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/dnaProbe.h src/hg/inc/dnaProbe.h index 0ddd41d..caab119 100644 --- src/hg/inc/dnaProbe.h +++ src/hg/inc/dnaProbe.h @@ -1,82 +1,85 @@ /* dnaProbe.h was originally generated by the autoSql program, which also * generated dnaProbe.c and dnaProbe.sql. This header links the database and * the RAM representation of objects. */ +/* Copyright (C) 2013 The Regents of the University of California + * See README in this or parent directory for licensing information. */ + #ifndef DNAPROBE_H #define DNAPROBE_H #ifndef JKSQL_H #include "jksql.h" #endif struct dnaProbe /* data about a dna probe used for microarrays */ { struct dnaProbe *next; /* Next in singly linked list. */ char *name; /* name of the dna probe */ char *dna; /* sequence of probe, {a,t,g,c} */ int size; /* size of sequence */ char *chrom; /* chromosome that sequence is from */ int start; /* start position in chromosome */ int end; /* end position in chromosome */ char strand[4]; /* strand that probe is on */ int tpDist; /* distance of from three prime end */ float tm; /* extimated binding tm */ float pGC; /* percentage of bases that are g's and c's */ int affyHeur; /* 1 if oligo passes affyMetrix heuristic, 0 otherwise */ float secStruct; /* gibbs free energy of secondary structure, higher is better */ int blatScore; /* blat score of the second greatest region of homology */ float comparison; /* weighted average of other scores used for comparison */ }; void dnaProbeStaticLoad(char **row, struct dnaProbe *ret); /* Load a row from dnaProbe table into ret. The contents of ret will * be replaced at the next call to this function. */ struct dnaProbe *dnaProbeLoad(char **row); /* Load a dnaProbe from row fetched with select * from dnaProbe * from database. Dispose of this with dnaProbeFree(). */ struct dnaProbe *dnaProbeLoadAll(char *fileName); /* Load all dnaProbe from a tab-separated file. * Dispose of this with dnaProbeFreeList(). */ struct dnaProbe *dnaProbeLoadByQuery(struct sqlConnection *conn, char *query); /* Load all dnaProbe 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 dnaProbeFreeList(). */ void dnaProbeSaveToDb(struct sqlConnection *conn, struct dnaProbe *el, char *tableName, int updateSize); /* Save dnaProbe 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 dnaProbe *dnaProbeCommaIn(char **pS, struct dnaProbe *ret); /* Create a dnaProbe out of a comma separated string. * This will fill in ret if non-null, otherwise will * return a new dnaProbe */ void dnaProbeFree(struct dnaProbe **pEl); /* Free a single dynamically allocated dnaProbe such as created * with dnaProbeLoad(). */ void dnaProbeFreeList(struct dnaProbe **pList); /* Free a list of dynamically allocated dnaProbe's */ void dnaProbeOutput(struct dnaProbe *el, FILE *f, char sep, char lastSep); /* Print out dnaProbe. Separate fields with sep. Follow last field with lastSep. */ #define dnaProbeTabOut(el,f) dnaProbeOutput(el,f,'\t','\n'); /* Print out dnaProbe as a line in a tab-separated file. */ #define dnaProbeCommaOut(el,f) dnaProbeOutput(el,f,',',','); /* Print out dnaProbe as a comma separated list including final comma. */ /* -------------------------------- End autoSql Generated Code -------------------------------- */ #endif /* DNAPROBE_H */