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/lib/pgPolyphenPred.c src/hg/lib/pgPolyphenPred.c deleted file mode 100644 index 9088c45..0000000 --- src/hg/lib/pgPolyphenPred.c +++ /dev/null @@ -1,222 +0,0 @@ -/* 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"); - } -} -