4cab7f311cadce7428c1d7e1c4dfdcb0d3a43033 angie Wed Jul 27 10:32:19 2011 -0700 Feature #3710 (vcfTabix UI options): Added controls for selection of centervariant for haplotype clustering/sorting. Also, some hgc improvements: made the Genotype Details table into a collapsible section; better display of QUAL and FILTER column values, which also involved improving the representation of those columns in src/inc/vcf.h. diff --git src/hg/inc/hui.h src/hg/inc/hui.h index bfb6f81..4c8ce4c 100644 --- src/hg/inc/hui.h +++ src/hg/inc/hui.h @@ -1,1228 +1,1234 @@ /* hui - human genome browser user interface controls that are shared * between more than one CGI. */ #ifndef HUI_H #define HUI_H #include "cart.h" #include "trackDb.h" #include "customTrack.h" #include "wiggle.h" struct lineFile; void setUdcCacheDir(); /* set the path to the udc cache dir */ char *hDownloadsServer(); /* get the downloads server from hg.conf or the default */ char *hUserCookie(); /* Return our cookie name. */ char *wrapWhiteFont(char *s); /* Write white font around s */ #define HELP_DIR "/goldenPath/help" /* 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 *encodeRestrictionDateDisplay(char *db,struct trackDb *trackDb); /* Create a string for ENCODE restriction date of this track if return is not null, then free it after use */ 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 *hBackgroundImage(); /* get the path to the configured background image to use, or the default */ /* 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" /* Definition for oligo match track. */ #define oligoMatchVar "hgt.oligoMatch" #define oligoMatchDefault "aaaaa" #define OLIGO_MATCH_TRACK_NAME "oligoMatch" #define OLIGO_MATCH_TRACK_LABEL "Short Match" #define OLIGO_MATCH_TRACK_LONGLABEL "Perfect Match to Short Sequence" /* 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_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" /* 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 790 /* 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 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, char *extra); /* 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, enum trackVisibility vis, boolean canPack, char *class,char *javascript); /* Make track visibility drop down for varName with style class and javascript */ #define hTvDropDownClass(varName,vis,canPack,class) \ hTvDropDownClassWithJavascript((varName),(vis),(canPack),(class),"") #define hTvDropDownWithJavascript(varName,vis,canPack,javascript) \ hTvDropDownClassWithJavascript((varName),(vis),(canPack),"normalText",(javascript)) #define hTvDropDown(varName,vis,canPack) \ hTvDropDownClassWithJavascript((varName),(vis),(canPack),"normalText","") #define SUPERTRACK_DEFAULT_VIS "hide" void hideShowDropDownWithClassAndExtra(char *varName, boolean show, char *class, char *extra); #define hideShowDropDown(varName,show,class) hideShowDropDownWithClassAndExtra(varName,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, }; 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_AGGREGATE_NONE "none" #define WIG_AGGREGATE_TRANSPARENT "transparentOverlay" #define WIG_AGGREGATE_SOLID "solidOverlay" /*** 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" /*** 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" 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. */ /*** Some Stuff for the base position (ruler) controls ***/ #define ZOOM_1PT5X "1.5x" #define ZOOM_3X "3x" #define ZOOM_10X "10x" #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 *key; /* 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 *filterTypeVar; /* cgi variable that holds type of filter. */ char *logicTypeVar; /* cgi variable 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, struct hash *trackHash); /* 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 a controlledVocabulary setting and the vocabType is found, then label will be wrapped with the link to display it. Return string is cloned. */ char *controlledVocabLink(char *file,char *term,char *value,char *title, char *label,char *suffix); // returns allocated string of HTML link to controlled vocabulary term char *metadataAsHtmlTable(char *db,struct trackDb *tdb,boolean showLongLabel,boolean showShortLabel, struct hash *trackHash); /* 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, struct hash *trackHash); /* If metadata from metaTbl exists, create a link that will allow toggling it's display */ boolean superTrackDropDownWithExtra(struct cart *cart, struct trackDb *tdb, int visibleChild,char *extra); /* Displays hide/show dropdown for supertrack. * Set visibleChild to indicate whether 'show' should be grayed * out to indicate that no supertrack members are visible: * 0 to gray out (no visible children) * 1 don't gray out (there are visible children) * -1 don't know (this function should determine) * If -1,i the subtracks field must be populated with the child trackDbs. * Returns false if not a supertrack */ #define superTrackDropDown(cart,tdb,visibleChild) superTrackDropDownWithExtra(cart,tdb,visibleChild,NULL) boolean dimensionsExist(struct trackDb *parentTdb); /* Does this parent track contain dimensions? */ int subgroupCount(struct trackDb *parentTdb); /* How many subGroup setting does this parent have? */ char * subgroupSettingByTagOrName(struct trackDb *parentTdb, char *groupNameOrTag); /* look for a subGroup by name (ie subGroup1) or tag (ie view) and return an unallocated char* */ boolean subgroupingExists(struct trackDb *parentTdb, char *groupNameOrTag); /* Does this parent track contain a particular subgrouping? */ boolean subgroupFind(struct trackDb *childTrack, char *name,char **value); /* looks for a single tag in a childTrack's subGroups setting */ void subgroupFree(char **value); /* frees subgroup memory */ int multViewCount(struct trackDb *parentTdb); /* returns the number of multiView views declared */ int tvConvertToNumericOrder(enum trackVisibility v); /* Convert the enum to numeric order of display power full=4,hide=0 */ int tvCompare(enum trackVisibility a, enum trackVisibility b); /* enum trackVis isn't in numeric order by visibility, so compare * symbolically: */ enum trackVisibility tvMin(enum trackVisibility a, enum trackVisibility b); /* Return the less visible of a and b. */ enum trackVisibility tdbLocalVisibility(struct cart *cart, struct trackDb *tdb,boolean *subtrackOverride); // returns visibility NOT limited by ancestry. Fills optional boolean if subtrack specific vis is found // If not NULL cart will be examined without ClosestToHome. Folders/supertracks resolve to hide/full enum trackVisibility tdbVisLimitedByAncestors(struct cart *cart, struct trackDb *tdb, boolean checkBoxToo, boolean foldersToo); // returns visibility limited by ancestry. This includes subtrack vis override and parents limit maximum. // 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 wigCfgUi(struct cart *cart, struct trackDb *tdb,char *name,char *title,boolean boxed); /* UI for the wiggle track */ #define NO_SCORE_FILTER "noScoreFilter" #define SCORE_FILTER "scoreFilter" #define SIGNAL_FILTER "signalFilter" #define PVALUE_FILTER "pValueFilter" #define QVALUE_FILTER "qValueFilter" #define _NO "No" #define _LIMITS "Limits" #define _MIN "Min" #define _MAX "Max" #define _BY_RANGE "ByRange" #define SCORE_MIN "scoreMin" #define GRAY_LEVEL_SCORE_MIN SCORE_MIN #define MIN_GRAY_LEVEL "minGrayLevel" void filterButtons(char *filterTypeVar, char *filterTypeVal, boolean none); /* Put up some filter buttons. */ void radioButton(char *var, char *val, char *ourVal); /* Print one radio button */ void oneMrnaFilterUi(struct controlGrid *cg, char *text, char *var, struct cart *cart); /* Print out user interface for one type of mrna filter. */ void bedUi(struct trackDb *tdb, struct cart *cart, char *title, boolean boxed); /* Put up UI for an bed track with filters. */ 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 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 */ #define ALL_SCORE_FILTERS_LOGIC #ifdef ALL_SCORE_FILTERS_LOGIC 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 */ #endif///def ALL_SCORE_FILTERS_LOGIC void encodePeakCfgUi(struct cart *cart, struct trackDb *tdb, char *name, char *title, boolean boxed); /* Put up UI for filtering wgEnocde peaks based on score, Pval and Qval */ void genePredCfgUi(struct cart *cart, struct trackDb *tdb, char *name, char *title, boolean boxed); /* Put up genePred-specific controls */ void wigMafCfgUi(struct cart *cart, struct trackDb *tdb,char *name, char *title, boolean boxed, char *db); /* UI for maf/wiggle track */ void bamCfgUi(struct cart *cart, struct trackDb *tdb, char *name, char *title, boolean boxed); /* BAM: short-read-oriented alignment file format. */ boolean tdbSortPrioritiesFromCart(struct cart *cart, struct trackDb **tdbList); /* Updates the tdb->priority from cart then sorts the list anew. Returns TRUE if priorities obtained from cart */ 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 isNameAtCompositeLevel(struct trackDb *tdb,char *name); /* cfgUi controls are passed a prefix name that may be at the composite or at the subtrack level returns TRUE for composite level name */ 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" typedef struct _filterBy { // A single filterBy set (from trackDb.ra filterBy column:Title=value,value [column:Title=value|label,value|label,value|label]) struct _filterBy *next; // SL list char*column; // field that will be filtered on char*title; // Title that User sees char*htmlName; // Name used in HTML/CGI boolean useIndex; // The returned values should be indexes boolean valueAndLabel; // If values list is value|label, then label is shown to the user boolean styleFollows; // style settings can follow like value|label[background-color:#660000] // legacy like value|label{#AA0000} is a just the style='color... that follows 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 */ 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 */ void filterBySetCfgUi(struct trackDb *tdb, filterBy_t *filterBySet, boolean onOneLine); /* Does the UI for a list of filterBy structure */ char *filterByClause(filterBy_t *filterBy); /* returns the SQL where clause for a single filterBy struct */ 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, struct hash *trackHash); // 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 hash *trackHash); /* Show downloads, schema and metadata links where appropriate */ boolean chainDbNormScoreAvailable(struct trackDb *tdb); /* check if normScore column is specified in trackDb as available */ void hPrintAbbreviationTable(struct sqlConnection *conn, char *sourceTable, char *label); /* Print out table of abbreviations. */ // Four State checkboxes can be checked/unchecked by enable/disabled // NOTE: fourState is not a bitmap because it is manipulated in javascript and int seemed easier at the time #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 cfgByCfgType(eCfgType cType,char *db, struct cart *cart, struct trackDb *tdb,char *prefix, char *title, boolean boxed); // Methods for putting up type specific cfgs used by composites/subtracks in hui.c and exported for common use +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 */ #endif /* HUI_H */