/* landmark.h was originally generated by the autoSql program, which also * generated landmark.c and landmark.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 LANDMARK_H #define LANDMARK_H #ifndef JKSQL_H #include "jksql.h" #endif #define LANDMARK_NUM_COLS 7 struct landmark /* track for regulatory regions and other landmarks from locus experts */ { struct landmark *next; /* Next in singly linked list. */ char *chrom; /* Chromosome */ unsigned chromStart; /* Start position in chrom */ unsigned chromEnd; /* End position in chrom */ char *name; /* name of landmark */ unsigned landmarkId; /* unique ID to identify this landmark */ char *landmarkType; /* type of landmark: HSS, promoter, .. */ unsigned short bin; /* A field to speed indexing */ }; void landmarkStaticLoad(char **row, struct landmark *ret); /* Load a row from landmark table into ret. The contents of ret will * be replaced at the next call to this function. */ struct landmark *landmarkLoad(char **row); /* Load a landmark from row fetched with select * from landmark * from database. Dispose of this with landmarkFree(). */ struct landmark *landmarkLoadAll(char *fileName); /* Load all landmark from whitespace-separated file. * Dispose of this with landmarkFreeList(). */ struct landmark *landmarkLoadAllByChar(char *fileName, char chopper); /* Load all landmark from chopper separated file. * Dispose of this with landmarkFreeList(). */ #define landmarkLoadAllByTab(a) landmarkLoadAllByChar(a, '\t'); /* Load all landmark from tab separated file. * Dispose of this with landmarkFreeList(). */ struct landmark *landmarkLoadByQuery(struct sqlConnection *conn, char *query); /* Load all landmark 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 landmarkFreeList(). */ void landmarkSaveToDb(struct sqlConnection *conn, struct landmark *el, char *tableName, int updateSize); /* Save landmark 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 landmark *landmarkCommaIn(char **pS, struct landmark *ret); /* Create a landmark out of a comma separated string. * This will fill in ret if non-null, otherwise will * return a new landmark */ void landmarkFree(struct landmark **pEl); /* Free a single dynamically allocated landmark such as created * with landmarkLoad(). */ void landmarkFreeList(struct landmark **pList); /* Free a list of dynamically allocated landmark's */ void landmarkOutput(struct landmark *el, FILE *f, char sep, char lastSep); /* Print out landmark. Separate fields with sep. Follow last field with lastSep. */ #define landmarkTabOut(el,f) landmarkOutput(el,f,'\t','\n'); /* Print out landmark as a line in a tab-separated file. */ #define landmarkCommaOut(el,f) landmarkOutput(el,f,',',','); /* Print out landmark as a comma separated list including final comma. */ #define LANDMARKATTR_NUM_COLS 4 struct landmarkAttr /* attributes associated with a landmark */ { struct landmarkAttr *next; /* Next in singly linked list. */ unsigned landmarkId; /* key into the landmark table */ unsigned linkId; /* key into the landmarkAttrLink table */ char *attribute; /* name of attribute being listed */ char *attrVal; /* value of this landmark attribute */ }; void landmarkAttrStaticLoad(char **row, struct landmarkAttr *ret); /* Load a row from landmarkAttr table into ret. The contents of ret will * be replaced at the next call to this function. */ struct landmarkAttr *landmarkAttrLoad(char **row); /* Load a landmarkAttr from row fetched with select * from landmarkAttr * from database. Dispose of this with landmarkAttrFree(). */ struct landmarkAttr *landmarkAttrLoadAll(char *fileName); /* Load all landmarkAttr from whitespace-separated file. * Dispose of this with landmarkAttrFreeList(). */ struct landmarkAttr *landmarkAttrLoadAllByChar(char *fileName, char chopper); /* Load all landmarkAttr from chopper separated file. * Dispose of this with landmarkAttrFreeList(). */ #define landmarkAttrLoadAllByTab(a) landmarkAttrLoadAllByChar(a, '\t'); /* Load all landmarkAttr from tab separated file. * Dispose of this with landmarkAttrFreeList(). */ struct landmarkAttr *landmarkAttrLoadByQuery(struct sqlConnection *conn, char *query); /* Load all landmarkAttr 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 landmarkAttrFreeList(). */ void landmarkAttrSaveToDb(struct sqlConnection *conn, struct landmarkAttr *el, char *tableName, int updateSize); /* Save landmarkAttr 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 landmarkAttr *landmarkAttrCommaIn(char **pS, struct landmarkAttr *ret); /* Create a landmarkAttr out of a comma separated string. * This will fill in ret if non-null, otherwise will * return a new landmarkAttr */ void landmarkAttrFree(struct landmarkAttr **pEl); /* Free a single dynamically allocated landmarkAttr such as created * with landmarkAttrLoad(). */ void landmarkAttrFreeList(struct landmarkAttr **pList); /* Free a list of dynamically allocated landmarkAttr's */ void landmarkAttrOutput(struct landmarkAttr *el, FILE *f, char sep, char lastSep); /* Print out landmarkAttr. Separate fields with sep. Follow last field with lastSep. */ #define landmarkAttrTabOut(el,f) landmarkAttrOutput(el,f,'\t','\n'); /* Print out landmarkAttr as a line in a tab-separated file. */ #define landmarkAttrCommaOut(el,f) landmarkAttrOutput(el,f,',',','); /* Print out landmarkAttr as a comma separated list including final comma. */ #define LANDMARKATTRLINK_NUM_COLS 4 struct landmarkAttrLink /* table to build links for landmarks */ { struct landmarkAttrLink *next; /* Next in singly linked list. */ unsigned attrId; /* key into the landmarkAttr table */ char *raKey; /* key into RA file, tells how to link */ char *attrAcc; /* accession used by link */ char *displayVal; /* how to display if different from acc */ }; void landmarkAttrLinkStaticLoad(char **row, struct landmarkAttrLink *ret); /* Load a row from landmarkAttrLink table into ret. The contents of ret will * be replaced at the next call to this function. */ struct landmarkAttrLink *landmarkAttrLinkLoad(char **row); /* Load a landmarkAttrLink from row fetched with select * from landmarkAttrLink * from database. Dispose of this with landmarkAttrLinkFree(). */ struct landmarkAttrLink *landmarkAttrLinkLoadAll(char *fileName); /* Load all landmarkAttrLink from whitespace-separated file. * Dispose of this with landmarkAttrLinkFreeList(). */ struct landmarkAttrLink *landmarkAttrLinkLoadAllByChar(char *fileName, char chopper); /* Load all landmarkAttrLink from chopper separated file. * Dispose of this with landmarkAttrLinkFreeList(). */ #define landmarkAttrLinkLoadAllByTab(a) landmarkAttrLinkLoadAllByChar(a, '\t'); /* Load all landmarkAttrLink from tab separated file. * Dispose of this with landmarkAttrLinkFreeList(). */ struct landmarkAttrLink *landmarkAttrLinkLoadByQuery(struct sqlConnection *conn, char *query); /* Load all landmarkAttrLink 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 landmarkAttrLinkFreeList(). */ void landmarkAttrLinkSaveToDb(struct sqlConnection *conn, struct landmarkAttrLink *el, char *tableName, int updateSize); /* Save landmarkAttrLink 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 landmarkAttrLink *landmarkAttrLinkCommaIn(char **pS, struct landmarkAttrLink *ret); /* Create a landmarkAttrLink out of a comma separated string. * This will fill in ret if non-null, otherwise will * return a new landmarkAttrLink */ void landmarkAttrLinkFree(struct landmarkAttrLink **pEl); /* Free a single dynamically allocated landmarkAttrLink such as created * with landmarkAttrLinkLoad(). */ void landmarkAttrLinkFreeList(struct landmarkAttrLink **pList); /* Free a list of dynamically allocated landmarkAttrLink's */ void landmarkAttrLinkOutput(struct landmarkAttrLink *el, FILE *f, char sep, char lastSep); /* Print out landmarkAttrLink. Separate fields with sep. Follow last field with lastSep. */ #define landmarkAttrLinkTabOut(el,f) landmarkAttrLinkOutput(el,f,'\t','\n'); /* Print out landmarkAttrLink as a line in a tab-separated file. */ #define landmarkAttrLinkCommaOut(el,f) landmarkAttrLinkOutput(el,f,',',','); /* Print out landmarkAttrLink as a comma separated list including final comma. */ /* -------------------------------- End autoSql Generated Code -------------------------------- */ #endif /* LANDMARK_H */