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/mammalPsg.c src/hg/cgilib/mammalPsg.c new file mode 100644 index 0000000..38e555b --- /dev/null +++ src/hg/cgilib/mammalPsg.c @@ -0,0 +1,295 @@ +/* mammalPsg.c was originally generated by the autoSql program, which also + * generated mammalPsg.h and mammalPsg.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 "mammalPsg.h" + + +struct mammalPsg *mammalPsgLoad(char **row) +/* Load a mammalPsg from row fetched with select * from mammalPsg + * from database. Dispose of this with mammalPsgFree(). */ +{ +struct mammalPsg *ret; + +AllocVar(ret); +ret->blockCount = sqlSigned(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]); +safecpy(ret->strand, sizeof(ret->strand), row[5]); +ret->thickStart = sqlUnsigned(row[6]); +ret->thickEnd = sqlUnsigned(row[7]); +ret->reserved = sqlUnsigned(row[8]); +{ +int sizeOne; +sqlSignedDynamicArray(row[10], &ret->blockSizes, &sizeOne); +assert(sizeOne == ret->blockCount); +} +{ +int sizeOne; +sqlSignedDynamicArray(row[11], &ret->chromStarts, &sizeOne); +assert(sizeOne == ret->blockCount); +} +ret->lrtAllPValue = sqlFloat(row[12]); +ret->lrtAllIsFdr = sqlUnsigned(row[13]); +ret->lrtPrimateBrPValue = sqlFloat(row[14]); +ret->lrtPrimateBrIsFdr = sqlUnsigned(row[15]); +ret->lrtPrimateClPValue = sqlFloat(row[16]); +ret->lrtPrimateClIsFdr = sqlUnsigned(row[17]); +ret->lrtRodentBrPValue = sqlFloat(row[18]); +ret->lrtRodentBrIsFdr = sqlUnsigned(row[19]); +ret->lrtRodentClPValue = sqlFloat(row[20]); +ret->lrtRodentClIsFdr = sqlUnsigned(row[21]); +ret->lrtHumanPValue = sqlFloat(row[22]); +ret->lrtHumanIsFdr = sqlUnsigned(row[23]); +ret->lrtChimpPValue = sqlFloat(row[24]); +ret->lrtChimpIsFdr = sqlUnsigned(row[25]); +ret->lrtHominidPValue = sqlFloat(row[26]); +ret->lrtHominidIsFdr = sqlUnsigned(row[27]); +ret->lrtMacaquePValue = sqlFloat(row[28]); +ret->lrtMacaqueIsFdr = sqlUnsigned(row[29]); +ret->bestHist = sqlUnsigned(row[30]); +ret->bestHistPP = sqlFloat(row[31]); +ret->nextBestHist = sqlUnsigned(row[32]); +ret->nextBestHistPP = sqlFloat(row[33]); +return ret; +} + +struct mammalPsg *mammalPsgLoadAll(char *fileName) +/* Load all mammalPsg from a whitespace-separated file. + * Dispose of this with mammalPsgFreeList(). */ +{ +struct mammalPsg *list = NULL, *el; +struct lineFile *lf = lineFileOpen(fileName, TRUE); +char *row[34]; + +while (lineFileRow(lf, row)) + { + el = mammalPsgLoad(row); + slAddHead(&list, el); + } +lineFileClose(&lf); +slReverse(&list); +return list; +} + +struct mammalPsg *mammalPsgLoadAllByChar(char *fileName, char chopper) +/* Load all mammalPsg from a chopper separated file. + * Dispose of this with mammalPsgFreeList(). */ +{ +struct mammalPsg *list = NULL, *el; +struct lineFile *lf = lineFileOpen(fileName, TRUE); +char *row[34]; + +while (lineFileNextCharRow(lf, chopper, row, ArraySize(row))) + { + el = mammalPsgLoad(row); + slAddHead(&list, el); + } +lineFileClose(&lf); +slReverse(&list); +return list; +} + +struct mammalPsg *mammalPsgCommaIn(char **pS, struct mammalPsg *ret) +/* Create a mammalPsg out of a comma separated string. + * This will fill in ret if non-null, otherwise will + * return a new mammalPsg */ +{ +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->reserved = sqlUnsignedComma(&s); +ret->blockCount = sqlSignedComma(&s); +{ +int i; +s = sqlEatChar(s, '{'); +AllocArray(ret->blockSizes, ret->blockCount); +for (i=0; i<ret->blockCount; ++i) + { + ret->blockSizes[i] = sqlSignedComma(&s); + } +s = sqlEatChar(s, '}'); +s = sqlEatChar(s, ','); +} +{ +int i; +s = sqlEatChar(s, '{'); +AllocArray(ret->chromStarts, ret->blockCount); +for (i=0; i<ret->blockCount; ++i) + { + ret->chromStarts[i] = sqlSignedComma(&s); + } +s = sqlEatChar(s, '}'); +s = sqlEatChar(s, ','); +} +ret->lrtAllPValue = sqlFloatComma(&s); +ret->lrtAllIsFdr = sqlUnsignedComma(&s); +ret->lrtPrimateBrPValue = sqlFloatComma(&s); +ret->lrtPrimateBrIsFdr = sqlUnsignedComma(&s); +ret->lrtPrimateClPValue = sqlFloatComma(&s); +ret->lrtPrimateClIsFdr = sqlUnsignedComma(&s); +ret->lrtRodentBrPValue = sqlFloatComma(&s); +ret->lrtRodentBrIsFdr = sqlUnsignedComma(&s); +ret->lrtRodentClPValue = sqlFloatComma(&s); +ret->lrtRodentClIsFdr = sqlUnsignedComma(&s); +ret->lrtHumanPValue = sqlFloatComma(&s); +ret->lrtHumanIsFdr = sqlUnsignedComma(&s); +ret->lrtChimpPValue = sqlFloatComma(&s); +ret->lrtChimpIsFdr = sqlUnsignedComma(&s); +ret->lrtHominidPValue = sqlFloatComma(&s); +ret->lrtHominidIsFdr = sqlUnsignedComma(&s); +ret->lrtMacaquePValue = sqlFloatComma(&s); +ret->lrtMacaqueIsFdr = sqlUnsignedComma(&s); +ret->bestHist = sqlUnsignedComma(&s); +ret->bestHistPP = sqlFloatComma(&s); +ret->nextBestHist = sqlUnsignedComma(&s); +ret->nextBestHistPP = sqlFloatComma(&s); +*pS = s; +return ret; +} + +void mammalPsgFree(struct mammalPsg **pEl) +/* Free a single dynamically allocated mammalPsg such as created + * with mammalPsgLoad(). */ +{ +struct mammalPsg *el; + +if ((el = *pEl) == NULL) return; +freeMem(el->chrom); +freeMem(el->name); +freeMem(el->blockSizes); +freeMem(el->chromStarts); +freez(pEl); +} + +void mammalPsgFreeList(struct mammalPsg **pList) +/* Free a list of dynamically allocated mammalPsg's */ +{ +struct mammalPsg *el, *next; + +for (el = *pList; el != NULL; el = next) + { + next = el->next; + mammalPsgFree(&el); + } +*pList = NULL; +} + +void mammalPsgOutput(struct mammalPsg *el, FILE *f, char sep, char lastSep) +/* Print out mammalPsg. 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->reserved); +fputc(sep,f); +fprintf(f, "%d", el->blockCount); +fputc(sep,f); +{ +int i; +if (sep == ',') fputc('{',f); +for (i=0; i<el->blockCount; ++i) + { + fprintf(f, "%d", el->blockSizes[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, "%d", el->chromStarts[i]); + fputc(',', f); + } +if (sep == ',') fputc('}',f); +} +fputc(sep,f); +fprintf(f, "%g", el->lrtAllPValue); +fputc(sep,f); +fprintf(f, "%u", el->lrtAllIsFdr); +fputc(sep,f); +fprintf(f, "%g", el->lrtPrimateBrPValue); +fputc(sep,f); +fprintf(f, "%u", el->lrtPrimateBrIsFdr); +fputc(sep,f); +fprintf(f, "%g", el->lrtPrimateClPValue); +fputc(sep,f); +fprintf(f, "%u", el->lrtPrimateClIsFdr); +fputc(sep,f); +fprintf(f, "%g", el->lrtRodentBrPValue); +fputc(sep,f); +fprintf(f, "%u", el->lrtRodentBrIsFdr); +fputc(sep,f); +fprintf(f, "%g", el->lrtRodentClPValue); +fputc(sep,f); +fprintf(f, "%u", el->lrtRodentClIsFdr); +fputc(sep,f); +fprintf(f, "%g", el->lrtHumanPValue); +fputc(sep,f); +fprintf(f, "%u", el->lrtHumanIsFdr); +fputc(sep,f); +fprintf(f, "%g", el->lrtChimpPValue); +fputc(sep,f); +fprintf(f, "%u", el->lrtChimpIsFdr); +fputc(sep,f); +fprintf(f, "%g", el->lrtHominidPValue); +fputc(sep,f); +fprintf(f, "%u", el->lrtHominidIsFdr); +fputc(sep,f); +fprintf(f, "%g", el->lrtMacaquePValue); +fputc(sep,f); +fprintf(f, "%u", el->lrtMacaqueIsFdr); +fputc(sep,f); +fprintf(f, "%u", el->bestHist); +fputc(sep,f); +fprintf(f, "%g", el->bestHistPP); +fputc(sep,f); +fprintf(f, "%u", el->nextBestHist); +fputc(sep,f); +fprintf(f, "%g", el->nextBestHistPP); +fputc(lastSep,f); +} + +/* -------------------------------- End autoSql Generated Code -------------------------------- */ +