src/hg/hgGenome/hgGenome.h 1.37

Index: src/hg/hgGenome/hgGenome.h
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/hgGenome/hgGenome.h,v
retrieving revision 1.36
retrieving revision 1.37
diff -b -B -U 1000000 -r1.36 -r1.37
--- src/hg/hgGenome/hgGenome.h	16 Nov 2007 14:52:55 -0000	1.36
+++ src/hg/hgGenome/hgGenome.h	10 Apr 2009 20:02:13 -0000	1.37
@@ -1,332 +1,332 @@
 /* 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. */
 
 #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. */
 
-struct customTrack *lookupCt(char *name);
-/* Find named custom track. */
+#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(struct sqlConnection *conn);
 /* 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. */
 
 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 */
 
 char *getBedGraphField(char *table, char *type);
 /* get the bedGraph dataValue field name from the track type */
 
 
 #endif /* HGGENOME_H */