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/dnaProbe.c src/hg/cgilib/dnaProbe.c new file mode 100644 index 0000000..8629643 --- /dev/null +++ src/hg/cgilib/dnaProbe.c @@ -0,0 +1,209 @@ +/* dnaProbe.c was originally generated by the autoSql program, which also + * generated dnaProbe.h and dnaProbe.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 "dnaProbe.h" + + +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. */ +{ + +ret->name = row[0]; +ret->dna = row[1]; +ret->size = sqlSigned(row[2]); +ret->chrom = row[3]; +ret->start = sqlSigned(row[4]); +ret->end = sqlSigned(row[5]); +strcpy(ret->strand, row[6]); +ret->tpDist = sqlSigned(row[7]); +ret->tm = atof(row[8]); +ret->pGC = atof(row[9]); +ret->affyHeur = sqlSigned(row[10]); +ret->secStruct = atof(row[11]); +ret->blatScore = sqlSigned(row[12]); +ret->comparison = atof(row[13]); +} + +struct dnaProbe *dnaProbeLoad(char **row) +/* Load a dnaProbe from row fetched with select * from dnaProbe + * from database. Dispose of this with dnaProbeFree(). */ +{ +struct dnaProbe *ret; + +AllocVar(ret); +ret->name = cloneString(row[0]); +ret->dna = cloneString(row[1]); +ret->size = sqlSigned(row[2]); +ret->chrom = cloneString(row[3]); +ret->start = sqlSigned(row[4]); +ret->end = sqlSigned(row[5]); +strcpy(ret->strand, row[6]); +ret->tpDist = sqlSigned(row[7]); +ret->tm = atof(row[8]); +ret->pGC = atof(row[9]); +ret->affyHeur = sqlSigned(row[10]); +ret->secStruct = atof(row[11]); +ret->blatScore = sqlSigned(row[12]); +ret->comparison = atof(row[13]); +return ret; +} + +struct dnaProbe *dnaProbeLoadAll(char *fileName) +/* Load all dnaProbe from a tab-separated file. + * Dispose of this with dnaProbeFreeList(). */ +{ +struct dnaProbe *list = NULL, *el; +struct lineFile *lf = lineFileOpen(fileName, TRUE); +char *row[14]; + +while (lineFileRow(lf, row)) + { + el = dnaProbeLoad(row); + slAddHead(&list, el); + } +lineFileClose(&lf); +slReverse(&list); +return list; +} + +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(). */ +{ +struct dnaProbe *list = NULL, *el; +struct sqlResult *sr; +char **row; + +sr = sqlGetResult(conn, query); +while ((row = sqlNextRow(sr)) != NULL) + { + el = dnaProbeLoad(row); + slAddHead(&list, el); + } +slReverse(&list); +sqlFreeResult(&sr); +return list; +} + +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 dyString *update = newDyString(updateSize); +sqlDyStringPrintf(update, "insert into %s values ( '%s','%s',%d,'%s',%d,%d,'%s',%d,%f,%f,%d,%f,%d,%f)", + tableName, el->name, el->dna, el->size, el->chrom, el->start, el->end, el->strand, el->tpDist, el->tm, el->pGC, el->affyHeur, el->secStruct, el->blatScore, el->comparison); +sqlUpdate(conn, update->string); +freeDyString(&update); +} + +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 */ +{ +char *s = *pS; + +if (ret == NULL) + AllocVar(ret); +ret->name = sqlStringComma(&s); +ret->dna = sqlStringComma(&s); +ret->size = sqlSignedComma(&s); +ret->chrom = sqlStringComma(&s); +ret->start = sqlSignedComma(&s); +ret->end = sqlSignedComma(&s); +sqlFixedStringComma(&s, ret->strand, sizeof(ret->strand)); +ret->tpDist = sqlSignedComma(&s); +ret->tm = sqlFloatComma(&s); +ret->pGC = sqlFloatComma(&s); +ret->affyHeur = sqlSignedComma(&s); +ret->secStruct = sqlFloatComma(&s); +ret->blatScore = sqlSignedComma(&s); +ret->comparison = sqlFloatComma(&s); +*pS = s; +return ret; +} + +void dnaProbeFree(struct dnaProbe **pEl) +/* Free a single dynamically allocated dnaProbe such as created + * with dnaProbeLoad(). */ +{ +struct dnaProbe *el; + +if ((el = *pEl) == NULL) return; +freeMem(el->name); +freeMem(el->dna); +freeMem(el->chrom); +freez(pEl); +} + +void dnaProbeFreeList(struct dnaProbe **pList) +/* Free a list of dynamically allocated dnaProbe's */ +{ +struct dnaProbe *el, *next; + +for (el = *pList; el != NULL; el = next) + { + next = el->next; + dnaProbeFree(&el); + } +*pList = NULL; +} + +void dnaProbeOutput(struct dnaProbe *el, FILE *f, char sep, char lastSep) +/* Print out dnaProbe. Separate fields with sep. Follow last field with lastSep. */ +{ +if (sep == ',') fputc('"',f); +fprintf(f, "%s", el->name); +if (sep == ',') fputc('"',f); +fputc(sep,f); +if (sep == ',') fputc('"',f); +fprintf(f, "%s", el->dna); +if (sep == ',') fputc('"',f); +fputc(sep,f); +fprintf(f, "%d", el->size); +fputc(sep,f); +if (sep == ',') fputc('"',f); +fprintf(f, "%s", el->chrom); +if (sep == ',') fputc('"',f); +fputc(sep,f); +fprintf(f, "%d", el->start); +fputc(sep,f); +fprintf(f, "%d", el->end); +fputc(sep,f); +if (sep == ',') fputc('"',f); +fprintf(f, "%s", el->strand); +if (sep == ',') fputc('"',f); +fputc(sep,f); +fprintf(f, "%d", el->tpDist); +fputc(sep,f); +fprintf(f, "%f", el->tm); +fputc(sep,f); +fprintf(f, "%f", el->pGC); +fputc(sep,f); +fprintf(f, "%d", el->affyHeur); +fputc(sep,f); +fprintf(f, "%f", el->secStruct); +fputc(sep,f); +fprintf(f, "%d", el->blatScore); +fputc(sep,f); +fprintf(f, "%f", el->comparison); +fputc(lastSep,f); +} + +/* -------------------------------- End autoSql Generated Code -------------------------------- */ +