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/pgPolyphenPred.c src/hg/cgilib/pgPolyphenPred.c new file mode 100644 index 0000000..9088c45 --- /dev/null +++ src/hg/cgilib/pgPolyphenPred.c @@ -0,0 +1,222 @@ +/* pgPolyphenPred.c was originally generated by the autoSql program, which also + * generated pgPolyphenPred.h and pgPolyphenPred.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 "pgPolyphenPred.h" +#include "hdb.h" + + +void pgPolyphenPredStaticLoadWithNull(char **row, struct pgPolyphenPred *ret) +/* Load a row from pgPolyphenPred table into ret. The contents of ret will + * be replaced at the next call to this function. */ +{ + +ret->chrom = row[0]; +if (row[1] != NULL) + { + ret->chromStart = needMem(sizeof(*(ret->chromStart))); + *(ret->chromStart) = sqlUnsigned(row[1]); + } +else + { + ret->chromStart = NULL; + } +if (row[2] != NULL) + { + ret->chromEnd = needMem(sizeof(*(ret->chromEnd))); + *(ret->chromEnd) = sqlUnsigned(row[2]); + } +else + { + ret->chromEnd = NULL; + } +ret->prediction = row[3]; +ret->basedOn = row[4]; +ret->geneName = row[5]; +ret->aaChange = row[6]; +} + +struct pgPolyphenPred *pgPolyphenPredLoadWithNull(char **row) +/* Load a pgPolyphenPred from row fetched with select * from pgPolyphenPred + * from database. Dispose of this with pgPolyphenPredFree(). */ +{ +struct pgPolyphenPred *ret; + +AllocVar(ret); +ret->chrom = cloneString(row[0]); +if (row[1] != NULL) + { + ret->chromStart = needMem(sizeof(*(ret->chromStart))); + *(ret->chromStart) = sqlUnsigned(row[1]); + } +else + { + ret->chromStart = NULL; + } +if (row[2] != NULL) + { + ret->chromEnd = needMem(sizeof(*(ret->chromEnd))); + *(ret->chromEnd) = sqlUnsigned(row[2]); + } +else + { + ret->chromEnd = NULL; + } +ret->prediction = cloneString(row[3]); +ret->basedOn = cloneString(row[4]); +ret->geneName = cloneString(row[5]); +ret->aaChange = cloneString(row[6]); +return ret; +} + +struct pgPolyphenPred *pgPolyphenPredLoadAll(char *fileName) +/* Load all pgPolyphenPred from a whitespace-separated file. + * Dispose of this with pgPolyphenPredFreeList(). */ +{ +struct pgPolyphenPred *list = NULL, *el; +struct lineFile *lf = lineFileOpen(fileName, TRUE); +char *row[7]; + +while (lineFileRow(lf, row)) + { + el = pgPolyphenPredLoadWithNull(row); + slAddHead(&list, el); + } +lineFileClose(&lf); +slReverse(&list); +return list; +} + +struct pgPolyphenPred *pgPolyphenPredLoadAllByChar(char *fileName, char chopper) +/* Load all pgPolyphenPred from a chopper separated file. + * Dispose of this with pgPolyphenPredFreeList(). */ +{ +struct pgPolyphenPred *list = NULL, *el; +struct lineFile *lf = lineFileOpen(fileName, TRUE); +char *row[7]; + +while (lineFileNextCharRow(lf, chopper, row, ArraySize(row))) + { + el = pgPolyphenPredLoadWithNull(row); + slAddHead(&list, el); + } +lineFileClose(&lf); +slReverse(&list); +return list; +} + +struct pgPolyphenPred *pgPolyphenPredCommaIn(char **pS, struct pgPolyphenPred *ret) +/* Create a pgPolyphenPred out of a comma separated string. + * This will fill in ret if non-null, otherwise will + * return a new pgPolyphenPred */ +{ +char *s = *pS; + +if (ret == NULL) + AllocVar(ret); +ret->chrom = sqlStringComma(&s); +ret->chromStart = needMem(sizeof(unsigned)); +*(ret->chromStart) = sqlUnsignedComma(&s); +ret->chromEnd = needMem(sizeof(unsigned)); +*(ret->chromEnd) = sqlUnsignedComma(&s); +ret->prediction = sqlStringComma(&s); +ret->basedOn = sqlStringComma(&s); +ret->geneName = sqlStringComma(&s); +ret->aaChange = sqlStringComma(&s); +*pS = s; +return ret; +} + +void pgPolyphenPredFree(struct pgPolyphenPred **pEl) +/* Free a single dynamically allocated pgPolyphenPred such as created + * with pgPolyphenPredLoad(). */ +{ +struct pgPolyphenPred *el; + +if ((el = *pEl) == NULL) return; +freeMem(el->chrom); +freeMem(el->prediction); +freeMem(el->basedOn); +freeMem(el->geneName); +freeMem(el->aaChange); +freez(pEl); +} + +void pgPolyphenPredFreeList(struct pgPolyphenPred **pList) +/* Free a list of dynamically allocated pgPolyphenPred's */ +{ +struct pgPolyphenPred *el, *next; + +for (el = *pList; el != NULL; el = next) + { + next = el->next; + pgPolyphenPredFree(&el); + } +*pList = NULL; +} + +void pgPolyphenPredOutput(struct pgPolyphenPred *el, FILE *f, char sep, char lastSep) +/* Print out pgPolyphenPred. 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->prediction); +if (sep == ',') fputc('"',f); +fputc(sep,f); +if (sep == ',') fputc('"',f); +fprintf(f, "%s", el->basedOn); +if (sep == ',') fputc('"',f); +fputc(sep,f); +if (sep == ',') fputc('"',f); +fprintf(f, "%s", el->geneName); +if (sep == ',') fputc('"',f); +fputc(sep,f); +if (sep == ',') fputc('"',f); +fprintf(f, "%s", el->aaChange); +if (sep == ',') fputc('"',f); +fputc(lastSep,f); +} + +/* -------------------------------- End autoSql Generated Code -------------------------------- */ + +void printPgPolyphenPred (char *db, char *tableName, struct pgSnp *item) +/* print the predictions for an hgc item click for a pgSnp track */ +{ +struct pgPolyphenPred *el; +struct sqlResult *sr; +char **row; +char query[512]; +struct sqlConnection *conn = hAllocConn(db); + +sqlSafef(query, sizeof(query), "select * from %s where chrom = '%s' and chromStart = %d and chromEnd = %d", + tableName, item->chrom, item->chromStart, item->chromEnd); +sr = sqlGetResult(conn, query); +while ((row = sqlNextRow(sr)) != NULL) + { + el = pgPolyphenPredLoadWithNull(row); + printf("
Polyphen prediction: %s\n", el->prediction); + printf("\n"); + } +} +