533112afe2a2005e80cdb1f82904ea65032d4302 braney Sat Oct 2 11:37:34 2021 -0700 split hg/lib into two separate libaries, one only used by the cgis diff --git src/hg/cgilib/simpleRepeat.c src/hg/cgilib/simpleRepeat.c new file mode 100644 index 0000000..9893599 --- /dev/null +++ src/hg/cgilib/simpleRepeat.c @@ -0,0 +1,204 @@ +/* simpleRepeat.c was originally generated by the autoSql program, which also + * generated simpleRepeat.h and simpleRepeat.sql. This module links the database and + * the RAM representation of objects. */ + +/* Copyright (C) 2014 The Regents of the University of California + * See README in this or parent directory for licensing information. */ + +#include "common.h" +#include "linefile.h" +#include "dystring.h" +#include "jksql.h" +#include "simpleRepeat.h" + + +void simpleRepeatStaticLoad(char **row, struct simpleRepeat *ret) +/* Load a row from simpleRepeat table into ret. The contents of ret will + * be replaced at the next call to this function. */ +{ + +ret->chrom = row[0]; +ret->chromStart = sqlUnsigned(row[1]); +ret->chromEnd = sqlUnsigned(row[2]); +ret->name = row[3]; +ret->period = sqlUnsigned(row[4]); +ret->copyNum = atof(row[5]); +ret->consensusSize = sqlUnsigned(row[6]); +ret->perMatch = sqlUnsigned(row[7]); +ret->perIndel = sqlUnsigned(row[8]); +ret->score = sqlUnsigned(row[9]); +ret->A = sqlUnsigned(row[10]); +ret->C = sqlUnsigned(row[11]); +ret->G = sqlUnsigned(row[12]); +ret->T = sqlUnsigned(row[13]); +ret->entropy = atof(row[14]); +ret->sequence = row[15]; +} + +struct simpleRepeat *simpleRepeatLoad(char **row) +/* Load a simpleRepeat from row fetched with select * from simpleRepeat + * from database. Dispose of this with simpleRepeatFree(). */ +{ +struct simpleRepeat *ret; + +AllocVar(ret); +ret->chrom = cloneString(row[0]); +ret->chromStart = sqlUnsigned(row[1]); +ret->chromEnd = sqlUnsigned(row[2]); +ret->name = cloneString(row[3]); +ret->period = sqlUnsigned(row[4]); +ret->copyNum = atof(row[5]); +ret->consensusSize = sqlUnsigned(row[6]); +ret->perMatch = sqlUnsigned(row[7]); +ret->perIndel = sqlUnsigned(row[8]); +ret->score = sqlUnsigned(row[9]); +ret->A = sqlUnsigned(row[10]); +ret->C = sqlUnsigned(row[11]); +ret->G = sqlUnsigned(row[12]); +ret->T = sqlUnsigned(row[13]); +ret->entropy = atof(row[14]); +ret->sequence = cloneString(row[15]); +return ret; +} + +struct simpleRepeat *simpleRepeatLoadAll(char *fileName) +/* Load all simpleRepeat from a tab-separated file. + * Dispose of this with simpleRepeatFreeList(). */ +{ +struct simpleRepeat *list = NULL, *el; +struct lineFile *lf = lineFileOpen(fileName, TRUE); +char *row[16]; + +while (lineFileRow(lf, row)) + { + el = simpleRepeatLoad(row); + slAddHead(&list, el); + } +lineFileClose(&lf); +slReverse(&list); +return list; +} + +struct simpleRepeat *simpleRepeatLoadWhere(struct sqlConnection *conn, char *table, char *where) +/* Load all simpleRepeat from table that satisfy where clause. The + * where clause may be NULL in which case whole table is loaded + * Dispose of this with simpleRepeatFreeList(). */ +{ +struct simpleRepeat *list = NULL, *el; +struct dyString *query = dyStringNew(256); +struct sqlResult *sr; +char **row; + +sqlDyStringPrintf(query, "select * from %s", table); +if (where != NULL) + dyStringPrintf(query, " where %s", where); +sr = sqlGetResult(conn, query->string); +while ((row = sqlNextRow(sr)) != NULL) + { + el = simpleRepeatLoad(row); + slAddHead(&list, el); + } +slReverse(&list); +sqlFreeResult(&sr); +dyStringFree(&query); +return list; +} + +struct simpleRepeat *simpleRepeatCommaIn(char **pS, struct simpleRepeat *ret) +/* Create a simpleRepeat out of a comma separated string. + * This will fill in ret if non-null, otherwise will + * return a new simpleRepeat */ +{ +char *s = *pS; + +if (ret == NULL) + AllocVar(ret); +ret->chrom = sqlStringComma(&s); +ret->chromStart = sqlUnsignedComma(&s); +ret->chromEnd = sqlUnsignedComma(&s); +ret->name = sqlStringComma(&s); +ret->period = sqlUnsignedComma(&s); +ret->copyNum = sqlFloatComma(&s); +ret->consensusSize = sqlUnsignedComma(&s); +ret->perMatch = sqlUnsignedComma(&s); +ret->perIndel = sqlUnsignedComma(&s); +ret->score = sqlUnsignedComma(&s); +ret->A = sqlUnsignedComma(&s); +ret->C = sqlUnsignedComma(&s); +ret->G = sqlUnsignedComma(&s); +ret->T = sqlUnsignedComma(&s); +ret->entropy = sqlFloatComma(&s); +ret->sequence = sqlStringComma(&s); +*pS = s; +return ret; +} + +void simpleRepeatFree(struct simpleRepeat **pEl) +/* Free a single dynamically allocated simpleRepeat such as created + * with simpleRepeatLoad(). */ +{ +struct simpleRepeat *el; + +if ((el = *pEl) == NULL) return; +freeMem(el->chrom); +freeMem(el->name); +freeMem(el->sequence); +freez(pEl); +} + +void simpleRepeatFreeList(struct simpleRepeat **pList) +/* Free a list of dynamically allocated simpleRepeat's */ +{ +struct simpleRepeat *el, *next; + +for (el = *pList; el != NULL; el = next) + { + next = el->next; + simpleRepeatFree(&el); + } +*pList = NULL; +} + +void simpleRepeatOutput(struct simpleRepeat *el, FILE *f, char sep, char lastSep) +/* Print out simpleRepeat. Separate fields with sep. Follow last field with lastSep. */ +{ +if (sep == ',') fputc('"',f); +fprintf(f, "%s", el->chrom); +if (sep == ',') fputc('"',f); +fputc(sep,f); +fprintf(f, "%u", el->chromStart); +fputc(sep,f); +fprintf(f, "%u", el->chromEnd); +fputc(sep,f); +if (sep == ',') fputc('"',f); +fprintf(f, "%s", el->name); +if (sep == ',') fputc('"',f); +fputc(sep,f); +fprintf(f, "%u", el->period); +fputc(sep,f); +fprintf(f, "%f", el->copyNum); +fputc(sep,f); +fprintf(f, "%u", el->consensusSize); +fputc(sep,f); +fprintf(f, "%u", el->perMatch); +fputc(sep,f); +fprintf(f, "%u", el->perIndel); +fputc(sep,f); +fprintf(f, "%u", el->score); +fputc(sep,f); +fprintf(f, "%u", el->A); +fputc(sep,f); +fprintf(f, "%u", el->C); +fputc(sep,f); +fprintf(f, "%u", el->G); +fputc(sep,f); +fprintf(f, "%u", el->T); +fputc(sep,f); +fprintf(f, "%f", el->entropy); +fputc(sep,f); +if (sep == ',') fputc('"',f); +fprintf(f, "%s", el->sequence); +if (sep == ',') fputc('"',f); +fputc(lastSep,f); +} +