/* oreganno.h was originally generated by the autoSql program, which also * generated oreganno.c and oreganno.sql. This header links the database and * the RAM representation of objects. */ /* Copyright (C) 2013 The Regents of the University of California * See kent/LICENSE or http://genome.ucsc.edu/license/ for licensing information. */ #ifndef OREGANNO_H #define OREGANNO_H #ifndef JKSQL_H #include "jksql.h" #endif #define OREGANNO_NUM_COLS 7 struct oreganno /* track for regulatory regions from ORegAnno */ { struct oreganno *next; /* Next in singly linked list. */ char *chrom; /* Chromosome */ unsigned chromStart; /* Start position in chrom */ unsigned chromEnd; /* End position in chrom */ char *id; /* unique ID to identify this regulatory region */ char strand[2]; /* + or - */ char *name; /* name of regulatory region */ unsigned short bin; /* A field to speed indexing */ }; void oregannoStaticLoad(char **row, struct oreganno *ret); /* Load a row from oreganno table into ret. The contents of ret will * be replaced at the next call to this function. */ struct oreganno *oregannoLoad(char **row); /* Load a oreganno from row fetched with select * from oreganno * from database. Dispose of this with oregannoFree(). */ struct oreganno *oregannoLoadAll(char *fileName); /* Load all oreganno from whitespace-separated file. * Dispose of this with oregannoFreeList(). */ struct oreganno *oregannoLoadAllByChar(char *fileName, char chopper); /* Load all oreganno from chopper separated file. * Dispose of this with oregannoFreeList(). */ #define oregannoLoadAllByTab(a) oregannoLoadAllByChar(a, '\t'); /* Load all oreganno from tab separated file. * Dispose of this with oregannoFreeList(). */ struct oreganno *oregannoLoadByQuery(struct sqlConnection *conn, char *query); /* Load all oreganno 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 oregannoFreeList(). */ void oregannoSaveToDb(struct sqlConnection *conn, struct oreganno *el, char *tableName, int updateSize); /* Save oreganno 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. Strings are automatically escaped to allow insertion into the database. */ struct oreganno *oregannoCommaIn(char **pS, struct oreganno *ret); /* Create a oreganno out of a comma separated string. * This will fill in ret if non-null, otherwise will * return a new oreganno */ void oregannoFree(struct oreganno **pEl); /* Free a single dynamically allocated oreganno such as created * with oregannoLoad(). */ void oregannoFreeList(struct oreganno **pList); /* Free a list of dynamically allocated oreganno's */ void oregannoOutput(struct oreganno *el, FILE *f, char sep, char lastSep); /* Print out oreganno. Separate fields with sep. Follow last field with lastSep. */ #define oregannoTabOut(el,f) oregannoOutput(el,f,'\t','\n'); /* Print out oreganno as a line in a tab-separated file. */ #define oregannoCommaOut(el,f) oregannoOutput(el,f,',',','); /* Print out oreganno as a comma separated list including final comma. */ #define OREGANNOATTR_NUM_COLS 3 struct oregannoAttr /* attributes associated with an ORegAnno regulatory region */ { struct oregannoAttr *next; /* Next in singly linked list. */ char *id; /* key into the oreganno table */ char *attribute; /* name of attribute being listed */ char *attrVal; /* value of this oreganno attribute */ }; void oregannoAttrStaticLoad(char **row, struct oregannoAttr *ret); /* Load a row from oregannoAttr table into ret. The contents of ret will * be replaced at the next call to this function. */ struct oregannoAttr *oregannoAttrLoad(char **row); /* Load a oregannoAttr from row fetched with select * from oregannoAttr * from database. Dispose of this with oregannoAttrFree(). */ struct oregannoAttr *oregannoAttrLoadAll(char *fileName); /* Load all oregannoAttr from whitespace-separated file. * Dispose of this with oregannoAttrFreeList(). */ struct oregannoAttr *oregannoAttrLoadAllByChar(char *fileName, char chopper); /* Load all oregannoAttr from chopper separated file. * Dispose of this with oregannoAttrFreeList(). */ #define oregannoAttrLoadAllByTab(a) oregannoAttrLoadAllByChar(a, '\t'); /* Load all oregannoAttr from tab separated file. * Dispose of this with oregannoAttrFreeList(). */ struct oregannoAttr *oregannoAttrLoadByQuery(struct sqlConnection *conn, char *query); /* Load all oregannoAttr 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 oregannoAttrFreeList(). */ void oregannoAttrSaveToDb(struct sqlConnection *conn, struct oregannoAttr *el, char *tableName, int updateSize); /* Save oregannoAttr 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. Strings are automatically escaped to allow insertion into the database. */ struct oregannoAttr *oregannoAttrCommaIn(char **pS, struct oregannoAttr *ret); /* Create a oregannoAttr out of a comma separated string. * This will fill in ret if non-null, otherwise will * return a new oregannoAttr */ void oregannoAttrFree(struct oregannoAttr **pEl); /* Free a single dynamically allocated oregannoAttr such as created * with oregannoAttrLoad(). */ void oregannoAttrFreeList(struct oregannoAttr **pList); /* Free a list of dynamically allocated oregannoAttr's */ void oregannoAttrOutput(struct oregannoAttr *el, FILE *f, char sep, char lastSep); /* Print out oregannoAttr. Separate fields with sep. Follow last field with lastSep. */ #define oregannoAttrTabOut(el,f) oregannoAttrOutput(el,f,'\t','\n'); /* Print out oregannoAttr as a line in a tab-separated file. */ #define oregannoAttrCommaOut(el,f) oregannoAttrOutput(el,f,',',','); /* Print out oregannoAttr as a comma separated list including final comma. */ #define OREGANNOLINK_NUM_COLS 4 struct oregannoLink /* links for ORegAnno regulatory region */ { struct oregannoLink *next; /* Next in singly linked list. */ char *id; /* key into the oreganno table */ char *attribute; /* name of attribute being listed */ char *raKey; /* key into RA file, tells how to link */ char *attrAcc; /* accession used by link */ }; void oregannoLinkStaticLoad(char **row, struct oregannoLink *ret); /* Load a row from oregannoLink table into ret. The contents of ret will * be replaced at the next call to this function. */ struct oregannoLink *oregannoLinkLoad(char **row); /* Load a oregannoLink from row fetched with select * from oregannoLink * from database. Dispose of this with oregannoLinkFree(). */ struct oregannoLink *oregannoLinkLoadAll(char *fileName); /* Load all oregannoLink from whitespace-separated file. * Dispose of this with oregannoLinkFreeList(). */ struct oregannoLink *oregannoLinkLoadAllByChar(char *fileName, char chopper); /* Load all oregannoLink from chopper separated file. * Dispose of this with oregannoLinkFreeList(). */ #define oregannoLinkLoadAllByTab(a) oregannoLinkLoadAllByChar(a, '\t'); /* Load all oregannoLink from tab separated file. * Dispose of this with oregannoLinkFreeList(). */ struct oregannoLink *oregannoLinkLoadByQuery(struct sqlConnection *conn, char *query); /* Load all oregannoLink 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 oregannoLinkFreeList(). */ void oregannoLinkSaveToDb(struct sqlConnection *conn, struct oregannoLink *el, char *tableName, int updateSize); /* Save oregannoLink 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. Strings are automatically escaped to allow insertion into the database. */ struct oregannoLink *oregannoLinkCommaIn(char **pS, struct oregannoLink *ret); /* Create a oregannoLink out of a comma separated string. * This will fill in ret if non-null, otherwise will * return a new oregannoLink */ void oregannoLinkFree(struct oregannoLink **pEl); /* Free a single dynamically allocated oregannoLink such as created * with oregannoLinkLoad(). */ void oregannoLinkFreeList(struct oregannoLink **pList); /* Free a list of dynamically allocated oregannoLink's */ void oregannoLinkOutput(struct oregannoLink *el, FILE *f, char sep, char lastSep); /* Print out oregannoLink. Separate fields with sep. Follow last field with lastSep. */ #define oregannoLinkTabOut(el,f) oregannoLinkOutput(el,f,'\t','\n'); /* Print out oregannoLink as a line in a tab-separated file. */ #define oregannoLinkCommaOut(el,f) oregannoLinkOutput(el,f,',',','); /* Print out oregannoLink as a comma separated list including final comma. */ /* -------------------------------- End autoSql Generated Code -------------------------------- */ struct hash *oregannoLoadAttrHash(struct sqlConnection *conn); /* Construct a hash table of the entries in the oregannoAttr table, indexed by ID. * Free with hashFreeWithVals(&attrHash, oregannoAttrFree). */ #endif /* OREGANNO_H */