/* omicia.h was originally generated by the autoSql program, which also * generated omicia.c and omicia.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 OMICIA_H #define OMICIA_H #ifndef JKSQL_H #include "jksql.h" #endif #define OMICIAAUTO_NUM_COLS 7 struct omiciaAuto /* table for OMICIA auto-generated data */ { struct omiciaAuto *next; /* Next in singly linked list. */ unsigned short bin; /* A field to speed indexing */ char *chrom; /* Chromosome */ unsigned chromStart; /* Start position in chrom */ unsigned chromEnd; /* End position in chrom */ char *name; /* ID for this mutation */ unsigned score; /* confidence score */ char strand[2]; /* + or - */ }; void omiciaAutoStaticLoad(char **row, struct omiciaAuto *ret); /* Load a row from omiciaAuto table into ret. The contents of ret will * be replaced at the next call to this function. */ struct omiciaAuto *omiciaAutoLoad(char **row); /* Load a omiciaAuto from row fetched with select * from omiciaAuto * from database. Dispose of this with omiciaAutoFree(). */ struct omiciaAuto *omiciaAutoLoadAll(char *fileName); /* Load all omiciaAuto from whitespace-separated file. * Dispose of this with omiciaAutoFreeList(). */ struct omiciaAuto *omiciaAutoLoadAllByChar(char *fileName, char chopper); /* Load all omiciaAuto from chopper separated file. * Dispose of this with omiciaAutoFreeList(). */ #define omiciaAutoLoadAllByTab(a) omiciaAutoLoadAllByChar(a, '\t'); /* Load all omiciaAuto from tab separated file. * Dispose of this with omiciaAutoFreeList(). */ struct omiciaAuto *omiciaAutoLoadByQuery(struct sqlConnection *conn, char *query); /* Load all omiciaAuto 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 omiciaAutoFreeList(). */ void omiciaAutoSaveToDb(struct sqlConnection *conn, struct omiciaAuto *el, char *tableName, int updateSize); /* Save omiciaAuto 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 omiciaAuto *omiciaAutoCommaIn(char **pS, struct omiciaAuto *ret); /* Create a omiciaAuto out of a comma separated string. * This will fill in ret if non-null, otherwise will * return a new omiciaAuto */ void omiciaAutoFree(struct omiciaAuto **pEl); /* Free a single dynamically allocated omiciaAuto such as created * with omiciaAutoLoad(). */ void omiciaAutoFreeList(struct omiciaAuto **pList); /* Free a list of dynamically allocated omiciaAuto's */ void omiciaAutoOutput(struct omiciaAuto *el, FILE *f, char sep, char lastSep); /* Print out omiciaAuto. Separate fields with sep. Follow last field with lastSep. */ #define omiciaAutoTabOut(el,f) omiciaAutoOutput(el,f,'\t','\n'); /* Print out omiciaAuto as a line in a tab-separated file. */ #define omiciaAutoCommaOut(el,f) omiciaAutoOutput(el,f,',',','); /* Print out omiciaAuto as a comma separated list including final comma. */ #define OMICIAHAND_NUM_COLS 7 struct omiciaHand /* table for OMICIA hand curated data */ { struct omiciaHand *next; /* Next in singly linked list. */ unsigned short bin; /* A field to speed indexing */ char *chrom; /* Chromosome */ unsigned chromStart; /* Start position in chrom */ unsigned chromEnd; /* End position in chrom */ char *name; /* ID for this mutation */ unsigned score; /* confidence score */ char strand[2]; /* + or - */ }; void omiciaHandStaticLoad(char **row, struct omiciaHand *ret); /* Load a row from omiciaHand table into ret. The contents of ret will * be replaced at the next call to this function. */ struct omiciaHand *omiciaHandLoad(char **row); /* Load a omiciaHand from row fetched with select * from omiciaHand * from database. Dispose of this with omiciaHandFree(). */ struct omiciaHand *omiciaHandLoadAll(char *fileName); /* Load all omiciaHand from whitespace-separated file. * Dispose of this with omiciaHandFreeList(). */ struct omiciaHand *omiciaHandLoadAllByChar(char *fileName, char chopper); /* Load all omiciaHand from chopper separated file. * Dispose of this with omiciaHandFreeList(). */ #define omiciaHandLoadAllByTab(a) omiciaHandLoadAllByChar(a, '\t'); /* Load all omiciaHand from tab separated file. * Dispose of this with omiciaHandFreeList(). */ struct omiciaHand *omiciaHandLoadByQuery(struct sqlConnection *conn, char *query); /* Load all omiciaHand 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 omiciaHandFreeList(). */ void omiciaHandSaveToDb(struct sqlConnection *conn, struct omiciaHand *el, char *tableName, int updateSize); /* Save omiciaHand 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 omiciaHand *omiciaHandCommaIn(char **pS, struct omiciaHand *ret); /* Create a omiciaHand out of a comma separated string. * This will fill in ret if non-null, otherwise will * return a new omiciaHand */ void omiciaHandFree(struct omiciaHand **pEl); /* Free a single dynamically allocated omiciaHand such as created * with omiciaHandLoad(). */ void omiciaHandFreeList(struct omiciaHand **pList); /* Free a list of dynamically allocated omiciaHand's */ void omiciaHandOutput(struct omiciaHand *el, FILE *f, char sep, char lastSep); /* Print out omiciaHand. Separate fields with sep. Follow last field with lastSep. */ #define omiciaHandTabOut(el,f) omiciaHandOutput(el,f,'\t','\n'); /* Print out omiciaHand as a line in a tab-separated file. */ #define omiciaHandCommaOut(el,f) omiciaHandOutput(el,f,',',','); /* Print out omiciaHand as a comma separated list including final comma. */ #define OMICIALINK_NUM_COLS 5 struct omiciaLink /* links */ { struct omiciaLink *next; /* Next in singly linked list. */ char *id; /* id into the omicia composite table */ char *attrType; /* attribute type */ char *raKey; /* key into .ra file on how to do link */ char *acc; /* accession or id used by link */ char *displayVal; /* value to display if different from acc */ }; void omiciaLinkStaticLoad(char **row, struct omiciaLink *ret); /* Load a row from omiciaLink table into ret. The contents of ret will * be replaced at the next call to this function. */ struct omiciaLink *omiciaLinkLoad(char **row); /* Load a omiciaLink from row fetched with select * from omiciaLink * from database. Dispose of this with omiciaLinkFree(). */ struct omiciaLink *omiciaLinkLoadAll(char *fileName); /* Load all omiciaLink from whitespace-separated file. * Dispose of this with omiciaLinkFreeList(). */ struct omiciaLink *omiciaLinkLoadAllByChar(char *fileName, char chopper); /* Load all omiciaLink from chopper separated file. * Dispose of this with omiciaLinkFreeList(). */ #define omiciaLinkLoadAllByTab(a) omiciaLinkLoadAllByChar(a, '\t'); /* Load all omiciaLink from tab separated file. * Dispose of this with omiciaLinkFreeList(). */ struct omiciaLink *omiciaLinkLoadByQuery(struct sqlConnection *conn, char *query); /* Load all omiciaLink 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 omiciaLinkFreeList(). */ void omiciaLinkSaveToDb(struct sqlConnection *conn, struct omiciaLink *el, char *tableName, int updateSize); /* Save omiciaLink 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 omiciaLink *omiciaLinkCommaIn(char **pS, struct omiciaLink *ret); /* Create a omiciaLink out of a comma separated string. * This will fill in ret if non-null, otherwise will * return a new omiciaLink */ void omiciaLinkFree(struct omiciaLink **pEl); /* Free a single dynamically allocated omiciaLink such as created * with omiciaLinkLoad(). */ void omiciaLinkFreeList(struct omiciaLink **pList); /* Free a list of dynamically allocated omiciaLink's */ void omiciaLinkOutput(struct omiciaLink *el, FILE *f, char sep, char lastSep); /* Print out omiciaLink. Separate fields with sep. Follow last field with lastSep. */ #define omiciaLinkTabOut(el,f) omiciaLinkOutput(el,f,'\t','\n'); /* Print out omiciaLink as a line in a tab-separated file. */ #define omiciaLinkCommaOut(el,f) omiciaLinkOutput(el,f,',',','); /* Print out omiciaLink as a comma separated list including final comma. */ #define OMICIAATTR_NUM_COLS 3 struct omiciaAttr /* attributes */ { struct omiciaAttr *next; /* Next in singly linked list. */ char *id; /* id into the omicia composite table */ char *attrType; /* attribute type, label */ char *attrVal; /* value for this attribute */ }; void omiciaAttrStaticLoad(char **row, struct omiciaAttr *ret); /* Load a row from omiciaAttr table into ret. The contents of ret will * be replaced at the next call to this function. */ struct omiciaAttr *omiciaAttrLoad(char **row); /* Load a omiciaAttr from row fetched with select * from omiciaAttr * from database. Dispose of this with omiciaAttrFree(). */ struct omiciaAttr *omiciaAttrLoadAll(char *fileName); /* Load all omiciaAttr from whitespace-separated file. * Dispose of this with omiciaAttrFreeList(). */ struct omiciaAttr *omiciaAttrLoadAllByChar(char *fileName, char chopper); /* Load all omiciaAttr from chopper separated file. * Dispose of this with omiciaAttrFreeList(). */ #define omiciaAttrLoadAllByTab(a) omiciaAttrLoadAllByChar(a, '\t'); /* Load all omiciaAttr from tab separated file. * Dispose of this with omiciaAttrFreeList(). */ struct omiciaAttr *omiciaAttrLoadByQuery(struct sqlConnection *conn, char *query); /* Load all omiciaAttr 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 omiciaAttrFreeList(). */ void omiciaAttrSaveToDb(struct sqlConnection *conn, struct omiciaAttr *el, char *tableName, int updateSize); /* Save omiciaAttr 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 omiciaAttr *omiciaAttrCommaIn(char **pS, struct omiciaAttr *ret); /* Create a omiciaAttr out of a comma separated string. * This will fill in ret if non-null, otherwise will * return a new omiciaAttr */ void omiciaAttrFree(struct omiciaAttr **pEl); /* Free a single dynamically allocated omiciaAttr such as created * with omiciaAttrLoad(). */ void omiciaAttrFreeList(struct omiciaAttr **pList); /* Free a list of dynamically allocated omiciaAttr's */ void omiciaAttrOutput(struct omiciaAttr *el, FILE *f, char sep, char lastSep); /* Print out omiciaAttr. Separate fields with sep. Follow last field with lastSep. */ #define omiciaAttrTabOut(el,f) omiciaAttrOutput(el,f,'\t','\n'); /* Print out omiciaAttr as a line in a tab-separated file. */ #define omiciaAttrCommaOut(el,f) omiciaAttrOutput(el,f,',',','); /* Print out omiciaAttr as a comma separated list including final comma. */ /* -------------------------------- End autoSql Generated Code -------------------------------- */ #endif /* OMICIA_H */