30c30147c744aa9a6e9115a67ec50e918759204a tdreszer Tue Jul 10 16:44:21 2012 -0700 Next batch of many checkins as dictated by Jim. Formatting space after if and limiting lines to 100 chars. Changes limited to lines last touched by tdreszer (git blame) so as not to ruin history. This checkin also includes removal of SUBTRACK_CFG ifdefs, and a bug fix for downloads link. diff --git src/hg/inc/hui.h src/hg/inc/hui.h index 2b364cf..f0d790e 100644 --- src/hg/inc/hui.h +++ src/hg/inc/hui.h @@ -1,29 +1,26 @@ /* hui - human genome browser user interface controls that are shared * between more than one CGI. */ #ifndef HUI_H #define HUI_H #include "cart.h" #include "trackDb.h" #include "customTrack.h" #include "wiggle.h" #include "asParse.h" -// This temporary define shouuld be removed after rollout of hgTrackUi subtrack cfg changes -#define SUBTRACK_CFG - struct lineFile; void setUdcCacheDir(); /* set the path to the udc cache dir */ char *hDownloadsServer(); /* get the downloads server from hg.conf or the default */ char *hUserCookie(); /* Return our cookie name. */ char *wrapWhiteFont(char *s); /* Write white font around s */ #define HELP_DIR "/goldenPath/help" @@ -859,34 +856,36 @@ struct trackNameAndLabel /* Store track name and label. */ { struct trackNameAndLabel *next; char *name; /* Name (not allocated here) */ char *label; /* Label (not allocated here) */ }; int trackNameAndLabelCmp(const void *va, const void *vb); /* Compare to sort on label. */ void rAddTrackListToHash(struct hash *trackHash, struct trackDb *tdbList, char *chrom, boolean leafOnly); /* Recursively add trackList to trackHash */ -struct hash *trackHashMakeWithComposites(char *db,char *chrom,struct trackDb **tdbList,bool withComposites); +struct hash *trackHashMakeWithComposites(char *db,char *chrom,struct trackDb **tdbList, + bool withComposites); // Make hash of trackDb items for this chromosome, including composites, not just the subtracks. // May pass in prepopulated trackDb list, or may receive the trackDb list as an inout. -#define makeTrackHashWithComposites(db,chrom,withComposites) trackHashMakeWithComposites(db,chrom,NULL,withComposites) +#define makeTrackHashWithComposites(db,chrom,withComposites) \ + trackHashMakeWithComposites(db,chrom,NULL,withComposites) #define makeTrackHash(db,chrom) trackHashMakeWithComposites(db,chrom,NULL,FALSE) 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. */ /****** Stuff for acembly related options *******/ enum acemblyOptEnum { acemblyAll =0, acemblyMain=1, acemblyPutative=2, }; @@ -926,31 +925,32 @@ boolean compositeMetadataToggle(char *db,struct trackDb *tdb,char *title, boolean embeddedInText,boolean showLongLabel); /* If metadata from metaTbl exists, create a link that will allow toggling it's display */ boolean superTrackDropDownWithExtra(struct cart *cart, struct trackDb *tdb, int visibleChild,char *extra); /* 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 */ -#define superTrackDropDown(cart,tdb,visibleChild) superTrackDropDownWithExtra(cart,tdb,visibleChild,NULL) +#define superTrackDropDown(cart,tdb,visibleChild) \ + superTrackDropDownWithExtra(cart,tdb,visibleChild,NULL) boolean dimensionsExist(struct trackDb *parentTdb); /* Does this parent track contain dimensions? */ int subgroupCount(struct trackDb *parentTdb); /* How many subGroup setting does this parent have? */ char * subgroupSettingByTagOrName(struct trackDb *parentTdb, char *groupNameOrTag); /* look for a subGroup by name (ie subGroup1) or tag (ie view) and return an unallocated char* */ boolean subgroupingExists(struct trackDb *parentTdb, char *groupNameOrTag); /* Does this parent track contain a particular subgrouping? */ boolean subgroupFind(struct trackDb *childTrack, char *name,char **value); /* looks for a single tag in a childTrack's subGroups setting */ @@ -959,70 +959,77 @@ /* frees subgroup memory */ int multViewCount(struct trackDb *parentTdb); /* returns the number of multiView views declared */ int tvConvertToNumericOrder(enum trackVisibility v); /* Convert the enum to numeric order of display power full=4,hide=0 */ int tvCompare(enum trackVisibility a, enum trackVisibility b); /* enum trackVis isn't in numeric order by visibility, so compare * symbolically: */ enum trackVisibility tvMin(enum trackVisibility a, enum trackVisibility b); /* Return the less visible of a and b. */ -enum trackVisibility tdbLocalVisibility(struct cart *cart, struct trackDb *tdb,boolean *subtrackOverride); -// returns visibility NOT limited by ancestry. Fills optional boolean if subtrack specific vis is found -// If not NULL cart will be examined without ClosestToHome. Folders/supertracks resolve to hide/full - -enum trackVisibility tdbVisLimitedByAncestors(struct cart *cart, struct trackDb *tdb, boolean checkBoxToo, boolean foldersToo); -// returns visibility limited by ancestry. This includes subtrack vis override and parents limit maximum. +enum trackVisibility tdbLocalVisibility(struct cart *cart, struct trackDb *tdb, + boolean *subtrackOverride); +// returns visibility NOT limited by ancestry. +// Fills optional boolean if subtrack specific vis is found +// If not NULL cart will be examined without ClosestToHome. +// Folders/supertracks resolve to hide/full + +enum trackVisibility tdbVisLimitedByAncestors(struct cart *cart, struct trackDb *tdb, + boolean checkBoxToo, boolean foldersToo); +// returns visibility limited by ancestry. +// This includes subtrack vis override and parents limit maximum. // cart may be null, in which case, only trackDb settings (default state) are examined // checkBoxToo means ensure subtrack checkbox state is visible // foldersToo means limit by folders (aka superTracks) as well. -#define tdbVisLimitedByAncestry(cart,tdb,noFolders) tdbVisLimitedByAncestors(cart, tdb, TRUE, !(noFolders)) +#define tdbVisLimitedByAncestry(cart,tdb,noFolders) \ + tdbVisLimitedByAncestors(cart, tdb, TRUE, !(noFolders)) char *compositeViewControlNameFromTdb(struct trackDb *tdb); /* Returns a string with the composite view control name if one exists */ void compositeViewControlNameFree(char **name); /* frees a string allocated by compositeViewControlNameFromTdb */ void wigCfgUi(struct cart *cart, struct trackDb *tdb,char *name,char *title,boolean boxed); /* UI for the wiggle track */ #define NO_SCORE_FILTER "noScoreFilter" #define SCORE_FILTER "scoreFilter" #define SIGNAL_FILTER "signalFilter" #define PVALUE_FILTER "pValueFilter" #define QVALUE_FILTER "qValueFilter" #define _NO "No" #define _LIMITS "Limits" #define _MIN "Min" #define _MAX "Max" #define _BY_RANGE "ByRange" #define SCORE_MIN "scoreMin" #define GRAY_LEVEL_SCORE_MIN SCORE_MIN #define MIN_GRAY_LEVEL "minGrayLevel" void filterButtons(char *filterTypeVar, char *filterTypeVal, boolean none); /* Put up some filter buttons. */ void radioButton(char *var, char *val, char *ourVal); /* Print one radio button */ -void oneMrnaFilterUi(struct controlGrid *cg, struct trackDb *tdb, char *text, char *var, char *suffix, struct cart *cart); +void oneMrnaFilterUi(struct controlGrid *cg, struct trackDb *tdb, char *text, char *var, + char *suffix, struct cart *cart); /* Print out user interface for one type of mrna filter. */ void bedFiltCfgUi(struct cart *cart, struct trackDb *tdb, char *prefix, char *title, boolean boxed); /* Put up UI for an "bedFilter" tracks. */ void mrnaCfgUi(struct cart *cart, struct trackDb *tdb, char *prefix, char *title, boolean boxed); /* Put up UI for an mRNA (or EST) track. */ boolean bedScoreHasCfgUi(struct trackDb *tdb); // Confirms that this track has a bedScore Cfg UI void scoreCfgUi(char *db, struct cart *cart, struct trackDb *parentTdb, char *name,char *title,int maxScore,boolean boxed); /* Put up UI for filtering bed track based on a score */ void crossSpeciesCfgUi(struct cart *cart, struct trackDb *tdb); @@ -1031,244 +1038,260 @@ void pslCfgUi(char *db, struct cart *cart, struct trackDb *parentTdb, char *prefix ,char *title, boolean boxed); /* Put up UI for psl tracks */ void netAlignCfgUi(char *db, struct cart *cart, struct trackDb *parentTdb, char *prefix ,char *title, boolean boxed); /* Put up UI for net tracks */ void chainCfgUi(char *db, struct cart *cart, struct trackDb *parentTdb, char *prefix ,char *title, boolean boxed, char *chromosome); /* Put up UI for chain tracks */ 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. */ struct dyString *dyAddFilterAsInt(struct cart *cart, struct trackDb *tdb, struct dyString *extraWhere,char *filter,char *defaultVal, char*field, boolean *and); -/* creates the where clause condition to support numeric int filter range. - Filters are expected to follow - {fiterName}: trackDb min or min:max - default value(s); - {filterName}Min or {filterName}: min (user supplied) cart variable; - {filterName}Max: max (user supplied) cart variable; - {filterName}Limits: trackDb allowed range "0:1000" Optional - uses:{filterName}Min: old trackDb value if {filterName}Limits not found - {filterName}Max: old trackDb value if {filterName}Limits not found - defaultLimits: function param if no tdb limits settings found) - The 'and' param and dyString in/out allows stringing multiple where clauses together */ +// creates the where clause condition to support numeric int filter range. +// Filters are expected to follow +// {fiterName}: trackDb min or min:max - default value(s); +// {filterName}Min or {filterName}: min (user supplied) cart variable; +// {filterName}Max: max (user supplied) cart variable; +// {filterName}Limits: trackDb allowed range "0:1000" Optional +// uses:{filterName}Min: old trackDb value if {filterName}Limits not found +// {filterName}Max: old trackDb value if {filterName}Limits not found +// defaultLimits: function param if no tdb limits settings found) +// The 'and' param and dyString in/out allows stringing multiple where clauses together struct dyString *dyAddFilterAsDouble(struct cart *cart, struct trackDb *tdb, struct dyString *extraWhere,char *filter,char *defaultLimits, char*field, boolean *and); -/* creates the where clause condition to support numeric double filters. - Filters are expected to follow - {fiterName}: trackDb min or min:max - default value(s); - {filterName}Min or {filterName}: min (user supplied) cart variable; - {filterName}Max: max (user supplied) cart variable; - {filterName}Limits: trackDb allowed range "0.0:10.0" Optional - uses: defaultLimits: function param if no tdb limits settings found) - The 'and' param allows stringing multiple where clauses together */ - -struct dyString *dyAddAllScoreFilters(struct cart *cart, struct trackDb *tdb, struct dyString *extraWhere,boolean *and); -/* creates the where clause condition to gather together all random double filters - Filters are expected to follow - {fiterName}: trackDb min or min:max - default value(s); - {filterName}Min or {filterName}: min (user supplied) cart variable; - {filterName}Max: max (user supplied) cart variable; - {filterName}Limits: trackDb allowed range "0.0:10.0" Optional - uses: defaultLimits: function param if no tdb limits settings found) - The 'and' param and dyString in/out allows stringing multiple where clauses together */ +// creates the where clause condition to support numeric double filters. +// Filters are expected to follow +// {fiterName}: trackDb min or min:max - default value(s); +// {filterName}Min or {filterName}: min (user supplied) cart variable; +// {filterName}Max: max (user supplied) cart variable; +// {filterName}Limits: trackDb allowed range "0.0:10.0" Optional +// uses: defaultLimits: function param if no tdb limits settings found) +// The 'and' param allows stringing multiple where clauses together + +struct dyString *dyAddAllScoreFilters(struct cart *cart, struct trackDb *tdb, + struct dyString *extraWhere,boolean *and); +// creates the where clause condition to gather together all random double filters +// Filters are expected to follow +// {fiterName}: trackDb min or min:max - default value(s); +// {filterName}Min or {filterName}: min (user supplied) cart variable; +// {filterName}Max: max (user supplied) cart variable; +// {filterName}Limits: trackDb allowed range "0.0:10.0" Optional +// uses: defaultLimits: function param if no tdb limits settings found) +// The 'and' param and dyString in/out allows stringing multiple where clauses together boolean encodePeakHasCfgUi(struct trackDb *tdb); // Confirms that this track has encode Peak cfgUI -void encodePeakCfgUi(struct cart *cart, struct trackDb *tdb, char *name, char *title, boolean boxed); -/* Put up UI for filtering wgEnocde peaks based on score, Pval and Qval */ +void encodePeakCfgUi(struct cart *cart, struct trackDb *tdb, char *name, char *title, + boolean boxed); +// Put up UI for filtering wgEnocde peaks based on score, Pval and Qval void genePredCfgUi(struct cart *cart, struct trackDb *tdb, char *name, char *title, boolean boxed); -/* Put up genePred-specific controls */ +// Put up genePred-specific controls void wigMafCfgUi(struct cart *cart, struct trackDb *tdb,char *name, char *title, boolean boxed, char *db); /* UI for maf/wiggle track */ void bamCfgUi(struct cart *cart, struct trackDb *tdb, char *name, char *title, boolean boxed); /* BAM: short-read-oriented alignment file format. */ boolean tdbSortPrioritiesFromCart(struct cart *cart, struct trackDb **tdbList); -/* Updates the tdb->priority from cart then sorts the list anew. - Returns TRUE if priorities obtained from cart */ +// Updates the tdb->priority from cart then sorts the list anew. +// Returns TRUE if priorities obtained from cart boolean tdbRefSortPrioritiesFromCart(struct cart *cart, struct slRef **tdbRefList); /* Updates the tdb->priority from cart then sorts the list anew. Returns TRUE if priorities obtained from cart */ enum trackVisibility visCompositeViewDefault(struct trackDb *parentTdb,char *view); -/* returns the default track visibility of particular view within a composite track */ +// returns the default track visibility of particular view within a composite track boolean isNameAtParentLevel(struct trackDb *tdb,char *name); // cfgUi controls are passed a prefix name that may be at the composite, view or subtrack level // returns TRUE if name at view or composite level boolean hSameTrackDbType(char *type1, char *type2); /* Compare type strings: require same string unless both are wig tracks. */ -typedef struct _sortOrder { +typedef struct _sortOrder // Sort order is used for sorting trackDb entries (hgTrackDb) and setting up javascript sorting (hui.c) + { int count; char*sortOrder; // from cart (eg: CEL=+ FAC=- view=-) char*htmlId; // {tableName}.sortOrder char**column; // Always order in trackDb.ra (eg: FAC,CEL,view) TAG char**title; // Always order in trackDb.ra (eg: Factor,Cell Line,View) boolean* forward; // Always order in trackDb.ra but value of cart! (eg: -,+,-) int* order; // 1 based char *setting; } sortOrder_t; 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 */ +// 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 */ void sortOrderFree(sortOrder_t **sortOrder); -/* frees any previously obtained sortOrder settings */ +// frees any previously obtained sortOrder settings -typedef struct _sortColumn { +typedef struct _sortColumn // link list of columns to sort contained in sortableItem + { struct _sortColumn *next; char *value; // value to sort on boolean fwd; // direction } sortColumn; -typedef struct _sortableTdbItem { +typedef struct _sortableTdbItem // link list of tdb items to sort + { struct _sortableTdbItem *next; struct trackDb *tdb; // a contained item is actually a tdb entry sortColumn *columns; // a link list of values to sort on } sortableTdbItem; sortableTdbItem *sortableTdbItemCreate(struct trackDb *tdbChild,sortOrder_t *sortOrder); // creates a sortable tdb item struct, given a child tdb and its parents sort table void sortTdbItemsAndUpdatePriorities(sortableTdbItem **items); // sort tdb items in list and then update priorities of item tdbs void sortableTdbItemsFree(sortableTdbItem **items); // Frees all memory associated with a list of sortable tdb items #define FILTER_BY "filterBy" -typedef struct _filterBy { -// A single filterBy set (from trackDb.ra filterBy column:Title=value,value [column:Title=value|label,value|label,value|label]) +typedef struct _filterBy +// A single filterBy set (from trackDb.ra filterBy column:Title=value,value +// [column:Title=value|label,value|label,value|label]) + { struct _filterBy *next; // SL list char*column; // field that will be filtered on char*title; // Title that User sees char*htmlName; // Name used in HTML/CGI boolean useIndex; // The returned values should be indexes boolean valueAndLabel; // If values list is value|label, then label is shown to the user - boolean styleFollows; // style settings can follow like value|label[background-color:#660000] - // legacy like value|label{#AA0000} is a just the style='color... that follows + boolean styleFollows; // style settings can follow like: + // value|label{background-color:#660000} struct slName *slValues; // Values that can be filtered on (All is always implied) struct slName *slChoices; // Values that have been chosen } filterBy_t; filterBy_t *filterBySetGet(struct trackDb *tdb, struct cart *cart, char *name); -/* Gets one or more "filterBy" settings (ClosestToHome). returns NULL if not found */ +// Gets one or more "filterBy" settings (ClosestToHome). returns NULL if not found void filterBySetFree(filterBy_t **filterBySet); -/* Free a set of filterBy structs */ +// Free a set of filterBy structs char *filterBySetClause(filterBy_t *filterBySet); -/* returns the "column1 in (...) and column2 in (...)" clause for a set of filterBy structs */ +// returns the "column1 in (...) and column2 in (...)" clause for a set of filterBy structs void filterBySetCfgUi(struct cart *cart, struct trackDb *tdb, filterBy_t *filterBySet, boolean onOneLine); -/* Does the UI for a list of filterBy structure */ +// Does the UI for a list of filterBy structure char *filterByClause(filterBy_t *filterBy); -/* returns the SQL where clause for a single filterBy struct */ +// returns the SQL where clause for a single filterBy struct: "column in (...)" 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 -*/ +// 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 + boolean makeDownloadsLink(char *database, struct trackDb *tdb); // Make a downloads link (if appropriate and then returns TRUE) boolean makeSchemaLink(char *db,struct trackDb *tdb,char *label); // Make a table schema link (if appropriate and then returns TRUE) void makeTopLink(struct trackDb *tdb); -/* Link to top of UI page */ +// Link to top of UI page void extraUiLinks(char *db,struct trackDb *tdb); -/* Show downloads, schema and metadata links where appropriate */ +// Show downloads, schema and metadata links where appropriate boolean chainDbNormScoreAvailable(struct trackDb *tdb); /* check if normScore column is specified in trackDb as available */ void hPrintAbbreviationTable(struct sqlConnection *conn, char *sourceTable, char *label); /* Print out table of abbreviations. */ // 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 +// NOTE: fourState is not a bitmap because it is manipulated in javascript +// and int seemed easier at the time #define FOUR_STATE_UNCHECKED 0 #define FOUR_STATE_CHECKED 1 #define FOUR_STATE_CHECKED_DISABLED -1 -#define fourStateChecked(fourState) ((fourState) == FOUR_STATE_CHECKED || (fourState) == FOUR_STATE_CHECKED_DISABLED) +#define fourStateChecked(fourState) \ + ((fourState) == FOUR_STATE_CHECKED || (fourState) == FOUR_STATE_CHECKED_DISABLED) #define fourStateEnabled(fourState) ((fourState) >= FOUR_STATE_UNCHECKED) #define fourStateVisible(fourState) ((fourState) == FOUR_STATE_CHECKED) int subtrackFourStateChecked(struct trackDb *subtrack, struct cart *cart); -/* Returns the four state checked state of the subtrack */ +// Returns the four state checked state of the subtrack -void subtrackFourStateCheckedSet(struct trackDb *subtrack, struct cart *cart,boolean checked, boolean enabled); -/* Sets the fourState Checked in the cart and updates cached state */ +void subtrackFourStateCheckedSet(struct trackDb *subtrack, struct cart *cart, + boolean checked, boolean enabled); +// Sets the fourState Checked in the cart and updates cached state boolean hPrintPennantIcon(struct trackDb *tdb); -// Returns TRUE and prints out the "pennantIcon" when found. Example: ENCODE tracks in hgTracks config list. +// Returns TRUE and prints out the "pennantIcon" when found. +// Example: ENCODE tracks in hgTracks config list. boolean printPennantIconNote(struct trackDb *tdb); // Returns TRUE and prints out the "pennantIcon" and note when found. //This is used by hgTrackUi and hgc before printing out trackDb "html" -void cfgByCfgType(eCfgType cType,char *db, struct cart *cart, struct trackDb *tdb,char *prefix, char *title, boolean boxed); -// Methods for putting up type specific cfgs used by composites/subtracks in hui.c and exported for common use +void cfgByCfgType(eCfgType cType,char *db, struct cart *cart, struct trackDb *tdb, + char *prefix, char *title, boolean boxed); +// Methods for putting up type specific cfgs used by composites/subtracks boolean cfgBeginBoxAndTitle(struct trackDb *tdb, boolean boxed, char *title); /* Handle start of box and title for individual track type settings */ void cfgEndBox(boolean boxed); /* Handle end of box and title for individual track type settings */ void printUpdateTime(char *database, struct trackDb *tdb, struct customTrack *ct); /* display table update time, or in case of bbi file, file stat time */ void printBbiUpdateTime(time_t *timep); /* for bbi files, print out the timep value */ //#define EXTRA_FIELDS_SUPPORT #ifdef EXTRA_FIELDS_SUPPORT -enum fieldType { +enum fieldType + { ftString =0, ftInteger =1, ftFloat =2, }; -struct extraField { +struct extraField // extraFileds are defined in trackDb and provide labls and can be used in filtering + { struct extraField *next; char *name; // name of field char *label; // Label (which could include HTML) enum fieldType type; // string, int, float }; struct extraField *extraFieldsGet(char *db, struct trackDb *tdb); // returns any extraFields defined in trackDb struct extraField *extraFieldsFind(struct extraField *extras, char *name); // returns the extraField matching the name (case insensitive). Note: slNameFind does NOT work. void extraFieldsFree(struct extraField **pExtras); // frees all mem for extraFields list #endif///def EXTRA_FIELDS_SUPPORT