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/mammalPsg.c src/hg/lib/mammalPsg.c deleted file mode 100644 index 38e555b..0000000 --- src/hg/lib/mammalPsg.c +++ /dev/null @@ -1,295 +0,0 @@ -/* 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 -------------------------------- */ -