5ede442a609630efb2eeda3682214948faf6d5c9
tdreszer
  Mon Jun 25 16:18:54 2012 -0700
Next batch of many checkins as dictated by Jim.  Formatting space after if and limiting lines to 100 chars.  Changes limited to lines last touched by tdreszer (git blame) so as not to ruin history.  None of these changes should affect executables in any way.  Only affect is to my sanity and Jim's.
diff --git src/hg/inc/hgMaf.h src/hg/inc/hgMaf.h
index 64c0171..3b5f196 100644
--- src/hg/inc/hgMaf.h
+++ src/hg/inc/hgMaf.h
@@ -1,98 +1,99 @@
 /* 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(char *prefix, struct consWiggle *wig,char **suffix);
 // Return name of cart variable (and optionally the suffix) 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 *prefix, char *db, struct wigMafSpecies **list, int *groupCt);
+char **wigMafGetSpecies(struct cart *cart, struct trackDb *tdb, char *prefix, 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