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/dgvPlus.c src/hg/cgilib/dgvPlus.c new file mode 100644 index 0000000..e4566f5 --- /dev/null +++ src/hg/cgilib/dgvPlus.c @@ -0,0 +1,258 @@ +/* dgvPlus.c was originally generated by the autoSql program, which also + * generated dgvPlus.h and dgvPlus.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 "dgvPlus.h" + + + +char *dgvPlusCommaSepFieldNames = "chrom,chromStart,chromEnd,name,score,strand,thickStart,thickEnd,itemRgb,varType,reference,pubMedId,method,platform,mergedVariants,supportingVariants,sampleSize,observedGains,observedLosses,cohortDescription,genes,samples"; + +void dgvPlusStaticLoad(char **row, struct dgvPlus *ret) +/* Load a row from dgvPlus 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->score = sqlUnsigned(row[4]); +safecpy(ret->strand, sizeof(ret->strand), row[5]); +ret->thickStart = sqlUnsigned(row[6]); +ret->thickEnd = sqlUnsigned(row[7]); +ret->itemRgb = sqlUnsigned(row[8]); +ret->varType = row[9]; +ret->reference = row[10]; +ret->pubMedId = sqlUnsigned(row[11]); +ret->method = row[12]; +ret->platform = row[13]; +ret->mergedVariants = row[14]; +ret->supportingVariants = row[15]; +ret->sampleSize = sqlUnsigned(row[16]); +ret->observedGains = sqlUnsigned(row[17]); +ret->observedLosses = sqlUnsigned(row[18]); +ret->cohortDescription = row[19]; +ret->genes = row[20]; +ret->samples = row[21]; +} + +struct dgvPlus *dgvPlusLoad(char **row) +/* Load a dgvPlus from row fetched with select * from dgvPlus + * from database. Dispose of this with dgvPlusFree(). */ +{ +struct dgvPlus *ret; + +AllocVar(ret); +ret->chrom = cloneString(row[0]); +ret->chromStart = sqlUnsigned(row[1]); +ret->chromEnd = sqlUnsigned(row[2]); +ret->name = cloneString(row[3]); +ret->score = sqlUnsigned(row[4]); +safecpy(ret->strand, sizeof(ret->strand), row[5]); +ret->thickStart = sqlUnsigned(row[6]); +ret->thickEnd = sqlUnsigned(row[7]); +ret->itemRgb = sqlUnsigned(row[8]); +ret->varType = cloneString(row[9]); +ret->reference = cloneString(row[10]); +ret->pubMedId = sqlUnsigned(row[11]); +ret->method = cloneString(row[12]); +ret->platform = cloneString(row[13]); +ret->mergedVariants = cloneString(row[14]); +ret->supportingVariants = cloneString(row[15]); +ret->sampleSize = sqlUnsigned(row[16]); +ret->observedGains = sqlUnsigned(row[17]); +ret->observedLosses = sqlUnsigned(row[18]); +ret->cohortDescription = cloneString(row[19]); +ret->genes = cloneString(row[20]); +ret->samples = cloneString(row[21]); +return ret; +} + +struct dgvPlus *dgvPlusLoadAll(char *fileName) +/* Load all dgvPlus from a whitespace-separated file. + * Dispose of this with dgvPlusFreeList(). */ +{ +struct dgvPlus *list = NULL, *el; +struct lineFile *lf = lineFileOpen(fileName, TRUE); +char *row[22]; + +while (lineFileRow(lf, row)) + { + el = dgvPlusLoad(row); + slAddHead(&list, el); + } +lineFileClose(&lf); +slReverse(&list); +return list; +} + +struct dgvPlus *dgvPlusLoadAllByChar(char *fileName, char chopper) +/* Load all dgvPlus from a chopper separated file. + * Dispose of this with dgvPlusFreeList(). */ +{ +struct dgvPlus *list = NULL, *el; +struct lineFile *lf = lineFileOpen(fileName, TRUE); +char *row[22]; + +while (lineFileNextCharRow(lf, chopper, row, ArraySize(row))) + { + el = dgvPlusLoad(row); + slAddHead(&list, el); + } +lineFileClose(&lf); +slReverse(&list); +return list; +} + +struct dgvPlus *dgvPlusCommaIn(char **pS, struct dgvPlus *ret) +/* Create a dgvPlus out of a comma separated string. + * This will fill in ret if non-null, otherwise will + * return a new dgvPlus */ +{ +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->score = sqlUnsignedComma(&s); +sqlFixedStringComma(&s, ret->strand, sizeof(ret->strand)); +ret->thickStart = sqlUnsignedComma(&s); +ret->thickEnd = sqlUnsignedComma(&s); +ret->itemRgb = sqlUnsignedComma(&s); +ret->varType = sqlStringComma(&s); +ret->reference = sqlStringComma(&s); +ret->pubMedId = sqlUnsignedComma(&s); +ret->method = sqlStringComma(&s); +ret->platform = sqlStringComma(&s); +ret->mergedVariants = sqlStringComma(&s); +ret->supportingVariants = sqlStringComma(&s); +ret->sampleSize = sqlUnsignedComma(&s); +ret->observedGains = sqlUnsignedComma(&s); +ret->observedLosses = sqlUnsignedComma(&s); +ret->cohortDescription = sqlStringComma(&s); +ret->genes = sqlStringComma(&s); +ret->samples = sqlStringComma(&s); +*pS = s; +return ret; +} + +void dgvPlusFree(struct dgvPlus **pEl) +/* Free a single dynamically allocated dgvPlus such as created + * with dgvPlusLoad(). */ +{ +struct dgvPlus *el; + +if ((el = *pEl) == NULL) return; +freeMem(el->chrom); +freeMem(el->name); +freeMem(el->varType); +freeMem(el->reference); +freeMem(el->method); +freeMem(el->platform); +freeMem(el->mergedVariants); +freeMem(el->supportingVariants); +freeMem(el->cohortDescription); +freeMem(el->genes); +freeMem(el->samples); +freez(pEl); +} + +void dgvPlusFreeList(struct dgvPlus **pList) +/* Free a list of dynamically allocated dgvPlus's */ +{ +struct dgvPlus *el, *next; + +for (el = *pList; el != NULL; el = next) + { + next = el->next; + dgvPlusFree(&el); + } +*pList = NULL; +} + +void dgvPlusOutput(struct dgvPlus *el, FILE *f, char sep, char lastSep) +/* Print out dgvPlus. 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->score); +fputc(sep,f); +if (sep == ',') fputc('"',f); +fprintf(f, "%s", el->strand); +if (sep == ',') fputc('"',f); +fputc(sep,f); +fprintf(f, "%u", el->thickStart); +fputc(sep,f); +fprintf(f, "%u", el->thickEnd); +fputc(sep,f); +fprintf(f, "%u", el->itemRgb); +fputc(sep,f); +if (sep == ',') fputc('"',f); +fprintf(f, "%s", el->varType); +if (sep == ',') fputc('"',f); +fputc(sep,f); +if (sep == ',') fputc('"',f); +fprintf(f, "%s", el->reference); +if (sep == ',') fputc('"',f); +fputc(sep,f); +fprintf(f, "%u", el->pubMedId); +fputc(sep,f); +if (sep == ',') fputc('"',f); +fprintf(f, "%s", el->method); +if (sep == ',') fputc('"',f); +fputc(sep,f); +if (sep == ',') fputc('"',f); +fprintf(f, "%s", el->platform); +if (sep == ',') fputc('"',f); +fputc(sep,f); +if (sep == ',') fputc('"',f); +fprintf(f, "%s", el->mergedVariants); +if (sep == ',') fputc('"',f); +fputc(sep,f); +if (sep == ',') fputc('"',f); +fprintf(f, "%s", el->supportingVariants); +if (sep == ',') fputc('"',f); +fputc(sep,f); +fprintf(f, "%u", el->sampleSize); +fputc(sep,f); +fprintf(f, "%u", el->observedGains); +fputc(sep,f); +fprintf(f, "%u", el->observedLosses); +fputc(sep,f); +if (sep == ',') fputc('"',f); +fprintf(f, "%s", el->cohortDescription); +if (sep == ',') fputc('"',f); +fputc(sep,f); +if (sep == ',') fputc('"',f); +fprintf(f, "%s", el->genes); +if (sep == ',') fputc('"',f); +fputc(sep,f); +if (sep == ',') fputc('"',f); +fprintf(f, "%s", el->samples); +if (sep == ',') fputc('"',f); +fputc(lastSep,f); +} + +/* -------------------------------- End autoSql Generated Code -------------------------------- */ +