4898794edd81be5285ea6e544acbedeaeb31bf78 max Tue Nov 23 08:10:57 2021 -0800 Fixing pointers to README file for license in all source code files. refs #27614 diff --git src/hg/inc/hui.h src/hg/inc/hui.h index 52a92e5..db18064 100644 --- src/hg/inc/hui.h +++ src/hg/inc/hui.h @@ -1,1578 +1,1578 @@ /* 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 README in this or parent directory for licensing information. */ + * 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 */ #endif /* HUI_H */