src/hg/inc/hgMaf.h 1.23

Index: src/hg/inc/hgMaf.h
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/inc/hgMaf.h,v
retrieving revision 1.22
retrieving revision 1.23
diff -b -B -U 1000000 -r1.22 -r1.23
--- src/hg/inc/hgMaf.h	10 Apr 2009 19:52:43 -0000	1.22
+++ src/hg/inc/hgMaf.h	5 Jun 2009 21:23:08 -0000	1.23
@@ -1,95 +1,98 @@
 /* hgMaf.h - Stuff to load up mafs from the browser database.
  *           Also, items for maf track display */
 #ifndef HGMAF_H
 #define HGMAF_H
 
 
 #include "trackDb.h"
 #include "cart.h"
 
 /* Track settings and variables */
 #define SPECIES_TREE_VAR        "speciesTree"
 #define SPECIES_ORDER_VAR       "speciesOrder"
 #define SPECIES_GROUP_VAR       "speciesGroups"
 #define SPECIES_TARGET_VAR      "speciesTarget"
 #define SPECIES_DEFAULT_OFF_VAR "speciesDefaultOff"
 #define SPECIES_GROUP_PREFIX    "sGroup_"
 #define SPECIES_HTML_TARGET	"sT"
 #define SPECIES_CODON_DEFAULT	"speciesCodonDefault"
 #define SPECIES_USE_FILE        "speciesUseFile"
 #define PAIRWISE_VAR            "pairwise"
 #define PAIRWISE_HEIGHT         "pairwiseHeight"
 #define SUMMARY_VAR             "summary"
 #define BASE_COLORS_VAR         "baseColors"
 #define BASE_COLORS_OFFSET_VAR  "baseColorsOffset"
 #define CONS_WIGGLE             "wiggle"
 #define ITEM_FIRST_CHAR_CASE	"itemFirstCharCase"
 #define DEFAULT_CONS_LABEL      "Conservation"
 
 #define gsidSubjList "gsidTable.gsidSubjList"
 #define gsidSeqList "gsidTable.gsidSeqList"
 
+#define gisaidSubjList "gisaidTable.gisaidSubjList"
+#define gisaidSeqList "gisaidTable.gisaidSeqList"
+
 struct mafAli *mafLoadInRegion2(struct sqlConnection *conn,
     struct sqlConnection *conn2, char *table, char *chrom,
     int start, int end, char *file);
 /* Return list of alignments in region. */
 
 struct mafAli *mafLoadInRegion(struct sqlConnection *conn, char *table,
 	char *chrom, int start, int end);
 /* Return list of alignments in region. */
 
 struct mafAli *axtLoadAsMafInRegion(struct sqlConnection *conn, char *table,
 	char *chrom, int start, int end,
 	char *tPrefix, char *qPrefix, int tSize,  struct hash *qSizeHash);
 /* Return list of alignments in region from axt external file as a maf. */
 
 struct mafAli *hgMafFrag(
 	char *database,     /* Database, must already have hSetDb to this */
 	char *track, 	    /* Name of MAF track */
 	char *chrom, 	    /* Chromosome (in database genome) */
 	int start, int end, /* start/end in chromosome */
 	char strand, 	    /* Chromosome strand. */
 	char *outName, 	    /* Optional name to use in first component */
 	struct slName *orderList /* Optional order of organisms. */
 	);
 /* mafFrag- Extract maf sequences for a region from database.
  * This creates a somewhat unusual MAF that extends from start
  * to end whether or not there are actually alignments.  Where
  * there are no alignments (or alignments missing a species)
  * a . character fills in.   The score is always zero, and
  * the sources just indicate the species.  You can mafFree this
  * as normal. */
 
 int mafCmp(const void *va, const void *vb);
 /* Compare to sort based on start of first component. */
 
 struct consWiggle {
     struct consWiggle *next;    /* Next in list */
     char *table;                /* phastCons table */
     char *leftLabel;            /* Left label for hgTracks */
     char *uiLabel;              /* Label to print on trackUi */
 };
 
 struct consWiggle *wigMafWiggles(char *db, struct trackDb *tdb);
 /* get conservation wiggle table names and labels from trackDb setting,
    ignoring those where table doesn't exist */
 
 char *wigMafWiggleVar(struct trackDb *tdb, struct consWiggle *wig);
 /* Return name of cart variable for this cons wiggle */
 
 struct wigMafSpecies
     {
     struct wigMafSpecies *next;
     char *name;
     int group;
     boolean on;
     };
 
 struct wigMafSpecies * wigMafSpeciesTable(struct cart *cart,
     struct trackDb *tdb, char *name, char *db) ;
 char **wigMafGetSpecies(struct cart *cart, struct trackDb *tdb, char *db, struct wigMafSpecies **list, int *groupCt);
 
 struct consWiggle *consWiggleFind(char *db,struct trackDb *parent,char *table);
 /* Return conservation wig if it is found in the parent. */
 
 #endif//ndef HGMAF_H