src/hg/inc/pgSnp.h 1.4

Index: src/hg/inc/pgSnp.h
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/inc/pgSnp.h,v
retrieving revision 1.3
retrieving revision 1.4
diff -b -B -U 1000000 -r1.3 -r1.4
--- src/hg/inc/pgSnp.h	3 Sep 2008 19:19:12 -0000	1.3
+++ src/hg/inc/pgSnp.h	8 Mar 2010 17:52:10 -0000	1.4
@@ -1,115 +1,119 @@
 /* pgSnp.h was originally generated by the autoSql program, which also 
  * generated pgSnp.c and pgSnp.sql.  This header links the database and
  * the RAM representation of objects. */
 
 #ifndef PGSNP_H
 #define PGSNP_H
 
 #include "jksql.h"
+#include "trackDb.h"
 #define PGSNP_NUM_COLS 8
 
 #ifndef BED_H
 #include "bed.h"
 #endif
 
 struct pgSnp
 /* personal genome SNP */
     {
     struct pgSnp *next;  /* Next in singly linked list. */
     char *chrom;	/* Chromosome */
     unsigned chromStart;	/* Start position in chrom */
     unsigned chromEnd;	/* End position in chrom */
     char *name;	/* alleles */
     int alleleCount;	/* number of alleles */
     char *alleleFreq;	/* comma separated list of frequency of each allele */
     char *alleleScores;	/* comma separated list of quality scores */
     unsigned short bin; /* A field to speed indexing */
     };
 
 void pgSnpStaticLoad(char **row, struct pgSnp *ret);
 /* Load a row from pgSnp table into ret.  The contents of ret will
  * be replaced at the next call to this function. */
 
 struct pgSnp *pgSnpLoad(char **row);
 /* Load a pgSnp from row fetched with select * from pgSnp
  * from database.  Dispose of this with pgSnpFree(). */
 
 struct pgSnp *pgSnpLoadAll(char *fileName);
 /* Load all pgSnp from whitespace-separated file.
  * Dispose of this with pgSnpFreeList(). */
 
 struct pgSnp *pgSnpLoadAllByChar(char *fileName, char chopper);
 /* Load all pgSnp from chopper separated file.
  * Dispose of this with pgSnpFreeList(). */
 
 #define pgSnpLoadAllByTab(a) pgSnpLoadAllByChar(a, '\t');
 /* Load all pgSnp from tab separated file.
  * Dispose of this with pgSnpFreeList(). */
 
 struct pgSnp *pgSnpLoadByQuery(struct sqlConnection *conn, char *query);
 /* Load all pgSnp from table that satisfy the query given.  
  * Where query is of the form 'select * from example where something=something'
  * or 'select example.* from example, anotherTable where example.something = 
  * anotherTable.something'.
  * Dispose of this with pgSnpFreeList(). */
 
 void pgSnpSaveToDb(struct sqlConnection *conn, struct pgSnp *el, char *tableName, int updateSize);
 /* Save pgSnp as a row to the table specified by tableName. 
  * As blob fields may be arbitrary size updateSize specifies the approx size
  * of a string that would contain the entire query. Arrays of native types are
  * converted to comma separated strings and loaded as such, User defined types are
  * inserted as NULL. Note that strings must be escaped to allow insertion into the database.
  * For example "autosql's features include" --> "autosql\'s features include" 
  * If worried about this use pgSnpSaveToDbEscaped() */
 
 void pgSnpSaveToDbEscaped(struct sqlConnection *conn, struct pgSnp *el, char *tableName, int updateSize);
 /* Save pgSnp as a row to the table specified by tableName. 
  * As blob fields may be arbitrary size updateSize specifies the approx size.
  * of a string that would contain the entire query. Automatically 
  * escapes all simple strings (not arrays of string) but may be slower than pgSnpSaveToDb().
  * For example automatically copies and converts: 
  * "autosql's features include" --> "autosql\'s features include" 
  * before inserting into database. */ 
 
 struct pgSnp *pgSnpCommaIn(char **pS, struct pgSnp *ret);
 /* Create a pgSnp out of a comma separated string. 
  * This will fill in ret if non-null, otherwise will
  * return a new pgSnp */
 
 void pgSnpFree(struct pgSnp **pEl);
 /* Free a single dynamically allocated pgSnp such as created
  * with pgSnpLoad(). */
 
 void pgSnpFreeList(struct pgSnp **pList);
 /* Free a list of dynamically allocated pgSnp's */
 
 void pgSnpOutput(struct pgSnp *el, FILE *f, char sep, char lastSep);
 /* Print out pgSnp.  Separate fields with sep. Follow last field with lastSep. */
 
 #define pgSnpTabOut(el,f) pgSnpOutput(el,f,'\t','\n');
 /* Print out pgSnp as a line in a tab-separated file. */
 
 #define pgSnpCommaOut(el,f) pgSnpOutput(el,f,',',',');
 /* Print out pgSnp as a comma separated list including final comma. */
 
 /* -------------------------------- End autoSql Generated Code -------------------------------- */
 
 struct pgCodon
 /* codons covering region */
     {
     char *seq;
     int cdStart;
     int cdEnd;
     int firstCodon;
     int regStart; /* in coding sequence positions */
     int regEnd;
     };
 
 struct pgCodon *fetchCodons (char *db, struct bed *gene, unsigned chrStart, unsigned chrEnd);
 /* get codon sequence to compute aa changes */
 
 void printSeqCodDisplay (char *db, struct pgSnp *item);
 /* print the display of sequence changes for a coding variant */
 
+void printPgDbLink(char *db, struct trackDb *tdb, struct pgSnp *item);
+/* print the links to phenotype and other databases for pgSnps */
+
 #endif /* PGSNP_H */