/* gv.h was originally generated by the autoSql program, which also * generated gv.c and gv.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 GV_H #define GV_H #ifndef JKSQL_H #include "jksql.h" #endif #define GV_NUM_COLS 6 struct gv /* track for mutation data */ { struct gv *next; /* Next in singly linked list. */ char *id; /* unique ID for this mutation */ char *name; /* Official nomenclature description of mutation */ char *srcId; /* source ID for this mutation */ char *baseChangeType; /* enum('insertion', 'deletion', 'substitution','duplication','complex','unknown') */ char *location; /* enum('intron', 'exon', '5'' UTR', '3'' UTR', 'not within known transcription unit') */ unsigned char coordinateAccuracy; /* 0=estimated, 1=definite, others? */ }; void gvStaticLoad(char **row, struct gv *ret); /* Load a row from gv table into ret. The contents of ret will * be replaced at the next call to this function. */ struct gv *gvLoad(char **row); /* Load a gv from row fetched with select * from gv * from database. Dispose of this with gvFree(). */ struct gv *gvLoadAll(char *fileName); /* Load all gv from whitespace-separated file. * Dispose of this with gvFreeList(). */ struct gv *gvLoadAllByChar(char *fileName, char chopper); /* Load all gv from chopper separated file. * Dispose of this with gvFreeList(). */ #define gvLoadAllByTab(a) gvLoadAllByChar(a, '\t'); /* Load all gv from tab separated file. * Dispose of this with gvFreeList(). */ struct gv *gvLoadByQuery(struct sqlConnection *conn, char *query); /* Load all gv 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 gvFreeList(). */ void gvSaveToDb(struct sqlConnection *conn, struct gv *el, char *tableName, int updateSize); /* Save gv 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 gv *gvCommaIn(char **pS, struct gv *ret); /* Create a gv out of a comma separated string. * This will fill in ret if non-null, otherwise will * return a new gv */ void gvFree(struct gv **pEl); /* Free a single dynamically allocated gv such as created * with gvLoad(). */ void gvFreeList(struct gv **pList); /* Free a list of dynamically allocated gv's */ void gvOutput(struct gv *el, FILE *f, char sep, char lastSep); /* Print out gv. Separate fields with sep. Follow last field with lastSep. */ #define gvTabOut(el,f) gvOutput(el,f,'\t','\n'); /* Print out gv as a line in a tab-separated file. */ #define gvCommaOut(el,f) gvOutput(el,f,',',','); /* Print out gv as a comma separated list including final comma. */ #define GVPOS_NUM_COLS 7 struct gvPos /* location of mutation */ { struct gvPos *next; /* Next in singly linked list. */ char *chrom; /* Chromosome */ unsigned chromStart; /* Start position in chrom */ unsigned chromEnd; /* End position in chrom */ char *name; /* ID for this mutation */ char strand[2]; /* + or - */ char *label; /* short official name for this mutation */ char *id; /* Added field to hold ID if change name */ unsigned short bin; /* A field to speed indexing */ }; void gvPosStaticLoad(char **row, struct gvPos *ret); /* Load a row from gvPos table into ret. The contents of ret will * be replaced at the next call to this function. */ struct gvPos *gvPosLoad(char **row); /* Load a gvPos from row fetched with select * from gvPos * from database. Dispose of this with gvPosFree(). */ struct gvPos *gvPosLoadAll(char *fileName); /* Load all gvPos from whitespace-separated file. * Dispose of this with gvPosFreeList(). */ struct gvPos *gvPosLoadAllByChar(char *fileName, char chopper); /* Load all gvPos from chopper separated file. * Dispose of this with gvPosFreeList(). */ #define gvPosLoadAllByTab(a) gvPosLoadAllByChar(a, '\t'); /* Load all gvPos from tab separated file. * Dispose of this with gvPosFreeList(). */ struct gvPos *gvPosLoadByQuery(struct sqlConnection *conn, char *query); /* Load all gvPos 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 gvPosFreeList(). */ void gvPosSaveToDb(struct sqlConnection *conn, struct gvPos *el, char *tableName, int updateSize); /* Save gvPos 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 gvPos *gvPosCommaIn(char **pS, struct gvPos *ret); /* Create a gvPos out of a comma separated string. * This will fill in ret if non-null, otherwise will * return a new gvPos */ void gvPosFree(struct gvPos **pEl); /* Free a single dynamically allocated gvPos such as created * with gvPosLoad(). */ void gvPosFreeList(struct gvPos **pList); /* Free a list of dynamically allocated gvPos's */ void gvPosOutput(struct gvPos *el, FILE *f, char sep, char lastSep); /* Print out gvPos. Separate fields with sep. Follow last field with lastSep. */ #define gvPosTabOut(el,f) gvPosOutput(el,f,'\t','\n'); /* Print out gvPos as a line in a tab-separated file. */ #define gvPosCommaOut(el,f) gvPosOutput(el,f,',',','); /* Print out gvPos as a comma separated list including final comma. */ #define GVSRC_NUM_COLS 3 struct gvSrc /* sources for mutation track */ { struct gvSrc *next; /* Next in singly linked list. */ char *srcId; /* key into gv table */ char *src; /* name of genome wide source or LSDB */ char *lsdb; /* for LSDB name of actual source DB */ }; void gvSrcStaticLoad(char **row, struct gvSrc *ret); /* Load a row from gvSrc table into ret. The contents of ret will * be replaced at the next call to this function. */ struct gvSrc *gvSrcLoad(char **row); /* Load a gvSrc from row fetched with select * from gvSrc * from database. Dispose of this with gvSrcFree(). */ struct gvSrc *gvSrcLoadAll(char *fileName); /* Load all gvSrc from whitespace-separated file. * Dispose of this with gvSrcFreeList(). */ struct gvSrc *gvSrcLoadAllByChar(char *fileName, char chopper); /* Load all gvSrc from chopper separated file. * Dispose of this with gvSrcFreeList(). */ #define gvSrcLoadAllByTab(a) gvSrcLoadAllByChar(a, '\t'); /* Load all gvSrc from tab separated file. * Dispose of this with gvSrcFreeList(). */ struct gvSrc *gvSrcLoadByQuery(struct sqlConnection *conn, char *query); /* Load all gvSrc 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 gvSrcFreeList(). */ void gvSrcSaveToDb(struct sqlConnection *conn, struct gvSrc *el, char *tableName, int updateSize); /* Save gvSrc 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 gvSrc *gvSrcCommaIn(char **pS, struct gvSrc *ret); /* Create a gvSrc out of a comma separated string. * This will fill in ret if non-null, otherwise will * return a new gvSrc */ void gvSrcFree(struct gvSrc **pEl); /* Free a single dynamically allocated gvSrc such as created * with gvSrcLoad(). */ void gvSrcFreeList(struct gvSrc **pList); /* Free a list of dynamically allocated gvSrc's */ void gvSrcOutput(struct gvSrc *el, FILE *f, char sep, char lastSep); /* Print out gvSrc. Separate fields with sep. Follow last field with lastSep. */ #define gvSrcTabOut(el,f) gvSrcOutput(el,f,'\t','\n'); /* Print out gvSrc as a line in a tab-separated file. */ #define gvSrcCommaOut(el,f) gvSrcOutput(el,f,',',','); /* Print out gvSrc as a comma separated list including final comma. */ #define GVATTR_NUM_COLS 3 struct gvAttr /* attributes asssociated with the mutation */ { struct gvAttr *next; /* Next in singly linked list. */ char *id; /* mutation ID */ char *attrType; /* attribute type */ char *attrVal; /* value for this attribute */ }; void gvAttrStaticLoad(char **row, struct gvAttr *ret); /* Load a row from gvAttr table into ret. The contents of ret will * be replaced at the next call to this function. */ struct gvAttr *gvAttrLoad(char **row); /* Load a gvAttr from row fetched with select * from gvAttr * from database. Dispose of this with gvAttrFree(). */ struct gvAttr *gvAttrLoadAll(char *fileName); /* Load all gvAttr from whitespace-separated file. * Dispose of this with gvAttrFreeList(). */ struct gvAttr *gvAttrLoadAllByChar(char *fileName, char chopper); /* Load all gvAttr from chopper separated file. * Dispose of this with gvAttrFreeList(). */ #define gvAttrLoadAllByTab(a) gvAttrLoadAllByChar(a, '\t'); /* Load all gvAttr from tab separated file. * Dispose of this with gvAttrFreeList(). */ struct gvAttr *gvAttrLoadByQuery(struct sqlConnection *conn, char *query); /* Load all gvAttr 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 gvAttrFreeList(). */ void gvAttrSaveToDb(struct sqlConnection *conn, struct gvAttr *el, char *tableName, int updateSize); /* Save gvAttr 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 gvAttr *gvAttrCommaIn(char **pS, struct gvAttr *ret); /* Create a gvAttr out of a comma separated string. * This will fill in ret if non-null, otherwise will * return a new gvAttr */ void gvAttrFree(struct gvAttr **pEl); /* Free a single dynamically allocated gvAttr such as created * with gvAttrLoad(). */ void gvAttrFreeList(struct gvAttr **pList); /* Free a list of dynamically allocated gvAttr's */ void gvAttrOutput(struct gvAttr *el, FILE *f, char sep, char lastSep); /* Print out gvAttr. Separate fields with sep. Follow last field with lastSep. */ #define gvAttrTabOut(el,f) gvAttrOutput(el,f,'\t','\n'); /* Print out gvAttr as a line in a tab-separated file. */ #define gvAttrCommaOut(el,f) gvAttrOutput(el,f,',',','); /* Print out gvAttr as a comma separated list including final comma. */ #define GVLINK_NUM_COLS 5 struct gvLink /* links both urls and local table lookups */ { struct gvLink *next; /* Next in singly linked list. */ char *id; /* id for attribute link */ 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 gvLinkStaticLoad(char **row, struct gvLink *ret); /* Load a row from gvLink table into ret. The contents of ret will * be replaced at the next call to this function. */ struct gvLink *gvLinkLoad(char **row); /* Load a gvLink from row fetched with select * from gvLink * from database. Dispose of this with gvLinkFree(). */ struct gvLink *gvLinkLoadAll(char *fileName); /* Load all gvLink from whitespace-separated file. * Dispose of this with gvLinkFreeList(). */ struct gvLink *gvLinkLoadAllByChar(char *fileName, char chopper); /* Load all gvLink from chopper separated file. * Dispose of this with gvLinkFreeList(). */ #define gvLinkLoadAllByTab(a) gvLinkLoadAllByChar(a, '\t'); /* Load all gvLink from tab separated file. * Dispose of this with gvLinkFreeList(). */ struct gvLink *gvLinkLoadByQuery(struct sqlConnection *conn, char *query); /* Load all gvLink 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 gvLinkFreeList(). */ void gvLinkSaveToDb(struct sqlConnection *conn, struct gvLink *el, char *tableName, int updateSize); /* Save gvLink 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 gvLink *gvLinkCommaIn(char **pS, struct gvLink *ret); /* Create a gvLink out of a comma separated string. * This will fill in ret if non-null, otherwise will * return a new gvLink */ void gvLinkFree(struct gvLink **pEl); /* Free a single dynamically allocated gvLink such as created * with gvLinkLoad(). */ void gvLinkFreeList(struct gvLink **pList); /* Free a list of dynamically allocated gvLink's */ void gvLinkOutput(struct gvLink *el, FILE *f, char sep, char lastSep); /* Print out gvLink. Separate fields with sep. Follow last field with lastSep. */ #define gvLinkTabOut(el,f) gvLinkOutput(el,f,'\t','\n'); /* Print out gvLink as a line in a tab-separated file. */ #define gvLinkCommaOut(el,f) gvLinkOutput(el,f,',',','); /* Print out gvLink as a comma separated list including final comma. */ #define GVATTRLONG_NUM_COLS 3 struct gvAttrLong /* attributes associated with a mutation that need long text */ { struct gvAttrLong *next; /* Next in singly linked list. */ char *id; /* mutation ID */ char *attrType; /* attribute type */ char *attrVal; /* value for this attribute */ }; void gvAttrLongStaticLoad(char **row, struct gvAttrLong *ret); /* Load a row from gvAttrLong table into ret. The contents of ret will * be replaced at the next call to this function. */ struct gvAttrLong *gvAttrLongLoad(char **row); /* Load a gvAttrLong from row fetched with select * from gvAttrLong * from database. Dispose of this with gvAttrLongFree(). */ struct gvAttrLong *gvAttrLongLoadAll(char *fileName); /* Load all gvAttrLong from whitespace-separated file. * Dispose of this with gvAttrLongFreeList(). */ struct gvAttrLong *gvAttrLongLoadAllByChar(char *fileName, char chopper); /* Load all gvAttrLong from chopper separated file. * Dispose of this with gvAttrLongFreeList(). */ #define gvAttrLongLoadAllByTab(a) gvAttrLongLoadAllByChar(a, '\t'); /* Load all gvAttrLong from tab separated file. * Dispose of this with gvAttrLongFreeList(). */ struct gvAttrLong *gvAttrLongLoadByQuery(struct sqlConnection *conn, char *query); /* Load all gvAttrLong 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 gvAttrLongFreeList(). */ void gvAttrLongSaveToDb(struct sqlConnection *conn, struct gvAttrLong *el, char *tableName, int updateSize); /* Save gvAttrLong 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 gvAttrLong *gvAttrLongCommaIn(char **pS, struct gvAttrLong *ret); /* Create a gvAttrLong out of a comma separated string. * This will fill in ret if non-null, otherwise will * return a new gvAttrLong */ void gvAttrLongFree(struct gvAttrLong **pEl); /* Free a single dynamically allocated gvAttrLong such as created * with gvAttrLongLoad(). */ void gvAttrLongFreeList(struct gvAttrLong **pList); /* Free a list of dynamically allocated gvAttrLong's */ void gvAttrLongOutput(struct gvAttrLong *el, FILE *f, char sep, char lastSep); /* Print out gvAttrLong. Separate fields with sep. Follow last field with lastSep. */ #define gvAttrLongTabOut(el,f) gvAttrLongOutput(el,f,'\t','\n'); /* Print out gvAttrLong as a line in a tab-separated file. */ #define gvAttrLongCommaOut(el,f) gvAttrLongOutput(el,f,',',','); /* Print out gvAttrLong as a comma separated list including final comma. */ /* -------------------------------- End autoSql Generated Code -------------------------------- */ #endif /* GV_H */