/* protVar.h was originally generated by the autoSql program, which also * generated protVar.c and protVar.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 PROTVAR_H #define PROTVAR_H #ifndef JKSQL_H #include "jksql.h" #endif #define PROTVAR_NUM_COLS 6 struct protVar /* track for mutation data */ { struct protVar *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 protVarStaticLoad(char **row, struct protVar *ret); /* Load a row from protVar table into ret. The contents of ret will * be replaced at the next call to this function. */ struct protVar *protVarLoad(char **row); /* Load a protVar from row fetched with select * from protVar * from database. Dispose of this with protVarFree(). */ struct protVar *protVarLoadAll(char *fileName); /* Load all protVar from whitespace-separated file. * Dispose of this with protVarFreeList(). */ struct protVar *protVarLoadAllByChar(char *fileName, char chopper); /* Load all protVar from chopper separated file. * Dispose of this with protVarFreeList(). */ #define protVarLoadAllByTab(a) protVarLoadAllByChar(a, '\t'); /* Load all protVar from tab separated file. * Dispose of this with protVarFreeList(). */ struct protVar *protVarLoadByQuery(struct sqlConnection *conn, char *query); /* Load all protVar 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 protVarFreeList(). */ void protVarSaveToDb(struct sqlConnection *conn, struct protVar *el, char *tableName, int updateSize); /* Save protVar 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 protVar *protVarCommaIn(char **pS, struct protVar *ret); /* Create a protVar out of a comma separated string. * This will fill in ret if non-null, otherwise will * return a new protVar */ void protVarFree(struct protVar **pEl); /* Free a single dynamically allocated protVar such as created * with protVarLoad(). */ void protVarFreeList(struct protVar **pList); /* Free a list of dynamically allocated protVar's */ void protVarOutput(struct protVar *el, FILE *f, char sep, char lastSep); /* Print out protVar. Separate fields with sep. Follow last field with lastSep. */ #define protVarTabOut(el,f) protVarOutput(el,f,'\t','\n'); /* Print out protVar as a line in a tab-separated file. */ #define protVarCommaOut(el,f) protVarOutput(el,f,',',','); /* Print out protVar as a comma separated list including final comma. */ #define PROTVARPOS_NUM_COLS 7 struct protVarPos /* location of mutation */ { struct protVarPos *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 */ unsigned short bin; /* A field to speed indexing */ }; void protVarPosStaticLoad(char **row, struct protVarPos *ret); /* Load a row from protVarPos table into ret. The contents of ret will * be replaced at the next call to this function. */ struct protVarPos *protVarPosLoad(char **row); /* Load a protVarPos from row fetched with select * from protVarPos * from database. Dispose of this with protVarPosFree(). */ struct protVarPos *protVarPosLoadAll(char *fileName); /* Load all protVarPos from whitespace-separated file. * Dispose of this with protVarPosFreeList(). */ struct protVarPos *protVarPosLoadAllByChar(char *fileName, char chopper); /* Load all protVarPos from chopper separated file. * Dispose of this with protVarPosFreeList(). */ #define protVarPosLoadAllByTab(a) protVarPosLoadAllByChar(a, '\t'); /* Load all protVarPos from tab separated file. * Dispose of this with protVarPosFreeList(). */ struct protVarPos *protVarPosLoadByQuery(struct sqlConnection *conn, char *query); /* Load all protVarPos 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 protVarPosFreeList(). */ void protVarPosSaveToDb(struct sqlConnection *conn, struct protVarPos *el, char *tableName, int updateSize); /* Save protVarPos 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 protVarPos *protVarPosCommaIn(char **pS, struct protVarPos *ret); /* Create a protVarPos out of a comma separated string. * This will fill in ret if non-null, otherwise will * return a new protVarPos */ void protVarPosFree(struct protVarPos **pEl); /* Free a single dynamically allocated protVarPos such as created * with protVarPosLoad(). */ void protVarPosFreeList(struct protVarPos **pList); /* Free a list of dynamically allocated protVarPos's */ void protVarPosOutput(struct protVarPos *el, FILE *f, char sep, char lastSep); /* Print out protVarPos. Separate fields with sep. Follow last field with lastSep. */ #define protVarPosTabOut(el,f) protVarPosOutput(el,f,'\t','\n'); /* Print out protVarPos as a line in a tab-separated file. */ #define protVarPosCommaOut(el,f) protVarPosOutput(el,f,',',','); /* Print out protVarPos as a comma separated list including final comma. */ #define PROTVARATTR_NUM_COLS 3 struct protVarAttr /* attributes asssociated with the mutation */ { struct protVarAttr *next; /* Next in singly linked list. */ char *id; /* mutation ID */ char *attrType; /* attribute type */ char *attrVal; /* value for this attribute */ }; void protVarAttrStaticLoad(char **row, struct protVarAttr *ret); /* Load a row from protVarAttr table into ret. The contents of ret will * be replaced at the next call to this function. */ struct protVarAttr *protVarAttrLoad(char **row); /* Load a protVarAttr from row fetched with select * from protVarAttr * from database. Dispose of this with protVarAttrFree(). */ struct protVarAttr *protVarAttrLoadAll(char *fileName); /* Load all protVarAttr from whitespace-separated file. * Dispose of this with protVarAttrFreeList(). */ struct protVarAttr *protVarAttrLoadAllByChar(char *fileName, char chopper); /* Load all protVarAttr from chopper separated file. * Dispose of this with protVarAttrFreeList(). */ #define protVarAttrLoadAllByTab(a) protVarAttrLoadAllByChar(a, '\t'); /* Load all protVarAttr from tab separated file. * Dispose of this with protVarAttrFreeList(). */ struct protVarAttr *protVarAttrLoadByQuery(struct sqlConnection *conn, char *query); /* Load all protVarAttr 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 protVarAttrFreeList(). */ void protVarAttrSaveToDb(struct sqlConnection *conn, struct protVarAttr *el, char *tableName, int updateSize); /* Save protVarAttr 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 protVarAttr *protVarAttrCommaIn(char **pS, struct protVarAttr *ret); /* Create a protVarAttr out of a comma separated string. * This will fill in ret if non-null, otherwise will * return a new protVarAttr */ void protVarAttrFree(struct protVarAttr **pEl); /* Free a single dynamically allocated protVarAttr such as created * with protVarAttrLoad(). */ void protVarAttrFreeList(struct protVarAttr **pList); /* Free a list of dynamically allocated protVarAttr's */ void protVarAttrOutput(struct protVarAttr *el, FILE *f, char sep, char lastSep); /* Print out protVarAttr. Separate fields with sep. Follow last field with lastSep. */ #define protVarAttrTabOut(el,f) protVarAttrOutput(el,f,'\t','\n'); /* Print out protVarAttr as a line in a tab-separated file. */ #define protVarAttrCommaOut(el,f) protVarAttrOutput(el,f,',',','); /* Print out protVarAttr as a comma separated list including final comma. */ #define PROTVARLINK_NUM_COLS 5 struct protVarLink /* links both urls and local table lookups */ { struct protVarLink *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 protVarLinkStaticLoad(char **row, struct protVarLink *ret); /* Load a row from protVarLink table into ret. The contents of ret will * be replaced at the next call to this function. */ struct protVarLink *protVarLinkLoad(char **row); /* Load a protVarLink from row fetched with select * from protVarLink * from database. Dispose of this with protVarLinkFree(). */ struct protVarLink *protVarLinkLoadAll(char *fileName); /* Load all protVarLink from whitespace-separated file. * Dispose of this with protVarLinkFreeList(). */ struct protVarLink *protVarLinkLoadAllByChar(char *fileName, char chopper); /* Load all protVarLink from chopper separated file. * Dispose of this with protVarLinkFreeList(). */ #define protVarLinkLoadAllByTab(a) protVarLinkLoadAllByChar(a, '\t'); /* Load all protVarLink from tab separated file. * Dispose of this with protVarLinkFreeList(). */ struct protVarLink *protVarLinkLoadByQuery(struct sqlConnection *conn, char *query); /* Load all protVarLink 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 protVarLinkFreeList(). */ void protVarLinkSaveToDb(struct sqlConnection *conn, struct protVarLink *el, char *tableName, int updateSize); /* Save protVarLink 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 protVarLink *protVarLinkCommaIn(char **pS, struct protVarLink *ret); /* Create a protVarLink out of a comma separated string. * This will fill in ret if non-null, otherwise will * return a new protVarLink */ void protVarLinkFree(struct protVarLink **pEl); /* Free a single dynamically allocated protVarLink such as created * with protVarLinkLoad(). */ void protVarLinkFreeList(struct protVarLink **pList); /* Free a list of dynamically allocated protVarLink's */ void protVarLinkOutput(struct protVarLink *el, FILE *f, char sep, char lastSep); /* Print out protVarLink. Separate fields with sep. Follow last field with lastSep. */ #define protVarLinkTabOut(el,f) protVarLinkOutput(el,f,'\t','\n'); /* Print out protVarLink as a line in a tab-separated file. */ #define protVarLinkCommaOut(el,f) protVarLinkOutput(el,f,',',','); /* Print out protVarLink as a comma separated list including final comma. */ /* -------------------------------- End autoSql Generated Code -------------------------------- */ #endif /* PROTVAR_H */