src/hg/inc/trackDb.h 1.45
1.45 2009/03/15 00:16:45 tdreszer
Checked in cfgNetAlign to get passed compiler error
Index: src/hg/inc/trackDb.h
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/inc/trackDb.h,v
retrieving revision 1.44
retrieving revision 1.45
diff -b -B -U 1000000 -r1.44 -r1.45
--- src/hg/inc/trackDb.h 12 Mar 2009 00:05:42 -0000 1.44
+++ src/hg/inc/trackDb.h 15 Mar 2009 00:16:45 -0000 1.45
@@ -1,280 +1,281 @@
/* trackDb.h was originally generated by the autoSql program, which also
* generated trackDb.c and trackDb.sql. This header links the database and
* the RAM representation of objects. */
#ifndef TRACKDB_H
#define TRACKDB_H
#include "common.h"
#ifndef JKSQL_H
#include "jksql.h"
#endif
#define TRACKDB_NUM_COLS 21
struct trackDb
/* This describes an annotation track. */
{
struct trackDb *next; /* Next in singly linked list. */
char *tableName; /* Symbolic ID of Track */
char *shortLabel; /* Short label displayed on left */
char *type; /* Track type: bed, psl, genePred, etc. */
char *longLabel; /* Long label displayed in middle */
unsigned char visibility; /* 0=hide, 1=dense, 2=full, 3=pack, 4=squish */
float priority; /* 0-100 - where to position. 0 is top */
unsigned char colorR; /* Color red component 0-255 */
unsigned char colorG; /* Color green component 0-255 */
unsigned char colorB; /* Color blue component 0-255 */
unsigned char altColorR; /* Light color red component 0-255 */
unsigned char altColorG; /* Light color green component 0-255 */
unsigned char altColorB; /* Light color blue component 0-255 */
unsigned char useScore; /* 1 if use score, 0 if not */
#ifndef __cplusplus
unsigned char private; /* 1 if only want to show it on test site */
#else
unsigned char priv; /* don't conflict with C++ keyword */
#endif
int restrictCount; /* Number of chromosomes this is on (0=all though!) */
char **restrictList; /* List of chromosomes this is on */
char *url; /* URL to link to when they click on an item */
char *html; /* Some html to display when they click on an item */
char *grp; /* Which group track belongs to */
unsigned char canPack; /* 1 if can pack track display, 0 otherwise */
char *settings; /* Name/value pairs for track-specific stuff */
struct hash *settingsHash; /* Hash for settings. Not saved in database.
* Don't use directly, rely on trackDbSetting to access. */
/* additional info, determined from settings */
char treeNodeType; /* bit map containing defining supertrack, composite and children of same (may be parent & child) */
struct trackDb *parent; /* parent of composite or superTracks */
struct trackDb *subtracks; /* children of composite (TODO: or supertrack) */ // NOTE: can only be on one sl at a time!
char *parentName; /* set if this is a supertrack member */
boolean isShow; /* for supertracks tracks: true if this is a supertrack with pseudo-vis 'show' */
struct hash *overrides; /* If not NULL, this is an override
* entry. It contains the names, but not the
* values of the fields and settings that were
* specified in the entry. */
};
#define SUPERTRACK_MASK 0x10
#define COMPOSITE_MASK 0x20
#define SUPERTRACK_CHILD_MASK 0x01
#define COMPOSITE_CHILD_MASK 0x02
#define PARENT_MASK 0xF0
#define CHILD_MASK 0x0F
#define TREETYPE_MASK 0xFF
#define PARENT_NODE(nodeType) ((nodeType) & PARENT_MASK)
#define CHILD_NODE(nodeType) ((nodeType) & CHILD_MASK)
#define SUPERTRACK_NODE(nodeType) (((nodeType) & SUPERTRACK_MASK) == SUPERTRACK_MASK)
#define COMPOSITE_NODE(nodeType) (((nodeType) & COMPOSITE_MASK ) == COMPOSITE_MASK )
#define SUPERTRACK_CHILD_NODE(nodeType) (((nodeType) & SUPERTRACK_CHILD_MASK) == SUPERTRACK_CHILD_MASK)
#define COMPOSITE_CHILD_NODE(nodeType) (((nodeType) & COMPOSITE_CHILD_MASK ) == COMPOSITE_CHILD_MASK )
#define INDEPENDENT_NODE(nodeType) (((nodeType) & TREETYPE_MASK ) == 0 )
//#define tdbIsParent(tdb) ((tdb)->subtracks)
//#define tdbIsChild(tdb) ((tdb)->parent )
//#define tdbIsTreeLeaf(tdb) ( CHILD_NODE((tdb)->treeNodeType) && !tdbIsParent(tdb))
//#define tdbIsTreeRoot(tdb) (PARENT_NODE((tdb)->treeNodeType) && !tdbIsChild(tdb) )
//#define tdbIsTreeBranch(tdb) (!INDEPENDENT_NODE((tdb)->treeNodeType) && tdbIsParent(tdb) && tdbIsChild(tdb))
//#define tdbIsNotInTree(tdb) ( INDEPENDENT_NODE((tdb)->treeNodeType) && !tdbIsParent(tdb) && !tdbIsChild(tdb))
INLINE boolean tdbIsSuper(struct trackDb *tdb)
/* Is this trackDb struct marked as a supertrack ? */
{
return tdb && SUPERTRACK_NODE(tdb->treeNodeType);
}
INLINE boolean tdbIsSuperTrack(struct trackDb *tdb)
/* Is this trackDb struct marked as a supertrack ? */
{
return tdb && /*tdb->subtracks &&*/ SUPERTRACK_NODE(tdb->treeNodeType); // TODO: superTrack code needs rewrite to contain it's children
}
INLINE boolean tdbIsComposite( struct trackDb *tdb)
/* Is this trackDb struct marked as a composite with children ? */
{
return tdb && tdb->subtracks && COMPOSITE_NODE( tdb->treeNodeType);
}
INLINE boolean tdbIsSuperTrackChild(struct trackDb *tdb)
/* Is this trackDb struct marked as a child of a supertrack ? */
{
return tdb && tdb->parent && SUPERTRACK_CHILD_NODE(tdb->treeNodeType);
}
INLINE boolean tdbIsCompositeChild(struct trackDb *tdb)
/* Is this trackDb struct marked as a child of a composite track ? */
{
return tdb && tdb->parent && COMPOSITE_CHILD_NODE( tdb->treeNodeType);
}
INLINE void tdbMarkAsSuperTrack(struct trackDb *tdb)
/* Marks a trackDb struct as a supertrack */
{
tdb->treeNodeType |= SUPERTRACK_MASK;
}
INLINE void tdbMarkAsComposite( struct trackDb *tdb)
/* Marks a trackDb struct as a composite track */
{
tdb->treeNodeType |= COMPOSITE_MASK;
}
INLINE void tdbMarkAsSuperTrackChild(struct trackDb *tdb)
/* Marks a trackDb struct as a child of a supertrack */
{
tdb->treeNodeType |= SUPERTRACK_CHILD_MASK;
}
INLINE void tdbMarkAsCompositeChild( struct trackDb *tdb)
/* Marks a trackDb struct as a child of a composite track */
{
tdb->treeNodeType |= COMPOSITE_CHILD_MASK;
}
struct trackDb *trackDbLoad(char **row);
/* Load a trackDb from row fetched with select * from trackDb
* from database. Dispose of this with trackDbFree(). */
struct trackDb *trackDbLoadAll(char *fileName);
/* Load all trackDb from whitespace-separated file.
* Dispose of this with trackDbFreeList(). */
struct trackDb *trackDbLoadWhere(struct sqlConnection *conn, char *table,
char *where);
/* Load all trackDb from table that satisfy where clause. The
* where clause may be NULL in which case whole table is loaded
* Dispose of this with trackDbFreeList(). */
struct trackDb *trackDbLoadAllByChar(char *fileName, char chopper);
/* Load all trackDb from chopper separated file.
* Dispose of this with trackDbFreeList(). */
#define trackDbLoadAllByTab(a) trackDbLoadAllByChar(a, '\t');
/* Load all trackDb from tab separated file.
* Dispose of this with trackDbFreeList(). */
struct trackDb *trackDbCommaIn(char **pS, struct trackDb *ret);
/* Create a trackDb out of a comma separated string.
* This will fill in ret if non-null, otherwise will
* return a new trackDb */
void trackDbFree(struct trackDb **pEl);
/* Free a single dynamically allocated trackDb such as created
* with trackDbLoad(). */
void trackDbFreeList(struct trackDb **pList);
/* Free a list of dynamically allocated trackDb's */
void trackDbOutput(struct trackDb *el, FILE *f, char sep, char lastSep);
/* Print out trackDb. Separate fields with sep. Follow last field with lastSep. */
#define trackDbTabOut(el,f) trackDbOutput(el,f,'\t','\n');
/* Print out trackDb as a line in a tab-separated file. */
#define trackDbCommaOut(el,f) trackDbOutput(el,f,',',',');
/* Print out trackDb as a comma separated list including final comma. */
/* ----------- End of AutoSQL generated code --------------------- */
int trackDbCmp(const void *va, const void *vb);
/* Sort track by priority. */
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. */
void trackDbOverridePriority(struct hash *tdHash, char *priorityRa);
/* Override priority settings using a ra file. */
struct trackDb *trackDbFromRa(char *raFile);
/* Load track info from ra file into list. */
void trackDbPolish(struct trackDb *bt);
/* Fill in missing values with defaults. */
struct hash *trackDbHashSettings(struct trackDb *tdb);
/* Force trackDb to hash up it's settings. Usually this is just
* done on demand. Returns settings hash. */
char *trackDbSetting(struct trackDb *tdb, char *name);
/* Return setting string or NULL if none exists. */
boolean trackDbSettingOn(struct trackDb *tdb, char *name);
/* Return true if a tdb setting is "on" "true" or "enabled". */
char *trackDbRequiredSetting(struct trackDb *tdb, char *name);
/* Return setting string or squawk and die. */
char *trackDbSettingOrDefault(struct trackDb *tdb, char *name, char *defaultVal);
/* Return setting string, or defaultVal if none exists */
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. */
char *trackDbGetSupertrackName(struct trackDb *tdb);
/* Find name of supertrack if this track is a member */
float trackDbFloatSettingOrDefault(struct trackDb *tdb, char *name, float defaultVal);
/* Return setting, convert to a float, or defaultVal if none exists */
void trackDbSuperMemberSettings(struct trackDb *tdb);
/* Set fields in trackDb to indicate this is a member of a
* supertrack. */
void trackDbSuperSettings(struct trackDb *tdbList);
/* Get info from supertrack setting. There are 2 forms:
* Parent: 'supertrack on [show]'
* Child: 'supertrack <parent> [vis]
* Returns NULL if there is no such setting */
char *trackDbInclude(char *raFile, char *line);
/* Get include filename from trackDb line.
Return NULL if line doesn't contain include */
char *trackDbOrigAssembly(struct trackDb *tdb);
/* return setting from trackDb, if any */
void trackDbPrintOrigAssembly(struct trackDb *tdb, char *database);
/* Print lift information from trackDb, if any */
// Not all track types have separate configuration
typedef enum _eCfgType
{
cfgNone =0,
cfgBedScore =1,
cfgWig =2,
cfgWigMaf =3,
cfgPeak =4,
cfgGenePred =5,
- cfgChain =6
+ cfgChain =6,
+ cfgNetAlign =7
} eCfgType;
eCfgType cfgTypeFromTdb(struct trackDb *tdb, boolean warnIfNecessary);
/* determine what kind of track specific configuration is needed,
warn if not multi-view compatible */
void trackDbOverride(struct trackDb *td, struct trackDb *overTd);
/* apply an trackOverride trackDb entry to a trackDb entry */
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 *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 */
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 *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 */
boolean trackDbSettingClosestToHomeOn(struct trackDb *tdb, char *name);
/* Return true if a tdb setting closest to home is "on" "true" or "enabled". */
#endif /* TRACKDB_H */