/* hgGenome.h - Include file used by all modules in hgGenome. * hgGenome is a CGI script that produces a web page containing * a graphic with all chromosomes in genome, and a graph or two * on top of them. */ /* Copyright (C) 2010 The Regents of the University of California * See kent/LICENSE or http://genome.ucsc.edu/license/ for licensing information. */ #ifndef HGGENOME_H #define HGGENOME_H #include "grp.h" #include "hPrint.h" #include "customTrack.h" /*** Prefixes for variables in cart we don't share with other apps. ***/ #define hggPrefix "hgGenome_" #define hggDo hggPrefix "do" /*** Our various cart variables. ***/ #define hggGraphPrefix hggPrefix "graph" #define hggGraphColorPrefix hggPrefix "graphColor" #define hggGraphHeight hggPrefix "graphHeight" #define hggLabels hggPrefix "labels" #define hggThreshold hggPrefix "threshold" #define defaultThreshold 3.5 #define hggGraphsPerLine hggPrefix "graphsPerLine" #define hggChromLayout hggPrefix "chromLayout" #define hggLinesOfGraphs hggPrefix "linesOfGraphs" #define hggDataSetName hggPrefix "dataSetName" #define hggDataSetDescription hggPrefix "dataSetDescription" #define hggMarkerType hggPrefix "markerType" #define hggFormatType hggPrefix "formatType" #define hggColumnLabels hggPrefix "columnLabels" #define hggMinVal hggPrefix "minVal" #define hggMaxVal hggPrefix "maxVal" #define hggLabelVals hggPrefix "labelVals" #define hggMaxGapToFill hggPrefix "maxGapToFill" #define hggUploadFile hggPrefix "uploadFile" #define hggUploadUrl hggPrefix "uploadUrl" #define hggUploadRa hggPrefix "uploadRa" #define hggImageWidth hggPrefix "imageWidth" #define hggRegionPad hggPrefix "regionPad" #define hggYellowMissing hggPrefix "yellowMissing" #define hggRegionPadDefault 25000 /*** Command variables. ***/ #define hggConfigure hggDo "Configure" #define hggConfigureOne hggDo "ConfigureOne" #define hggBrowse hggDo "Browse" #define hggSort hggDo "Sort" #define hggCorrelate hggDo "Correlate" #define hggUpload hggDo "Upload" #define hggSubmitUpload hggDo "SubmitUpload" #define hggImport hggDo "Import" #define hggSubmitImport hggDo "SubmitImport" #define hggClick hggDo "Click" #define hggPsOutput hggDo "PsOutput" #define hggClickX hggClick ".x" #define hggClickY hggClick ".y" /* -- import-track related -- */ #define hggGroup hggPrefix "group" #define hggTrack hggPrefix "track" #define hggTable hggPrefix "table" #define hggBedConvertType hggPrefix "bedConvertType" #define hggBedConvertTypeJs "js_bedConvertType" #define hggBedCoverage "coverage" #define hggBedDepth "depth" /* Global variables - generally set during initialization and then read-only. */ extern char *curTable; /* Current selected table. */ extern struct trackDb *curTrack; /* Currently selected track. */ struct trackDb *getFullTrackList(); /* Get all tracks including custom tracks if any. */ struct customTrack *getCustomTracks(); /* Get custom track list. */ struct trackDb *findSelectedTrack(struct trackDb *trackList, struct grp *group, char *varName); /* Find selected track - from CGI variable if possible, else * via various defaults. */ #define lookupCt(name) ctFind(getCustomTracks(),name) struct customTrack *newCt(char *ctName, char *ctDesc, int visNum, char *ctUrl, int fields); /* Make a new custom track record for the query results. */ void removeNamedCustom(struct customTrack **pList, char *name); /* Remove named custom track from list if it's on there. */ struct hTableInfo *ctToHti(struct customTrack *ct); /* Create an hTableInfo from a customTrack. */ struct hTableInfo *getHti(char *db, char *table); /* Return primary table info. */ struct hTableInfo *maybeGetHti(char *db, char *table); /* Return primary table info, but don't abort if table not there. */ #define hgtaCtName "hgta_ctName" #define hgtaCtDesc "hgta_ctDesc" #define hgtaCtVis "hgta_ctVis" #define hgtaCtUrl "hgta_ctUrl" #define hgtaCtWigOutType "hgta_ctWigOutType" /* Prefix for temp name files created for custom tracks */ #define hgtaCtTempNamePrefix "hgtct" /* Prefix for variables containing filters themselves. */ #define hgtaFilterVarPrefix hgtaFilterPrefix "v." /* Prefix for variables managed by filter page. */ #define hgtaFilterPrefix "hgta_fil." #define hgtaPrintCustomTrackHeaders "hgta_printCustomTrackHeaders" #define outWigData "wigData" #define hgtaIntersectTable "hgta_intersectTable" #define hgtaIntersectTrack "hgta_intersectTrack" #define hgtaInvertTable2 "hgta_invertTable2" #define hgtaIntersectOp "hgta_intersectOp" /*** External vars declared in hgGenome.c ***/ extern struct cart *cart; extern struct hash *oldCart; extern char *database; extern char *genome; extern struct genoGraph *ggUserList; /* List of user graphs */ extern struct genoGraph *ggDbList; /* List of graphs in database. */ extern struct trackLayout tl; /* Dimensions of things, fonts, etc. */ extern struct slRef *ggList; /* List of active genome graphs */ extern struct hash *ggHash; /* Hash of active genome graphs */ extern boolean withLabels; /* Draw labels? */ /*** Name prefixes to separate user from db graphs. */ #define hggUserTag "user_" #define hggDbTag "" /*** Info on a single graph. ***/ struct genoGraph /* A genomic graph */ { struct genoGraph *next; /* Next in list. */ char *name; /* Graph name. */ char *shortLabel; /* Short label. */ char *longLabel; /* Long label. */ char *binFileName; /* Binary file associated with graph. */ struct chromGraphSettings *settings; /* Display settings */ boolean didRefine; /* Set to true after refined */ struct chromGraphBin *cgb; /* Binary data handle. */ boolean isSubGraph; /* Set to TRUE if the graph is part of a composite. */ boolean isComposite; /* Set to TRUE if this just has composite settings. */ }; /*** Routines from hgGenome.h ***/ int regionPad(); /* Number of bases to pad regions by. */ char *getThresholdName(); /* Return threshold name. */ double getThreshold(); /* Return user-set threshold */ boolean getYellowMissing(); /* Return draw background in yellow for missing data flag. */ struct bed3 *regionsOverThreshold(); /* Get list of regions over threshold */ int graphHeight(); /* Return height of graph. */ #define betweenRowPad 3 #define minGraphsPerLine 1 #define maxGraphsPerLine 4 #define defaultGraphsPerLine 2 int graphsPerLine(); /* Return number of graphs to draw per line. */ #define minLinesOfGraphs 1 #define maxLinesOfGraphs 10 #define defaultLinesOfGraphs 1 int linesOfGraphs(); /* Return number of lines of graphs */ #define layTwoPerLine "two per line" #define layOnePerLine "one per line" #define layAllOneLine "all in one line" char *chromLayout(); /* Return one of above strings specifying layout. */ void getGenoGraphs(struct sqlConnection *conn); /* Set up ggList and ggHash with all available genome graphs */ char *graphVarName(int row, int col); /* Get graph data source variable for given row and column. Returns * static buffer. */ char *graphColorVarName(int row, int col); /* Get graph color variable for givein row and column. Returns * static buffer. */ char *graphSourceAt(int row, int col); /* Return graph source at given row/column, NULL if none. */ char *graphColorAt(int row, int col); /* Return graph color at given row/column, NULL if nonw. */ struct genoLay *ggLayout(struct sqlConnection *conn, int graphRows, int graphCols); /* Figure out how to lay out image. */ struct genoGraph *ggFirstVisible(); /* Return first visible graph, or NULL if none. */ struct slRef *ggAllVisible(); /* Return list of references to all visible graphs */ void hggDoUsualHttp(); /* Wrap html page dispatcher with code that writes out * HTTP header and write cart back to database. */ /*** Functions imported from other modules. ***/ void handlePostscript(struct sqlConnection *conn); /* Do graphic as eps/pdf. */ void mainPage(struct sqlConnection *conn); /* Do main page of application: hotlinks bar, controls, graphic. */ void printMainHelp(); /* Put up main page help info. */ void uploadPage(); /* Put up initial upload page. */ void importPage(); /* Put up initial import page. */ void configurePage(); /* Put up configuration page. */ void configureOnePage(); /* Put up configuration for one graph. */ void correlatePage(struct sqlConnection *conn); /* Put up correlation page. */ void submitUpload(struct sqlConnection *conn); /* Called when they've submitted from uploads page */ void submitUpload2(struct sqlConnection *conn); /* Called when they've submitted from uploads page */ void submitImport(); /* Called when they've submitted from import page */ void browseRegions(struct sqlConnection *conn); /* Put up a frame with a list of links on the left and the * first link selected on the right. */ void sortGenes(struct sqlConnection *conn); /* Put up sort gene page. */ void clickOnImage(struct sqlConnection *conn); /* Handle click on image - calculate position in forward to genome browser. */ /* ----------- Wiggle business in wiggle.c -------------------- */ #define MAX_REGION_DISPLAY 1000 boolean isWiggle(char *db, char *table); /* Return TRUE if db.table is a wiggle. */ boolean isBedGraph(char *table); /* Return TRUE if table is specified as a bedGraph in the current database's * trackDb. */ char *getBedGraphType(char *table); /* Return bedgraph track type if table is a bedGraph in the current database's * trackDb. */ int getBedGraphColumnNum(char *table); /* get the bedGraph dataValue column num from the track type */ void wiggleMinMax(struct trackDb *tdb, double *min, double *max); /* obtain wiggle data limits from trackDb or cart or settings */ struct wiggleDataStream *wigChromRawStats(char *chrom); /* Fetch stats for wig data in chrom. * Returns a wiggleDataStream, free it with wiggleDataStreamFree() */ /* ------------ */ struct sqlResult *chromQuery(struct sqlConnection *conn, char *table, char *fields, char *chrom, boolean isPositional, char *extraWhere); /* Construct and execute query for table on chrom. Returns NULL if * table doesn't exist (e.g. missing split table for chrom). */ struct bed *getBeds(char *chrom, struct lm *lm, int *retFieldCount); /* Get list of beds on single chrom. */ struct bed *customTrackGetBedsForChrom(char *name, char *chrom, struct lm *lm, int *retFieldCount); /* Get list of beds from custom track of given name that are * in given chrom. You can bedFree this when done. */ boolean isMafTable(char *database, struct trackDb *track, char *table); /* Return TRUE if table is maf. */ boolean isChromGraph(struct trackDb *track); /* Return TRUE if it's a chromGraph track */ #endif /* HGGENOME_H */