1b074613b1c6b7f84953c3f490631b91d844c9a9 galt Thu Sep 8 22:40:20 2022 -0700 Adapting Angie's existing variant effects to the new dbSnp that uses SPDI and provided via json formatted data. So users can see variant effects with version 153 or later. refs #29989 diff --git src/hg/inc/hui.h src/hg/inc/hui.h index db18064..b69c6d7 100644 --- src/hg/inc/hui.h +++ src/hg/inc/hui.h @@ -1,1578 +1,1595 @@ /* hui - human genome browser user interface controls that are shared * between more than one CGI. */ /* Copyright (C) 2014 The Regents of the University of California * See kent/LICENSE or http://genome.ucsc.edu/license/ for licensing information. */ #ifndef HUI_H #define HUI_H #include "common.h" #include "cart.h" #include "trackDb.h" #include "customTrack.h" #include "wiggle.h" #include "asParse.h" struct lineFile; void setUdcTimeout(struct cart *cart); /* set the udc cache timeout */ 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" /* will be appended to DOCUMENT_ROOT */ #define DOCUMENT_ROOT "/usr/local/apache/htdocs" /* default DocumentRoot as configured in Apache httpd.conf */ /* DocumentRoot can be set in hg.conf as browser.documentRoot */ #define DEFAULT_BACKGROUND "../images/floret.jpg" /* full path is determined by Apache's DocumentRoot since this is a * relative URL reference */ #define ENCODE_DATA_RELEASE_POLICY "/ENCODE/terms.html" char *encodeRestrictionDate(char *db,struct trackDb *trackDb,boolean excludePast); /* Create a string for ENCODE restriction date of this track if return is not null, then free it after use */ #define encodeRestrictionDateDisplay(db,tdb) encodeRestrictionDate(db,tdb,TRUE) char *hDocumentRoot(); /* get the path to the DocumentRoot, or the default */ 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. */ 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. */ char *hCgiRoot(); /* get the path to the CGI directory. * Returns NULL when not running as a CGI (unless specified by browser.cgiRoot) */ char *hTrackUiForTrack(char *trackName); /* Relative URL to extended track UI, delegated to a track-specific UI if available. */ /* Definitions for ruler pseudo-track. It's not yet a full-fledged * track, so it can't appear in trackDb. */ #define RULER_TRACK_NAME "ruler" #define RULER_TRACK_LABEL "Base Position" #define RULER_TRACK_LONGLABEL "Genome Base Position" #define SCALE_BAR_LABEL "Scale" #define WIN_POS_LABEL "Window Position" #define WIN_TITLE_LABEL "" /* "Title" */ /* Definitions for restriction enzyme track. */ #define cutterVar "hgt.cutters" #define cutterDefault "" #define CUTTERS_POPULAR "ClaI,BamHI,BglII,EcoRI,EcoRV,HindIII,PstI,SalI,SmaI,XbaI,KpnI,SacI,SphI" #define CUTTERS_TRACK_NAME "cutters" #define CUTTERS_TRACK_LABEL "Restr Enzymes" #define CUTTERS_TRACK_LONGLABEL "Restriction Enzymes from REBASE" #define CUTTERS_TRACK_PRIORITY 100 /* Definition for oligo match track. */ #define oligoMatchVar "hgt.oligoMatch" #define oligoMatchDefault "" #define OLIGO_MATCH_TRACK_NAME "oligoMatch" #define OLIGO_MATCH_TRACK_LABEL "Short Match" #define OLIGO_MATCH_TRACK_LONGLABEL "Perfect Match to Short Sequence" #define OLIGO_MATCH_TRACK_PRIORITY 100 /* Definitions for User Psl track (hgBlat results). */ #define USER_PSL_TRACK_NAME "hgUserPsl" #define USER_PSL_TRACK_LABEL "Blat Sequence" #define USER_PSL_TRACK_LONGLABEL "Your Sequence from BLAT Search" /* Display of bases on the ruler, and multiple alignments. * If present, indicates reverse strand */ #define COMPLEMENT_BASES_VAR "complement" /* For trackUi and hgTracks, motif highlight options */ #define BASE_MOTIFS "hgt.motifs" #define MOTIF_COMPLEMENT "hgt.motifComplement" #define BASE_SCALE_BAR "hgt.baseShowScaleBar" #define BASE_SHOWRULER "hgt.baseShowRuler" #define BASE_SHOWPOS "hgt.baseShowPos" #define BASE_SHOWASM "hgt.baseShowAsm" #define BASE_SHOWASM_SCALEBAR "hgt.baseShowAsmScaleBar" #define BASE_TITLE "hgt.baseTitle" #define REV_CMPL_DISP "hgt.revCmplDisp" /* Configuration variable to cause ruler zoom to zoom to base level */ #define RULER_BASE_ZOOM_VAR "rulerBaseZoom" /* Maf track display variables and their values */ #define MAF_GENEPRED_VAR "mafGenePred" #define MAF_FRAMING_VAR "mafFrame" #define MAF_DOT_VAR "mafDot" #define MAF_CHAIN_VAR "mafChain" #define MAF_SHOW_SNP "mafShowSnp" /* display of bases for tracks that are type psl and have sequence e.g. ESTs */ #define PSL_SEQUENCE_BASES "pslSequenceBases" #define PSL_SEQUENCE_DEFAULT "no" /****** Some stuff for tables of controls ******/ #define CONTROL_TABLE_WIDTH 940 /* this number is 10 less than hgDefaultPixWidth and DEFAULT_PIX_WIDTH * defined in hCommon.h */ #define EXTENDED_DNA_BUTTON "extended case/color options" /* Net track option */ #define NET_OPT_TOP_ONLY "netTopOnly" /* Microarray default setting. */ #define MICROARRAY_CLICK_LIMIT 200 /* itemImagePath trackDb variable names */ #define ITEM_IMAGE_PATH "itemImagePath" #define ITEM_BIG_IMAGE_PATH "itemBigImagePath" /* SwitchGear TSS default filter. */ #define SWITCHDBTSS_FILTER 10 /* Subtrack color support in UI */ #define SUBTRACK_COLOR_PATCH "showSubtrackColorOnUi" // for use with subGroup and sortOrder settings // ie. subGroup1 subtrackColor Color; sortOrder subtrackColor=+ cellType=+ #define SUBTRACK_COLOR_SUBGROUP "subtrackColor" // trackDb setting and cart/cgi var #define SUBTRACK_HIDE_EMPTY "hideEmptySubtracks" #define SUBTRACK_HIDE_EMPTY_LABEL "hideEmptySubtracksLabel" #define SUBTRACK_HIDE_EMPTY_MULTIBED_URL "hideEmptySubtracksMultiBedUrl" #define SUBTRACK_HIDE_EMPTY_SOURCES_URL "hideEmptySubtracksSourcesUrl" // multi-region #define MULTI_REGION_CHROM "multi" #define OLD_MULTI_REGION_CHROM "virt" #define MULTI_REGION_BED_PADDING "multiRegionBedPadding" #define MULTI_REGION_BED_WIN_FULL "virtWinFull" void netUi(struct trackDb *tdb); struct controlGrid /* Keep track of a control grid (table) */ { int columns; /* How many columns in grid. */ int columnIx; /* Index (0 based) of current column. */ char *align; /* Which way to align. */ boolean rowOpen; /* True if have opened a row. */ }; struct controlGrid *startControlGrid(int columns, char *align); /* Start up a control grid. */ void controlGridStartCell(struct controlGrid *cg); /* Start a new cell in control grid. */ void controlGridEndCell(struct controlGrid *cg); /* End cell in control grid. */ void endControlGrid(struct controlGrid **pCg); /* Finish up a control grid. */ void controlGridEndRow(struct controlGrid *cg); /* Force end of row. */ /****** Some stuff for hide/dense/full controls ******/ enum trackVisibility /* How to look at a track. */ { tvHide=0, /* Hide it. */ tvDense=1, /* Squish it together. */ tvFull=2, /* Expand it out. */ tvPack=3, /* Zig zag it up and down. */ tvSquish=4, /* Pack with thin boxes and no labels. */ }; #define tvShow tvFull enum trackVisibility hTvFromString(char *s); /* Given a string representation of track visibility, return as * equivalent enum. */ enum trackVisibility hTvFromStringNoAbort(char *s); /* Given a string representation of track visibility, return as * equivalent enum. */ char *hStringFromTv(enum trackVisibility vis); /* Given enum representation convert to string. */ /* Standard width for visibility dropdowns */ #define TV_DROPDOWN_STYLE "width: 70px" void hTvDropDownClassVisOnlyAndExtra(char *varName, enum trackVisibility vis, boolean canPack, char *class, char *visOnly, struct slPair *events); /* Make track visibility drop down for varName with style class, and potentially limited to visOnly */ #define hTvDropDownClassVisOnly(varName,vis,canPack,class,visOnly) \ hTvDropDownClassVisOnlyAndExtra(varName,vis,canPack,class,visOnly,NULL) void hTvDropDownClassWithJavascript(char *varName, char *id, enum trackVisibility vis, boolean canPack, char *class, struct slPair *events); /* Make track visibility drop down for varName with style class and javascript */ #define hTvDropDownClass(varName,vis,canPack,class) \ hTvDropDownClassWithJavascript((varName),NULL,(vis),(canPack),(class),NULL) #define hTvDropDownWithJavascript(varName,vis,canPack,javascript) \ hTvDropDownClassWithJavascript((varName),NULL,(vis),(canPack),"normalText",(javascript)) #define hTvDropDown(varName,vis,canPack) \ hTvDropDownClassWithJavascript((varName),NULL,(vis),(canPack),"normalText",NULL) #define SUPERTRACK_DEFAULT_VIS "hide" void hideShowDropDownWithClassAndExtra(char *varName, char *id, boolean show, char *class, struct slPair *events); #define hideShowDropDown(varName,show,class) \ hideShowDropDownWithClassAndExtra(varName,NULL,show,class,NULL) /* Make hide/show dropdown for varName */ /****** Some stuff for stsMap related controls *******/ enum stsMapOptEnum { smoeGenetic = 0, smoeGenethon = 1, smoeMarshfield = 2, smoeDecode = 3, smoeGm99 = 4, smoeWiYac = 5, smoeWiRh = 6, smoeTng = 7, }; enum stsMapOptEnum smoeStringToEnum(char *string); /* Convert from string to enum representation. */ char *smoeEnumToString(enum stsMapOptEnum x); /* Convert from enum to string representation. */ void smoeDropDown(char *var, char *curVal); /* Make drop down of options. */ /****** Some stuff for stsMapMouseNew related controls *******/ enum stsMapMouseOptEnum { smmoeGenetic = 0, smmoeWig = 1, smmoeMgi = 2, smmoeRh = 3, }; enum stsMapMouseOptEnum smmoeStringToEnum(char *string); /* Convert from string to enum representation. */ char *smmoeEnumToString(enum stsMapMouseOptEnum x); /* Convert from enum to string representation. */ void smmoeDropDown(char *var, char *curVal); /* Make drop down of options. */ /****** Some stuff for stsMapRat related controls *******/ enum stsMapRatOptEnum { smroeGenetic = 0, smroeFhh = 1, smroeShrsp = 2, smroeRh = 3, }; enum stsMapRatOptEnum smroeStringToEnum(char *string); /* Convert from string to enum representation. */ char *smroeEnumToString(enum stsMapRatOptEnum x); /* Convert from enum to string representation. */ void smroeDropDown(char *var, char *curVal); /* Make drop down of options. */ /****** Some stuff for fishClones related controls *******/ enum fishClonesOptEnum { fcoeFHCRC = 0, fcoeNCI = 1, fcoeSC = 2, fcoeRPCI = 3, fcoeCSMC = 4, fcoeLANL = 5, fcoeUCSF = 6, }; enum fishClonesOptEnum fcoeStringToEnum(char *string); /* Convert from string to enum representation. */ char *fcoeEnumToString(enum fishClonesOptEnum x); /* Convert from enum to string representation. */ void fcoeDropDown(char *var, char *curVal); /* Make drop down of options. */ /****** Some stuff for recombRate related controls *******/ enum recombRateOptEnum { rroeDecodeAvg = 0, rroeDecodeFemale = 1, rroeDecodeMale = 2, rroeMarshfieldAvg = 3, rroeMarshfieldFemale = 4, rroeMarshfieldMale = 5, rroeGenethonAvg = 6, rroeGenethonFemale = 7, rroeGenethonMale = 8, }; enum recombRateOptEnum rroeStringToEnum(char *string); /* Convert from string to enum representation. */ char *rroeEnumToString(enum recombRateOptEnum x); /* Convert from enum to string representation. */ void rroeDropDown(char *var, char *curVal); /* Make drop down of options. */ /****** Some stuff for recombRateRat related controls *******/ enum recombRateRatOptEnum { rrroeShrspAvg = 0, rrroeFhhAvg = 1, }; enum recombRateRatOptEnum rrroeStringToEnum(char *string); /* Convert from string to enum representation. */ char *rrroeEnumToString(enum recombRateRatOptEnum x); /* Convert from enum to string representation. */ void rrroeDropDown(char *var, char *curVal); /* Make drop down of options. */ /****** Some stuff for recombRateMouse related controls *******/ enum recombRateMouseOptEnum { rrmoeWiAvg = 0, rrmoeMgdAvg = 1, }; enum recombRateMouseOptEnum rrmoeStringToEnum(char *string); /* Convert from string to enum representation. */ char *rrmoeEnumToString(enum recombRateMouseOptEnum x); /* Convert from enum to string representation. */ void rrmoeDropDown(char *var, char *curVal); /* Make drop down of options. */ /****** Some stuff for cghNci60 related controls *******/ enum cghNci60OptEnum { cghoeTissue = 0, cghoeBreast = 1, cghoeCns = 2, cghoeColon = 3, cghoeLeukemia = 4, cghoeLung = 5, cghoeMelanoma = 6, cghoeOvary = 7, cghoeProstate = 8, cghoeRenal = 9, cghoeAll = 10, }; enum cghNci60OptEnum cghoeStringToEnum(char *string); /* Convert from string to enum representation. */ char *cghoeEnumToString(enum cghNci60OptEnum x); /* Convert from enum to string representation. */ void cghoeDropDown(char *var, char *curVal); /* Make drop down of options. */ /****** Some stuff for Expression Data tracks in general *******/ struct expdFilter /* Info on one type of expression data filter. */ { struct expdFilter *next; /* Next in list. */ char *filterInclude; /* Identifier associated with items to include, NULL indicates include all. */ char *filterExclude; /* Identifier associated with items to exclude, NULL indicates exclude none. */ boolean redGreen; /* True if red/green color scheme, Otherwise blue/red color scheme. */ }; /*** Some Stuff for the NCI60 track ***/ enum nci60OptEnum { nci60Tissue = 0, nci60All = 1, nci60Breast = 2, nci60Cns = 3, nci60Colon = 4, nci60Leukemia = 5, nci60Melanoma = 6, nci60Ovary = 7, nci60Prostate = 8, nci60Renal = 9, nci60Nsclc = 10, nci60Duplicates = 11, nci60Unknown = 12 }; enum nci60OptEnum nci60StringToEnum(char *string); /* Convert from string to enum representation. */ char *nci60EnumToString(enum nci60OptEnum x); /* Convert from enum to string representation. */ void nci60DropDown(char *var, char *curVal); /* Make drop down of options. */ /* net track level display options */ enum netLevelEnum { netLevel0 = 0, netLevel1 = 1, netLevel2 = 2, netLevel3 = 3, netLevel4 = 4, netLevel5 = 5, netLevel6 = 6, }; enum netLevelEnum netLevelStringToEnum(char *string); /* Convert from string to enum representation. */ char *netLevelEnumToString(enum netLevelEnum x); /* Convert from enum to string representation. */ void netLevelDropDown(char *var, char *curVal); /* Make drop down of options. */ /* net track color options */ enum netColorEnum { netColorChromColors = 0, netColorGrayScale = 1, }; enum netColorEnum netColorStringToEnum(char *string); /* Convert from string to enum representation. */ char *netColorEnumToString(enum netColorEnum x); /* Convert from enum to string representation. */ void netColorDropDown(char *var, char *curVal); /* Make drop down of options. */ /* chain track color options */ enum chainColorEnum { chainColorChromColors = 0, chainColorScoreColors = 1, chainColorNoColors = 2, }; enum chainColorEnum chainColorStringToEnum(char *string); /* Convert from string to enum representation. */ char *chainColorEnumToString(enum chainColorEnum x); /* Convert from enum to string representation. */ void chainColorDropDown(char *var, char *curVal); /* Make drop down of options. */ /* Wiggle track Windowing combining function option */ enum wiggleWindowingEnum { wiggleWindowingWhiskers = 0, wiggleWindowingMax = 1, wiggleWindowingMean = 2, wiggleWindowingMin = 3, }; enum wiggleWindowingEnum wiggleWindowingStringToEnum(char *string); /* Convert from string to enum representation. */ char *wiggleWindowingEnumToString(enum wiggleWindowingEnum x); /* Convert from enum to string representation. */ void wiggleWindowingDropDown(char *var, char *curVal); /* Make drop down of options. */ /* Wiggle track use Smoothing option, 0 and 1 is the same as Off */ enum wiggleSmoothingEnum { wiggleSmoothingOff = 0, wiggleSmoothing2 = 1, wiggleSmoothing3 = 2, wiggleSmoothing4 = 3, wiggleSmoothing5 = 4, wiggleSmoothing6 = 5, wiggleSmoothing7 = 6, wiggleSmoothing8 = 7, wiggleSmoothing9 = 8, wiggleSmoothing10 = 9, wiggleSmoothing11 = 10, wiggleSmoothing12 = 11, wiggleSmoothing13 = 12, wiggleSmoothing14 = 13, wiggleSmoothing15 = 14, wiggleSmoothing16 = 15, wiggleSmoothingMax = MAX_SMOOTHING, /* Not an option, but lets us keep track of memory to use */ }; enum wiggleSmoothingEnum wiggleSmoothingStringToEnum(char *string); /* Convert from string to enum representation. */ char *wiggleSmoothingEnumToString(enum wiggleSmoothingEnum x); /* Convert from enum to string representation. */ void wiggleSmoothingDropDown(char *var, char *curVal); /* Make drop down of options. */ /* Wiggle track y Line Mark on/off option */ enum wiggleYLineMarkEnum { wiggleYLineMarkOff = 0, wiggleYLineMarkOn = 1, }; enum wiggleYLineMarkEnum wiggleYLineMarkStringToEnum(char *string); /* Convert from string to enum representation. */ char *wiggleYLineMarkEnumToString(enum wiggleYLineMarkEnum x); /* Convert from enum to string representation. */ void wiggleYLineMarkDropDown(char *var, char *curVal); /* Make drop down of options. */ /* Wiggle track use AutoScale option */ enum wiggleScaleOptEnum { wiggleScaleManual = 0, wiggleScaleAuto = 1, wiggleScaleCumulative = 2, }; enum wiggleScaleOptEnum wiggleScaleStringToEnum(char *string); /* Convert from string to enum representation. */ char *wiggleScaleEnumToString(enum wiggleScaleOptEnum x); /* Convert from enum to string representation. */ void wiggleScaleDropDown(char *var, char *curVal); /* Make drop down of options. */ /* Wiggle track type of graph option */ enum wiggleGraphOptEnum { wiggleGraphPoints = 0, wiggleGraphBar = 1, }; enum wiggleGraphOptEnum wiggleGraphStringToEnum(char *string); /* Convert from string to enum representation. */ char *wiggleGraphEnumToString(enum wiggleGraphOptEnum x); /* Convert from enum to string representation. */ void wiggleGraphDropDown(char *var, char *curVal); /* Make drop down of options. */ /* Wiggle track transform func*/ enum wiggleTransformFuncEnum { wiggleTransformFuncNone = 0, wiggleTransformFuncLog = 1, }; enum wiggleTransformFuncEnum wiggleTransformFuncToEnum(char *string); /* Convert from string to enum representation. */ /* Wiggle track always include zero */ enum wiggleAlwaysZeroEnum { wiggleAlwaysZeroOff = 0, wiggleAlwaysZeroOn = 1, }; enum wiggleAlwaysZeroEnum wiggleAlwaysZeroToEnum(char *string); /* Convert from string to enum representation. */ /* Wiggle track Grid lines on/off option */ enum wiggleGridOptEnum { wiggleHorizontalGridOn = 0, wiggleHorizontalGridOff = 1, }; enum wiggleGridOptEnum wiggleGridStringToEnum(char *string); /* Convert from string to enum representation. */ char *wiggleGridEnumToString(enum wiggleGridOptEnum x); /* Convert from enum to string representation. */ void wiggleGridDropDown(char *var, char *curVal); /* Make drop down of options. */ #define WIG_VIEWFUNC_SHOW_ALL "showAll" #define WIG_VIEWFUNC_ADD_ALL "addAll" #define WIG_VIEWFUNC_SUBTRACT_ALL "subtractAll" /* Wiggle track aggregate option */ enum wiggleViewFuncEnum { wiggleViewFuncShowAll = 0, wiggleViewFuncAddAll = 1, wiggleViewFuncSubtractAll = 2, }; char *wiggleViewFuncEnumToString(enum wiggleViewFuncEnum x); /* Convert from enum to string representation. */ enum wiggleViewFuncEnum wiggleViewFuncStringToEnum(char *string); #define WIG_AGGREGATE_NONE "none" #define WIG_AGGREGATE_TRANSPARENT "transparentOverlay" #define WIG_AGGREGATE_SOLID "solidOverlay" #define WIG_AGGREGATE_STACKED "stacked" #define WIG_AGGREGATE_ADD "add" #define WIG_AGGREGATE_SUBTRACT "subtract" /* Wiggle track aggregate option */ enum wiggleAggregateFunctionEnum { wiggleAggregateNone = 0, wiggleAggregateTransparent = 1, wiggleAggregateSolid = 2, wiggleAggregateStacked = 3, wiggleAggregateAdd = 4, wiggleAggregateSubtract = 5, }; char *wiggleAggregateFunctionEnumToString(enum wiggleAggregateFunctionEnum x); /* Convert from enum to string representation. */ enum wiggleAggregateFunctionEnum wiggleAggregateFunctionStringToEnum(char *string); /*** BAM alignment track coloring code: ***/ // tdbSettings / cart var suffixes and default values: #define BAM_PAIR_ENDS_BY_NAME "pairEndsByName" #define BAM_SHOW_NAMES "showNames" #define BAM_MIN_ALI_QUAL "minAliQual" #define BAM_MIN_ALI_QUAL_DEFAULT "0" #define BAM_COLOR_MODE "bamColorMode" #define BAM_COLOR_MODE_GRAY "gray" #define BAM_COLOR_MODE_STRAND "strand" #define BAM_COLOR_MODE_TAG "tag" #define BAM_COLOR_MODE_OFF "off" #define BAM_COLOR_MODE_DEFAULT BAM_COLOR_MODE_STRAND #define BAM_GRAY_MODE "bamGrayMode" #define BAM_GRAY_MODE_ALI_QUAL "aliQual" #define BAM_GRAY_MODE_BASE_QUAL "baseQual" #define BAM_GRAY_MODE_UNPAIRED "unpaired" #define BAM_GRAY_MODE_DEFAULT BAM_GRAY_MODE_ALI_QUAL #define BAM_COLOR_TAG "bamColorTag" #define BAM_COLOR_TAG_DEFAULT "YC" #define BAMWIG_MODE "bamWigMode" /*** Control of base/codon coloring code: ***/ /* Drawing modes: values <= baseColorDrawOff don't render at base or codon * level */ enum baseColorDrawOpt { baseColorDrawCds = -1, /* not a selection option, a fall back when * zoomed out. */ baseColorDrawOff = 0, baseColorDrawGenomicCodons = 1, baseColorDrawItemCodons = 2, baseColorDrawDiffCodons = 3, baseColorDrawItemBases = 4, baseColorDrawDiffBases = 5, }; /* Drawing mode select box labels: */ #define BASE_COLOR_DRAW_OFF_LABEL "OFF" #define BASE_COLOR_DRAW_GENOMIC_CODONS_LABEL "genomic codons" #define BASE_COLOR_DRAW_ITEM_CODONS_LABEL "mRNA codons" #define BASE_COLOR_DRAW_DIFF_CODONS_LABEL "nonsynonymous mRNA codons" #define BASE_COLOR_DRAW_ITEM_BASES_CDS_LABEL "mRNA bases" #define BASE_COLOR_DRAW_DIFF_BASES_CDS_LABEL "different mRNA bases" #define BASE_COLOR_DRAW_ITEM_BASES_NC_LABEL "item bases" #define BASE_COLOR_DRAW_DIFF_BASES_NC_LABEL "different item bases" /* Drawing mode select box values: */ #define BASE_COLOR_DRAW_OFF "none" #define BASE_COLOR_DRAW_GENOMIC_CODONS "genomicCodons" #define BASE_COLOR_DRAW_ITEM_CODONS "itemCodons" #define BASE_COLOR_DRAW_DIFF_CODONS "diffCodons" #define BASE_COLOR_DRAW_ITEM_BASES "itemBases" #define BASE_COLOR_DRAW_DIFF_BASES "diffBases" /* Drawing mode per-track cart variable suffix: */ #define BASE_COLOR_VAR_SUFFIX "baseColorDrawOpt" #define CODON_NUMBERING_SUFFIX "codonNumbering" /* trackDb settings: */ #define BASE_COLOR_USE_CDS "baseColorUseCds" #define BASE_COLOR_USE_SEQUENCE "baseColorUseSequence" #define BASE_COLOR_DEFAULT "baseColorDefault" #define SHOW_DIFF_BASES_ALL_SCALES "showDiffBasesAllScales" /* Coloring help pages: */ #define CDS_HELP_PAGE "../goldenPath/help/hgCodonColoring.html" #define CDS_MRNA_HELP_PAGE "../goldenPath/help/hgCodonColoringMrna.html" #define CDS_BASE_HELP_PAGE "../goldenPath/help/hgBaseLabel.html" /* Settings for coloring and filtering genePred tables from an item class table. */ #define GENEPRED_CLASS_VAR "geneClasses" #define GENEPRED_CLASS_PREFIX "gClass_" #define GENEPRED_CLASS_TBL "itemClassTbl" #define GENEPRED_CLASS_NAME_COLUMN "itemClassNameColumn" #define GENEPRED_CLASS_NAME_COLUMN_DEFAULT "name" #define GENEPRED_CLASS_CLASS_COLUMN "itemClassClassColumn" #define GENEPRED_CLASS_CLASS_COLUMN_DEFAULT "class" /* genbank track cart variable suffixes: */ #define SHOW_PATENT_SEQUENCES_SUFFIX "showPatentSequences" void baseColorDrawOptDropDown(struct cart *cart, struct trackDb *tdb); /* Make appropriately labeled drop down of options if any are applicable.*/ enum baseColorDrawOpt baseColorDrawOptEnabled(struct cart *cart, struct trackDb *tdb); /* Query cart & trackDb to determine what drawing mode (if any) is enabled. */ /*** Other Gene Prediction type options: ***/ #define HIDE_NONCODING_SUFFIX "hideNoncoding" #define HIDE_NONCODING_DEFAULT FALSE /*** Control of fancy indel display code: ***/ /* trackDb settings: */ #define INDEL_DOUBLE_INSERT "indelDoubleInsert" #define INDEL_QUERY_INSERT "indelQueryInsert" #define INDEL_POLY_A "indelPolyA" #define INDEL_HELP_PAGE "../goldenPath/help/hgIndelDisplay.html" void indelShowOptions(struct cart *cart, struct trackDb *tdb); /* Make HTML inputs for indel display options if any are applicable. */ 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 -1.0 to disable check for zoom level. */ void bamAddBaseAndIndelSettings(struct trackDb *tdb); /* Unless already set in tdb, add settings to enable base-level differences and indel display. */ /*** Some Stuff for the base position (ruler) controls ***/ #define ZOOM_1PT5X "1.5x" #define ZOOM_3X "3x" #define ZOOM_10X "10x" #define ZOOM_100X "100x" #define ZOOM_BASE "base" void zoomRadioButtons(char *var, char *curVal); /* Make a list of radio buttons for all zoom options */ /*** Some Stuff for the wiggle track ***/ enum wiggleOptEnum { wiggleNoInterpolation = 0, wiggleLinearInterpolation = 1, }; enum wiggleOptEnum wiggleStringToEnum(char *string); /* Convert from string to enum representation. */ char *wiggleEnumToString(enum wiggleOptEnum x); /* Convert from enum to string representation. */ void wiggleDropDown(char *var, char *curVal); /* Make drop down of options. */ /*** Some Stuff for the GCwiggle track ***/ enum GCwiggleOptEnum { GCwiggleNoInterpolation = 0, GCwiggleLinearInterpolation = 1, }; enum GCwiggleOptEnum GCwiggleStringToEnum(char *string); /* Convert from string to enum representation. */ char *GCwiggleEnumToString(enum GCwiggleOptEnum x); /* Convert from enum to string representation. */ void GCwiggleDropDown(char *var, char *curVal); /* Make drop down of options. */ /*** Some Stuff for the chimp track ***/ enum chimpOptEnum { chimpNoInterpolation = 0, chimpLinearInterpolation = 1, }; enum chimpOptEnum chimpStringToEnum(char *string); /* Convert from string to enum representation. */ char *chimpEnumToString(enum chimpOptEnum x); /* Convert from enum to string representation. */ void wiggleDropDown(char *var, char *curVal); /* Make drop down of options. */ /*** Some Stuff for the AFFY track ***/ enum affyOptEnum { affyChipType = 0, affyId = 1, affyTissue = 2, affyAllData = 3, }; enum affyOptEnum affyStringToEnum(char *string); /* Convert from string to enum representation. */ char *affyEnumToString(enum affyOptEnum x); /* Convert from enum to string representation. */ void affyDropDown(char *var, char *curVal); /* Make drop down of options. */ /*** Some Stuff for the affy all exon track ***/ enum affyAllExonOptEnum { affyAllExonChip = 0, affyAllExonTissue = 1, affyAllExonAllData = 2, }; enum affyAllExonOptEnum affyAllExonStringToEnum(char *string); /* Convert from string to enum representation. */ char *affyAllExonEnumToString(enum affyAllExonOptEnum x); /* Convert from enum to string representation. */ void affyAllExonDropDown(char *var, char *curVal); /* Make drop down of options. */ /****** Some stuff for Rosetta related controls *******/ enum rosettaOptEnum { rosettaAll =0, rosettaPoolOther=1, rosettaPool=2, rosettaOther=3 }; enum rosettaExonOptEnum { rosettaConfEx, rosettaPredEx, rosettaAllEx }; enum rosettaOptEnum rosettaStringToEnum(char *string); /* Convert from string to enum representation. */ char *rosettaEnumToString(enum rosettaOptEnum x); /* Convert from enum to string representation. */ void rosettaDropDown(char *var, char *curVal); /* Make drop down of options. */ enum rosettaExonOptEnum rosettaStringToExonEnum(char *string); /* Convert from string to enum representation of exon types. */ char *rosettaExonEnumToString(enum rosettaExonOptEnum x); /* Convert from enum to string representation of exon types. */ void rosettaExonDropDown(char *var, char *curVal); /* Make drop down of exon type options. */ /****** Some stuff for mRNA and EST related controls *******/ struct mrnaFilter /* Info on one type of mrna filter. */ { struct mrnaFilter *next; /* Next in list. */ char *label; /* Filter label. */ char *suffix; /* Suffix of cgi variable holding search pattern. */ char *table; /* Associated table to search. */ char *pattern; /* Pattern to find. */ int mrnaTableIx; /* Index of field in mrna table. */ struct hash *hash; /* Hash of id's in table that match pattern */ }; struct mrnaUiData /* Data for mrna-specific user interface. */ { char *filterTypeSuffix; /* cgi variable suffix that holds type of filter. */ char *logicTypeSuffix; /* cgi variable suffix that indicates logic. */ struct mrnaFilter *filterList; /* List of filters that can be applied. */ }; struct mrnaUiData *newBedUiData(char *track); /* Make a new in extra-ui data structure for a bed. */ struct mrnaUiData *newMrnaUiData(char *track, boolean isXeno); /* Make a new in extra-ui data structure for mRNA. */ 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); // 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 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, }; enum acemblyOptEnum acemblyStringToEnum(char *string); /* Convert from string to enum representation. */ char *acemblyEnumToString(enum acemblyOptEnum x); /* Convert from enum to string representation. */ void acemblyDropDown(char *var, char *curVal); /* Make drop down of options. */ 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. */ char *compositeGroupLabel(struct trackDb *childTdb, char *group, char *id); /* Given ID from group, return corresponding label, looking through parent's subGroupN's */ char *compositeGroupId(struct trackDb *tdb, char *group, char *id); /* Given label, return id, looking through parent's subGroupN's */ char *compositeLabelWithVocabLink(char *db,struct trackDb *parentTdb, struct trackDb *childTdb, char *vocabType, char *label); /* If the parentTdb has an ENCODE controlledVocabulary setting and the vocabType is found, then label will be wrapped with the link to display it. Return string is cloned. */ boolean compositeHideEmptySubtracksSetting(struct trackDb *tdb, boolean *retDefault, char **retMultiBedFile, char **retSubtrackIdFile); /* Parse hideEmptySubtracks settings * Format: hideEmptySubtracks on|off * Optional index files for performance: * hideEmptySubtracksMultiBedUrl multiBed.bigBed * hideEmptySubtracksSourceUrl subtrackIds.tab * MultiBed.bed is a bed3Sources bigBed, generated with UCSC tool trackDbIndexBb * (for single view subtracks, can use bedtools multiinter * post-processed by UCSC multiBed.pl tool) * subtrackIds.tab is a tab-sep file: id subtrackName * * Return TRUE if setting is present. retDefault is TRUE if set to 'on', o/w FALSE */ boolean compositeHideEmptySubtracks(struct cart *cart, struct trackDb *tdb, char **retMultiBedFile, char **retSubtrackIdFile); /* Parse hideEmptySubtracks setting and check cart * Return TRUE if we should hide empties */ boolean compositeChildHideEmptySubtracks(struct cart *cart, struct trackDb *childTdb, char **retMultiBedFile, char **retSubtrackIdFile); /* Parse hideEmptySubtracks setting and check cart * Return TRUE if we should hide empties */ char *wgEncodeVocabLink(char *file,char *term,char *value,char *title, char *label,char *suffix); // returns allocated string of HTML link to ENCODE controlled vocabulary term char *metadataAsHtmlTable(char *db,struct trackDb *tdb,boolean showLongLabel,boolean showShortLabel); /* If metadata from metaDb exists, return string of html with table definition */ 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, struct slPair *events); /* 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) typedef struct _dimensions { int count; char**names; char**subgroups; char* setting; } dimensions_t; boolean dimensionsExist(struct trackDb *parentTdb); /* Does this parent track contain dimensions? */ 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; typedef struct _membersForAll { int abcCount; int dimMax; // Arrays of "members" structs will be ordered as // [view][dimX][dimY][dimA]... with first 3 in fixed spots // and rest as found (and non-empty) boolean filters; // ABCs use filterComp boxes (as upposed to check boxes dimensions_t *dimensions; // One struct describing "deimensions" setting" // (e.g. dimX:cell dimY:antibody dimA:treatment) members_t* members[27]; // One struct for each dimension describing groups in dimension // (e.g. cell: GM12878,K562) char* checkedTags[27]; // FIXME: Should move checkedTags into // membersForAll->members[ix]->selected; char letters[27]; } membersForAll_t; membersForAll_t* membersForAllSubGroupsGet(struct trackDb *parentTdb, struct cart *cart); // Returns all the parents subGroups and members membership_t *subgroupMembershipGet(struct trackDb *childTdb); /* gets all the subgroup membership for a child track */ 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 */ void subgroupFree(char **value); /* frees subgroup memory */ boolean subgroupRequired(char *value); /* Returns whether subgroup much be specified for each track. * Generally true. Exceptions are specially defined subgroups */ 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. // 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)) 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 wigOption(struct cart *cart, char *name, char *title, struct trackDb *tdb); /* let the user choose to see the track in wiggle mode */ void wigCfgUi(struct cart *cart, struct trackDb *tdb,char *name,char *title,boolean boxed); /* UI for the wiggle track */ void labelCfgUi(char *db, struct cart *cart, struct trackDb *tdb, char *prefix); /* Put up a choice for labels. */ #define MERGESPAN_TDB_SETTING "mergeSpannedItems" // also used in hgTracks.js! #define MERGESPAN_CART_SETTING "doMergeItems" void mergeSpanCfgUi(struct cart *cart, struct trackDb *tdb, char *prefix); /* If this track offers a merge spanned items option, put up the cfg for it, which * is just a checkbox with a small explanation. Comparing tdb->track to prefix * ensures we don't offer this control at the composite level, as this is a * subtrack only config */ #define NO_SCORE_FILTER "noScoreFilter" #define SCORE_FILTER "scoreFilter" #define SCORE_LABEL "scoreLabel" #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" boolean colonPairToDoubles(char * colonPair,double *first,double *second); // Non-destructive. Only sets values if found. No colon: value goes to *first boolean colonPairToInts(char * colonPair,int *first,int *second); // Non-destructive. Only sets values if found. No colon: value goes to *first void getScoreIntRangeFromCart(struct cart *cart, struct trackDb *tdb, boolean parentLevel, 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) // void getScoreFloatRangeFromCart(struct cart *cart, struct trackDb *tdb, boolean parentLevel, 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) 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); /* 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); // Put up UI for selecting rainbow chromosome color or intensity score. 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 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 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 genePredCfgUi(char *db, struct cart *cart, struct trackDb *tdb, char *name, char *title, boolean boxed); // 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. */ void lrgCfgUi(struct cart *cart, struct trackDb *tdb, char *name, char *title, boolean boxed); /* LRG: Locus Reference Genomic sequences mapped to assembly. */ void lrgTranscriptAliCfgUi(struct cart *cart, struct trackDb *tdb, char *name, char *title, boolean boxed); /* LRG Transcripts: Locus Reference Genomic transcript sequences mapped to assembly. */ 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 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 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 // 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 */ void sortOrderFree(sortOrder_t **sortOrder); // frees any previously obtained sortOrder settings 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 // 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" #define HIGHLIGHT_BY "highlightBy" 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} 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 filterBy_t *highlightBySetGet(struct trackDb *tdb, struct cart *cart, char *name); /* Gets one or more "highlightBy" settings (ClosestToHome). returns NULL if not found */ void filterBySetFree(filterBy_t **filterBySet); // 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 INLINE boolean filterByAllChosen(filterBy_t *filterBy) /* Is "All" chosen in the filter list? */ { return ((filterBy->slChoices == NULL) || (slNameInList(filterBy->slChoices,"All"))); } void filterBySetCfgUi(struct cart *cart, struct trackDb *tdb, filterBy_t *filterBySet, boolean onOneLine, char *prefix); // Does the UI for a list of filterBy structure char *filterByClause(filterBy_t *filterBy); // 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 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 void extraUiLinks(char *db, struct trackDb *tdb, struct cart *cart); // Show downloads, schema and metadata links where appropriate boolean chainDbNormScoreAvailable(struct trackDb *tdb); /* check if normScore column is specified in trackDb as available */ /* UI for factorSource track type */ /* trackDb settings: */ #define SOURCE_TABLE "sourceTable" void hPrintAbbreviationTable(struct sqlConnection *conn, char *sourceTable, char *label); /* Print out table of abbreviations. */ void hPrintFactorSourceAbbrevTable(struct sqlConnection *conn, struct trackDb *tdb); /* Print out table of abbreviations. With 'pack' setting, * show cell name only (before '+') and uniqify */ // 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 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 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 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. 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 hPrintIcons(struct trackDb *tdb); /* prints optional folder and pennants icons and a space, if any icons were printed */ 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 { ftString =0, ftInteger =1, ftFloat =2, }; 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 struct asObject *asFromTableDescriptions(struct sqlConnection *conn, char *table); // If there is a tableDescriptions table and it has an entry for table, return // a parsed autoSql object; otherwise return NULL. struct asObject *asForTdb(struct sqlConnection *conn, struct trackDb *tdb); // Get autoSQL description if any associated with table, ignoring errAborts if any. struct asObject *asForDb(struct trackDb *tdb, char* database); /* return asObject given a database name. NULL if not found */ struct asColumn *asColumnFind(struct asObject *asObj, char *name); // Return named column. struct slName *asColNames(struct asObject *as); // Get list of column names. /********************/ /* Basic info for controlled vocabulary terms (e.g. to display for composites, or cluster tracks */ char *vocabLink(struct hash *vocabFieldHash, char *term, char *title); /* Make an anchor with mouseover containing description and link if present */ struct hash *vocabBasicFromSetting(struct trackDb *parentTdb, struct cart *cart); /* Get description and URL for all vocabTables. Returns a hash of hashes */ boolean vocabSettingIsEncode(char *setting); /* Distinguish ENCODE controlled vocab settings (first arg is cv.ra filename) from non-ENCODE (table-based vocabs) */ boolean isEncode2(char *database, char *track); /* Return true for tracks created by UCSC DCC during ENCODE production phase */ char *replaceInUrl(char *url, char *idInUrl, struct cart *cart, char *db, char *seqName, int winStart, int winEnd, char *track, boolean encode, struct slPair *fields) ; /* replace $$ in url with idInUrl. Supports many other wildchards, and custom fields $<field> */ char *replaceFieldInPattern(char *pattern, int fieldCount, char **fieldNames, char **fieldVals); /* Replace $fieldName in pattern with value. Used in trackDb mouseOver setting */ struct slPair *buildFieldList(struct trackDb *tdb, char *trackDbVar, struct asObject *as); /* Build up a hash of a list of fields in an AS file. */ char *checkDataVersion(char *database, struct trackDb *tdb); /* see if trackDb has a dataVersion setting and check that file for version */ void printDataVersion(char *database, struct trackDb *tdb); /* If this annotation has a dataVersion setting, print it. * check hgFixed.trackVersion, meta data and trackDb 'dataVersion'. */ void labelMakeCheckBox(struct cart *cart, struct trackDb *tdb, char *sym, char *desc, boolean defaultOn); /* add a checkbox for the user to select a component of a label (e.g. ID, name, other info). * NOTE: This does not have a track name argument, so the correct tdb must be passed in: * if setting is at composite level, then pass in composite tdb, likewise for view. */ int defaultFieldLocation(char *field); /* Sometimes we get bigBed filters with field names that are not in the AS file. * Try to guess what the user means. */ void printInfoIcon(char *mouseover); /* Print info icon (i) with explanatory text on mouseover * Uses jquery icon set, with style customized to GB in jquery-ui.css */ void printRelatedTracks(char *database, struct hash *trackHash, struct trackDb *tdb, struct cart *cart); /* Maybe print a "related track" section */ +struct trackDb *snp125FetchGeneTracks(char *database, struct cart *cart); +/* Get a list of genePred tracks. */ + +struct trackDb *tdbOrAncestorByName(struct trackDb *tdb, char *name); +/* For reasons Angie cannot fathom, if a composite or view is passed to cfgByCfgType then + * cfgByCfgType passes a leaf subtrack to its callees like bigDbSnpCfgUi. That is why we + * see so many calls to isNameAtParentLevel, which returns true if the tdb was originally + * at the composite or view level, which we can only tell by comparing with the original track name. + * labelMakeCheckBox, called by many handlers in hgTrackUi that must be always top-level + * (or have a special handler that bypasses cfgByCfgType like refSeqComposite), + * is blissfully unaware of this. It uses the same tdb for looking in cart ClosestToHome + * and for making the HTML element's cart var name, trusting that the correct tdb has been + * handed to it. + * So in order for a callee of cfgByCfgType to call labelMakeCheckBox with the correct tdb, + * we need to walk back up comparing name like isNameAtParentLevel does. + * If name doesn't match tdb or any of its ancestors then this returns NULL. */ + #endif /* HUI_H */