/* models.h was originally generated by the autoSql program, which also * generated models.c and models.sql. This header links the database and * the RAM representation of objects. */ #ifndef MODELS_H #define MODELS_H #define QUAKESAMPLE_NUM_COLS 12 extern char *quakeSampleCommaSepFieldNames; struct quakeSample /* Sample from quake lab */ { struct quakeSample *next; /* Next in singly linked list. */ char *date; /* DD/MM/YY format date string */ char *subdir; /* Subdirectory where files live */ char *fluidPlateAcc; /* Shorter 5 char accession corresponding to plate? */ unsigned unknown1; /* Seems to be number 1-8 with some gaps */ char *seqFormat; /* Form like 151 (8) (8) 151 or 101 (6) 101 */ char *sequencer; /* Looks like a sequencing machine id */ char *sample; /* Looks like a unique ID for each sample */ char *user; /* User name */ char *lab; /* Lab name */ char *ilAcc; /* SOme sort of accession starting with IL */ char *captureArrayBarcode; /* Seems to vary in lock-step with ilAcc */ char *cellPos; /* Position of cell in plate I think */ }; void quakeSampleStaticLoad(char **row, struct quakeSample *ret); /* Load a row from quakeSample table into ret. The contents of ret will * be replaced at the next call to this function. */ struct quakeSample *quakeSampleLoad(char **row); /* Load a quakeSample from row fetched with select * from quakeSample * from database. Dispose of this with quakeSampleFree(). */ struct quakeSample *quakeSampleLoadAll(char *fileName); /* Load all quakeSample from whitespace-separated file. * Dispose of this with quakeSampleFreeList(). */ struct quakeSample *quakeSampleLoadAllByChar(char *fileName, char chopper); /* Load all quakeSample from chopper separated file. * Dispose of this with quakeSampleFreeList(). */ #define quakeSampleLoadAllByTab(a) quakeSampleLoadAllByChar(a, '\t'); /* Load all quakeSample from tab separated file. * Dispose of this with quakeSampleFreeList(). */ struct quakeSample *quakeSampleCommaIn(char **pS, struct quakeSample *ret); /* Create a quakeSample out of a comma separated string. * This will fill in ret if non-null, otherwise will * return a new quakeSample */ void quakeSampleFree(struct quakeSample **pEl); /* Free a single dynamically allocated quakeSample such as created * with quakeSampleLoad(). */ void quakeSampleFreeList(struct quakeSample **pList); /* Free a list of dynamically allocated quakeSample's */ void quakeSampleOutput(struct quakeSample *el, FILE *f, char sep, char lastSep); /* Print out quakeSample. Separate fields with sep. Follow last field with lastSep. */ #define quakeSampleTabOut(el,f) quakeSampleOutput(el,f,'\t','\n'); /* Print out quakeSample as a line in a tab-separated file. */ #define quakeSampleCommaOut(el,f) quakeSampleOutput(el,f,',',','); /* Print out quakeSample as a comma separated list including final comma. */ #define QUAKECHIP_NUM_COLS 15 extern char *quakeChipCommaSepFieldNames; struct quakeChip /* A microfluidics chip from quake lab */ { struct quakeChip *next; /* Next in singly linked list. */ char *captureArrayBarcode; /* Long unique id */ char *date; /* MM/DD/YY format */ char *machineName; /* Name of machine run on */ char *user; /* User name */ char *lab; /* Lab */ char *sampleType; /* Overall type of cell */ char *tissue; /* Tissue or organ */ char *species; /* M. musculus, etc */ char *strain; /* Black 6 etc */ char *age; /* Adult, etc */ char *targetCell; /* Epithelium, etc */ char *sortMethod; /* FACS usually */ char *markers; /* Space delimited markers like CD45 etc */ char *attiRun; /* Seems to include data and other info */ char *description; /* Typically not very descriptive.... */ }; void quakeChipStaticLoad(char **row, struct quakeChip *ret); /* Load a row from quakeChip table into ret. The contents of ret will * be replaced at the next call to this function. */ struct quakeChip *quakeChipLoad(char **row); /* Load a quakeChip from row fetched with select * from quakeChip * from database. Dispose of this with quakeChipFree(). */ struct quakeChip *quakeChipLoadAll(char *fileName); /* Load all quakeChip from whitespace-separated file. * Dispose of this with quakeChipFreeList(). */ struct quakeChip *quakeChipLoadAllByChar(char *fileName, char chopper); /* Load all quakeChip from chopper separated file. * Dispose of this with quakeChipFreeList(). */ #define quakeChipLoadAllByTab(a) quakeChipLoadAllByChar(a, '\t'); /* Load all quakeChip from tab separated file. * Dispose of this with quakeChipFreeList(). */ struct quakeChip *quakeChipCommaIn(char **pS, struct quakeChip *ret); /* Create a quakeChip out of a comma separated string. * This will fill in ret if non-null, otherwise will * return a new quakeChip */ void quakeChipFree(struct quakeChip **pEl); /* Free a single dynamically allocated quakeChip such as created * with quakeChipLoad(). */ void quakeChipFreeList(struct quakeChip **pList); /* Free a list of dynamically allocated quakeChip's */ void quakeChipOutput(struct quakeChip *el, FILE *f, char sep, char lastSep); /* Print out quakeChip. Separate fields with sep. Follow last field with lastSep. */ #define quakeChipTabOut(el,f) quakeChipOutput(el,f,'\t','\n'); /* Print out quakeChip as a line in a tab-separated file. */ #define quakeChipCommaOut(el,f) quakeChipOutput(el,f,',',','); /* Print out quakeChip as a comma separated list including final comma. */ #define QUAKESHEET_NUM_COLS 10 extern char *quakeSheetCommaSepFieldNames; struct quakeSheet /* SampleSheet file info */ { struct quakeSheet *next; /* Next in singly linked list. */ char *fcid; /* Flow cell ID */ int lane; /* Sequencing lane - small number */ char *sampleId; /* Same as quakeSample.sample */ char *sampleRef; /* Always SampleRef? */ char *seqIndex; /* Nucleotides used to separate out multiplexing in lane */ char *description; /* Looks like some sort of IL # */ char *control; /* N */ char *recipe; /* Recipe */ char *operator; /* GM? */ char *SampleProject; /* Looks like this actually has operator */ }; void quakeSheetStaticLoad(char **row, struct quakeSheet *ret); /* Load a row from quakeSheet table into ret. The contents of ret will * be replaced at the next call to this function. */ struct quakeSheet *quakeSheetLoad(char **row); /* Load a quakeSheet from row fetched with select * from quakeSheet * from database. Dispose of this with quakeSheetFree(). */ struct quakeSheet *quakeSheetLoadAll(char *fileName); /* Load all quakeSheet from whitespace-separated file. * Dispose of this with quakeSheetFreeList(). */ struct quakeSheet *quakeSheetLoadAllByChar(char *fileName, char chopper); /* Load all quakeSheet from chopper separated file. * Dispose of this with quakeSheetFreeList(). */ #define quakeSheetLoadAllByTab(a) quakeSheetLoadAllByChar(a, '\t'); /* Load all quakeSheet from tab separated file. * Dispose of this with quakeSheetFreeList(). */ struct quakeSheet *quakeSheetCommaIn(char **pS, struct quakeSheet *ret); /* Create a quakeSheet out of a comma separated string. * This will fill in ret if non-null, otherwise will * return a new quakeSheet */ void quakeSheetFree(struct quakeSheet **pEl); /* Free a single dynamically allocated quakeSheet such as created * with quakeSheetLoad(). */ void quakeSheetFreeList(struct quakeSheet **pList); /* Free a list of dynamically allocated quakeSheet's */ void quakeSheetOutput(struct quakeSheet *el, FILE *f, char sep, char lastSep); /* Print out quakeSheet. Separate fields with sep. Follow last field with lastSep. */ #define quakeSheetTabOut(el,f) quakeSheetOutput(el,f,'\t','\n'); /* Print out quakeSheet as a line in a tab-separated file. */ #define quakeSheetCommaOut(el,f) quakeSheetOutput(el,f,',',','); /* Print out quakeSheet as a comma separated list including final comma. */ /* -------------------------------- End autoSql Generated Code -------------------------------- */ #endif /* MODELS_H */