4dcb41c179c6fae38abffb52dd2b764b74301c7c
angie
  Mon Jul 30 16:39:17 2012 -0700
Feature #8551 (Sequence Ontology terms for predicted functional effects on SNP details pages):at Ensembl's request, instead of displaying dbSNP's predicted function terms, instead show
terms from the Sequence Ontology (SO).  Where possible, terms from Ensembl's list at
http://staging.ensembl.org/info/docs/variation/predicted_data.html are used.

diff --git src/hg/inc/snp125Ui.h src/hg/inc/snp125Ui.h
index 73d7912..3733cc0 100644
--- src/hg/inc/snp125Ui.h
+++ src/hg/inc/snp125Ui.h
@@ -1,136 +1,141 @@
 /* snp125Ui.c - enums & char arrays for snp UI features and shared util code */
 #include "common.h"
 
 #ifndef SNP125UI_H
 #define SNP125UI_H
 
 #include "cart.h"
 #include "trackDb.h"
 
 char *snp125OrthoTable(struct trackDb *tdb, int *retSpeciesCount);
 /* Look for a setting that specifies a table with orthologous alleles.
  * If retSpeciesCount is not null, set it to the number of other species
  * whose alleles are in the table. Do not free the returned string. */
 
 struct slName *snp125FilterFromCart(struct cart *cart, char *track, char *attribute,
 				    boolean *retFoundInCart);
 /* Look up snp125 filter settings in the cart, keeping backwards compatibility with old
  * cart variable names. */
 
 char *snp125OldColorVarToNew(char *oldVar, char *attribute);
 /* Abbreviate an old cart var name -- new name is based on track plus this. Don't free result. */
 
 #define SNP125_DEFAULT_MAX_WEIGHT 1
 #define SNP125_DEFAULT_MIN_AVHET 0.0
 #define SNP132_DEFAULT_MIN_SUBMITTERS 0
 #define SNP132_DEFAULT_MIN_MINOR_AL_FREQ 0.0
 #define SNP132_DEFAULT_MAX_MINOR_AL_FREQ 0.5
 #define SNP132_DEFAULT_MIN_AL_FREQ_2N 0
 
 extern boolean snp125ExtendedNames;
 
 enum snp125Color {
     snp125ColorRed,
     snp125ColorGreen,
     snp125ColorBlue,
     snp125ColorGray,
     snp125ColorBlack,
 };
 
 extern char *snp125ColorLabel[];
 extern int snp125ColorArraySize;
 
 /****** Color source related controls *******/
 /* Molecule Type, Class, Validation, Function */
 
 enum snp125ColorSource {
     snp125ColorSourceLocType,
     snp125ColorSourceClass,
     snp125ColorSourceValid,
     snp125ColorSourceFunc,
     snp125ColorSourceMolType,
     snp125ColorSourceExceptions,
     snp125ColorSourceBitfields,
     snp125ColorSourceAlleleFreq,
 };
 
 #define SNP125_DEFAULT_COLOR_SOURCE snp125ColorSourceFunc
 
 enum snp125ColorSource snp125ColorSourceFromCart(struct cart *cart, struct trackDb *tdb);
 /* Look up color source in cart, keeping backwards compatibility with old cart var names. */
 
 char *snp125ColorSourceToLabel(struct trackDb *tdb, enum snp125ColorSource cs);
 /* Due to availability of different color sources in several different versions,
  * this is not just an array lookup, hence the encapsulation. Don't modify return value. */
 
 extern char *snp125ColorSourceLabels[];
 extern char *snp125ColorSourceOldVar;
 extern int snp125ColorSourceArraySize;
 
 extern char *snp128ColorSourceLabels[];
 extern int snp128ColorSourceArraySize;
 
 extern char *snp132ColorSourceLabels[];
 extern int snp132ColorSourceArraySize;
 
 /****** MolType related controls *******/
 /* unknown, genomic, cDNA */
 
 extern char *snp125MolTypeLabels[];
 extern char *snp125MolTypeOldColorVars[];
 extern char *snp125MolTypeDataName[];
 extern char *snp125MolTypeDefault[];
 extern int snp125MolTypeArraySize;
 
 /****** Class related controls *******/
 
 extern char *snp125ClassLabels[];
 extern char *snp125ClassOldColorVars[];
 extern char *snp125ClassDataName[];
 extern char *snp125ClassDefault[];
 extern int snp125ClassArraySize;
 
 /****** Valid related controls *******/
 
 extern char *snp125ValidLabels[];
 extern char *snp125ValidOldColorVars[];
 extern char *snp125ValidDataName[];
 extern char *snp125ValidDefault[];
 extern int snp125ValidArraySize;
 
 /****** Func related controls *******/
 
+char *snpMisoLinkFromFunc(char *funcTerm);
+/* If we can map funcTerm to a Sequence Ontology term, return a link to the MISO SO browser;
+ * otherwise just return the same term. */
+
 extern char *snp125FuncLabels[];
 extern char *snp125FuncOldColorVars[];
 extern char *snp125FuncDataName[];
 extern char *snp125FuncDefault[];
 extern char **snp125FuncDataSynonyms[];
 extern int snp125FuncArraySize;
 
+
 /****** LocType related controls *******/
 /* unknown, range, exact, between,
    rangeInsertion, rangeSubstitution, rangeDeletion */
 
 extern char *snp125LocTypeLabels[];
 extern char *snp125LocTypeOldColorVars[];
 extern char *snp125LocTypeDataName[];
 extern char *snp125LocTypeDefault[];
 extern int snp125LocTypeArraySize;
 
 /****** Exception related controls *******/
 
 extern char *snp132ExceptionLabels[];
 extern char *snp132ExceptionVarName[];
 extern char *snp132ExceptionDefault[];
 extern int snp132ExceptionArraySize;
 
 /****** Miscellaneous attributes (bitfields) related controls *******/
 
 extern char *snp132BitfieldLabels[];
 extern char *snp132BitfieldVarName[];
 extern char *snp132BitfieldDataName[];
 extern char *snp132BitfieldDefault[];
 extern int snp132BitfieldArraySize;
 
 #endif /* SNP125UI_H */