src/hg/lib/trackDbCustom.c 1.73
1.73 2010/01/04 19:12:30 kent
Merging viewInTheMiddle branch.
Index: src/hg/lib/trackDbCustom.c
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/lib/trackDbCustom.c,v
retrieving revision 1.72
retrieving revision 1.73
diff -b -B -U 1000000 -r1.72 -r1.73
--- src/hg/lib/trackDbCustom.c 30 Nov 2009 17:58:11 -0000 1.72
+++ src/hg/lib/trackDbCustom.c 4 Jan 2010 19:12:30 -0000 1.73
@@ -1,928 +1,1041 @@
/* trackDbCustom - custom (not autoSQL generated) code for working
* with trackDb. This code is concerned with making the trackDb
* MySQL table out of the trackDb.ra files. */
#include "common.h"
#include "linefile.h"
#include "jksql.h"
#include "trackDb.h"
#include "hdb.h"
#include "hui.h"
#include "ra.h"
#include "hash.h"
#include "sqlNum.h"
#include "obscure.h"
#include "hgMaf.h"
#include "customTrack.h"
static char const rcsid[] = "$Id$";
/* ----------- End of AutoSQL generated code --------------------- */
int trackDbCmp(const void *va, const void *vb)
/* Compare to sort based on priority; use shortLabel as secondary sort key.
* Note: parallel code to hgTracks.c:tgCmpPriority */
{
const struct trackDb *a = *((struct trackDb **)va);
const struct trackDb *b = *((struct trackDb **)vb);
float dif = a->priority - b->priority;
if (dif < 0)
return -1;
else if (dif == 0.0)
return strcasecmp(a->shortLabel, b->shortLabel);
else
return 1;
}
void parseColor(char *text, unsigned char *r, unsigned char *g, unsigned char *b)
/* Turn comma-separated string of three numbers into three
* color components. */
{
char *words[4];
int wordCount;
wordCount = chopString(text, ", \t", words, ArraySize(words));
if (wordCount != 3)
errAbort("Expecting 3 comma separated values in %s.", text);
*r = atoi(words[0]);
*g = atoi(words[1]);
*b = atoi(words[2]);
}
static unsigned char parseVisibility(char *value, struct lineFile *lf)
/* Parse a visibility value */
{
if (sameString(value, "hide") || sameString(value, "0"))
return tvHide;
else if (sameString(value, "dense") || sameString(value, "1"))
return tvDense;
else if (sameString(value, "full") || sameString(value, "2"))
return tvFull;
else if (sameString(value, "pack") || sameString(value, "3"))
return tvPack;
else if (sameString(value, "squish") || sameString(value, "4"))
return tvSquish;
else
errAbort("Unknown visibility %s line %d of %s",
value, lf->lineIx, lf->fileName);
return tvHide; /* never reached */
}
static void parseTrackLine(struct trackDb *bt, char *value,
struct lineFile *lf)
/* parse the track line */
{
char *val2 = cloneString(value);
bt->tableName = nextWord(&val2);
// check for override option
if (val2 != NULL)
{
val2 = trimSpaces(val2);
if (!sameString(val2, "override"))
errAbort("invalid track line: %s:%d: track %s", lf->fileName, lf->lineIx, value);
bt->overrides = hashNew(0);
}
}
static void trackDbAddInfo(struct trackDb *bt,
char *var, char *value, struct lineFile *lf)
/* Add info from a variable/value pair to browser table. */
{
if (sameString(var, "track"))
parseTrackLine(bt, value, lf);
else if (sameString(var, "shortLabel") || sameString(var, "name"))
bt->shortLabel = cloneString(value);
else if (sameString(var, "longLabel") || sameString(var, "description"))
bt->longLabel = cloneString(value);
else if (sameString(var, "priority"))
bt->priority = atof(value);
else if (sameWord(var, "url"))
bt->url = cloneString(value);
else if (sameString(var, "visibility"))
{
bt->visibility = parseVisibility(value, lf);
}
else if (sameWord(var, "color"))
{
parseColor(value, &bt->colorR, &bt->colorG, &bt->colorB);
}
else if (sameWord(var, "altColor"))
{
parseColor(value, &bt->altColorR, &bt->altColorG, &bt->altColorB);
}
else if (sameWord(var, "type"))
{
bt->type = cloneString(value);
}
else if (sameWord(var, "spectrum") || sameWord(var, "useScore"))
{
bt->useScore = TRUE;
}
else if (sameWord(var, "canPack"))
{
bt->canPack = !(sameString(value, "0") || sameString(value, "off"));
}
else if (sameWord(var, "chromosomes"))
sqlStringDynamicArray(value, &bt->restrictList, &bt->restrictCount);
else if (sameWord(var, "private"))
bt->private = TRUE;
else if (sameWord(var, "group"))
{
bt->grp = cloneString(value);
}
-else /* Add to settings. */
- {
- if (bt->settingsHash == NULL)
+if (bt->settingsHash == NULL)
bt->settingsHash = hashNew(7);
- hashAdd(bt->settingsHash, var, cloneString(value));
- }
+hashAdd(bt->settingsHash, var, cloneString(value));
+
if (bt->overrides != NULL)
hashAdd(bt->overrides, var, NULL);
}
static void replaceStr(char **varPtr, char *val)
/** replace string in varPtr with val */
{
freeMem(*varPtr);
*varPtr = cloneString(val);
}
static void overrideField(struct trackDb *td, struct trackDb *overTd,
char *var)
/* Update override one field from override. */
{
if (sameString(var, "track"))
{
// skip
}
else if (sameString(var, "shortLabel") || sameString(var, "name"))
replaceStr(&td->shortLabel, overTd->shortLabel);
else if (sameString(var, "longLabel") || sameString(var, "description"))
replaceStr(&td->longLabel, overTd->longLabel);
else if (sameString(var, "priority"))
td->priority = overTd->priority;
else if (sameWord(var, "url"))
replaceStr(&td->url, overTd->url);
else if (sameString(var, "visibility"))
td->visibility = overTd->visibility;
else if (sameWord(var, "color"))
{
td->colorR = overTd->colorR;
td->colorG = overTd->colorG;
td->colorB = overTd->colorB;
}
else if (sameWord(var, "altColor"))
{
td->altColorR = overTd->altColorR;
td->altColorG = overTd->altColorG;
td->altColorB = overTd->altColorB;
}
else if (sameWord(var, "type"))
replaceStr(&td->type, overTd->type);
else if (sameWord(var, "spectrum") || sameWord(var, "useScore"))
td->useScore = overTd->useScore;
else if (sameWord(var, "canPack"))
td->canPack = overTd->canPack;
else if (sameWord(var, "chromosomes"))
{
// just format and re-parse
char *sa = sqlStringArrayToString(overTd->restrictList, overTd->restrictCount);
sqlStringFreeDynamicArray(&td->restrictList);
sqlStringDynamicArray(sa, &td->restrictList, &td->restrictCount);
freeMem(sa);
}
else if (sameWord(var, "private"))
td->private = overTd->private;
else if (sameWord(var, "group"))
{
replaceStr(&td->grp, overTd->grp);
}
else if (sameWord(var, "release"))
{
// ignore -- it was pruned by pruneRelease before this was called.
}
else /* Add to settings. */
{
if (td->settingsHash == NULL)
td->settingsHash = hashNew(7);
char *val = hashMustFindVal(overTd->settingsHash, var);
struct hashEl *hel = hashStore(td->settingsHash, var);
replaceStr((char**)&hel->val, val);
}
}
void trackDbOverride(struct trackDb *td, struct trackDb *overTd)
/* apply an trackOverride trackDb entry to a trackDb entry */
{
assert(overTd->overrides != NULL);
struct hashEl *hel;
struct hashCookie hc = hashFirst(overTd->overrides);
while ((hel = hashNext(&hc)) != NULL)
overrideField(td, overTd, hel->name);
}
static boolean packableType(char *type)
/* Return TRUE if we can pack this type. */
{
char *t = cloneString(type);
char *s = firstWordInLine(t);
boolean canPack = (sameString("psl", s) || sameString("chain", s) ||
sameString("bed", s) || sameString("genePred", s) ||
sameString("bigBed", s) ||
sameString("expRatio", s) || sameString("wigMaf", s) ||
sameString("factorSource", s) || sameString("bed5FloatScore", s) ||
sameString("bed6FloatScore", s) || sameString("altGraphX", s) ||
sameString("bam", s));
freeMem(t);
return canPack;
}
-void trackDbInherit(struct trackDb *bt, struct trackDb *composite)
-/* Fill in some missing values with values from parent track */
-{
-if (bt->type == NULL)
- bt->type = cloneString(composite->type);
-if (bt->url == NULL && composite->url != NULL)
- bt->url = cloneString(composite->url);
-if (bt->grp == NULL)
- bt->grp = cloneString(composite->grp);
-if (bt->canPack == 2 && composite->canPack != 2)
- bt->canPack = composite->canPack;
-if (composite->private)
- bt->private = TRUE;
-if (composite->useScore)
- bt->useScore = TRUE;
-}
-
void trackDbPolish(struct trackDb *bt)
/* Fill in missing values with defaults. */
{
if (bt->shortLabel == NULL)
bt->shortLabel = cloneString(bt->tableName);
if (bt->longLabel == NULL)
bt->longLabel = cloneString(bt->shortLabel);
if (bt->altColorR == 0 && bt->altColorG == 0 && bt->altColorB == 0)
{
bt->altColorR = (255+bt->colorR)/2;
bt->altColorG = (255+bt->colorG)/2;
bt->altColorB = (255+bt->colorB)/2;
}
if (bt->type == NULL)
bt->type = cloneString("");
if (bt->priority == 0)
bt->priority = 100.0;
if (bt->url == NULL)
bt->url = cloneString("");
if (bt->html == NULL)
bt->html = cloneString("");
if (bt->grp == NULL)
bt->grp = cloneString("x");
if (bt->canPack == 2)
bt->canPack = packableType(bt->type);
if (bt->settings == NULL)
bt->settings = cloneString("");
}
char *trackDbInclude(char *raFile, char *line)
/* Get include filename from trackDb line.
Return NULL if line doesn't contain include */
{
static char incFile[256];
char *file;
if (startsWith("include", line))
{
splitPath(raFile, incFile, NULL, NULL);
nextWord(&line);
file = nextQuotedWord(&line);
strcat(incFile, file);
return cloneString(incFile);
}
else
return NULL;
}
struct trackDb *trackDbFromRa(char *raFile)
/* Load track info from ra file into list. */
{
struct lineFile *lf = lineFileOpen(raFile, TRUE);
char *line, *word;
struct trackDb *btList = NULL, *bt;
boolean done = FALSE;
struct hash *compositeHash = hashNew(8);
char *incFile;
for (;;)
{
/* Seek to next line that starts with 'track' */
for (;;)
{
if (!lineFileNext(lf, &line, NULL))
{
done = TRUE;
break;
}
line = skipLeadingSpaces(line);
if (startsWithWord("track", line))
{
lineFileReuse(lf);
break;
}
else if ((incFile = trackDbInclude(raFile, line)) != NULL)
{
struct trackDb *incTdb = trackDbFromRa(incFile);
btList = slCat(btList, incTdb);
}
}
if (done)
break;
/* Allocate track structure and fill it in until next blank line. */
AllocVar(bt);
bt->canPack = 2; /* Unknown value */
slAddHead(&btList, bt);
for (;;)
{
/* Break at blank line or EOF. */
if (!lineFileNext(lf, &line, NULL))
break;
line = skipLeadingSpaces(line);
if (line == NULL || line[0] == 0)
break;
/* Skip comments. */
if (line[0] == '#')
continue;
/* Parse out first word and decide what to do. */
word = nextWord(&line);
if (line == NULL)
errAbort("No value for %s line %d of %s", word, lf->lineIx, lf->fileName);
line = trimSpaces(line);
trackDbAddInfo(bt, word, line, lf);
}
- if (trackDbSetting(bt, "compositeTrack") != NULL)
+ if (trackDbLocalSetting(bt, "compositeTrack") != NULL)
hashAdd(compositeHash, bt->tableName, bt);
}
lineFileClose(&lf);
-for (bt = btList; bt != NULL; bt = bt->next)
- {
- struct trackDb *compositeTdb;
- char *compositeName;
- if ((compositeName = trackDbSetting(bt, "subTrack")) != NULL &&
- trackDbSettingClosestToHome(bt, "noInherit") == NULL)
- if ((compositeTdb =
- hashFindVal(compositeHash, compositeName)) != NULL)
- trackDbInherit(bt, compositeTdb);
- trackDbPolish(bt);
- }
slReverse(&btList);
return btList;
}
void trackDbOverrideVisbility(struct hash *tdHash, char *visibilityRa,
boolean hideFirst)
/* Override visbility settings using a ra file. If hideFirst, set all
* visibilities to hide before applying visibilityRa. */
{
struct lineFile *lf;
struct hash *raRecord;
if (hideFirst)
{
/* Set visibility to hide on all entries */
struct hashEl *hel;
struct hashCookie cookie;
cookie = hashFirst(tdHash);
while ((hel = hashNext(&cookie)) != NULL)
((struct trackDb *)hel->val)->visibility = tvHide;
}
/* Parse the ra file, adjusting visibility accordingly */
lf = lineFileOpen(visibilityRa, TRUE);
while ((raRecord = raNextRecord(lf)) != NULL)
{
char *trackName = hashFindVal(raRecord, "track");
char *visibility = hashFindVal(raRecord, "visibility");
if ((trackName != NULL) && (visibility != NULL))
{
struct trackDb *td = hashFindVal(tdHash, trackName);
if (td != NULL)
td->visibility = parseVisibility(visibility, lf);
}
hashFree(&raRecord);
}
lineFileClose(&lf);
}
+#ifdef OLD
void trackDbOverridePriority(struct hash *tdHash, char *priorityRa)
/* Override priority settings using a ra file. */
{
struct lineFile *lf;
struct hash *raRecord;
/* Parse the ra file, adjusting priority accordingly */
lf = lineFileOpen(priorityRa, TRUE);
while ((raRecord = raNextRecord(lf)) != NULL)
{
char *trackName = hashFindVal(raRecord, "track");
char *priority = hashFindVal(raRecord, "priority");
if ((trackName != NULL) && (priority != NULL))
{
struct trackDb *td = hashFindVal(tdHash, trackName);
if (td != NULL)
{
td->priority = atof(priority);
trackDbPolish(td);
}
}
hashFree(&raRecord);
}
lineFileClose(&lf);
}
+#endif /* OLD */
struct hash *trackDbHashSettings(struct trackDb *tdb)
/* Force trackDb to hash up it's settings. Usually this is just
* done on demand. Returns settings hash. */
{
if (tdb->settingsHash == NULL)
tdb->settingsHash = raFromString(tdb->settings);
return tdb->settingsHash;
}
-char *trackDbSetting(struct trackDb *tdb, char *name)
-/* Return setting string or NULL if none exists. */
+char *trackDbLocalSetting(struct trackDb *tdb, char *name)
+/* Return setting from tdb, but *not* any of it's parents. */
{
if (tdb == NULL)
errAbort("Program error: null tdb passed to trackDbSetting.");
if (tdb->settingsHash == NULL)
tdb->settingsHash = raFromString(tdb->settings);
return hashFindVal(tdb->settingsHash, name);
}
boolean trackDbSettingOn(struct trackDb *tdb, char *name)
/* Return true if a tdb setting is "on" "true" or "enabled". */
{
char *setting = trackDbSetting(tdb,name);
return (setting && ( sameWord(setting,"on")
|| sameWord(setting,"true")
|| sameWord(setting,"enabled")));
}
char *trackDbRequiredSetting(struct trackDb *tdb, char *name)
/* Return setting string or squawk and die. */
{
char *ret = trackDbSetting(tdb, name);
if (ret == NULL)
errAbort("Missing required %s setting in %s track", name, tdb->tableName);
return ret;
}
char *trackDbSettingOrDefault(struct trackDb *tdb, char *name, char *defaultVal)
/* Return setting string, or defaultVal if none exists */
{
char *val = trackDbSetting(tdb, name);
return (val == NULL ? defaultVal : val);
}
float trackDbFloatSettingOrDefault(struct trackDb *tdb, char *name, float defaultVal)
/* Return setting, convert to a float, or defaultVal if none exists */
{
char *val = trackDbSetting(tdb, name);
if (val == NULL)
return defaultVal;
else
return sqlFloat(trimSpaces(val));
}
struct hashEl *trackDbSettingsLike(struct trackDb *tdb, char *wildStr)
/* Return a list of settings whose names match wildStr (may contain wildcard
* characters). Free the result with hashElFreeList. */
{
struct hashEl *allSettings = hashElListHash(tdb->settingsHash);
struct hashEl *matchingSettings = NULL;
struct hashEl *hel = allSettings;
while (hel != NULL)
{
struct hashEl *next = hel->next;
if (wildMatch(wildStr, hel->name))
{
slAddHead(&matchingSettings, hel);
}
else
hashElFree(&hel);
hel = next;
}
return matchingSettings;
}
struct superTrackInfo {
boolean isSuper;
boolean isShow;
char *parentName;
enum trackVisibility defaultVis;
};
static struct superTrackInfo *getSuperTrackInfo(struct trackDb *tdb)
/* Get info from supertrack setting. There are 2 forms:
* Parent: 'superTrack on [show]'
* Child: 'superTrack <parent> [vis]
* Return null if there is no such setting. */
{
char *setting = trackDbSetting(tdb, "superTrack");
if (!setting)
return NULL;
char *words[8];
int wordCt = chopLine(cloneString(setting), words);
if (wordCt < 1)
return NULL;
struct superTrackInfo *stInfo;
AllocVar(stInfo);
if (sameString("on", words[0]))
{
/* parent */
stInfo->isSuper = TRUE;
if ((wordCt > 1) && sameString("show", words[1]))
stInfo->isShow = TRUE;
}
else
{
/* child */
stInfo->parentName = cloneString(words[0]);
if (wordCt > 1)
stInfo->defaultVis = max(0, hTvFromStringNoAbort(words[1]));
}
return stInfo;
}
char *trackDbGetSupertrackName(struct trackDb *tdb)
/* Find name of supertrack if this track is a member */
{
char *ret = NULL;
struct superTrackInfo *stInfo = getSuperTrackInfo(tdb);
if (stInfo)
{
if (stInfo->parentName)
ret = cloneString(stInfo->parentName);
freeMem(stInfo);
}
return ret;
}
void trackDbSuperMemberSettings(struct trackDb *tdb)
/* Set fields in trackDb to indicate this is a member of a
* supertrack. */
{
struct superTrackInfo *stInfo = getSuperTrackInfo(tdb);
tdb->parentName = cloneString(stInfo->parentName);
tdb->visibility = stInfo->defaultVis;
tdbMarkAsSuperTrackChild(tdb);
if(tdb->parent)
{
tdbMarkAsSuperTrack(tdb->parent);
- //if(tdb->parent->subtracks || tdb->next == NULL) // TODO: Currently supertracks Sometimes don't contain their subtracks!
- // slAddHead(&tdb->parent->subtracks, tdb);
}
freeMem(stInfo);
}
-void trackDbSuperSettings(struct trackDb *tdbList)
+void trackDbSuperMarkup(struct trackDb *tdbList)
/* Set trackDb from superTrack setting */
{
struct trackDb *tdb;
struct hash *superHash = hashNew(0);
struct superTrackInfo *stInfo;
/* find supertracks, setup their settings */
for (tdb = tdbList; tdb != NULL; tdb = tdb->next)
{
stInfo = getSuperTrackInfo(tdb);
if (!stInfo)
continue;
if (stInfo->isSuper)
{
tdbMarkAsSuperTrack(tdb);
tdb->isShow = stInfo->isShow;
if (!hashLookup(superHash, tdb->tableName))
hashAdd(superHash, tdb->tableName, tdb);
}
freeMem(stInfo);
}
/* adjust settings on supertrack members after verifying they have
* a supertrack configured in this trackDb */
for (tdb = tdbList; tdb != NULL; tdb = tdb->next)
{
stInfo = getSuperTrackInfo(tdb);
if (!stInfo)
continue;
if(!stInfo->isSuper)
{
- tdb->parent = hashFindVal(superHash, stInfo->parentName); // TODO: Parent wont contain children: and can't in this list!
+ tdb->parent = hashFindVal(superHash, stInfo->parentName);
if (tdb->parent)
+ {
trackDbSuperMemberSettings(tdb);
}
+ }
freeMem(stInfo);
}
}
char *trackDbOrigAssembly(struct trackDb *tdb)
/* return setting from trackDb, if any */
{
return (trackDbSetting(tdb, "origAssembly"));
}
void trackDbPrintOrigAssembly(struct trackDb *tdb, char *database)
/* Print lift information from trackDb, if any */
{
char *origAssembly = trackDbOrigAssembly(tdb);
if (origAssembly)
{
if (differentString(origAssembly, database))
{
char *freeze = hFreezeFromDb(origAssembly);
printf("<B>Data coordinates converted via <A TARGET=_BLANK HREF=\"../goldenPath/help/hgTracksHelp.html#Liftover\">liftOver</A> from:</B> %s %s%s%s<BR>\n", freeze ? freeze : "", freeze ? "(" : "", origAssembly, freeze ? ")":"");
}
}
}
eCfgType cfgTypeFromTdb(struct trackDb *tdb, boolean warnIfNecessary)
/* determine what kind of track specific configuration is needed,
warn if not multi-view compatible */
{
eCfgType cType = cfgNone;
-if(startsWith("wigMaf", tdb->type))
+char *type = tdb->type;
+if(startsWith("wigMaf", type))
cType = cfgWigMaf;
-else if(startsWith("wig", tdb->type))
+else if(startsWith("wig", type))
cType = cfgWig;
-else if(startsWith("bigWig", tdb->type))
+else if(startsWith("bigWig", type))
cType = cfgWig;
-else if(startsWith("bedGraph", tdb->type))
+else if(startsWith("bedGraph", type))
cType = cfgWig;
-else if(startsWith("netAlign", tdb->type))
+else if(startsWith("netAlign", type))
{
cType = cfgNetAlign;
warnIfNecessary = FALSE;
}
-else if(sameWord("bed5FloatScore", tdb->type)
- || sameWord("bed5FloatScoreWithFdr",tdb->type))
+else if(sameWord("bed5FloatScore", type)
+ || sameWord("bed5FloatScoreWithFdr",type))
cType = cfgBedScore;
-else if(sameWord("narrowPeak",tdb->type)
- || sameWord("broadPeak", tdb->type)
- || sameWord("encodePeak",tdb->type)
- || sameWord("gappedPeak",tdb->type))
+else if(sameWord("narrowPeak",type)
+ || sameWord("broadPeak", type)
+ || sameWord("encodePeak",type)
+ || sameWord("gappedPeak",type))
cType = cfgPeak;
-else if(sameWord("genePred",tdb->type))
+else if(sameWord("genePred",type))
cType = cfgGenePred;
-else if(startsWith("bed ", tdb->type) || startsWith("bigBed ", tdb->type)) // TODO: Only these are configurable so far
+else if(startsWith("bed ", type) || startsWith("bigBed ", type))
{
char *words[3];
- chopLine(cloneString( tdb->type), words);
+ chopLine(cloneString( type), words);
if (trackDbSetting(tdb, "bedFilter") != NULL)
cType = cfgBedFilt;
else if (atoi(words[1]) >= 5 && trackDbSettingClosestToHome(tdb, "noScoreFilter") == NULL)
cType = cfgBedScore;
}
-else if(startsWith("chain",tdb->type))
+else if(startsWith("chain",type))
cType = cfgChain;
+// TODO: Only these are configurable so far
+// uglyAbort("cfgTypeFromTdb 3 tdb=%s type=%s", tdb->tableName,type);
if(cType == cfgNone && warnIfNecessary)
{
- if(!startsWith("bed ", tdb->type) && !startsWith("bigBed", tdb->type)
+ if(!startsWith("bed ", type) && !startsWith("bigBed", type)
&& subgroupFind(tdb,"view",NULL))
- warn("Track type \"%s\" is not yet supported in multi-view composites for %s.",tdb->type,tdb->tableName);
+ warn("Track type \"%s\" is not yet supported in multi-view composites for %s.",type,tdb->tableName);
}
return cType;
}
-
-char *trackDbCompositeSettingByView(struct trackDb *parentTdb, char* view, char *name)
-/* Get a trackDb setting at the view level for a multiview composite.
- returns a string that must be freed */
+char *trackDbSetting(struct trackDb *tdb, char *name)
+/* Look for a trackDb setting from lowest level on up chain of parents. */
{
+struct trackDb *generation;
char *trackSetting = NULL;
-char *settingsByView = cloneString(trackDbSetting(parentTdb,"settingsByView"));
-if(settingsByView != NULL)
- {
- char *settingForAView = NULL;
- char *words[32];
- int cnt,ix;
- // parse settingsByView "Signal:viewLimits=5:500,viewLimitsMax=0:20910 ..."
- cnt = chopLine(cloneString(settingsByView), words);
- for(ix=0;ix<cnt;ix++)
+for (generation = tdb; generation != NULL; generation = generation->parent)
{
- if(startsWithWordByDelimiter(view,':',words[ix]))
- {
- settingForAView = cloneString(words[ix]+(strlen(view)+1));
+ trackSetting = trackDbLocalSetting(generation,name);
+ if (trackSetting != NULL)
break;
}
- }
- freeMem(settingsByView);
- if(settingForAView != NULL) // found a match
- {
- // parse settingByView: "viewLimits=5:500,viewLimitsMax=0:20910"
- cnt = chopByChar(settingForAView,',',words,ArraySize(words));
- for(ix=0;ix<cnt;ix++)
- {
- if(startsWithWordByDelimiter(name,'=',words[ix]))
- {
- trackSetting = cloneString(words[ix]+strlen(name)+1);
- break;
- }
- }
- freeMem(settingForAView);
- }
- }
return trackSetting;
}
char *trackDbSettingByView(struct trackDb *tdb, char *name)
-/* For a subtrack of a multiview composite, get a setting stored in the parent settingByView.
- returns a string that must be freed */
+/* For a subtrack of a multiview composite, get a setting stored in the view or any other
+ * ancestor. */
{
-char * view;
-if(tdbIsCompositeChild(tdb) && subgroupFind(tdb,"view",&view))
- {
- return trackDbCompositeSettingByView(tdb->parent,view,name);
- }
+if (tdb->parent == NULL)
+ return NULL;
+return trackDbSettingClosestToHome(tdb->parent, name);
return NULL;
}
-char *trackDbSettingClosestToHome(struct trackDb *tdb, char *name)
-/* Look for a trackDb setting from lowest level on up:
- from subtrack, then composite, then settingsByView, then composite */
-{
-char *trackSetting = trackDbSetting(tdb,name);
-if(trackSetting == NULL && tdbIsCompositeChild(tdb))
- {
- trackSetting = trackDbSettingByView(tdb,name);
- if(trackSetting == NULL)
- trackSetting = trackDbSetting(tdb->parent,name);
- }
-return trackSetting;
-}
-
char *trackDbSettingClosestToHomeOrDefault(struct trackDb *tdb, char *name, char *defaultVal)
-/* Look for a trackDb setting (or default) from lowest level on up:
- from subtrack, then composite, then settingsByView, then composite */
+/* Look for a trackDb setting (or default) from lowest level on up chain of parents. */
{
char *trackSetting = trackDbSettingClosestToHome(tdb,name);
if(trackSetting == NULL)
trackSetting = defaultVal;
return trackSetting;
}
boolean trackDbSettingClosestToHomeOn(struct trackDb *tdb, char *name)
/* Return true if a tdb setting closest to home is "on" "true" or "enabled". */
{
char *setting = trackDbSettingClosestToHome(tdb,name);
return (setting && ( sameWord(setting,"on")
|| sameWord(setting,"true")
|| sameWord(setting,"enabled")
|| atoi(setting) != 0));
}
struct trackDb *subTdbFind(struct trackDb *parent,char *table)
/* Return subTrack tdb if it exists in parent. */
{
if(parent == NULL)
return NULL;
-struct trackDb *tdb;
-for (tdb = parent->subtracks;
- tdb != NULL && differentString(tdb->tableName,table);
- tdb = tdb->next) {}
-return tdb;
+struct trackDb *found = NULL;
+struct slRef *tdbRef, *tdbRefList = trackDbListGetRefsToDescendants(parent->subtracks);
+for (tdbRef = tdbRefList; tdbRef != NULL; tdbRef = tdbRef->next)
+ {
+ struct trackDb *tdb = tdbRef->val;
+ if (sameString(tdb->tableName, table))
+ {
+ found = tdb;
+ break;
+ }
+ }
+slFreeList(&tdbRefList);
+return found;
}
struct trackDb *tdbFindOrCreate(char *db,struct trackDb *parent,char *table)
/* Find or creates the tdb for this table. May return NULL. */
{
struct trackDb *tdb = NULL;
if (parent != NULL)
{
if(sameString(parent->tableName, table))
tdb = parent;
else if(consWiggleFind(db,parent,table) != NULL)
tdb = parent;
else
tdb = subTdbFind(parent,table);
}
if(tdb == NULL && db != NULL)
{
struct sqlConnection *conn = hAllocConn(db);
tdb = hMaybeTrackInfo(conn, table);
hFreeConn(&conn);
}
return tdb;
}
metadata_t *metadataSettingGet(struct trackDb *tdb)
/* Looks for a metadata tag and parses the setting into arrays of tags and values */
{
char *setting = trackDbSetting(tdb, "metadata");
if(setting == NULL)
return NULL;
int count = countChars(setting,'='); // <= actual count, since value may contain a =
if(count <= 0)
return NULL;
metadata_t *metadata = needMem(sizeof(metadata_t));
metadata->setting = cloneString(setting);
metadata->tags = needMem(sizeof(char*)*count);
metadata->values = needMem(sizeof(char*)*count);
char *cp = metadata->setting;
for(metadata->count=0;*cp != '\0' && metadata->count<count;metadata->count++)
{
metadata->tags[metadata->count] = cloneNextWordByDelimiter(&cp,'=');
if(*cp != '"')
metadata->values[metadata->count] = cloneNextWordByDelimiter(&cp,' ');
else
{
metadata->values[metadata->count] = ++cp;
for(;*cp != '\0';cp++)
{
if(*cp == '"' && *(cp - 1) != '\\') // Not escaped
{
*cp = '\0';
metadata->values[metadata->count] = replaceChars(metadata->values[metadata->count],"\\\"","\"");
*cp = '"'; // Put it baaack!
break;
}
}
if(*cp == '\0') // Didn't find close quote!
metadata->values[metadata->count] = cloneString(metadata->values[metadata->count]);
else
cp++;
}
}
return metadata;
}
void metadataFree(metadata_t **metadata)
/* frees any previously obtained metadata setting */
{
if(metadata && *metadata)
{
for(;(*metadata)->count > 0;(*metadata)->count--)
{
freeMem((*metadata)->tags[ (*metadata)->count - 1]);
freeMem((*metadata)->values[(*metadata)->count - 1]);
}
freeMem((*metadata)->setting);
freez(metadata);
}
}
char *metadataSettingFind(struct trackDb *tdb,char *name)
/* Looks for a specific metadata setting and returns the value or null
returned value should be freed */
{
metadata_t *metadata = metadataSettingGet(tdb);
if(metadata == NULL)
return NULL;
int ix=0;
char *setting = NULL;
for(;ix<metadata->count;ix++)
{
if (sameString(metadata->tags[ix],name))
{
setting = cloneString(metadata->values[ix]);
break;
}
}
metadataFree(&metadata);
return setting;
}
-int parentTdbAbandonTablelessChildren(char *db, struct trackDb *parentTdb)
-/* abandons tableless children from a container tdb, such as a composite
- returns count of children that have been abandoned */
-{
-struct trackDb *goodKids = NULL;
-struct trackDb *childTdb;
-int badKids = 0;
+struct trackDb *trackDbLinkUpGenerations(struct trackDb *tdbList)
+/* Convert a list to a forest - filling in parent and subtrack pointers.
+ * The exact topology of the forest is a little complex due to the
+ * fact there are two "inheritance" systems - the superTrack system
+ * and the subTrack system. In the superTrack system (which is on it's
+ * way out) the superTrack's themselves have the tag:
+ * superTrack on
+ * and the children of superTracks have the tag:
+ * superTrack parentName
+ * In the subTrack system the parents have the tag:
+ * compositeTrack on
+ * and the children have the tag:
+ * subTrack parentName
+ * In this routine the subtracks are removed from the list, and stuffed into
+ * the subtracks lists of their parents. The highest level parents stay on
+ * the list. There can be multiple levels of inheritance.
+ * For the supertracks the _parents_ are removed from the list. The only
+ * reference to them in the returned forest is that they are in the parent
+ * field of their children. The parents of supertracks have no subtracks
+ * after this call currently. */
+{
+struct trackDb *forest = NULL;
+struct hash *trackHash = hashNew(0);
+struct trackDb *tdb, *next;
+for (tdb = tdbList; tdb != NULL; tdb = tdb->next)
+ hashAdd(trackHash, tdb->tableName, tdb);
+
+/* Do superTrack inheritance. This involves setting up the parent pointers to superTracks,
+ * but removing the superTracks themselves from the list. */
+struct trackDb *superlessList = NULL;
+for (tdb = tdbList; tdb != NULL; tdb = next)
+ {
+ next = tdb->next;
+ char *superTrack = trackDbSetting(tdb, "superTrack");
+ if (superTrack != NULL)
+ {
+ if (sameWord(superTrack, "on"))
+ {
+ tdb->next = NULL;
+ }
+ else
+ {
+ char *parentName = tdb->parentName = cloneFirstWord(superTrack);
+ struct trackDb *parent = hashFindVal(trackHash, parentName);
+ if (parent == NULL)
+ errAbort("Parent track %s of supertrack %s doesn't exist",
+ parentName, tdb->tableName);
+ tdb->parent = parent;
+ slAddHead(&superlessList, tdb);
+ }
+ }
+ else
+ {
+ slAddHead(&superlessList, tdb);
+ }
+ }
-while((childTdb = slPopHead(&(parentTdb->subtracks))) != NULL)
+/* Do subtrack hierarchy - filling in parent and subtracks fields. */
+for (tdb = superlessList; tdb != NULL; tdb = next)
+ {
+ next = tdb->next;
+ char *subtrackSetting = trackDbLocalSetting(tdb, "subTrack");
+ if (subtrackSetting != NULL)
{
- if (hTableOrSplitExists(db, childTdb->tableName))
- slAddHead(&goodKids,childTdb);
+ char *parentName = cloneFirstWord(subtrackSetting);
+ struct trackDb *parent = hashFindVal(trackHash, parentName);
+ if (parent != NULL)
+ {
+ slAddHead(&parent->subtracks, tdb);
+ tdb->parent = parent;
+ }
else
{
- badKids++;
- trackDbFree(&childTdb);
+ errAbort("Parent track %s of subTrack %s doesn't exist", parentName, tdb->tableName);
+ }
+ freez(&parentName);
+ }
+ else
+ {
+ slAddHead(&forest, tdb);
+ }
+ }
+
+hashFree(&trackHash);
+return forest;
+}
+
+void rGetRefsToDescendants(struct slRef **pList, struct trackDb *tdbList)
+/* Add all member of tdbList, and all of their children to pList recursively. */
+/* Convert a list to a forest - filling in parent and subtrack pointers.
+ * The exact topology of the forest is a little complex due to the
+ * fact there are two "inheritance" systems - the superTrack system
+ * and the subTrack system. In the superTrack system (which is on it's
+ * way out) the superTrack's themselves have the tag:
+ * superTrack on
+ * and the children of superTracks have the tag:
+ * superTrack parentName
+ * In the subTrack system the parents have the tag:
+ * compositeTrack on
+ * and the children have the tag:
+ * subTrack parentName
+ * In this routine the subtracks are removed from the list, and stuffed into
+ * the subtracks lists of their parents. The highest level parents stay on
+ * the list. There can be multiple levels of inheritance.
+ * For the supertracks the _parents_ are removed from the list. The only
+ * reference to them in the returned forest is that they are in the parent
+ * field of their children. The parents of supertracks have no subtracks
+ * after this call currently. */
+{
+struct trackDb *tdb;
+for (tdb = tdbList; tdb != NULL; tdb = tdb->next)
+ {
+ refAdd(pList, tdb);
+ rGetRefsToDescendants(pList, tdb->subtracks);
+ }
+}
+
+struct slRef *trackDbListGetRefsToDescendants(struct trackDb *tdbList)
+/* Return reference list to everything in forest. Do slFreeList when done. */
+{
+struct slRef *refList = NULL;
+rGetRefsToDescendants(&refList, tdbList);
+slReverse(&refList);
+return refList;
+}
+
+int trackDbCountDescendants(struct trackDb *tdb)
+/* Count the number of tracks in subtracks list and their subtracks too . */
+{
+struct slRef *tdbRefList = trackDbListGetRefsToDescendants(tdb->subtracks);
+int result = slCount(tdbRefList);
+slFreeList(&tdbRefList);
+return result;
+}
+
+void rGetRefsToDescendantLeaves(struct slRef **pList, struct trackDb *tdbList)
+/* Add all leaf members of trackList, and any leaf descendants to pList recursively. */
+{
+struct trackDb *tdb;
+for (tdb = tdbList; tdb != NULL; tdb = tdb->next)
+ {
+ if (tdb->subtracks)
+ rGetRefsToDescendantLeaves(pList, tdb->subtracks);
+ else
+ refAdd(pList, tdb);
}
+}
+
+struct slRef *trackDbListGetRefsToDescendantLeaves(struct trackDb *tdbList)
+/* Return reference list all leaves in forest. Do slFreeList when done. */
+{
+struct slRef *refList = NULL;
+rGetRefsToDescendantLeaves(&refList, tdbList);
+slReverse(&refList);
+return refList;
+}
+
+int trackDbCountDescendantLeaves(struct trackDb *tdb)
+/* Count the number of leaves in children list and their children. */
+{
+struct slRef *leafRefs = trackDbListGetRefsToDescendantLeaves(tdb->subtracks);
+int result = slCount(leafRefs);
+slFreeList(&leafRefs);
+return result;
+}
+
+int trackDbRefCmp(const void *va, const void *vb)
+/* Do trackDbCmp on list of references as opposed to actual trackDbs. */
+{
+const struct slRef *aRef = *((struct slRef **)va);
+const struct slRef *bRef = *((struct slRef **)vb);
+struct trackDb *a = aRef->val, *b = bRef->val;
+return trackDbCmp(&a, &b);
+}
+
+struct trackDb *trackDbCompositeParent(struct trackDb *tdb)
+/* Return closest ancestor who is a composite track. */
+{
+struct trackDb *parent;
+for (parent = tdb->parent; parent != NULL; parent = parent->parent)
+ {
+ if (trackDbLocalSetting(parent, "compositeTrack"))
+ return parent;
}
-if(goodKids != NULL)
- slReverse(&goodKids);
-parentTdb->subtracks = goodKids;
-return badKids;
+return NULL;
+}
+
+struct trackDb *trackDbTopLevelSelfOrParent(struct trackDb *tdb)
+/* Look for a parent who is a composite track and return that. Failing that
+ * just return self. */
+{
+struct trackDb *parent = trackDbCompositeParent(tdb);
+if (parent != NULL)
+ return parent;
+else
+ return tdb;
}