e70152e44cc66cc599ff6b699eb8adc07f3e656a kent Sat May 24 21:09:34 2014 -0700 Adding Copyright NNNN Regents of the University of California to all files I believe with reasonable certainty were developed under UCSC employ or as part of Genome Browser copyright assignment. diff --git src/hg/inc/fbTables.h src/hg/inc/fbTables.h index f6f2bac..53006bc 100644 --- src/hg/inc/fbTables.h +++ src/hg/inc/fbTables.h @@ -1,426 +1,429 @@ /* fbTables.h was originally generated by the autoSql program, which also * generated fbTables.c and fbTables.sql. This header links the database and * the RAM representation of objects. */ +/* Copyright (C) 2004 The Regents of the University of California + * See README in this or parent directory for licensing information. */ + #ifndef FBTABLES_H #define FBTABLES_H #define FBGENE_NUM_COLS 3 struct fbGene /* Links FlyBase IDs, gene symbols and gene names */ { struct fbGene *next; /* Next in singly linked list. */ char *geneId; /* FlyBase ID */ char *geneSym; /* Short gene symbol */ char *geneName; /* Gene name - up to a couple of words */ }; void fbGeneStaticLoad(char **row, struct fbGene *ret); /* Load a row from fbGene table into ret. The contents of ret will * be replaced at the next call to this function. */ struct fbGene *fbGeneLoad(char **row); /* Load a fbGene from row fetched with select * from fbGene * from database. Dispose of this with fbGeneFree(). */ struct fbGene *fbGeneLoadAll(char *fileName); /* Load all fbGene from whitespace-separated file. * Dispose of this with fbGeneFreeList(). */ struct fbGene *fbGeneLoadAllByChar(char *fileName, char chopper); /* Load all fbGene from chopper separated file. * Dispose of this with fbGeneFreeList(). */ #define fbGeneLoadAllByTab(a) fbGeneLoadAllByChar(a, '\t'); /* Load all fbGene from tab separated file. * Dispose of this with fbGeneFreeList(). */ struct fbGene *fbGeneCommaIn(char **pS, struct fbGene *ret); /* Create a fbGene out of a comma separated string. * This will fill in ret if non-null, otherwise will * return a new fbGene */ void fbGeneFree(struct fbGene **pEl); /* Free a single dynamically allocated fbGene such as created * with fbGeneLoad(). */ void fbGeneFreeList(struct fbGene **pList); /* Free a list of dynamically allocated fbGene's */ void fbGeneOutput(struct fbGene *el, FILE *f, char sep, char lastSep); /* Print out fbGene. Separate fields with sep. Follow last field with lastSep. */ #define fbGeneTabOut(el,f) fbGeneOutput(el,f,'\t','\n'); /* Print out fbGene as a line in a tab-separated file. */ #define fbGeneCommaOut(el,f) fbGeneOutput(el,f,',',','); /* Print out fbGene as a comma separated list including final comma. */ #define FBTRANSCRIPT_NUM_COLS 2 struct fbTranscript /* Links FlyBase gene IDs and BDGP transcript IDs */ { struct fbTranscript *next; /* Next in singly linked list. */ char *geneId; /* FlyBase Gene ID */ char *transcriptId; /* BDGP Transcript ID */ }; void fbTranscriptStaticLoad(char **row, struct fbTranscript *ret); /* Load a row from fbTranscript table into ret. The contents of ret will * be replaced at the next call to this function. */ struct fbTranscript *fbTranscriptLoad(char **row); /* Load a fbTranscript from row fetched with select * from fbTranscript * from database. Dispose of this with fbTranscriptFree(). */ struct fbTranscript *fbTranscriptLoadAll(char *fileName); /* Load all fbTranscript from whitespace-separated file. * Dispose of this with fbTranscriptFreeList(). */ struct fbTranscript *fbTranscriptLoadAllByChar(char *fileName, char chopper); /* Load all fbTranscript from chopper separated file. * Dispose of this with fbTranscriptFreeList(). */ #define fbTranscriptLoadAllByTab(a) fbTranscriptLoadAllByChar(a, '\t'); /* Load all fbTranscript from tab separated file. * Dispose of this with fbTranscriptFreeList(). */ struct fbTranscript *fbTranscriptCommaIn(char **pS, struct fbTranscript *ret); /* Create a fbTranscript out of a comma separated string. * This will fill in ret if non-null, otherwise will * return a new fbTranscript */ void fbTranscriptFree(struct fbTranscript **pEl); /* Free a single dynamically allocated fbTranscript such as created * with fbTranscriptLoad(). */ void fbTranscriptFreeList(struct fbTranscript **pList); /* Free a list of dynamically allocated fbTranscript's */ void fbTranscriptOutput(struct fbTranscript *el, FILE *f, char sep, char lastSep); /* Print out fbTranscript. Separate fields with sep. Follow last field with lastSep. */ #define fbTranscriptTabOut(el,f) fbTranscriptOutput(el,f,'\t','\n'); /* Print out fbTranscript as a line in a tab-separated file. */ #define fbTranscriptCommaOut(el,f) fbTranscriptOutput(el,f,',',','); /* Print out fbTranscript as a comma separated list including final comma. */ #define FBSYNONYM_NUM_COLS 2 struct fbSynonym /* Links all the names we call a gene to it's flybase ID */ { struct fbSynonym *next; /* Next in singly linked list. */ char *geneId; /* FlyBase ID */ char *name; /* A name (synonym or real) */ }; void fbSynonymStaticLoad(char **row, struct fbSynonym *ret); /* Load a row from fbSynonym table into ret. The contents of ret will * be replaced at the next call to this function. */ struct fbSynonym *fbSynonymLoad(char **row); /* Load a fbSynonym from row fetched with select * from fbSynonym * from database. Dispose of this with fbSynonymFree(). */ struct fbSynonym *fbSynonymLoadAll(char *fileName); /* Load all fbSynonym from whitespace-separated file. * Dispose of this with fbSynonymFreeList(). */ struct fbSynonym *fbSynonymLoadAllByChar(char *fileName, char chopper); /* Load all fbSynonym from chopper separated file. * Dispose of this with fbSynonymFreeList(). */ #define fbSynonymLoadAllByTab(a) fbSynonymLoadAllByChar(a, '\t'); /* Load all fbSynonym from tab separated file. * Dispose of this with fbSynonymFreeList(). */ struct fbSynonym *fbSynonymCommaIn(char **pS, struct fbSynonym *ret); /* Create a fbSynonym out of a comma separated string. * This will fill in ret if non-null, otherwise will * return a new fbSynonym */ void fbSynonymFree(struct fbSynonym **pEl); /* Free a single dynamically allocated fbSynonym such as created * with fbSynonymLoad(). */ void fbSynonymFreeList(struct fbSynonym **pList); /* Free a list of dynamically allocated fbSynonym's */ void fbSynonymOutput(struct fbSynonym *el, FILE *f, char sep, char lastSep); /* Print out fbSynonym. Separate fields with sep. Follow last field with lastSep. */ #define fbSynonymTabOut(el,f) fbSynonymOutput(el,f,'\t','\n'); /* Print out fbSynonym as a line in a tab-separated file. */ #define fbSynonymCommaOut(el,f) fbSynonymOutput(el,f,',',','); /* Print out fbSynonym as a comma separated list including final comma. */ #define FBALLELE_NUM_COLS 3 struct fbAllele /* The alleles of a gene */ { struct fbAllele *next; /* Next in singly linked list. */ int id; /* Allele ID */ char *geneId; /* Flybase ID of gene */ char *name; /* Allele name */ }; void fbAlleleStaticLoad(char **row, struct fbAllele *ret); /* Load a row from fbAllele table into ret. The contents of ret will * be replaced at the next call to this function. */ struct fbAllele *fbAlleleLoad(char **row); /* Load a fbAllele from row fetched with select * from fbAllele * from database. Dispose of this with fbAlleleFree(). */ struct fbAllele *fbAlleleLoadAll(char *fileName); /* Load all fbAllele from whitespace-separated file. * Dispose of this with fbAlleleFreeList(). */ struct fbAllele *fbAlleleLoadAllByChar(char *fileName, char chopper); /* Load all fbAllele from chopper separated file. * Dispose of this with fbAlleleFreeList(). */ #define fbAlleleLoadAllByTab(a) fbAlleleLoadAllByChar(a, '\t'); /* Load all fbAllele from tab separated file. * Dispose of this with fbAlleleFreeList(). */ struct fbAllele *fbAlleleCommaIn(char **pS, struct fbAllele *ret); /* Create a fbAllele out of a comma separated string. * This will fill in ret if non-null, otherwise will * return a new fbAllele */ void fbAlleleFree(struct fbAllele **pEl); /* Free a single dynamically allocated fbAllele such as created * with fbAlleleLoad(). */ void fbAlleleFreeList(struct fbAllele **pList); /* Free a list of dynamically allocated fbAllele's */ void fbAlleleOutput(struct fbAllele *el, FILE *f, char sep, char lastSep); /* Print out fbAllele. Separate fields with sep. Follow last field with lastSep. */ #define fbAlleleTabOut(el,f) fbAlleleOutput(el,f,'\t','\n'); /* Print out fbAllele as a line in a tab-separated file. */ #define fbAlleleCommaOut(el,f) fbAlleleOutput(el,f,',',','); /* Print out fbAllele as a comma separated list including final comma. */ #define FBREF_NUM_COLS 2 struct fbRef /* A literature or sometimes database reference */ { struct fbRef *next; /* Next in singly linked list. */ int id; /* Reference ID */ char *text; /* Usually begins with flybase ref ID, but not always */ }; void fbRefStaticLoad(char **row, struct fbRef *ret); /* Load a row from fbRef table into ret. The contents of ret will * be replaced at the next call to this function. */ struct fbRef *fbRefLoad(char **row); /* Load a fbRef from row fetched with select * from fbRef * from database. Dispose of this with fbRefFree(). */ struct fbRef *fbRefLoadAll(char *fileName); /* Load all fbRef from whitespace-separated file. * Dispose of this with fbRefFreeList(). */ struct fbRef *fbRefLoadAllByChar(char *fileName, char chopper); /* Load all fbRef from chopper separated file. * Dispose of this with fbRefFreeList(). */ #define fbRefLoadAllByTab(a) fbRefLoadAllByChar(a, '\t'); /* Load all fbRef from tab separated file. * Dispose of this with fbRefFreeList(). */ struct fbRef *fbRefCommaIn(char **pS, struct fbRef *ret); /* Create a fbRef out of a comma separated string. * This will fill in ret if non-null, otherwise will * return a new fbRef */ void fbRefFree(struct fbRef **pEl); /* Free a single dynamically allocated fbRef such as created * with fbRefLoad(). */ void fbRefFreeList(struct fbRef **pList); /* Free a list of dynamically allocated fbRef's */ void fbRefOutput(struct fbRef *el, FILE *f, char sep, char lastSep); /* Print out fbRef. Separate fields with sep. Follow last field with lastSep. */ #define fbRefTabOut(el,f) fbRefOutput(el,f,'\t','\n'); /* Print out fbRef as a line in a tab-separated file. */ #define fbRefCommaOut(el,f) fbRefOutput(el,f,',',','); /* Print out fbRef as a comma separated list including final comma. */ #define FBROLE_NUM_COLS 4 struct fbRole /* Role of gene in wildType */ { struct fbRole *next; /* Next in singly linked list. */ char *geneId; /* Flybase Gene ID */ int fbAllele; /* ID in fbAllele table or 0 if not allele-specific */ int fbRef; /* ID in fbRef table */ char *text; /* Descriptive text */ }; void fbRoleStaticLoad(char **row, struct fbRole *ret); /* Load a row from fbRole table into ret. The contents of ret will * be replaced at the next call to this function. */ struct fbRole *fbRoleLoad(char **row); /* Load a fbRole from row fetched with select * from fbRole * from database. Dispose of this with fbRoleFree(). */ struct fbRole *fbRoleLoadAll(char *fileName); /* Load all fbRole from whitespace-separated file. * Dispose of this with fbRoleFreeList(). */ struct fbRole *fbRoleLoadAllByChar(char *fileName, char chopper); /* Load all fbRole from chopper separated file. * Dispose of this with fbRoleFreeList(). */ #define fbRoleLoadAllByTab(a) fbRoleLoadAllByChar(a, '\t'); /* Load all fbRole from tab separated file. * Dispose of this with fbRoleFreeList(). */ struct fbRole *fbRoleCommaIn(char **pS, struct fbRole *ret); /* Create a fbRole out of a comma separated string. * This will fill in ret if non-null, otherwise will * return a new fbRole */ void fbRoleFree(struct fbRole **pEl); /* Free a single dynamically allocated fbRole such as created * with fbRoleLoad(). */ void fbRoleFreeList(struct fbRole **pList); /* Free a list of dynamically allocated fbRole's */ void fbRoleOutput(struct fbRole *el, FILE *f, char sep, char lastSep); /* Print out fbRole. Separate fields with sep. Follow last field with lastSep. */ #define fbRoleTabOut(el,f) fbRoleOutput(el,f,'\t','\n'); /* Print out fbRole as a line in a tab-separated file. */ #define fbRoleCommaOut(el,f) fbRoleOutput(el,f,',',','); /* Print out fbRole as a comma separated list including final comma. */ #define FBPHENOTYPE_NUM_COLS 4 struct fbPhenotype /* Observed phenotype in mutant. Sometimes contains gene function info */ { struct fbPhenotype *next; /* Next in singly linked list. */ char *geneId; /* Flybase Gene ID */ int fbAllele; /* ID in fbAllele table or 0 if not allele-specific */ int fbRef; /* ID in fbRef table */ char *text; /* Descriptive text */ }; void fbPhenotypeStaticLoad(char **row, struct fbPhenotype *ret); /* Load a row from fbPhenotype table into ret. The contents of ret will * be replaced at the next call to this function. */ struct fbPhenotype *fbPhenotypeLoad(char **row); /* Load a fbPhenotype from row fetched with select * from fbPhenotype * from database. Dispose of this with fbPhenotypeFree(). */ struct fbPhenotype *fbPhenotypeLoadAll(char *fileName); /* Load all fbPhenotype from whitespace-separated file. * Dispose of this with fbPhenotypeFreeList(). */ struct fbPhenotype *fbPhenotypeLoadAllByChar(char *fileName, char chopper); /* Load all fbPhenotype from chopper separated file. * Dispose of this with fbPhenotypeFreeList(). */ #define fbPhenotypeLoadAllByTab(a) fbPhenotypeLoadAllByChar(a, '\t'); /* Load all fbPhenotype from tab separated file. * Dispose of this with fbPhenotypeFreeList(). */ struct fbPhenotype *fbPhenotypeCommaIn(char **pS, struct fbPhenotype *ret); /* Create a fbPhenotype out of a comma separated string. * This will fill in ret if non-null, otherwise will * return a new fbPhenotype */ void fbPhenotypeFree(struct fbPhenotype **pEl); /* Free a single dynamically allocated fbPhenotype such as created * with fbPhenotypeLoad(). */ void fbPhenotypeFreeList(struct fbPhenotype **pList); /* Free a list of dynamically allocated fbPhenotype's */ void fbPhenotypeOutput(struct fbPhenotype *el, FILE *f, char sep, char lastSep); /* Print out fbPhenotype. Separate fields with sep. Follow last field with lastSep. */ #define fbPhenotypeTabOut(el,f) fbPhenotypeOutput(el,f,'\t','\n'); /* Print out fbPhenotype as a line in a tab-separated file. */ #define fbPhenotypeCommaOut(el,f) fbPhenotypeOutput(el,f,',',','); /* Print out fbPhenotype as a comma separated list including final comma. */ #define FBGO_NUM_COLS 3 struct fbGo /* Links FlyBase gene IDs and GO IDs/aspects */ { struct fbGo *next; /* Next in singly linked list. */ char *geneId; /* Flybase Gene ID */ char *goId; /* GO ID */ char *aspect; /* P (process), F (function) or C (cellular component) */ }; void fbGoStaticLoad(char **row, struct fbGo *ret); /* Load a row from fbGo table into ret. The contents of ret will * be replaced at the next call to this function. */ struct fbGo *fbGoLoad(char **row); /* Load a fbGo from row fetched with select * from fbGo * from database. Dispose of this with fbGoFree(). */ struct fbGo *fbGoLoadAll(char *fileName); /* Load all fbGo from whitespace-separated file. * Dispose of this with fbGoFreeList(). */ struct fbGo *fbGoLoadAllByChar(char *fileName, char chopper); /* Load all fbGo from chopper separated file. * Dispose of this with fbGoFreeList(). */ #define fbGoLoadAllByTab(a) fbGoLoadAllByChar(a, '\t'); /* Load all fbGo from tab separated file. * Dispose of this with fbGoFreeList(). */ struct fbGo *fbGoCommaIn(char **pS, struct fbGo *ret); /* Create a fbGo out of a comma separated string. * This will fill in ret if non-null, otherwise will * return a new fbGo */ void fbGoFree(struct fbGo **pEl); /* Free a single dynamically allocated fbGo such as created * with fbGoLoad(). */ void fbGoFreeList(struct fbGo **pList); /* Free a list of dynamically allocated fbGo's */ void fbGoOutput(struct fbGo *el, FILE *f, char sep, char lastSep); /* Print out fbGo. Separate fields with sep. Follow last field with lastSep. */ #define fbGoTabOut(el,f) fbGoOutput(el,f,'\t','\n'); /* Print out fbGo as a line in a tab-separated file. */ #define fbGoCommaOut(el,f) fbGoOutput(el,f,',',','); /* Print out fbGo as a comma separated list including final comma. */ /* -------------------------------- End autoSql Generated Code -------------------------------- */ #endif /* FBTABLES_H */