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/putaInfo.c src/hg/cgilib/putaInfo.c new file mode 100644 index 0000000..0ee0709 --- /dev/null +++ src/hg/cgilib/putaInfo.c @@ -0,0 +1,347 @@ +/* putaInfo.c was originally generated by the autoSql program, which also + * generated putaInfo.h and putaInfo.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 "putaInfo.h" + + +struct putaInfo *putaInfoLoad(char **row) +/* Load a putaInfo from row fetched with select * from putaInfo + * from database. Dispose of this with putaInfoFree(). */ +{ +struct putaInfo *ret; + +AllocVar(ret); +ret->blockCount = sqlUnsigned(row[9]); +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]); +ret->strand = cloneString(row[5]); +ret->oChrom = cloneString(row[6]); +ret->oChromStart = sqlUnsigned(row[7]); +ret->oChromEnd = sqlUnsigned(row[8]); +ret->stop = sqlUnsigned(row[10]); +sqlUnsignedArray(row[11], ret->tExons, 2); +sqlUnsignedArray(row[12], ret->qExons, 4); +sqlUnsignedArray(row[13], ret->qBases, 4); +sqlUnsignedArray(row[14], ret->repeats, 2); +{ +int sizeOne; +sqlUnsignedDynamicArray(row[15], &ret->stops, &sizeOne); +assert(sizeOne == ret->blockCount); +} +sqlDoubleArray(row[16], ret->id, 2); +return ret; +} + +struct putaInfo *putaInfoLoadAll(char *fileName) +/* Load all putaInfo from a whitespace-separated file. + * Dispose of this with putaInfoFreeList(). */ +{ +struct putaInfo *list = NULL, *el; +struct lineFile *lf = lineFileOpen(fileName, TRUE); +char *row[17]; + +while (lineFileRow(lf, row)) + { + el = putaInfoLoad(row); + slAddHead(&list, el); + } +lineFileClose(&lf); +slReverse(&list); +return list; +} + +struct putaInfo *putaInfoLoadAllByChar(char *fileName, char chopper) +/* Load all putaInfo from a chopper separated file. + * Dispose of this with putaInfoFreeList(). */ +{ +struct putaInfo *list = NULL, *el; +struct lineFile *lf = lineFileOpen(fileName, TRUE); +char *row[17]; + +while (lineFileNextCharRow(lf, chopper, row, ArraySize(row))) + { + el = putaInfoLoad(row); + slAddHead(&list, el); + } +lineFileClose(&lf); +slReverse(&list); +return list; +} + +struct putaInfo *putaInfoLoadByQuery(struct sqlConnection *conn, char *query) +/* Load all putaInfo 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 putaInfoFreeList(). */ +{ +struct putaInfo *list = NULL, *el; +struct sqlResult *sr; +char **row; + +sr = sqlGetResult(conn, query); +while ((row = sqlNextRow(sr)) != NULL) + { + el = putaInfoLoad(row); + slAddHead(&list, el); + } +slReverse(&list); +sqlFreeResult(&sr); +return list; +} + +void putaInfoSaveToDb(struct sqlConnection *conn, struct putaInfo *el, char *tableName, int updateSize) +/* Save putaInfo 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); +char *tExonsArray, *qExonsArray, *qBasesArray, *repeatsArray, *stopsArray, *idArray; +tExonsArray = sqlUnsignedArrayToString(el->tExons, 2); +qExonsArray = sqlUnsignedArrayToString(el->qExons, 4); +qBasesArray = sqlUnsignedArrayToString(el->qBases, 4); +repeatsArray = sqlUnsignedArrayToString(el->repeats, 2); +stopsArray = sqlUnsignedArrayToString(el->stops, el->blockCount); +idArray = sqlDoubleArrayToString(el->id, 2); +sqlDyStringPrintf(update, "insert into %s values ( '%s',%u,%u,'%s',%u,'%s','%s',%u,%u,%u,%u,'%s','%s','%s','%s','%s','%s')", + tableName, el->chrom, el->chromStart, el->chromEnd, el->name, el->score, el->strand, el->oChrom, el->oChromStart, el->oChromEnd, el->blockCount, el->stop, tExonsArray , qExonsArray , qBasesArray , repeatsArray , stopsArray , idArray ); +sqlUpdate(conn, update->string); +freeDyString(&update); +freez(&tExonsArray); +freez(&qExonsArray); +freez(&qBasesArray); +freez(&repeatsArray); +freez(&stopsArray); +freez(&idArray); +} + + +struct putaInfo *putaInfoCommaIn(char **pS, struct putaInfo *ret) +/* Create a putaInfo out of a comma separated string. + * This will fill in ret if non-null, otherwise will + * return a new putaInfo */ +{ +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); +ret->strand = sqlStringComma(&s); +ret->oChrom = sqlStringComma(&s); +ret->oChromStart = sqlUnsignedComma(&s); +ret->oChromEnd = sqlUnsignedComma(&s); +ret->blockCount = sqlUnsignedComma(&s); +ret->stop = sqlUnsignedComma(&s); +{ +int i; +s = sqlEatChar(s, '{'); +for (i=0; i<2; ++i) + { + ret->tExons[i] = sqlUnsignedComma(&s); + } +s = sqlEatChar(s, '}'); +s = sqlEatChar(s, ','); +} +{ +int i; +s = sqlEatChar(s, '{'); +for (i=0; i<4; ++i) + { + ret->qExons[i] = sqlUnsignedComma(&s); + } +s = sqlEatChar(s, '}'); +s = sqlEatChar(s, ','); +} +{ +int i; +s = sqlEatChar(s, '{'); +for (i=0; i<4; ++i) + { + ret->qBases[i] = sqlUnsignedComma(&s); + } +s = sqlEatChar(s, '}'); +s = sqlEatChar(s, ','); +} +{ +int i; +s = sqlEatChar(s, '{'); +for (i=0; i<2; ++i) + { + ret->repeats[i] = sqlUnsignedComma(&s); + } +s = sqlEatChar(s, '}'); +s = sqlEatChar(s, ','); +} +{ +int i; +s = sqlEatChar(s, '{'); +AllocArray(ret->stops, ret->blockCount); +for (i=0; i<ret->blockCount; ++i) + { + ret->stops[i] = sqlUnsignedComma(&s); + } +s = sqlEatChar(s, '}'); +s = sqlEatChar(s, ','); +} +{ +int i; +s = sqlEatChar(s, '{'); +for (i=0; i<2; ++i) + { + ret->id[i] = sqlDoubleComma(&s); + } +s = sqlEatChar(s, '}'); +s = sqlEatChar(s, ','); +} +*pS = s; +return ret; +} + +void putaInfoFree(struct putaInfo **pEl) +/* Free a single dynamically allocated putaInfo such as created + * with putaInfoLoad(). */ +{ +struct putaInfo *el; + +if ((el = *pEl) == NULL) return; +freeMem(el->chrom); +freeMem(el->name); +freeMem(el->strand); +freeMem(el->oChrom); +freeMem(el->stops); +freez(pEl); +} + +void putaInfoFreeList(struct putaInfo **pList) +/* Free a list of dynamically allocated putaInfo's */ +{ +struct putaInfo *el, *next; + +for (el = *pList; el != NULL; el = next) + { + next = el->next; + putaInfoFree(&el); + } +*pList = NULL; +} + +void putaInfoOutput(struct putaInfo *el, FILE *f, char sep, char lastSep) +/* Print out putaInfo. 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); +if (sep == ',') fputc('"',f); +fprintf(f, "%s", el->oChrom); +if (sep == ',') fputc('"',f); +fputc(sep,f); +fprintf(f, "%u", el->oChromStart); +fputc(sep,f); +fprintf(f, "%u", el->oChromEnd); +fputc(sep,f); +fprintf(f, "%u", el->blockCount); +fputc(sep,f); +fprintf(f, "%u", el->stop); +fputc(sep,f); +{ +int i; +if (sep == ',') fputc('{',f); +for (i=0; i<2; ++i) + { + fprintf(f, "%u", el->tExons[i]); + fputc(',', f); + } +if (sep == ',') fputc('}',f); +} +fputc(sep,f); +{ +int i; +if (sep == ',') fputc('{',f); +for (i=0; i<4; ++i) + { + fprintf(f, "%u", el->qExons[i]); + fputc(',', f); + } +if (sep == ',') fputc('}',f); +} +fputc(sep,f); +{ +int i; +if (sep == ',') fputc('{',f); +for (i=0; i<4; ++i) + { + fprintf(f, "%u", el->qBases[i]); + fputc(',', f); + } +if (sep == ',') fputc('}',f); +} +fputc(sep,f); +{ +int i; +if (sep == ',') fputc('{',f); +for (i=0; i<2; ++i) + { + fprintf(f, "%u", el->repeats[i]); + fputc(',', f); + } +if (sep == ',') fputc('}',f); +} +fputc(sep,f); +{ +int i; +if (sep == ',') fputc('{',f); +for (i=0; i<el->blockCount; ++i) + { + fprintf(f, "%u", el->stops[i]); + fputc(',', f); + } +if (sep == ',') fputc('}',f); +} +fputc(sep,f); +{ +int i; +if (sep == ',') fputc('{',f); +for (i=0; i<2; ++i) + { + fprintf(f, "%g", el->id[i]); + fputc(',', f); + } +if (sep == ',') fputc('}',f); +} +fputc(lastSep,f); +} + +/* -------------------------------- End autoSql Generated Code -------------------------------- */ +