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/dbSnpDetails.c src/hg/lib/dbSnpDetails.c deleted file mode 100644 index bbe8a1a..0000000 --- src/hg/lib/dbSnpDetails.c +++ /dev/null @@ -1,346 +0,0 @@ -/* dbSnpDetails.c was originally generated by the autoSql program, which also - * generated dbSnpDetails.h and dbSnpDetails.sql. This module links the database and - * the RAM representation of objects. */ - -#include "common.h" -#include "linefile.h" -#include "dystring.h" -#include "jksql.h" -#include "dbSnpDetails.h" - - - -char *dbSnpDetailsCommaSepFieldNames = "name,freqSourceCount,alleleCounts,alleleTotals,soTermCount,soTerms,clinVarCount,clinVarAccs,clinVarSigs,submitterCount,submitters,pubMedIdCount,pubMedIds"; - -struct dbSnpDetails *dbSnpDetailsLoad(char **row) -/* Load a dbSnpDetails from row fetched with select * from dbSnpDetails - * from database. Dispose of this with dbSnpDetailsFree(). */ -{ -struct dbSnpDetails *ret; - -AllocVar(ret); -ret->freqSourceCount = sqlSigned(row[1]); -ret->soTermCount = sqlSigned(row[4]); -ret->clinVarCount = sqlSigned(row[6]); -ret->submitterCount = sqlSigned(row[9]); -ret->pubMedIdCount = sqlSigned(row[11]); -ret->name = cloneString(row[0]); -{ -int sizeOne; -sqlStringDynamicArray(row[2], &ret->alleleCounts, &sizeOne); -assert(sizeOne == ret->freqSourceCount); -} -{ -int sizeOne; -sqlSignedDynamicArray(row[3], &ret->alleleTotals, &sizeOne); -assert(sizeOne == ret->freqSourceCount); -} -{ -int sizeOne; -sqlSignedDynamicArray(row[5], &ret->soTerms, &sizeOne); -assert(sizeOne == ret->soTermCount); -} -{ -int sizeOne; -sqlStringDynamicArray(row[7], &ret->clinVarAccs, &sizeOne); -assert(sizeOne == ret->clinVarCount); -} -{ -int sizeOne; -sqlStringDynamicArray(row[8], &ret->clinVarSigs, &sizeOne); -assert(sizeOne == ret->clinVarCount); -} -{ -int sizeOne; -sqlStringDynamicArray(row[10], &ret->submitters, &sizeOne); -assert(sizeOne == ret->submitterCount); -} -{ -int sizeOne; -sqlSignedDynamicArray(row[12], &ret->pubMedIds, &sizeOne); -assert(sizeOne == ret->pubMedIdCount); -} -return ret; -} - -struct dbSnpDetails *dbSnpDetailsLoadAll(char *fileName) -/* Load all dbSnpDetails from a whitespace-separated file. - * Dispose of this with dbSnpDetailsFreeList(). */ -{ -struct dbSnpDetails *list = NULL, *el; -struct lineFile *lf = lineFileOpen(fileName, TRUE); -char *row[13]; - -while (lineFileRow(lf, row)) - { - el = dbSnpDetailsLoad(row); - slAddHead(&list, el); - } -lineFileClose(&lf); -slReverse(&list); -return list; -} - -struct dbSnpDetails *dbSnpDetailsLoadAllByChar(char *fileName, char chopper) -/* Load all dbSnpDetails from a chopper separated file. - * Dispose of this with dbSnpDetailsFreeList(). */ -{ -struct dbSnpDetails *list = NULL, *el; -struct lineFile *lf = lineFileOpen(fileName, TRUE); -char *row[13]; - -while (lineFileNextCharRow(lf, chopper, row, ArraySize(row))) - { - el = dbSnpDetailsLoad(row); - slAddHead(&list, el); - } -lineFileClose(&lf); -slReverse(&list); -return list; -} - -struct dbSnpDetails *dbSnpDetailsCommaIn(char **pS, struct dbSnpDetails *ret) -/* Create a dbSnpDetails out of a comma separated string. - * This will fill in ret if non-null, otherwise will - * return a new dbSnpDetails */ -{ -char *s = *pS; - -if (ret == NULL) - AllocVar(ret); -ret->name = sqlStringComma(&s); -ret->freqSourceCount = sqlSignedComma(&s); -{ -int i; -s = sqlEatChar(s, '{'); -AllocArray(ret->alleleCounts, ret->freqSourceCount); -for (i=0; i<ret->freqSourceCount; ++i) - { - ret->alleleCounts[i] = sqlStringComma(&s); - } -s = sqlEatChar(s, '}'); -s = sqlEatChar(s, ','); -} -{ -int i; -s = sqlEatChar(s, '{'); -AllocArray(ret->alleleTotals, ret->freqSourceCount); -for (i=0; i<ret->freqSourceCount; ++i) - { - ret->alleleTotals[i] = sqlSignedComma(&s); - } -s = sqlEatChar(s, '}'); -s = sqlEatChar(s, ','); -} -ret->soTermCount = sqlSignedComma(&s); -{ -int i; -s = sqlEatChar(s, '{'); -AllocArray(ret->soTerms, ret->soTermCount); -for (i=0; i<ret->soTermCount; ++i) - { - ret->soTerms[i] = sqlSignedComma(&s); - } -s = sqlEatChar(s, '}'); -s = sqlEatChar(s, ','); -} -ret->clinVarCount = sqlSignedComma(&s); -{ -int i; -s = sqlEatChar(s, '{'); -AllocArray(ret->clinVarAccs, ret->clinVarCount); -for (i=0; i<ret->clinVarCount; ++i) - { - ret->clinVarAccs[i] = sqlStringComma(&s); - } -s = sqlEatChar(s, '}'); -s = sqlEatChar(s, ','); -} -{ -int i; -s = sqlEatChar(s, '{'); -AllocArray(ret->clinVarSigs, ret->clinVarCount); -for (i=0; i<ret->clinVarCount; ++i) - { - ret->clinVarSigs[i] = sqlStringComma(&s); - } -s = sqlEatChar(s, '}'); -s = sqlEatChar(s, ','); -} -ret->submitterCount = sqlSignedComma(&s); -{ -int i; -s = sqlEatChar(s, '{'); -AllocArray(ret->submitters, ret->submitterCount); -for (i=0; i<ret->submitterCount; ++i) - { - ret->submitters[i] = sqlStringComma(&s); - } -s = sqlEatChar(s, '}'); -s = sqlEatChar(s, ','); -} -ret->pubMedIdCount = sqlSignedComma(&s); -{ -int i; -s = sqlEatChar(s, '{'); -AllocArray(ret->pubMedIds, ret->pubMedIdCount); -for (i=0; i<ret->pubMedIdCount; ++i) - { - ret->pubMedIds[i] = sqlSignedComma(&s); - } -s = sqlEatChar(s, '}'); -s = sqlEatChar(s, ','); -} -*pS = s; -return ret; -} - -void dbSnpDetailsFree(struct dbSnpDetails **pEl) -/* Free a single dynamically allocated dbSnpDetails such as created - * with dbSnpDetailsLoad(). */ -{ -struct dbSnpDetails *el; - -if ((el = *pEl) == NULL) return; -freeMem(el->name); -/* All strings in alleleCounts are allocated at once, so only need to free first. */ -if (el->alleleCounts != NULL) - freeMem(el->alleleCounts[0]); -freeMem(el->alleleCounts); -freeMem(el->alleleTotals); -freeMem(el->soTerms); -/* All strings in clinVarAccs are allocated at once, so only need to free first. */ -if (el->clinVarAccs != NULL) - freeMem(el->clinVarAccs[0]); -freeMem(el->clinVarAccs); -/* All strings in clinVarSigs are allocated at once, so only need to free first. */ -if (el->clinVarSigs != NULL) - freeMem(el->clinVarSigs[0]); -freeMem(el->clinVarSigs); -/* All strings in submitters are allocated at once, so only need to free first. */ -if (el->submitters != NULL) - freeMem(el->submitters[0]); -freeMem(el->submitters); -freeMem(el->pubMedIds); -freez(pEl); -} - -void dbSnpDetailsFreeList(struct dbSnpDetails **pList) -/* Free a list of dynamically allocated dbSnpDetails's */ -{ -struct dbSnpDetails *el, *next; - -for (el = *pList; el != NULL; el = next) - { - next = el->next; - dbSnpDetailsFree(&el); - } -*pList = NULL; -} - -void dbSnpDetailsOutput(struct dbSnpDetails *el, FILE *f, char sep, char lastSep) -/* Print out dbSnpDetails. 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); -fprintf(f, "%d", el->freqSourceCount); -fputc(sep,f); -{ -int i; -if (sep == ',') fputc('{',f); -for (i=0; i<el->freqSourceCount; ++i) - { - if (sep == ',') fputc('"',f); - fprintf(f, "%s", el->alleleCounts[i]); - if (sep == ',') fputc('"',f); - fputc(',', f); - } -if (sep == ',') fputc('}',f); -} -fputc(sep,f); -{ -int i; -if (sep == ',') fputc('{',f); -for (i=0; i<el->freqSourceCount; ++i) - { - fprintf(f, "%d", el->alleleTotals[i]); - fputc(',', f); - } -if (sep == ',') fputc('}',f); -} -fputc(sep,f); -fprintf(f, "%d", el->soTermCount); -fputc(sep,f); -{ -int i; -if (sep == ',') fputc('{',f); -for (i=0; i<el->soTermCount; ++i) - { - fprintf(f, "%d", el->soTerms[i]); - fputc(',', f); - } -if (sep == ',') fputc('}',f); -} -fputc(sep,f); -fprintf(f, "%d", el->clinVarCount); -fputc(sep,f); -{ -int i; -if (sep == ',') fputc('{',f); -for (i=0; i<el->clinVarCount; ++i) - { - if (sep == ',') fputc('"',f); - fprintf(f, "%s", el->clinVarAccs[i]); - if (sep == ',') fputc('"',f); - fputc(',', f); - } -if (sep == ',') fputc('}',f); -} -fputc(sep,f); -{ -int i; -if (sep == ',') fputc('{',f); -for (i=0; i<el->clinVarCount; ++i) - { - if (sep == ',') fputc('"',f); - fprintf(f, "%s", el->clinVarSigs[i]); - if (sep == ',') fputc('"',f); - fputc(',', f); - } -if (sep == ',') fputc('}',f); -} -fputc(sep,f); -fprintf(f, "%d", el->submitterCount); -fputc(sep,f); -{ -int i; -if (sep == ',') fputc('{',f); -for (i=0; i<el->submitterCount; ++i) - { - if (sep == ',') fputc('"',f); - fprintf(f, "%s", el->submitters[i]); - if (sep == ',') fputc('"',f); - fputc(',', f); - } -if (sep == ',') fputc('}',f); -} -fputc(sep,f); -fprintf(f, "%d", el->pubMedIdCount); -fputc(sep,f); -{ -int i; -if (sep == ',') fputc('{',f); -for (i=0; i<el->pubMedIdCount; ++i) - { - fprintf(f, "%d", el->pubMedIds[i]); - fputc(',', f); - } -if (sep == ',') fputc('}',f); -} -fputc(lastSep,f); -} - -/* -------------------------------- End autoSql Generated Code -------------------------------- */ -