* knownGenes, then refGenes. */
if (cartTrack != NULL)
selectedName = trackFindLabel(nameList, cartTrack);
if (selectedName == NULL)
selectedName = trackFindLabel(nameList, "Known Genes");
if (selectedName == NULL)
selectedName = trackFindLabel(nameList, "SGD Genes");
if (selectedName == NULL)
selectedName = trackFindLabel(nameList, "BDGP Genes");
if (selectedName == NULL)
selectedName = trackFindLabel(nameList, "WormBase Genes");
if (selectedName == NULL)
selectedName = trackFindLabel(nameList, "RefSeq Genes");
if (selectedName == NULL)
selectedName = nameList->name;
/* Make drop-down list. */
{
char javascript[SMALLBUF], *autoSubmit;
int nameCount = slCount(nameList);
char **menu;
int i;
AllocArray(menu, nameCount);
for (name = nameList, i=0; name != NULL; name = name->next, ++i)
{
menu[i] = name->label;
}
if (formName == NULL)
autoSubmit = NULL;
else
{
safef(javascript, sizeof(javascript),
"onchange=\"document.%s.submit();\"", formName);
autoSubmit = javascript;
}
cgiMakeDropListFull(varName, menu, menu,
nameCount, selectedName, autoSubmit);
freez(&menu);
}
/* Convert to track name */
for (name = nameList; name != NULL; name = name->next)
{
if (sameString(selectedName, name->label))
trackName = name->name;
}
/* Clean up and return. */
slFreeList(&nameList);
slFreeList(&trackList);
return trackName;
}
static void rAddTrackListToHash(struct hash *trackHash, struct trackDb *tdbList, char *chrom,
boolean leafOnly)
/* Recursively add trackList to trackHash */
{
struct trackDb *tdb;
for (tdb = tdbList; tdb != NULL; tdb = tdb->next)
{
if (hTrackOnChrom(tdb, chrom))
{
if (tdb->subtracks == NULL || !leafOnly)
hashAdd(trackHash, tdb->track, tdb);
}
rAddTrackListToHash(trackHash, tdb->subtracks, chrom, leafOnly);
}
}
struct hash *makeTrackHashWithComposites(char *database, char *chrom,
bool withComposites)
/* Make hash of trackDb items for this chromosome, including composites,
not just the subtracks. */
{
struct trackDb *tdbs = hTrackDb(database, chrom);
struct hash *trackHash = newHash(7);
rAddTrackListToHash(trackHash, tdbs, chrom, !withComposites);
return trackHash;
}
struct hash *makeTrackHash(char *database, char *chrom)
/* Make hash of trackDb items for this chromosome. */
{
return makeTrackHashWithComposites(database, chrom, FALSE);
}
/****** Stuff for acembly related options *******/
static char *acemblyOptions[] = {
"all genes",
"main",
"putative",
};
enum acemblyOptEnum acemblyStringToEnum(char *string)
/* Convert from string to enum representation. */
{
int x = stringIx(string, acemblyOptions);
if (x < 0)
errAbort("hui::acemblyStringToEnum() - Unknown option %s", string);
return x;
}
char *acemblyEnumToString(enum acemblyOptEnum x)
/* Convert from enum to string representation. */
{
return acemblyOptions[x];
}
void acemblyDropDown(char *var, char *curVal)
/* Make drop down of options. */
{
cgiMakeDropList(var, acemblyOptions, ArraySize(acemblyOptions),
curVal);
}
static boolean parseAssignment(char *words, char **name, char **value)
/* parse =, destroying input words in the process */
{
char *p;
if ((p = index(words, '=')) == NULL)
return FALSE;
*p++ = 0;
if (name)
*name = words;
if (value)
*value = p;
return TRUE;
}
static char *getPrimaryType(char *primarySubtrack, struct trackDb *tdb)
/* Do not free when done. */
{
char *type = NULL;
if (primarySubtrack)
{
struct slRef *tdbRef, *tdbRefList = trackDbListGetRefsToDescendants(tdb->subtracks);
for (tdbRef = tdbRefList; tdbRef != NULL; tdbRef = tdbRef->next)
{
struct trackDb *subtrack = tdbRef->val;
if (sameString(subtrack->track, primarySubtrack))
{
type = subtrack->type;
break;
}
}
slFreeList(&tdbRefList);
}
return type;
}
boolean hSameTrackDbType(char *type1, char *type2)
/* Compare type strings: require same string unless both are wig tracks. */
{
return (sameString(type1, type2) ||
(startsWith("wig ", type1) && startsWith("wig ", type2)));
}
static char *labelRoot(char *label, char** suffix)
/* Parses a label which may be split with a into root and suffix
Always free labelRoot. suffix, which may be null does not need to be freed. */
{
char *root = cloneString(label);
char *extra=strstrNoCase(root," "); // mean don't include the reset as part of the link
if ((long)(extra)==-1)
extra=NULL;
if (extra!=NULL)
{
*extra='\0';
if(suffix != NULL)
{
extra+=5;
*extra=' '; // Converts the to ' ' and include the ' '
*suffix = extra;
}
}
return root;
}
typedef struct _dividers {
int count;
char**subgroups;
char* setting;
} dividers_t;
static dividers_t *dividersSettingGet(struct trackDb *parentTdb)
/* Parses any dividers setting in parent of subtracks */
{
dividers_t *dividers = needMem(sizeof(dividers_t));
dividers->setting = cloneString(trackDbSetting(parentTdb, "dividers"));
if(dividers->setting == NULL)
{
freeMem(dividers);
return NULL;
}
dividers->subgroups = needMem(24*sizeof(char*));
dividers->count = chopByWhite(dividers->setting, dividers->subgroups,24);
return dividers;
}
static void dividersFree(dividers_t **dividers)
/* frees any previously obtained dividers setting */
{
if(dividers && *dividers)
{
freeMem((*dividers)->subgroups);
freeMem((*dividers)->setting);
freez(dividers);
}
}
typedef struct _hierarchy {
int count;
char* subgroup;
char**membership;
int* indents;
char* setting;
} hierarchy_t;
static hierarchy_t *hierarchySettingGet(struct trackDb *parentTdb)
/* Parses any list hierachy instructions setting in parent of subtracks */
{
hierarchy_t *hierarchy = needMem(sizeof(hierarchy_t));
hierarchy->setting = cloneString(trackDbSetting(parentTdb, "hierarchy")); // To be freed later
if(hierarchy->setting == NULL)
{
freeMem(hierarchy);
return NULL;
}
int cnt,ix;
char *words[SMALLBUF];
cnt = chopLine(hierarchy->setting, words);
assert(cnt<=ArraySize(words));
if(cnt <= 1)
{
freeMem(hierarchy->setting);
freeMem(hierarchy);
return NULL;
}
hierarchy->membership = needMem(cnt*sizeof(char*));
hierarchy->indents = needMem(cnt*sizeof(int));
hierarchy->subgroup = words[0];
char *name,*value;
for (ix = 1,hierarchy->count=0; ix < cnt; ix++)
{
if (parseAssignment(words[ix], &name, &value))
{
hierarchy->membership[hierarchy->count] = name;
hierarchy->indents[hierarchy->count] = sqlUnsigned(value);
hierarchy->count++;
}
}
return hierarchy;
}
static void hierarchyFree(hierarchy_t **hierarchy)
/* frees any previously obtained hierachy settings */
{
if(hierarchy && *hierarchy)
{
freeMem((*hierarchy)->setting);
freeMem((*hierarchy)->membership);
freeMem((*hierarchy)->indents);
freez(hierarchy);
}
}
#define TV_HIDE "hide"
static boolean subtracksViewIsHidden(struct cart *cart,struct trackDb *subtrack)
// Returns TRUE if the subtrack belongs to a view that is hidden
{
if(subgroupFind(subtrack,"view",NULL) == FALSE)
return FALSE; // No view
if(subtrack->parent == NULL || subtrack->parent->parent == NULL)
return FALSE; // Not the subtrack
char * view = trackDbLocalSetting(subtrack->parent, "view");
assert(view != NULL);
char objName[SMALLBUF];
char *setting =trackDbLocalSetting(subtrack->parent, "visibility");
if(setting == NULL)
setting = TV_HIDE;
safef(objName, sizeof(objName), "%s.%s.vis", subtrack->parent->parent->track,view);
setting = cartUsualString(cart, objName, setting); // Not ClosestToHome
return sameWord(setting,TV_HIDE);
}
char *tdbResolveVis(struct cart *cart,struct trackDb *tdb, boolean applyMax)
// Determines the correct vis for a tdb as modified by parent
{
// Vis can be in trackDb and/or in cart
// vis at subtrack overrides higher up
// no subtrack vis then composite is max applied to view vis
// FIXME: This should become the main API for determining a subtrack's vis.
char objName[SMALLBUF];
char *setting = NULL;
struct trackDb *thisTdb;
enum trackVisibility vis = tvFull; // Successively limited
for(thisTdb = tdb;thisTdb != NULL;thisTdb = thisTdb->parent)
{
setting = trackDbLocalSetting(thisTdb, "visibility");
if(setting == NULL && thisTdb->subtracks != NULL)
{
setting = TV_HIDE;// non-subtrack must default to hide. subtracks default to NULL
// FIXME: If querying for subtrack, need to determine if subtrack checked.
//if(tdbIsCompositeChild(tdb))
// {
// char *subSetting = trackDbLocalSetting(tdb, "parent");
// if (subSetting != NULL && findWordByDelimiter("off",' ',subSetting) == NULL)
// setting = "full";// subtrack checked, so default to full and let applyMax do it's trick
// }
}
safef(objName, sizeof(objName), "%s.vis", thisTdb->track);
if(thisTdb->parent != NULL && thisTdb->subtracks != NULL) // middle level so probably view
{
char * view = trackDbLocalSetting(thisTdb, "view");
if(view != NULL)
safef(objName, sizeof(objName), "%s.%s.vis", thisTdb->parent->track,view);
}
setting = cartUsualString(cart, objName, setting); // Not ClosestToHome
if(setting != NULL && (thisTdb->subtracks == NULL || !applyMax))
return setting; // defined at lowest level so accept it.
if(setting != NULL && applyMax) // applyMax is assertable if settings is not NULL !
vis = tvMin(vis,hTvFromStringNoAbort(setting)); // successively limits
}
assert(setting != NULL);
assert(applyMax);
return hStringFromTv(vis);
}
// Four State checkboxes can be checked/unchecked by enable/disabled
// NOTE: fourState is not a bitmap because it is manipulated in javascript and int seemed easier at the time
#define FOURSTATE_KEY "fourState"
#define FOURSTATE_EMPTY 666
#define FOURSTATE_UNCHECKED 0
#define FOURSTATE_CHECKED 1
#define FOURSTATE_DISABLE(val) {while((val) >= 0) (val) -= 2;}
#define FOURSTATE_ENABLE(val) {while((val) < 0) (val) += 2;}
#define fourStateChecked(fourState) ((fourState) == 1 || (fourState) == -1)
#define fourStateEnabled(fourState) ((fourState) >= 0)
#define fourStateVisible(fourState) ((fourState) == 1)
static int subtrackFourStateChecked(struct trackDb *subtrack, struct cart *cart)
/* Returns the four state checked state of the subtrack */
{
char * setting = NULL;
char objName[SMALLBUF];
int fourState = (int)(long)tdbExtrasGetOrDefault(subtrack,FOURSTATE_KEY,(void *)FOURSTATE_EMPTY);
if(fourState != FOURSTATE_EMPTY)
return fourState;
fourState = FOURSTATE_UNCHECKED; // default to unchecked, enabled
if ((setting = trackDbLocalSetting(subtrack, "parent")) != NULL)
{
if(findWordByDelimiter("off",' ',setting) == NULL)
fourState = FOURSTATE_CHECKED;
}
// Now check visibility
setting = tdbResolveVis(cart,subtrack,FALSE);
// If subtrack's view is hide then fourstate includes disabled
if(sameWord(setting,TV_HIDE) && subtracksViewIsHidden(cart,subtrack))
FOURSTATE_DISABLE(fourState);
safef(objName, sizeof(objName), "%s_sel", subtrack->track);
fourState = cartUsualInt(cart, objName, fourState);
tdbExtrasAddOrUpdate(subtrack,FOURSTATE_KEY,(void *)(long)fourState);
return fourState;
}
typedef struct _dimensions {
int count;
char**names;
char**subgroups;
char* setting;
} dimensions_t;
boolean dimensionsExist(struct trackDb *parentTdb)
/* Does this parent track contain dimensions? */
{
return (trackDbSetting(parentTdb, "dimensions") != NULL);
}
//static boolean dimensionsSubtrackOf(struct trackDb *childTdb)
///* Does this child belong to a parent with dimensions? */
//{
// return (tdbIsCompositeChild(childTdb) && dimensionsExist(childTdb->parent));
//}
static dimensions_t *dimensionSettingsGet(struct trackDb *parentTdb)
/* Parses any dimemnions setting in parent of subtracks */
{
dimensions_t *dimensions = needMem(sizeof(dimensions_t));
dimensions->setting = cloneString(trackDbSetting(parentTdb, "dimensions")); // To be freed later
if(dimensions->setting == NULL)
{
freeMem(dimensions);
return NULL;
}
int cnt,ix;
char *words[SMALLBUF];
cnt = chopLine(dimensions->setting,words);
assert(cnt<=ArraySize(words));
if(cnt <= 0)
{
freeMem(dimensions->setting);
freeMem(dimensions);
return NULL;
}
dimensions->names = needMem(cnt*sizeof(char*));
dimensions->subgroups = needMem(cnt*sizeof(char*));
char *name,*value;
for (ix = 0,dimensions->count=0; ix < cnt; ix++)
{
if (parseAssignment(words[ix], &name, &value))
{
dimensions->names[dimensions->count] = name;
dimensions->subgroups[dimensions->count] = value;
dimensions->count++;
}
}
return dimensions;
}
static void dimensionsFree(dimensions_t **dimensions)
/* frees any previously obtained dividers setting */
{
if(dimensions && *dimensions)
{
freeMem((*dimensions)->setting);
freeMem((*dimensions)->names);
freeMem((*dimensions)->subgroups);
freez(dimensions);
}
}
#define SUBGROUP_MAX 9
#define FILTER_COMPOSITE_ONLYONE
#ifdef FILTER_COMPOSITE_ONLYONE
// FIXME: do we even support anything but multi??? If not, this is a boolean
enum filterCompositeType
/* How to look at a track. */
{
fctNone=0, // do not offer filter for this dimension
fctOne=1, // filter composite by one or all
fctOneOnly=2, // filter composite by only one
fctMulti=3, // filter composite by multiselect: all, one or many
};
#endif///def FILTER_COMPOSITE_ONLYONE
typedef struct _members {
int count;
char * groupTag;
char * groupTitle;
char **tags;
char **titles;
boolean *selected;
char * setting;
int *subtrackCount; // count of subtracks
int *currentlyVisible; // count of visible subtracks
struct slRef **subtrackList; // set of subtracks belonging to each subgroup member
#ifdef FILTER_COMPOSITE_ONLYONE
enum filterCompositeType fcType; // fctNone,fctOne,fctMulti
#endif///def FILTER_COMPOSITE_ONLYONE
} members_t;
int subgroupCount(struct trackDb *parentTdb)
/* How many subGroup setting does this parent have? */
{
int ix;
int count = 0;
for(ix=1;ix<=SUBGROUP_MAX;ix++)
{
char subGrp[16];
safef(subGrp, ArraySize(subGrp), "subGroup%d",ix);
if(trackDbSetting(parentTdb, subGrp) != NULL)
count++;
}
return count;
}
char * subgroupSettingByTagOrName(struct trackDb *parentTdb, char *groupNameOrTag)
/* look for a subGroup by name (ie subGroup1) or tag (ie view) and return an unallocated char* */
{
struct trackDb *ancestor;
for (ancestor = parentTdb; ancestor != NULL; ancestor = ancestor->parent)
{
int ix;
char *setting = NULL;
if(startsWith("subGroup",groupNameOrTag))
{
setting = trackDbSetting(ancestor, groupNameOrTag);
if(setting != NULL)
return setting;
}
for(ix=1;ix<=SUBGROUP_MAX;ix++) // How many do we support?
{
char subGrp[16];
safef(subGrp, ArraySize(subGrp), "subGroup%d",ix);
setting = trackDbSetting(ancestor, subGrp);
if(setting != NULL) // Doesn't require consecutive subgroups
{
if(startsWithWord(groupNameOrTag,setting))
return setting;
}
}
}
return NULL;
}
boolean subgroupingExists(struct trackDb *parentTdb, char *groupNameOrTag)
/* Does this parent track contain a particular subgrouping? */
{
return (subgroupSettingByTagOrName(parentTdb,groupNameOrTag) != NULL);
}
static members_t *subgroupMembersGet(struct trackDb *parentTdb, char *groupNameOrTag)
/* Parse a subGroup setting line into tag,title, names(optional) and values(optional), returning the count of members or 0 */
{
int ix,count;
char *setting = subgroupSettingByTagOrName(parentTdb, groupNameOrTag);
if(setting == NULL)
return NULL;
members_t *members = needMem(sizeof(members_t));
members->setting = cloneString(setting);
char *words[SMALLBUF];
count = chopLine(members->setting, words);
assert(count <= ArraySize(words));
if(count <= 1)
{
freeMem(members->setting);
freeMem(members);
return NULL;
}
members->groupTag = words[0];
members->groupTitle = strSwapChar(words[1],'_',' '); // Titles replace '_' with space
members->tags = needMem(count*sizeof(char*));
members->titles = needMem(count*sizeof(char*));
for (ix = 2,members->count=0; ix < count; ix++)
{
char *name,*value;
if (parseAssignment(words[ix], &name, &value))
{
members->tags[members->count] = name;
members->titles[members->count] = strSwapChar(value,'_',' ');
members->count++;
}
}
return members;
}
// No longer used, but it could come back!
//static members_t *subgroupMembersGetByDimension(struct trackDb *parentTdb, char dimension)
///* Finds the dimension requested and return its associated
// * subgroupMembership, returning the count of members or 0 */
//{
//int ix;
//dimensions_t *dimensions = dimensionSettingsGet(parentTdb);
//if(dimensions!=NULL)
// {
// for(ix=0;ixcount;ix++)
// {
// if(lastChar(dimensions->names[ix]) != dimension)
// continue;
// if((strlen(dimensions->names[ix]) == 10 && startsWith("dimension",dimensions->names[ix]))
// || (strlen(dimensions->names[ix]) == 4 && startsWith("dim",dimensions->names[ix])))
// {
// members_t *members = subgroupMembersGet(parentTdb, dimensions->subgroups[ix]);
// dimensionsFree(&dimensions);
// return members;
// }
// }
// dimensionsFree(&dimensions);
// }
//return NULL;
//}
static int membersSubGroupIx(members_t* members, char *tag)
{ // Returns the index of the subgroup within the members struct (or -1)
int ix = 0;
for(ix=0;ixcount;ix++)
{
if (members->tags[ix] != NULL && sameString(members->tags[ix],tag))
return ix;
}
return -1;
}
static void subgroupMembersFree(members_t **members)
/* frees memory for subgroupMembers lists */
{
if(members && *members)
{
// This should only get set through membersForAll which should not be freed.
if((*members)->selected != NULL || (*members)->subtrackList != NULL)
return;
freeMem((*members)->setting);
freeMem((*members)->tags);
freeMem((*members)->titles);
freez(members);
}
}
static members_t *subgroupMembersWeedOutEmpties(struct trackDb *parentTdb, members_t *members, struct cart *cart)
// Weed out members of a subgroup without any subtracks, alters memory in place!
{
// First tally all subtrack counts
int ixIn=0;
struct slRef *subtrackRef, *subtrackRefList = trackDbListGetRefsToDescendantLeaves(parentTdb->subtracks);
struct trackDb *subtrack;
members->subtrackCount = needMem(members->count * sizeof(int));
members->currentlyVisible = needMem(members->count * sizeof(int));
members->subtrackList = needMem(members->count * sizeof(struct slRef *));
for (subtrackRef = subtrackRefList; subtrackRef != NULL; subtrackRef = subtrackRef->next)
{
subtrack = subtrackRef->val;
char *belongsTo =NULL;
if(subgroupFind(subtrack,members->groupTag,&belongsTo))
{
for(ixIn=0;ixIncount;ixIn++)
{
if(sameString(members->tags[ixIn],belongsTo))
{
members->subtrackCount[ixIn]++;
if(cart && fourStateVisible(subtrackFourStateChecked(subtrack,cart)))
members->currentlyVisible[ixIn]++;
refAdd(&(members->subtrackList[ixIn]), subtrack);
break;
}
}
}
}
// Now weed out empty subgroup tags. Can do this in place since new count <= old count
// NOTE: Don't I wish I had made these as an slList ages ago! (tim)
int ixOut=0;
for(ixIn=ixOut;ixIncount;ixIn++)
{
if(members->subtrackCount[ixIn] > 0)
{
if(ixOut < ixIn)
{
members->tags[ixOut] = members->tags[ixIn];
members->titles[ixOut] = members->titles[ixIn];
members->subtrackCount[ixOut] = members->subtrackCount[ixIn];
members->currentlyVisible[ixOut] = members->currentlyVisible[ixIn];
members->subtrackList[ixOut] = members->subtrackList[ixIn];
if(members->selected != NULL)
members->selected[ixOut] = members->selected[ixIn];
}
ixOut++;
}
else
{
members->tags[ixIn] = NULL;
members->titles[ixIn] = NULL;
members->subtrackCount[ixIn] = 0;
members->currentlyVisible[ixIn] = 0;
//slFreeList(&members->subtrackList[ixIn]); // No freeing at this moment
members->subtrackList[ixIn] = NULL;
if(members->selected != NULL)
members->selected[ixIn] = FALSE;
}
}
members->count = ixOut;
if(members->count == 0) // No members of this subgroup had a subtrack
{
subgroupMembersFree(&members);
return NULL;
}
return members;
}
enum
{
dimV=0, // View first
dimX=1, // X & Y next
dimY=2,
dimA=3, // dimA is start of first of the optional non-matrix, non-view dimensions
};
typedef struct _membersForAll {
int abcCount;
int dimMax;
boolean filters;
dimensions_t *dimensions;
members_t* members[27];
char* checkedTags[27]; // FIXME: Should move checkedTags into membersForAll->members[ix]->selected;
} membersForAll_t;
static char* abcMembersChecked(struct trackDb *parentTdb, struct cart *cart, members_t* members, char letter)
/* returns a string of subGroup tags which are currently checked */
{
char settingName[SMALLBUF];
int mIx;
if (members->selected == NULL)
members->selected = needMem(members->count * sizeof(boolean));
safef(settingName, sizeof(settingName), "%s.filterComp.%s",parentTdb->track,members->groupTag);
struct slName *options = cartOptionalSlNameList(cart,settingName);
if(options != NULL)
{
struct slName *option;
for(option=options;option!=NULL;option=option->next)
{
mIx = membersSubGroupIx(members, option->name);
if(mIx >= 0)
members->selected[mIx] = TRUE;
}
return slNameListToString(options,',');
}
struct dyString *currentlyCheckedTags = NULL;
// Need a string of subGroup tags which are currently checked
safef(settingName,sizeof(settingName),"dimension%cchecked",letter);
char *dimCheckedDefaults = trackDbSettingOrDefault(parentTdb,settingName,"");
for(mIx=0;mIxcount;mIx++)
{
safef(settingName, sizeof(settingName), "%s.mat_%s_dim%c_cb",parentTdb->track,members->tags[mIx],letter);
members->selected[mIx] = (NULL!=findWordByDelimiter(members->tags[mIx],',',dimCheckedDefaults));
members->selected[mIx] = cartUsualBoolean(cart,settingName,members->selected[mIx]);
if(members->selected[mIx])
{
if(currentlyCheckedTags == NULL)
currentlyCheckedTags = dyStringCreate(members->tags[mIx]);
else
{
dyStringAppendC(currentlyCheckedTags,',');
dyStringAppend(currentlyCheckedTags,members->tags[mIx]);
}
}
}
if(currentlyCheckedTags)
return dyStringCannibalize(¤tlyCheckedTags);
return NULL;
}
static membersForAll_t *membersForAllSubGroupsWeedOutEmpties(struct trackDb *parentTdb, membersForAll_t *membersForAll, struct cart *cart)
// Weed through members, tossing those without subtracks
{
// View is always first
if (membersForAll->members[dimV] != NULL)
membersForAll->members[dimV] = subgroupMembersWeedOutEmpties(parentTdb, membersForAll->members[dimV],cart);
// X and Y are special
if (membersForAll->members[dimX] != NULL)
membersForAll->members[dimX] = subgroupMembersWeedOutEmpties(parentTdb, membersForAll->members[dimX],cart);
if (membersForAll->members[dimY] != NULL)
membersForAll->members[dimY] = subgroupMembersWeedOutEmpties(parentTdb, membersForAll->members[dimY],cart);
// Handle the ABC dimensions
int ixIn,ixOut=dimA;
for(ixIn=ixOut;ixIndimMax;ixIn++)
{
if(membersForAll->members[ixIn] != NULL)
membersForAll->members[ixIn] = subgroupMembersWeedOutEmpties(parentTdb, membersForAll->members[ixIn],cart);
if(membersForAll->members[ixIn] == NULL)
membersForAll->checkedTags[ixOut] = NULL;
else
{
if(ixOut < ixIn) // Collapse if necessary
{ // NOTE: Don't I wish I had made these as an slList ages ago! (tim)
membersForAll->members[ixOut] = membersForAll->members[ixIn];
membersForAll->checkedTags[ixOut] = membersForAll->checkedTags[ixIn];
}
ixOut++;
}
}
membersForAll->dimMax = ixOut;
membersForAll->abcCount = membersForAll->dimMax - dimA;
return membersForAll;
}
#define MEMBERS_FOR_ALL_KEY "membersForAll"
static membersForAll_t* membersForAllSubGroupsGet(struct trackDb *parentTdb, struct cart *cart)
/* Returns all the parents subGroups and members */
{
membersForAll_t *membersForAll =tdbExtrasGetOrDefault(parentTdb,MEMBERS_FOR_ALL_KEY,NULL);
if(membersForAll != NULL)
return membersForAll; // Already retrieved, so don't do it again
int ix;
membersForAll = needMem(sizeof(membersForAll_t));
membersForAll->members[dimV]=subgroupMembersGet(parentTdb,"view");
membersForAll->dimMax=dimA; // This can expand, depending upon ABC dimensions
membersForAll->dimensions = dimensionSettingsGet(parentTdb);
if(membersForAll->dimensions != NULL)
{
for(ix=0;ixdimensions->count;ix++)
{
char letter = lastChar(membersForAll->dimensions->names[ix]);
if(letter != 'X' && letter != 'Y')
{
membersForAll->members[membersForAll->dimMax]=subgroupMembersGet(parentTdb, membersForAll->dimensions->subgroups[ix]);
if(cart != NULL)
membersForAll->checkedTags[membersForAll->dimMax] = abcMembersChecked(parentTdb,cart,membersForAll->members[membersForAll->dimMax],letter);
membersForAll->dimMax++;
}
else if(letter == 'X')
membersForAll->members[dimX]=subgroupMembersGet(parentTdb, membersForAll->dimensions->subgroups[ix]);
else
membersForAll->members[dimY]=subgroupMembersGet(parentTdb, membersForAll->dimensions->subgroups[ix]);
}
}
membersForAll->abcCount = membersForAll->dimMax - dimA;
membersForAll = membersForAllSubGroupsWeedOutEmpties(parentTdb, membersForAll, cart);
// NOTE: Dimensions must be defined for filterComposite. Filter dimensioms are all and only ABCs. Use dimensionAchecked to define selected
char *filtering = trackDbSettingOrDefault(parentTdb,"filterComposite",NULL);
if(filtering && !sameWord(filtering,"off"))
{
if(membersForAll->dimensions == NULL)
errAbort("If 'filterComposite' defined, must define 'dimensions' also.");
membersForAll->filters = TRUE;
#ifdef FILTER_COMPOSITE_ONLYONE
// Default all to multi
for(ix=dimA;ixdimMax;ix++)
{
if(membersForAll->members[ix] != NULL)
membersForAll->members[ix]->fcType = fctMulti;
}
if(!sameWord(filtering,"on"))
{
// Example tdb setting: "filterComposite on" OR "filterComposite dimA=one dimB=multi dimC=onlyOne"
// FIXME: do we even support anything but multi???
char *filterGroups[27];
int count = chopLine(filtering,filterGroups);
for(ix=0;ixmembers[abcIx]->fcType = fctOne;
else if(sameWord(filterGroups[ix],"onlyOne") || sameWord(filterGroups[ix],"oneOnly"))
membersForAll->members[abcIx]->fcType = fctOneOnly;
}
}
#endif///def FILTER_COMPOSITE_ONLYONE
}
if(cart != NULL) // Only save this if it is fully populated!
tdbExtrasAddOrUpdate(parentTdb,MEMBERS_FOR_ALL_KEY,membersForAll);
return membersForAll;
}
static int membersForAllFindSubGroupIx(membersForAll_t* membersForAll, char *tag)
{ // Returns the index of the subgroups member struct within membersForAll (or -1)
int ix = 0;
for(ix=0;ixdimMax;ix++)
{
if (membersForAll->members[ix] != NULL && sameString(membersForAll->members[ix]->groupTag,tag))
return ix;
}
return -1;
}
const members_t*membersFindByTag(struct trackDb *parentTdb, char *tag)
{ // Uses membersForAll which may be in tdbExtraCache. Do not free
membersForAll_t* membersForAll = membersForAllSubGroupsGet(parentTdb,NULL);
if(membersForAll == NULL)
return NULL;
int ix = membersForAllFindSubGroupIx(membersForAll,tag);
if(ix >= 0)
return membersForAll->members[ix];
return NULL;
}
static void membersForAllSubGroupsFree(struct trackDb *parentTdb, membersForAll_t** membersForAllPtr)
/* frees memory for membersForAllSubGroups struct */
{
if(membersForAllPtr && *membersForAllPtr)
{
if(parentTdb != NULL)
{
if(*membersForAllPtr == tdbExtrasGetOrDefault(parentTdb,MEMBERS_FOR_ALL_KEY,NULL))
return; // Don't free something saved to the tdbExtras!
}
membersForAll_t* membersForAll = *membersForAllPtr;
subgroupMembersFree(&(membersForAll->members[dimX]));
subgroupMembersFree(&(membersForAll->members[dimY]));
subgroupMembersFree(&(membersForAll->members[dimV]));
int ix;
for(ix=dimA;ixdimMax;ix++)
{
//ASSERT(membersForAll->members[ix] != NULL);
subgroupMembersFree(&(membersForAll->members[ix]));
if(membersForAll->checkedTags[ix])
freeMem(membersForAll->checkedTags[ix]);
}
dimensionsFree(&(membersForAll->dimensions));
freez(membersForAllPtr);
}
}
int multViewCount(struct trackDb *parentTdb)
/* returns the number of multiView views declared */
{
char *setting = subgroupSettingByTagOrName(parentTdb,"view");
if(setting == NULL)
return 0;
setting = cloneString(setting);
int cnt;
char *words[32];
cnt = chopLine(setting, words);
freeMem(setting);
return (cnt - 1);
}
typedef struct _membership {
int count;
char **subgroups; // Ary of Tags in parentTdb->subGroupN and in childTdb->subGroups (ie view)
char **membership; // Ary of Tags of subGroups that child belongs to (ie PK)
char **titles; // Ary of Titles of subGroups a child belongs to (ie Peak)
char * setting;
} membership_t;
#define SUBTRACK_MEMBERSHIP_KEY "subgroupMembership"
static membership_t *subgroupMembershipGet(struct trackDb *childTdb)
/* gets all the subgroup membership for a child track */
{
membership_t *membership = tdbExtrasGetOrDefault(childTdb,SUBTRACK_MEMBERSHIP_KEY,NULL);
if(membership != NULL)
return membership; // Already retrieved, so don't do it again
membership = needMem(sizeof(membership_t));
membership->setting = cloneString(trackDbSetting(childTdb, "subGroups"));
if(membership->setting == NULL)
{
freeMem(membership);
return NULL;
}
int ix,cnt;
char *words[SMALLBUF];
cnt = chopLine(membership->setting, words);
assert(cnt <= ArraySize(words));
if(cnt <= 0)
{
freeMem(membership->setting);
freeMem(membership);
return NULL;
}
membership->subgroups = needMem(cnt*sizeof(char*));
membership->membership = needMem(cnt*sizeof(char*));
membership->titles = needMem(cnt*sizeof(char*));
for (ix = 0,membership->count=0; ix < cnt; ix++)
{
char *name,*value;
if (parseAssignment(words[ix], &name, &value))
{
membership->subgroups[membership->count] = name;
membership->membership[membership->count] = value;//strSwapChar(value,'_',' ');
members_t* members = subgroupMembersGet(childTdb->parent, name);
membership->titles[membership->count] = NULL; // default
if(members != NULL)
{
int ix2 = stringArrayIx(value,members->tags,members->count);
if(ix2 != -1)
membership->titles[membership->count] = strSwapChar(cloneString(members->titles[ix2]),'_',' ');
subgroupMembersFree(&members);
}
membership->count++;
}
}
tdbExtrasAddOrUpdate(childTdb,SUBTRACK_MEMBERSHIP_KEY,membership);
return membership;
}
static boolean membershipInAllCurrentABCs(membership_t *membership,membersForAll_t*membersForAll)
/* looks for a match between a membership set and ABC dimensions currently checked */
{
int mIx,aIx,tIx;
for (aIx = dimA; aIx < membersForAll->dimMax; aIx++) // for each ABC subGroup
{
assert(membersForAll->members[aIx]->selected);
// must find atleast one selected tag that we have membership in
boolean matched = FALSE;
for (mIx = 0; mIx members[aIx]->count;mIx++) // for each tag of that subgroup
{
if(membersForAll->members[aIx]->selected[mIx]) // The particular subgroup tag is selected
{
for(tIx=0;tIxcount;tIx++) // what we are members of
{
if(sameString(membersForAll->members[aIx]->groupTag, membership->subgroups[tIx]) // subTrack belongs to subGroup
&& sameWord(membersForAll->members[aIx]->tags[mIx],membership->membership[tIx])) // and tags match
{
matched = TRUE;
break;
}
}
}
}
if(!matched)
return FALSE;
}
return TRUE; // passed all tests so must be on all
}
// No longer free this because it is saved in subtrack tdbExtras
#define subgroupMembershipFree(membership)
//static void subgroupMembershipFree(membership_t **membership)
//// frees subgroupMembership memory
//{
//if(membership && *membership)
// {
// int ix;
// for(ix=0;ix<(*membership)->count;ix++) { freeMem((*membership)->titles[ix]); }
// freeMem((*membership)->titles);
// freeMem((*membership)->setting);
// freeMem((*membership)->subgroups);
// freeMem((*membership)->membership);
// freez(membership);
// }
//}
char *compositeGroupLabel(struct trackDb *tdb, char *group, char *id)
/* Given ID from group, return corresponding label, looking through parent's subGroupN's */
/* Given group ID, return group label, looking through parent's subGroupN's */
{
members_t *members = subgroupMembersGet(tdb, group);
char *result = NULL;
int i;
for (i=0; icount; ++i)
{
if (sameString(members->tags[i], id))
result = cloneString(members->titles[i]);
}
subgroupMembersFree(&members);
return result;
}
char *compositeGroupId(struct trackDb *tdb, char *group, char *label)
/* Given label, return id, looking through parent's subGroupN's */
{
members_t *members = subgroupMembersGet(tdb, group);
char *result = NULL;
int i;
for (i=0; icount; ++i)
{
if (sameString(members->titles[i], label))
result = cloneString(members->tags[i]);
}
subgroupMembersFree(&members);
return result;
}
static boolean subtrackInAllCurrentABCs(struct trackDb *childTdb,membersForAll_t*membersForAll)
/* looks for a match between a membership set and ABC dimensions currently checked */
{
membership_t *membership = subgroupMembershipGet(childTdb);
if(membership == NULL)
return FALSE;
boolean found = membershipInAllCurrentABCs(membership,membersForAll);
subgroupMembershipFree(&membership);
return found;
}
boolean subgroupFind(struct trackDb *childTdb, char *name,char **value)
/* looks for a single tag in a child track's subGroups setting */
{
if(value != NULL)
*value = NULL;
membership_t *membership = subgroupMembershipGet(childTdb);
if(membership != NULL)
{
int ix;
for(ix=0;ixcount;ix++)
{
if(sameString(name,membership->subgroups[ix]))
{
if(value != NULL)
*value = cloneString(membership->membership[ix]);
return TRUE;
}
}
}
return FALSE;
}
boolean subgroupFindTitle(struct trackDb *parentTdb, char *name,char **value)
/* looks for a a subgroup matching the name and returns the title if found */
{
if(value != (void*)NULL)
*value = NULL;
members_t*members=subgroupMembersGet(parentTdb, name);
//const members_t *members = membersFindByTag(parentTdb,name); // Can't use because of dimension dependence
if(members==NULL)
return FALSE;
*value = cloneString(members->groupTitle);
//subgroupMembersFree(&members);
return TRUE;
}
void subgroupFree(char **value)
/* frees subgroup memory */
{
if(value && *value)
freez(value);
}
sortOrder_t *sortOrderGet(struct cart *cart,struct trackDb *parentTdb)
/* Parses any list sort order instructions for parent of subtracks (from cart or trackDb)
Some trickiness here. sortOrder->sortOrder is from cart (changed by user action), as is sortOrder->order,
But columns are in original tdb order (unchanging)! However, if cart is null, all is from trackDb.ra */
{
int ix;
char *setting = trackDbSetting(parentTdb, "sortOrder");
if(setting == NULL) // Must be in trackDb or not a sortable table
return NULL;
sortOrder_t *sortOrder = needMem(sizeof(sortOrder_t));
sortOrder->htmlId = needMem(strlen(parentTdb->track)+15);
safef(sortOrder->htmlId, (strlen(parentTdb->track)+15), "%s.sortOrder", parentTdb->track);
char *cartSetting = NULL;
if(cart != NULL)
cartSetting = cartCgiUsualString(cart, sortOrder->htmlId, setting);
if(cart != NULL && strlen(cartSetting) == strlen(setting))
sortOrder->sortOrder = cloneString(cartSetting); // cart order
else
sortOrder->sortOrder = cloneString(setting); // old cart value is abandoned!
sortOrder->column = needMem(12*sizeof(char*)); // There aren't going to be more than 3 or 4!
sortOrder->setting = cloneString(setting);
sortOrder->count = chopByWhite(sortOrder->setting, sortOrder->column,12);
sortOrder->title = needMem(sortOrder->count*sizeof(char*));
sortOrder->forward = needMem(sortOrder->count*sizeof(boolean));
sortOrder->order = needMem(sortOrder->count*sizeof(int));
for (ix = 0; ixcount; ix++)
{
strSwapChar(sortOrder->column[ix],'=',0); // Don't want 'CEL=+' but 'CEL' and '+'
char *pos = stringIn(sortOrder->column[ix], sortOrder->sortOrder);// find tdb substr in cart current order string
//assert(pos != NULL && pos[strlen(sortOrder->column[ix])] == '=');
if(pos != NULL && pos[strlen(sortOrder->column[ix])] == '=')
{
int ord=1;
char* pos2 = sortOrder->sortOrder;
for(;*pos2 && pos2 < pos;pos2++)
{
if(*pos2 == '=') // Discovering sort order in cart
ord++;
}
sortOrder->forward[ix] = (pos[strlen(sortOrder->column[ix]) + 1] == '+');
sortOrder->order[ix] = ord;
}
else // give up on cartSetting
{
sortOrder->forward[ix] = TRUE;
sortOrder->order[ix] = ix+1;
}
subgroupFindTitle(parentTdb,sortOrder->column[ix],&(sortOrder->title[ix]));
}
return sortOrder; // NOTE cloneString:words[0]==*sortOrder->column[0] and will be freed when sortOrder is freed
}
void sortOrderFree(sortOrder_t **sortOrder)
/* frees any previously obtained sortOrder settings */
{
if(sortOrder && *sortOrder)
{
int ix;
for(ix=0;ix<(*sortOrder)->count;ix++) { subgroupFree(&((*sortOrder)->title[ix])); }
freeMem((*sortOrder)->sortOrder);
freeMem((*sortOrder)->htmlId);
freeMem((*sortOrder)->column);
freeMem((*sortOrder)->forward);
freeMem((*sortOrder)->order);
freeMem((*sortOrder)->setting);
freez(sortOrder);
}
}
sortableTdbItem *sortableTdbItemCreate(struct trackDb *tdbChild,sortOrder_t *sortOrder)
// creates a sortable tdb item struct, given a child tdb and its parent's sort table
// Errors in interpreting a passed in sortOrder will return NULL
{
sortableTdbItem *item = NULL;
if(tdbChild == NULL || tdbChild->shortLabel == NULL)
return NULL;
AllocVar(item);
item->tdb = tdbChild;
if(sortOrder != NULL) // Add some sort buttons
{
int sIx=0;
for(sIx=sortOrder->count - 1;sIx>=0;sIx--) // walk backwards to ensure sort order in columns
{
sortColumn *column = NULL;
AllocVar(column);
column->fwd = sortOrder->forward[sIx];
if(!subgroupFind(item->tdb,sortOrder->column[sIx],&(column->value)))
{
char *setting = trackDbSetting(item->tdb,sortOrder->column[sIx]);
if(setting != NULL)
column->value = cloneString(setting);
// No subgroup, assume there is a matching setting (eg longLabel)
}
if(column->value != NULL)
slAddHead(&(item->columns), column);
else
{
freez(&column);
if(item->columns != NULL)
slFreeList(&(item->columns));
freeMem(item);
return NULL; // sortOrder setting doesn't match items to be sorted.
}
}
}
return item;
}
static int sortableTdbItemsCmp(const void *va, const void *vb)
// Compare two sortable tdb items based upon sort columns.
{
const sortableTdbItem *a = *((sortableTdbItem **)va);
const sortableTdbItem *b = *((sortableTdbItem **)vb);
sortColumn *colA = a->columns;
sortColumn *colB = b->columns;
int compared = 0;
for (;compared==0 && colA!=NULL && colB!=NULL;colA=colA->next,colB=colB->next)
{
if(colA->value != NULL && colB->value != NULL)
compared = strcmp(colA->value, colB->value) * (colA->fwd? 1: -1);
}
if(compared != 0)
return compared;
return strcmp(a->tdb->shortLabel, b->tdb->shortLabel); // Last chance
}
void sortTdbItemsAndUpdatePriorities(sortableTdbItem **items)
// sort items in list and then update priorities of item tdbs
{
if(items != NULL && *items != NULL)
{
slSort(items, sortableTdbItemsCmp);
int priority=10001; // Setting priorities high allows new subtracks without cart entries to fall after existing subtracks
sortableTdbItem *item;
for (item = *items; item != NULL; item = item->next)
item->tdb->priority = (float)priority++;
}
}
void sortableTdbItemsFree(sortableTdbItem **items)
// Frees all memory associated with a list of sortable tdb items
{
if(items != NULL && *items != NULL)
{
sortableTdbItem *item;
for (item = *items; item != NULL; item = item->next)
{
sortColumn *column;
for (column = item->columns; column != NULL; column = column->next)
freeMem(column->value);
slFreeList(&(item->columns));
}
slFreeList(items);
}
}
static boolean colonPairToStrings(char * colonPair,char **first,char **second)
{ // Will set *first and *second to NULL. Must free any string returned! No colon: value goes to *first
if(first)
*first =NULL; // default to NULL !
if(second)
*second=NULL;
if(colonPair != NULL)
{
if(strchr(colonPair,':'))
{
if(second)
*second = cloneString(strchr(colonPair,':') + 1);
if(first)
*first = strSwapChar(cloneString(colonPair),':',0);
}
else if(first)
*first = cloneString(colonPair);
return (*first != NULL || *second != NULL);
}
return FALSE;
}
static boolean colonPairToInts(char * colonPair,int *first,int *second)
{ // Non-destructive. Only sets values if found. No colon: value goes to *first
char *a=NULL;
char *b=NULL;
if(colonPairToStrings(colonPair,&a,&b))
{
if(a!=NULL)
{
if(first)
*first = atoi(a);
freeMem(a);
}
if(b!=NULL)
{
if(second)
*second = atoi(b);
freeMem(b);
}
return TRUE;
}
return FALSE;
}
static boolean colonPairToDoubles(char * colonPair,double *first,double *second)
{ // Non-destructive. Only sets values if found. No colon: value goes to *first
char *a=NULL;
char *b=NULL;
if(colonPairToStrings(colonPair,&a,&b))
{
if(a!=NULL)
{
if(first)
*first = strtod(a,NULL);
freeMem(a);
}
if(b!=NULL)
{
if(second)
*second = strtod(b,NULL);
freeMem(b);
}
return TRUE;
}
return FALSE;
}
filterBy_t *filterBySetGet(struct trackDb *tdb, struct cart *cart, char *name)
/* Gets one or more "filterBy" settings (ClosestToHome). returns NULL if not found */
{
filterBy_t *filterBySet = NULL;
char *setting = trackDbSettingClosestToHome(tdb, FILTER_BY);
if(setting == NULL)
return NULL;
if( name == NULL )
name = tdb->track;
setting = cloneString(setting);
char *filters[10];
int filterCount = chopLine(setting, filters);
int ix;
for(ix=0;ixcolumn = filter;
filter += strlen(filter) + 1;
strSwapChar(filter,'=',0);
filterBy->title = strSwapChar(filter,'_',' '); // Title does not have underscores
filter += strlen(filter) + 1;
if(filter[0] == '+') // values are indexes to the string titles
{
filter += 1;
filterBy->useIndex = TRUE;
}
filterBy->valueAndLabel = (strchr(filter,'|') != NULL);
filterBy->slValues = slNameListFromComma(filter);
if(filterBy->valueAndLabel)
{
struct slName *val = filterBy->slValues;
for(;val!=NULL;val=val->next)
{
char * lab =strchr(val->name,'|');
if(lab == NULL)
{
warn("Using filterBy but only some values contain labels in form of value|label.");
filterBy->valueAndLabel = FALSE;
break;
}
*lab++ = 0;
strSwapChar(lab,'_',' '); // Title does not have underscores
}
}
slAddTail(&filterBySet,filterBy); // Keep them in order (only a few)
if(cart != NULL)
{
char suffix[64];
safef(suffix, sizeof(suffix), "filterBy.%s", filterBy->column);
boolean compositeLevel = isNameAtCompositeLevel(tdb,name);
if(cartLookUpVariableClosestToHome(cart,tdb,compositeLevel,suffix,&(filterBy->htmlName)))
filterBy->slChoices = cartOptionalSlNameList(cart,filterBy->htmlName);
}
if(filterBy->htmlName == NULL)
{
int len = strlen(name) + strlen(filterBy->column) + 15;
filterBy->htmlName = needMem(len);
safef(filterBy->htmlName, len, "%s.filterBy.%s", name,filterBy->column);
}
}
freeMem(setting);
return filterBySet;
}
void filterBySetFree(filterBy_t **filterBySet)
/* Free a set of filterBy structs */
{
if(filterBySet != NULL)
{
while(*filterBySet != NULL)
{
filterBy_t *filterBy = slPopHead(filterBySet);
if(filterBy->slValues != NULL)
slNameFreeList(filterBy->slValues);
if(filterBy->slChoices != NULL)
slNameFreeList(filterBy->slChoices);
if(filterBy->htmlName != NULL)
freeMem(filterBy->htmlName);
freeMem(filterBy->column);
freeMem(filterBy);
}
}
}
static char *filterByClause(filterBy_t *filterBy)
/* returns the "column in (...)" clause for a single filterBy struct */
{
int count = slCount(filterBy->slChoices);
if(count == 0)
return NULL;
if(slNameInList(filterBy->slChoices,"All"))
return NULL;
struct dyString *dyClause = newDyString(256);
dyStringAppend(dyClause, filterBy->column);
if(count == 1)
dyStringPrintf(dyClause, " = ");
else
dyStringPrintf(dyClause, " in (");
struct slName *slChoice = NULL;
boolean notFirst = FALSE;
for(slChoice = filterBy->slChoices;slChoice != NULL;slChoice=slChoice->next)
{
if(notFirst)
dyStringPrintf(dyClause, ",");
notFirst = TRUE;
if(filterBy->useIndex)
dyStringAppend(dyClause, slChoice->name);
else
dyStringPrintf(dyClause, "\"%s\"",slChoice->name);
}
if(dyStringLen(dyClause) == 0)
{
dyStringFree(&dyClause);
return NULL;
}
if(count > 1)
dyStringPrintf(dyClause, ")");
return dyStringCannibalize(&dyClause);
}
struct dyString *dyAddFilterByClause(struct cart *cart, struct trackDb *tdb,
struct dyString *extraWhere,char *column, boolean *and)
/* creates the where clause condition to support a filterBy setting.
Format: filterBy column:Title=value,value [column:Title=value|label,value|label,value|label])
filterBy filters are multiselect's so could have multiple values selected.
thus returns the "column1 in (...) and column2 in (...)" clause.
if 'column' is provided, and there are multiple filterBy columns, only the named column's clause is returned.
The 'and' param and dyString in/out allows stringing multiple where clauses together
*/
{
filterBy_t *filterBySet = filterBySetGet(tdb, cart,NULL);
if(filterBySet== NULL)
return extraWhere;
filterBy_t *filterBy = filterBySet;
for(;filterBy != NULL; filterBy = filterBy->next)
{
if(column != NULL && differentString(column,filterBy->column))
continue;
char *clause = filterByClause(filterBy);
if(clause != NULL)
{
if(*and)
dyStringPrintf(extraWhere, " AND ");
dyStringAppend(extraWhere, clause);
freeMem(clause);
*and = TRUE;
}
}
filterBySetFree(&filterBySet);
return extraWhere;
}
char *filterBySetClause(filterBy_t *filterBySet)
/* returns the "column1 in (...) and column2 in (...)" clause for a set of filterBy structs */
{
struct dyString *dyClause = newDyString(256);
boolean notFirst = FALSE;
filterBy_t *filterBy = NULL;
for(filterBy = filterBySet;filterBy != NULL; filterBy = filterBy->next)
{
char *clause = filterByClause(filterBy);
if(clause != NULL)
{
if(notFirst)
dyStringPrintf(dyClause, " AND ");
dyStringAppend(dyClause, clause);
freeMem(clause);
notFirst = TRUE;
}
}
if(dyStringLen(dyClause) == 0)
{
dyStringFree(&dyClause);
return NULL;
}
return dyStringCannibalize(&dyClause);
}
void filterBySetCfgUi(struct trackDb *tdb, filterBy_t *filterBySet)
/* Does the UI for a list of filterBy structure */
{
if(filterBySet == NULL)
return;
#define FILTERBY_HELP_LINK "help"
int count = slCount(filterBySet);
if(count == 1)
puts("
");
if(count == 1)
printf("Filter by %s (select multiple items - %s) \n",filterBy->title,FILTERBY_HELP_LINK);
else
printf("%s \n",filterBy->title);
// TODO: Scroll long lists
//#define FILTER_COMPOSITE_OPEN_SIZE 16
// TODO: columnCount (Number of filterBoxes per row) should be configurable through tdb setting
#define FILTER_BY_FORMAT "\n");
// The following is needed to make msie scroll to selected option.
printf("\n",tdb->track);
puts("
", sortOrder->htmlId, sortOrder->htmlId,sortOrder->sortOrder); // keeing track of priority
// Columns in tdb order (unchanging), sort in cart order (changed by user action)
int sIx=0;
for(sIx=0;sIxcount;sIx++)
{
printf ("
");
if (!primarySubtrack)
puts("");
if(dependentCfgsNeedBinding)
cfgLinkToDependentCfgs(parentTdb,parentTdb->track);
membersForAllSubGroupsFree(parentTdb,&membersForAll);
dyStringFree(&dyHtml)
sortOrderFree(&sortOrder);
dividersFree(÷rs);
hierarchyFree(&hierarchy);
}
static void compositeUiAllSubtracks(char *db, struct cart *cart, struct trackDb *tdb,
char *primarySubtrack)
/* Show checkboxes for all subtracks, not just selected ones. */
{
compositeUiSubtracks(db, cart, tdb, FALSE, primarySubtrack);
}
static void compositeUiSelectedSubtracks(char *db, struct cart *cart, struct trackDb *tdb,
char *primarySubtrack)
/* Show checkboxes only for selected subtracks. */
{
compositeUiSubtracks(db, cart, tdb, TRUE, primarySubtrack);
}
static void makeAddClearSubmitTweak(char javascript[JBUFSIZE], char *formName,
char *buttonVar, char *label)
/* safef into javascript a sequence of commands that will force a refresh
* of this same form, updating the values of whatever variables are necessary
* to say what we want to do. */
{
safef(javascript, JBUFSIZE*sizeof(char),
"document.%s.action = '%s'; document.%s.%s.value='%s'; "
"document.%s.submit();",
formName, cgiScriptName(), formName, buttonVar, label,
formName);
}
#define MANY_SUBTRACKS 8
#define WIGGLE_HELP_PAGE "../goldenPath/help/hgWiggleTrackHelp.html"
static boolean cfgBeginBoxAndTitle(struct trackDb *tdb, boolean boxed, char *title)
/* Handle start of box and title for individual track type settings */
{
if(!boxed)
{
boxed = trackDbSettingOn(tdb,"boxedCfg");
if(boxed)
printf(" ");
}
if (boxed)
{
printf("
", COLOR_BG_ALTDEFAULT, COLOR_BG_ALTDEFAULT);
if (title)
printf("
%s Configuration
\n", title);
}
else if (title)
printf("
%s ", title );
else
printf("
");
return boxed;
}
static void cfgEndBox(boolean boxed)
/* Handle end of box and title for individual track type settings */
{
if (boxed)
puts("
");
}
void wigCfgUi(struct cart *cart, struct trackDb *tdb, char *name, char *title, boolean boxed)
/* UI for the wiggle track */
{
char *typeLine = NULL; /* to parse the trackDb type line */
char *words[8]; /* to parse the trackDb type line */
int wordCount = 0; /* to parse the trackDb type line */
char option[256];
double minY; /* from trackDb or cart */
double maxY; /* from trackDb or cart */
double tDbMinY; /* data range limits from trackDb type line */
double tDbMaxY; /* data range limits from trackDb type line */
int defaultHeight; /* pixels per item */
char *horizontalGrid = NULL; /* Grid lines, off by default */
char *transformFunc = NULL; /* function to transform data points */
char *alwaysZero = NULL; /* Always include 0 in range */
char *lineBar; /* Line or Bar graph */
char *autoScale; /* Auto scaling on or off */
char *windowingFunction; /* Maximum, Mean, or Minimum */
char *smoothingWindow; /* OFF or [2:16] */
char *yLineMarkOnOff; /* user defined Y marker line to draw */
double yLineMark; /* from trackDb or cart */
int maxHeightPixels = atoi(DEFAULT_HEIGHT_PER);
int minHeightPixels = MIN_HEIGHT_PER;
boxed = cfgBeginBoxAndTitle(tdb, boxed, title);
wigFetchMinMaxPixelsWithCart(cart,tdb,name,&minHeightPixels, &maxHeightPixels, &defaultHeight);
typeLine = cloneString(tdb->type);
wordCount = chopLine(typeLine,words);
wigFetchMinMaxYWithCart(cart, tdb, name, &minY, &maxY, &tDbMinY, &tDbMaxY, wordCount, words);
freeMem(typeLine);
wigFetchTransformFuncWithCart(cart,tdb,name, &transformFunc);
wigFetchAlwaysZeroWithCart(cart,tdb,name, &alwaysZero);
wigFetchHorizontalGridWithCart(cart,tdb,name, &horizontalGrid);
wigFetchAutoScaleWithCart(cart,tdb,name, &autoScale);
wigFetchGraphTypeWithCart(cart,tdb,name, &lineBar);
wigFetchWindowingFunctionWithCart(cart,tdb,name, &windowingFunction);
wigFetchSmoothingWindowWithCart(cart,tdb,name, &smoothingWindow);
wigFetchYLineMarkWithCart(cart,tdb,name, &yLineMarkOnOff);
wigFetchYLineMarkValueWithCart(cart,tdb,name, &yLineMark);
printf("
");
printf("at y = 0.0:");
snprintf(option, sizeof(option), "%s.%s", name, HORIZGRID );
wiggleGridDropDown(option, horizontalGrid);
printf(" at y =");
snprintf(option, sizeof(option), "%s.%s", name, YLINEMARK );
cgiMakeDoubleVarWithLimits(option, yLineMark, "Indicator at Y", 0, tDbMinY, tDbMaxY);
snprintf(option, sizeof(option), "%s.%s", name, YLINEONOFF );
wiggleYLineMarkDropDown(option, yLineMarkOnOff);
printf("
");
if(boxed)
puts("
");
else
{
puts("
");
printf("Graph configuration help",WIGGLE_HELP_PAGE);
}
cfgEndBox(boxed);
}
void filterButtons(char *filterTypeVar, char *filterTypeVal, boolean none)
/* Put up some filter buttons. */
{
printf("Filter: ");
radioButton(filterTypeVar, filterTypeVal, "red");
radioButton(filterTypeVar, filterTypeVal, "green");
radioButton(filterTypeVar, filterTypeVal, "blue");
radioButton(filterTypeVar, filterTypeVal, "exclude");
radioButton(filterTypeVar, filterTypeVal, "include");
if (none)
radioButton(filterTypeVar, filterTypeVal, "none");
}
void radioButton(char *var, char *val, char *ourVal)
/* Print one radio button */
{
cgiMakeRadioButton(var, ourVal, sameString(ourVal, val));
printf("%s ", ourVal);
}
void oneMrnaFilterUi(struct controlGrid *cg, char *text, char *var, struct cart *cart)
/* Print out user interface for one type of mrna filter. */
{
controlGridStartCell(cg);
printf("%s: ", text);
cgiMakeTextVar(var, cartUsualString(cart, var, ""), 19);
controlGridEndCell(cg);
}
void bedUi(struct trackDb *tdb, struct cart *cart, char *title, boolean boxed)
/* Put up UI for an mRNA (or EST) track. */
{
struct mrnaUiData *mud = newBedUiData(tdb->track);
struct mrnaFilter *fil;
struct controlGrid *cg = NULL;
char *filterTypeVar = mud->filterTypeVar;
char *filterTypeVal = cartUsualString(cart, filterTypeVar, "red");
boxed = cfgBeginBoxAndTitle(tdb, boxed, title);
/* Define type of filter. */
printf("
\n");
filterButtons(filterTypeVar, filterTypeVal, FALSE);
printf("");
/* List various fields you can filter on. */
cg = startControlGrid(4, NULL);
for (fil = mud->filterList; fil != NULL; fil = fil->next)
oneMrnaFilterUi(cg, fil->label, fil->key, cart);
endControlGrid(&cg);
cfgEndBox(boxed);
}
void scoreGrayLevelCfgUi(struct cart *cart, struct trackDb *tdb, char *prefix, int scoreMax)
/* If scoreMin has been set, let user select the shade of gray for that score, in case
* the default is too light to see or darker than necessary. */
{
boolean compositeLevel = isNameAtCompositeLevel(tdb,prefix);
char *scoreMinStr = trackDbSettingClosestToHome(tdb, GRAY_LEVEL_SCORE_MIN);
if (scoreMinStr != NULL)
{
int scoreMin = atoi(scoreMinStr);
// maxShade=9 taken from hgTracks/simpleTracks.c. Ignore the 10 in shadesOfGray[10+1] --
// maxShade is used to access the array.
int maxShade = 9;
int scoreMinGrayLevel = scoreMin * maxShade/scoreMax;
if (scoreMinGrayLevel <= 0) scoreMinGrayLevel = 1;
char *setting = trackDbSettingClosestToHome(tdb, MIN_GRAY_LEVEL);
int minGrayLevel = cartUsualIntClosestToHome(cart, tdb, compositeLevel, MIN_GRAY_LEVEL,
setting ? atoi(setting) : scoreMinGrayLevel);
if (minGrayLevel <= 0) minGrayLevel = 1;
if (minGrayLevel > maxShade) minGrayLevel = maxShade;
puts("\n
Shade of lowest-scoring items: ");
// Add javascript to select so that its color is consistent with option colors:
int level = 255 - (255*minGrayLevel / maxShade);
printf("
\n");
}
}
static boolean getScoreDefaultsFromTdb(struct trackDb *tdb, char *scoreName,char *defaults,char**min,char**max)
/* returns TRUE if defaults exist and sets the string pointer (because they may be float or int)
if min or max are set, then they should be freed */
{
if(min)
*min = NULL; // default these outs!
if(max)
*max = NULL;
char *setting = trackDbSettingClosestToHome(tdb, scoreName);
if(setting)
{
if(strchr(setting,':') != NULL)
return colonPairToStrings(setting,min,max);
else if(min)
*min = cloneString(setting);
return TRUE;
}
return FALSE;
}
static boolean getScoreLimitsFromTdb(struct trackDb *tdb, char *scoreName,char *defaults,char**min,char**max)
/* returns TRUE if limits exist and sets the string pointer (because they may be float or int)
if min or max are set, then they should be freed */
{
if(min)
*min = NULL; // default these outs!
if(max)
*max = NULL;
char scoreLimitName[128];
safef(scoreLimitName, sizeof(scoreLimitName), "%s%s", scoreName, _LIMITS);
char *setting = trackDbSettingClosestToHome(tdb, scoreLimitName);
if(setting)
{
return colonPairToStrings(setting,min,max);
}
else
{
if(min)
{
safef(scoreLimitName, sizeof(scoreLimitName), "%s%s", scoreName, _MIN);
setting = trackDbSettingClosestToHome(tdb, scoreLimitName);
if(setting)
*min = cloneString(setting);
}
if(max)
{
safef(scoreLimitName, sizeof(scoreLimitName), "%s%s", scoreName, _MAX);
setting = trackDbSettingClosestToHome(tdb, scoreLimitName);
if(setting)
*max = cloneString(setting);
}
return TRUE;
}
if(defaults != NULL && ((min && *min == NULL) || (max && *max == NULL)))
{
char *minLoc=NULL;
char *maxLoc=NULL;
if(colonPairToStrings(defaults,&minLoc,&maxLoc))
{
if(min && *min == NULL && minLoc != NULL)
*min=minLoc;
else
freeMem(minLoc);
if(max && *max == NULL && maxLoc != NULL)
*max=maxLoc;
else
freeMem(maxLoc);
return TRUE;
}
}
return FALSE;
}
static void getScoreIntRangeFromCart(struct cart *cart, struct trackDb *tdb, char *scoreName,
int *limitMin, int *limitMax,int *min,int *max)
/* gets an integer score range from the cart, but the limits from trackDb
for any of the pointers provided, will return a value found, if found, else it's contents
are undisturbed (use NO_VALUE to recognize unavaliable values) */
{
char scoreLimitName[128];
char *deMin=NULL,*deMax=NULL;
if((limitMin || limitMax) && getScoreLimitsFromTdb(tdb,scoreName,NULL,&deMin,&deMax))
{
if(deMin != NULL && limitMin)
*limitMin = atoi(deMin);
if(deMax != NULL && limitMax)
*limitMax = atoi(deMax);
freeMem(deMin);
freeMem(deMax);
}
if((min || max) && getScoreDefaultsFromTdb(tdb,scoreName,NULL,&deMin,&deMax))
{
if(deMin != NULL && min)
*min = atoi(deMin);
if(deMax != NULL && max)
*max =atoi(deMax);
freeMem(deMin);
freeMem(deMax);
}
if(max)
{
safef(scoreLimitName, sizeof(scoreLimitName), "%s%s", scoreName, _MAX);
deMax = cartOptionalStringClosestToHome(cart, tdb,FALSE,scoreLimitName);
if(deMax != NULL)
*max = atoi(deMax);
}
if(min)
{
safef(scoreLimitName, sizeof(scoreLimitName), "%s%s", scoreName, (max && deMax? _MIN:"")); // Warning: name changes if max!
deMin = cartOptionalStringClosestToHome(cart, tdb,FALSE,scoreLimitName);
if(deMin != NULL)
*min = atoi(deMin);
}
if(min && limitMin && *min != NO_VALUE && *min < *limitMin) *min = *limitMin; // defaults within range
if(min && limitMax && *min != NO_VALUE && *min > *limitMax) *min = *limitMax;
if(max && limitMax && *max != NO_VALUE && *max > *limitMax) *max = *limitMax;
if(max && limitMin && *max != NO_VALUE && *max < *limitMin) *max = *limitMin;
}
static void getScoreFloatRangeFromCart(struct cart *cart, struct trackDb *tdb, char *scoreName,
double *limitMin,double *limitMax,double*min,double*max)
/* gets an double score range from the cart, but the limits from trackDb
for any of the pointers provided, will return a value found, if found, else it's contents
are undisturbed (use NO_VALUE to recognize unavaliable values) */
{
char scoreLimitName[128];
char *deMin=NULL,*deMax=NULL;
if((limitMin || limitMax) && getScoreLimitsFromTdb(tdb,scoreName,NULL,&deMin,&deMax))
{
if(deMin != NULL && limitMin)
*limitMin = strtod(deMin,NULL);
if(deMax != NULL && limitMax)
*limitMax =strtod(deMax,NULL);
freeMem(deMin);
freeMem(deMax);
}
if((min || max) && getScoreDefaultsFromTdb(tdb,scoreName,NULL,&deMin,&deMax))
{
if(deMin != NULL && min)
*min = strtod(deMin,NULL);
if(deMax != NULL && max)
*max =strtod(deMax,NULL);
freeMem(deMin);
freeMem(deMax);
}
if(max)
{
safef(scoreLimitName, sizeof(scoreLimitName), "%s%s", scoreName, _MAX);
deMax = cartOptionalStringClosestToHome(cart, tdb,FALSE,scoreLimitName);
if(deMax != NULL)
*max = strtod(deMax,NULL);
}
if(min)
{
safef(scoreLimitName, sizeof(scoreLimitName), "%s%s", scoreName, _MIN); // name is always {filterName}Min
deMin = cartOptionalStringClosestToHome(cart, tdb,FALSE,scoreLimitName);
if(deMin != NULL)
*min = strtod(deMin,NULL);
}
if(min && limitMin && (int)(*min) != NO_VALUE && *min < *limitMin) *min = *limitMin; // defaults within range
if(min && limitMax && (int)(*min) != NO_VALUE && *min > *limitMax) *min = *limitMax;
if(max && limitMax && (int)(*max) != NO_VALUE && *max > *limitMax) *max = *limitMax;
if(max && limitMin && (int)(*max) != NO_VALUE && *max < *limitMin) *max = *limitMin;
}
void scoreCfgUi(char *db, struct cart *cart, struct trackDb *tdb, char *name, char *title, int maxScore, boolean boxed)
/* Put up UI for filtering bed track based on a score */
{
char option[256];
boolean compositeLevel = isNameAtCompositeLevel(tdb,name);
filterBy_t *filterBySet = filterBySetGet(tdb,cart,name);
if(filterBySet != NULL)
{
if(!tdbIsComposite(tdb) && !tdbIsCompositeChild(tdb))
jsIncludeFile("hui.js",NULL);
filterBySetCfgUi(tdb,filterBySet);
filterBySetFree(&filterBySet);
return; // Cannot have both 'filterBy' score and 'scoreFilter'
}
boolean scoreFilterOk = (trackDbSettingClosestToHome(tdb, NO_SCORE_FILTER) == NULL);
boolean glvlScoreMin = (trackDbSettingClosestToHome(tdb, GRAY_LEVEL_SCORE_MIN) != NULL);
if (! (scoreFilterOk || glvlScoreMin))
return;
boxed = cfgBeginBoxAndTitle(tdb, boxed, title);
if (scoreFilterOk)
{
int minLimit=0,maxLimit=maxScore,minVal=0,maxVal=maxScore;
getScoreIntRangeFromCart(cart,tdb,SCORE_FILTER,&minLimit,&maxLimit,&minVal,&maxVal);
boolean filterByRange = trackDbSettingClosestToHomeOn(tdb, SCORE_FILTER _BY_RANGE);
if (filterByRange)
{
puts("Filter score range: min:");
snprintf(option, sizeof(option), "%s.%s", name,SCORE_FILTER _MIN);
cgiMakeIntVarWithLimits(option, minVal, "Minimum score",0, minLimit,maxLimit);
puts("max:");
snprintf(option, sizeof(option), "%s.%s", name,SCORE_FILTER _MAX);
cgiMakeIntVarWithLimits(option, maxVal, "Maximum score",0,minLimit,maxLimit);
printf("(%d to %d)\n",minLimit,maxLimit);
}
else
{
printf("Show only items with score at or above: ");
snprintf(option, sizeof(option), "%s.%s", name,SCORE_FILTER);
cgiMakeIntVarWithLimits(option, minVal, "Minimum score",0, minLimit,maxLimit);
printf(" (range: %d to %d)", minLimit, maxLimit);
}
}
if (glvlScoreMin)
scoreGrayLevelCfgUi(cart, tdb, name, maxScore);
/* filter top-scoring N items in track */
char *scoreCtString = trackDbSettingClosestToHome(tdb, "filterTopScorers");
if (scoreCtString != NULL)
{
/* show only top-scoring items. This option only displayed if trackDb
* setting exists. Format: filterTopScorers
");
}
if (hIsGsidServer())
numberPerRow = 6;
else
numberPerRow = 5;
/* new logic to decide if line break should be displayed here */
if ((j != 0 && (j % numberPerRow) == 0) && (lineBreakJustPrinted == FALSE))
{
puts("
");
lineBreakJustPrinted = TRUE;
}
char id[MAX_SP_SIZE];
boolean checked = TRUE;
if(defaultOffSpeciesCnt > 0)
{
if(stringArrayIx(wmSpecies->name,words,defaultOffSpeciesCnt) == -1)
safef(id, sizeof(id), "cb_maf_%s_%s", groups[group], wmSpecies->name);
else
{
safef(id, sizeof(id), "cb_maf_%s_%s_defOff", groups[group], wmSpecies->name);
checked = FALSE;
}
}
else
safef(id, sizeof(id), "cb_maf_%s_%s", groups[group], wmSpecies->name);
if (hIsGsidServer())
{
char *chp;
/* for GSID maf, display only entries belong to the specific MSA selected */
safef(option, sizeof(option), "%s.%s", name, wmSpecies->name);
label = hOrganism(wmSpecies->name);
if (label == NULL)
label = wmSpecies->name;
strcpy(trackName, tdb->track);
/* try AaMaf first */
chp = strstr(trackName, "AaMaf");
/* if it is not a AaMaf track, try Maf next */
if (chp == NULL) chp = strstr(trackName, "Maf");
/* test if the entry actually is part of the specific maf track data */
if (chp != NULL)
{
*chp = '\0';
safef(query, sizeof(query),
"select id from %sMsa where id = 'ss.%s'", trackName, label);
conn = hAllocConn(db);
sr = sqlGetResult(conn, query);
row = sqlNextRow(sr);
/* offer it only if the entry is found in current maf data set */
if (row != NULL)
{
puts("
");
cfgEndBox(boxed);
}
#endif//def USE_BAM
struct trackDb *rFindViewInList(struct trackDb *tdbList, char *view)
/* Return the trackDb on the list (or on any children of the list) that has matching view tag. */
{
struct trackDb *tdb;
for (tdb = tdbList; tdb != NULL; tdb = tdb->next)
{
char *viewSetting = trackDbSetting(tdb, "view");
if (sameOk(viewSetting, view))
return tdb;
}
for (tdb = tdbList; tdb != NULL; tdb = tdb->next)
{
struct trackDb *viewTdb = rFindViewInList(tdb->subtracks, view);
if (viewTdb != NULL)
return viewTdb;
}
return NULL;
}
static boolean compositeViewCfgExpandedByDefault(struct trackDb *parentTdb,char *view,
char **retVisibility)
/* returns true if the view cfg is expanded by default. Optionally allocates string of view
* setting (eg 'dense') */
{
boolean expanded = FALSE;
if ( retVisibility != NULL )
*retVisibility = cloneString(hStringFromTv(parentTdb->visibility));
struct trackDb *viewTdb = rFindViewInList(parentTdb->subtracks, view);
if (viewTdb == NULL)
return FALSE;
if (retVisibility != NULL)
*retVisibility = cloneString(hStringFromTv(viewTdb->visibility));
if (trackDbSetting(viewTdb, "viewUi"))
expanded = TRUE;
return expanded;
}
enum trackVisibility visCompositeViewDefault(struct trackDb *parentTdb,char *view)
/* returns the default track visibility of particular view within a composite track */
{
char *visibility = NULL;
compositeViewCfgExpandedByDefault(parentTdb,view,&visibility);
enum trackVisibility vis = hTvFromString(visibility);
freeMem(visibility);
return vis;
}
struct trackDb *rFindView(struct trackDb *forest, char *viewName)
/* Find a descendent with given view. */
{
struct trackDb *tdb;
for (tdb = forest; tdb != NULL; tdb = tdb->next)
{
char *viewSetting = trackDbSetting(tdb, "view");
if (sameOk(viewSetting, viewName))
return tdb;
struct trackDb *view = rFindView(tdb->subtracks, viewName);
if (view)
return view;
}
return NULL;
}
static boolean hCompositeDisplayViewDropDowns(char *db, struct cart *cart, struct trackDb *parentTdb)
/* UI for composite view drop down selections. */
{
int ix;
char varName[SMALLBUF];
char classes[SMALLBUF];
char javascript[JBUFSIZE];
#define CFG_LINK "%s\n"
#define MAKE_CFG_LINK(name,title,tbl,open) printf(CFG_LINK, (name),(name),(name),(name),(title),(title),(tbl),(name),((open)?"on":"off"))
members_t *membersOfView = subgroupMembersGet(parentTdb,"view");
if(membersOfView == NULL)
return FALSE;
char configurable[membersOfView->count];
memset(configurable,cfgNone,sizeof(configurable));
int firstOpened = -1;
boolean makeCfgRows = FALSE;
struct trackDb **matchedSubtracks = needMem(sizeof(struct trackDb *)*membersOfView->count);
for (ix = 0; ix < membersOfView->count; ix++)
{
char *viewName = membersOfView->tags[ix];
struct trackDb *view = rFindView(parentTdb->subtracks, viewName);
if (view != NULL)
{
matchedSubtracks[ix] = view;
configurable[ix] = (char)cfgTypeFromTdb(view->subtracks, TRUE);
if(configurable[ix] != cfgNone)
{
if(firstOpened == -1)
{
safef(varName, sizeof(varName), "%s.%s.showCfg", parentTdb->track, viewName);
if(cartUsualBoolean(cart,varName,FALSE))
firstOpened = ix;
}
makeCfgRows = TRUE;
}
}
}
toLowerN(membersOfView->groupTitle, 1);
printf("Select %s (help): \n", membersOfView->groupTitle);
puts("
");
// Make row of vis drop downs
for (ix = 0; ix < membersOfView->count; ix++)
{
struct trackDb *view = matchedSubtracks[ix];
char *viewName = membersOfView->tags[ix];
if (view != NULL)
{
printf("
",compositeLabelWithVocabLink(db,parentTdb,dimensionX->subtrackList[ixX]->val,dimensionX->groupTag,label));
freeMem(label);
cntX++;
}
}
// If dimension is big enough, then add Y buttons to right as well
if(cntX>MATRIX_RIGHT_BUTTONS_AFTER)
{
if(dimensionY)
{
printf("
%s
", dimensionX->groupTitle);
printf("
All ",top?"TOP":"BOTTOM");
buttonsForAll();
puts("
\n");
}
static void matrixXheadingsRow2(struct trackDb *parentTdb, membersForAll_t* membersForAll)
/* prints the 2nd row of a matrix: Y title; X buttons; title Y */
{
members_t *dimensionX = membersForAll->members[dimX];
members_t *dimensionY = membersForAll->members[dimY];
// If there are both X and Y dimensions, then there is a row of buttons in X
if(dimensionX && dimensionY)
{
int ixX,cntX=0;
printf("
%s
",COLOR_BG_ALTDEFAULT, dimensionY->groupTitle);
for (ixX = 0; ixX < dimensionX->count; ixX++) // Special row of +- +- +-
{
if(dimensionX->subtrackList && dimensionX->subtrackList[ixX] && dimensionX->subtrackList[ixX]->val)
{
char objName[SMALLBUF];
puts("
\n",compositeLabelWithVocabLink(db,parentTdb,childTdb,dimensionY->groupTag,dimensionY->titles[ixY]));
}
static int displayABCdimensions(char *db,struct cart *cart, struct trackDb *parentTdb, struct slRef *subtrackRefList, membersForAll_t* membersForAll)
/* This will walk through all declared nonX&Y dimensions (X and Y is the 2D matrix of CBs.
NOTE: ABC dims are only supported if there are X & Y both. Also expected number should be passed in */
{
int count=0,ix;
for(ix=dimA;ixdimMax;ix++)
{
if(membersForAll->members[ix]==NULL)
continue;
if(membersForAll->members[ix]->count<1)
continue;
count++;
if(count==1) // First time set up a table
puts("
");
char objName[SMALLBUF];
char javascript[JBUFSIZE];
boolean alreadySet=FALSE;
if(membersForAll->members[ix]->selected != NULL)
alreadySet = membersForAll->members[ix]->selected[aIx];
safef(objName, sizeof(objName), "%s.mat_%s_dim%c_cb",parentTdb->track,membersForAll->members[ix]->tags[aIx], 'A' + (ix - dimA));
safef(javascript,sizeof(javascript),"onclick='matCbClick(this);' class=\"matCB abc %s\"",membersForAll->members[ix]->tags[aIx]);
// TODO Set classes properly (if needed!!!) The class abc works but what about a b or c?
cgiMakeCheckBoxJS(objName,alreadySet,javascript);
printf("%s",compositeLabelWithVocabLink(db,parentTdb,membersForAll->members[ix]->subtrackList[aIx]->val,
membersForAll->members[ix]->groupTag,membersForAll->members[ix]->titles[aIx]));
puts("
");
}
}
puts("
");
}
if(count>0)
puts("
");
return count;
}
#ifdef DEBUG
static void dumpDimension(members_t *dimension, char *name, FILE *f)
/* Dump out information on dimension. */
{
int count = dimension->count;
fprintf(f, "%s: count=%d tag=%s title=%s setting=%s \n", name, count, dimension->tag, dimension->title, dimension->setting);
int i;
for (i=0; inames[i], dimension->values[i]);
fprintf(f, " \n");
}
#endif /* DEBUG */
static char *labelWithVocabLinkForMultiples(char *db,struct trackDb *parentTdb, members_t* members)
/* If the parentTdb has a controlledVocabulary setting and the vocabType is found,
then label will be wrapped with the link to all relevent terms. Return string is cloned. */
{
assert(members->subtrackList != NULL);
char *vocab = cloneString(trackDbSetting(parentTdb, "controlledVocabulary"));
if(vocab == NULL)
return cloneString(members->groupTitle); // No link wrapping!
char *words[15];
int count,ix;
boolean found=FALSE;
if((count = chopByWhite(vocab, words,15)) <= 1) // vocab now contains just the file name
return cloneString(members->groupTitle);
#define VOCAB_MULTILINK_BEG "%s"
struct dyString *dyLink = dyStringCreate(VOCAB_MULTILINK_BEG,vocab);
char *mdbVar = NULL;
// Find mdb var to look up based upon the groupTag and cv setting
for(ix=1;ixgroupTag,words[ix])) // controlledVocabulary setting matches tag so all labels are linked
{
mdbVar = members->groupTag;
break;
}
else if(startsWithWordByDelimiter(members->groupTag,'=',words[ix]))
{
mdbVar = words[ix] + strlen(members->groupTag) + 1;
break;
}
}
if(mdbVar == NULL)
{
dyStringFree(&dyLink);
freeMem(vocab);
return cloneString(members->groupTitle);
}
// Now build the comma delimited string of mdb vals (all have same mdb var)
boolean first = TRUE;
for(ix=0;ixcount;ix++)
{
if(members->subtrackList[ix] != NULL && members->subtrackList[ix]->val != NULL)
{
struct trackDb *childTdb = members->subtrackList[ix]->val;
(void)metadataForTable(db,childTdb,NULL); // Makes sure this has been populated
const char * mdbVal = metadataFindValue(childTdb,mdbVar); // one for each is enough
if(mdbVal != NULL)
{
if(!first)
dyStringAppendC(dyLink,',');
dyStringAppend(dyLink,(char *)mdbVal);
first = FALSE;
}
}
}
dyStringPrintf(dyLink,VOCAB_MULTILINK_END,members->groupTitle,members->groupTitle);
freeMem(vocab);
return dyStringCannibalize(&dyLink);
}
static boolean hCompositeUiByFilter(char *db, struct cart *cart, struct trackDb *parentTdb, char *formName)
/* UI for composite tracks: filter subgroups by multiselects to select subtracks. */
{
membersForAll_t* membersForAll = membersForAllSubGroupsGet(parentTdb,cart);
if(membersForAll == NULL || membersForAll->filters == FALSE) // Not Matrix or filters
return FALSE;
jsIncludeFile("ui.core.js",NULL);
jsIncludeFile("ui.dropdownchecklist.js",NULL);
printf("\n");
// TODO:
// 1) Make this work with matrix
// 2) Scroll long lists should be configurable through tdb setting
// #define FILTER_COMPOSITE_OPEN_SIZE 16
// 3) columnCount (Number of filterBoxes per row) should be configurable through tdb setting
printf("Filter subtracks by: (select multiple %sitems - %s) \n",(membersForAll->dimMax == dimA?"":"categories and "),FILTERBY_HELP_LINK);
printf("
\n");
// Do All [+][-] buttons
if(membersForAll->members[dimX] == NULL && membersForAll->members[dimY] == NULL) // No matrix
{
#define PM_BUTTON_FILTER_COMP ""
printf("
\n");
puts(" \n");
return TRUE;
}
static boolean hCompositeUiByMatrix(char *db, struct cart *cart, struct trackDb *parentTdb, char *formName)
/* UI for composite tracks: matrix of checkboxes. */
{
//int ix;
char objName[SMALLBUF];
membersForAll_t* membersForAll = membersForAllSubGroupsGet(parentTdb,cart);
if(membersForAll == NULL || membersForAll->dimensions == NULL) // Not Matrix!
return FALSE;
int ixX,ixY;
members_t *dimensionX = membersForAll->members[dimX];
members_t *dimensionY = membersForAll->members[dimY];
// use array of char determine all the cells (in X,Y,Z dimensions) that are actually populated
char *value;
int sizeOfX = dimensionX?dimensionX->count:1;
int sizeOfY = dimensionY?dimensionY->count:1;
int cells[sizeOfX][sizeOfY]; // There needs to be atleast one element in dimension
int chked[sizeOfX][sizeOfY]; // How many subCBs are checked per matCB?
int enabd[sizeOfX][sizeOfY]; // How many subCBs are enabled per matCB?
memset(cells, 0, sizeof(cells));
memset(chked, 0, sizeof(chked));
memset(enabd, 0, sizeof(chked));
struct slRef *subtrackRef, *subtrackRefList = trackDbListGetRefsToDescendantLeaves(parentTdb->subtracks);
struct trackDb *subtrack;
if (dimensionX || dimensionY) // Must be an X or Y dimension
{
// Fill the cells based upon subtrack membership
for (subtrackRef = subtrackRefList; subtrackRef != NULL; subtrackRef = subtrackRef->next)
{
subtrack = subtrackRef->val;
ixX = (dimensionX ? -1 : 0 );
ixY = (dimensionY ? -1 : 0 );
if(dimensionX && subgroupFind(subtrack,dimensionX->groupTag,&value))
{
ixX = stringArrayIx(value,dimensionX->tags,dimensionX->count);
subgroupFree(&value);
}
if(dimensionY && subgroupFind(subtrack,dimensionY->groupTag,&value))
{
ixY = stringArrayIx(value,dimensionY->tags,dimensionY->count);
subgroupFree(&value);
}
if(ixX > -1 && ixY > -1)
{
cells[ixX][ixY]++;
int fourState = subtrackFourStateChecked(subtrack,cart);
if(fourStateEnabled(fourState)) // hidden views are handled by 4-way CBs: only count enabled
{
if(subtrackInAllCurrentABCs(subtrack,membersForAll)) // Only bother if the subtrack is found in all ABC dims checked
{
enabd[ixX][ixY]++;
if(fourStateChecked(fourState) == 1)
chked[ixX][ixY]++;
}
}
}
}
}
if(!hCompositeUiByFilter(db, cart, parentTdb, formName))
{
char javascript[JBUFSIZE];
//puts("Select subtracks by characterization: ");
printf("Select subtracks by ");
if(dimensionX && !dimensionY)
safef(javascript, sizeof(javascript), "%s:",dimensionX->groupTitle);
else if(!dimensionX && dimensionY)
safef(javascript, sizeof(javascript), "%s:",dimensionY->groupTitle);
else if(dimensionX && dimensionY)
safef(javascript, sizeof(javascript), "%s and %s:",dimensionX->groupTitle,dimensionY->groupTitle);
else
safef(javascript, sizeof(javascript), "multiple variables:");
puts(strLower(javascript));
if(!subgroupingExists(parentTdb,"view"))
puts("(help)\n");
puts(" \n");
if(membersForAll->abcCount > 0)
{
displayABCdimensions(db,cart,parentTdb,subtrackRefList,membersForAll);
}
}
if(dimensionX == NULL && dimensionY == NULL) // Could have been just filterComposite. Must be an X or Y dimension
return FALSE;
printf("
\n",COLOR_BG_DEFAULT,COLOR_BG_DEFAULT);
matrixXheadings(db,parentTdb,membersForAll,TRUE);
// Now the Y by X matrix
int cntX=0,cntY=0;
for (ixY = 0; ixY < sizeOfY; ixY++)
{
if(dimensionY == NULL || (dimensionY->tags[ixY]))
{
cntY++;
assert(!dimensionY || ixY < dimensionY->count);
printf("
");
/* generate set & clear buttons for subgroups */
for (i = 0; i < MAX_SUBGROUP; i++)
{
char *subGroup;
safef(setting, sizeof setting, "subGroup%d", i+1);
if (trackDbSetting(parentTdb, setting) == NULL)
break;
wordCnt = chopLine(cloneString(trackDbSetting(parentTdb, setting)), words);
if (wordCnt < 2)
continue;
subGroup = cloneString(words[0]);
if(sameWord(subGroup,"view"))
continue; // Multi-view should have taken care of "view" subgroup already
puts ("
");
printf("
%s
", words[1]);
for (j = 2; j < wordCnt; j++)
{
if (!parseAssignment(words[j], &name, &value))
continue;
printf("
");
button = cgiOptionalString(buttonVar);
if (isEmpty(button))
continue;
struct slRef *tdbRefList = trackDbListGetRefsToDescendantLeaves(parentTdb->subtracks);
struct slRef *tdbRef;
for (tdbRef = tdbRefList; tdbRef != NULL; tdbRef = tdbRef->next)
{
subtrack = tdbRef->val;
char *p;
int n;
if ((p = trackDbSetting(subtrack, "subGroups")) == NULL)
continue;
n = chopLine(cloneString(p), words);
for (k = 0; k < n; k++)
{
char *subName, *subValue;
if (!parseAssignment(words[k], &subName, &subValue))
continue;
if (sameString(subName, subGroup) && sameString(subValue, name))
{
boolean newVal = FALSE;
safef(option, sizeof(option),"%s_sel", subtrack->track);
newVal = sameString(button, ADD_BUTTON_LABEL);
if (primarySubtrack)
{
if (sameString(subtrack->track, primarySubtrack))
newVal = TRUE;
if (hSameTrackDbType(primaryType, subtrack->type))
cartSetBoolean(cart, option, newVal);
}
else
cartSetBoolean(cart, option, newVal);
}
}
}
}
puts ("
");
}
return TRUE;
}
void hCompositeUi(char *db, struct cart *cart, struct trackDb *tdb,
char *primarySubtrack, char *fakeSubmit, char *formName)
/* UI for composite tracks: subtrack selection. If primarySubtrack is
* non-NULL, don't allow it to be cleared and only offer subtracks
* that have the same type. If fakeSubmit is non-NULL, add a hidden
* var with that name so it looks like it was pressed. */
{
bool hasSubgroups = (trackDbSetting(tdb, "subGroup1") != NULL);
boolean displayAll =
sameString(cartUsualString(cart, "displaySubtracks", "all"), "all");
boolean isMatrix = dimensionsExist(tdb);
boolean viewsOnly = FALSE;
if(trackDbSetting(tdb, "dragAndDrop") != NULL)
jsIncludeFile("jquery.tablednd.js", NULL);
jsIncludeFile("hui.js",NULL);
jsIncludeFile("ajax.js",NULL);
#ifdef TABLE_SCROLL
jsIncludeFile("jquery.fixedtable.js",NULL);
#endif//def TABLE_SCROLL
puts("
");
}
}
}
boolean superTrackDropDown(struct cart *cart, struct trackDb *tdb,
int visibleChild)
/* Displays hide/show dropdown for supertrack.
* Set visibleChild to indicate whether 'show' should be grayed
* out to indicate that no supertrack members are visible:
* 0 to gray out (no visible children)
* 1 don't gray out (there are visible children)
* -1 don't know (this function should determine)
* If -1,i the subtracks field must be populated with the child trackDbs.
* Returns false if not a supertrack */
{
if (!tdbIsSuperTrack(tdb))
return FALSE;
/* determine if supertrack is show/hide */
boolean show = FALSE;
char *setting =
cartUsualString(cart, tdb->track, tdb->isShow ? "show" : "hide");
if (sameString("show", setting))
show = TRUE;
/* Determine if any tracks in supertrack are visible; if not,
* the 'show' is grayed out */
if (show && (visibleChild == -1))
{
visibleChild = 0;
struct trackDb *cTdb;
for (cTdb = tdb->subtracks; cTdb != NULL; cTdb = tdb->next)
{
cTdb->visibility =
hTvFromString(cartUsualString(cart, cTdb->track,
hStringFromTv(cTdb->visibility)));
if (cTdb->visibility != tvHide)
visibleChild = 1;
}
}
hideShowDropDown(tdb->track, show, (show && visibleChild) ?
"normalText" : "hiddenText");
return TRUE;
}
int tvConvertToNumericOrder(enum trackVisibility v)
{
return ((v) == tvFull ? 4 : \
(v) == tvPack ? 3 : \
(v) == tvSquish ? 2 : \
(v) == tvDense ? 1 : 0);
}
int tvCompare(enum trackVisibility a, enum trackVisibility b)
/* enum trackVis isn't in numeric order by visibility, so compare
* symbolically: */
{
return (tvConvertToNumericOrder(b) - tvConvertToNumericOrder(a));
}
enum trackVisibility tvMin(enum trackVisibility a, enum trackVisibility b)
/* Return the less visible of a and b. */
{
if (tvCompare(a, b) >= 0)
return a;
else
return b;
}
char *compositeViewControlNameFromTdb(struct trackDb *tdb)
/* Returns a string with the composite view control name if one exists */
{
char *stView = NULL;
char *name = NULL;
char *rootName = NULL;
// This routine should give these results: compositeName.viewName or else subtrackName.viewName or else compositeName or else subtrackName
if(tdbIsCompositeChild(tdb) == TRUE && trackDbLocalSetting(tdb, "parent") != NULL)
{
if(trackDbSettingClosestToHomeOn(tdb, "configurable"))
rootName = tdb->track; // subtrackName
else
rootName = firstWordInLine(cloneString(trackDbLocalSetting(tdb, "parent"))); // compositeName
}
if(rootName != NULL)
{
if(subgroupFind(tdb,"view",&stView))
{
int len = strlen(rootName) + strlen(stView) + 3;
name = needMem(len);
safef(name,len,"%s.%s",rootName,stView);
subgroupFree(&stView);
}
else
name = cloneString(rootName);
}
else
name = cloneString(tdb->track);
return name;
}
void compositeViewControlNameFree(char **name)
/* frees a string allocated by compositeViewControlNameFromTdb */
{
if(name && *name)
freez(name);
}
boolean isNameAtCompositeLevel(struct trackDb *tdb,char *name)
/* cfgUi controls are passed a prefix name that may be at the composite or at the subtrack level
returns TRUE for composite level name */
{
struct trackDb *parent;
for (parent = tdb->parent; parent != NULL; parent = parent->parent)
if (startsWithWordByDelimiter(parent->track, '.', name))
return TRUE;
return FALSE;
}
boolean chainDbNormScoreAvailable(struct trackDb *tdb)
/* check if normScore column is specified in trackDb as available */
{
boolean normScoreAvailable = FALSE;
char * normScoreTest =
trackDbSettingClosestToHomeOrDefault(tdb, "chainNormScoreAvailable", "no");
if (differentWord(normScoreTest, "no"))
normScoreAvailable = TRUE;
return normScoreAvailable;
}
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