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/fishClones.c src/hg/lib/fishClones.c deleted file mode 100644 index 29f535c..0000000 --- src/hg/lib/fishClones.c +++ /dev/null @@ -1,278 +0,0 @@ -/* fishClones.c was originally generated by the autoSql program, which also - * generated fishClones.h and fishClones.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 "jksql.h" -#include "fishClones.h" - - -struct fishClones *fishClonesLoad(char **row) -/* Load a fishClones from row fetched with select * from fishClones - * from database. Dispose of this with fishClonesFree(). */ -{ -struct fishClones *ret; -int sizeOne; - -AllocVar(ret); -ret->placeCount = sqlUnsigned(row[5]); -ret->accCount = sqlUnsigned(row[10]); -ret->stsCount = sqlUnsigned(row[12]); -ret->beCount = sqlUnsigned(row[14]); -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]); -sqlStringDynamicArray(row[6], &ret->bandStarts, &sizeOne); -assert(sizeOne == ret->placeCount); -sqlStringDynamicArray(row[7], &ret->bandEnds, &sizeOne); -assert(sizeOne == ret->placeCount); -sqlStringDynamicArray(row[8], &ret->labs, &sizeOne); -assert(sizeOne == ret->placeCount); -ret->placeType = cloneString(row[9]); -sqlStringDynamicArray(row[11], &ret->accNames, &sizeOne); -assert(sizeOne == ret->accCount); -sqlStringDynamicArray(row[13], &ret->stsNames, &sizeOne); -assert(sizeOne == ret->stsCount); -sqlStringDynamicArray(row[15], &ret->beNames, &sizeOne); -assert(sizeOne == ret->beCount); -return ret; -} - -struct fishClones *fishClonesLoadAll(char *fileName) -/* Load all fishClones from a tab-separated file. - * Dispose of this with fishClonesFreeList(). */ -{ -struct fishClones *list = NULL, *el; -struct lineFile *lf = lineFileOpen(fileName, TRUE); -char *row[16]; - -while (lineFileRow(lf, row)) - { - el = fishClonesLoad(row); - slAddHead(&list, el); - } -lineFileClose(&lf); -slReverse(&list); -return list; -} - -struct fishClones *fishClonesCommaIn(char **pS, struct fishClones *ret) -/* Create a fishClones out of a comma separated string. - * This will fill in ret if non-null, otherwise will - * return a new fishClones */ -{ -char *s = *pS; -int i; - -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->placeCount = sqlUnsignedComma(&s); -s = sqlEatChar(s, '{'); -AllocArray(ret->bandStarts, ret->placeCount); -for (i=0; i<ret->placeCount; ++i) - { - ret->bandStarts[i] = sqlStringComma(&s); - } -s = sqlEatChar(s, '}'); -s = sqlEatChar(s, ','); -s = sqlEatChar(s, '{'); -AllocArray(ret->bandEnds, ret->placeCount); -for (i=0; i<ret->placeCount; ++i) - { - ret->bandEnds[i] = sqlStringComma(&s); - } -s = sqlEatChar(s, '}'); -s = sqlEatChar(s, ','); -s = sqlEatChar(s, '{'); -AllocArray(ret->labs, ret->placeCount); -for (i=0; i<ret->placeCount; ++i) - { - ret->labs[i] = sqlStringComma(&s); - } -s = sqlEatChar(s, '}'); -s = sqlEatChar(s, ','); -ret->placeType = sqlStringComma(&s); -ret->accCount = sqlUnsignedComma(&s); -s = sqlEatChar(s, '{'); -AllocArray(ret->accNames, ret->accCount); -for (i=0; i<ret->accCount; ++i) - { - ret->accNames[i] = sqlStringComma(&s); - } -s = sqlEatChar(s, '}'); -s = sqlEatChar(s, ','); -ret->stsCount = sqlUnsignedComma(&s); -s = sqlEatChar(s, '{'); -AllocArray(ret->stsNames, ret->stsCount); -for (i=0; i<ret->stsCount; ++i) - { - ret->stsNames[i] = sqlStringComma(&s); - } -s = sqlEatChar(s, '}'); -s = sqlEatChar(s, ','); -ret->beCount = sqlUnsignedComma(&s); -s = sqlEatChar(s, '{'); -AllocArray(ret->beNames, ret->beCount); -for (i=0; i<ret->beCount; ++i) - { - ret->beNames[i] = sqlStringComma(&s); - } -s = sqlEatChar(s, '}'); -s = sqlEatChar(s, ','); -*pS = s; -return ret; -} - -void fishClonesFree(struct fishClones **pEl) -/* Free a single dynamically allocated fishClones such as created - * with fishClonesLoad(). */ -{ -struct fishClones *el; - -if ((el = *pEl) == NULL) return; -freeMem(el->chrom); -freeMem(el->name); -/* All strings in bandStarts are allocated at once, so only need to free first. */ -if (el->bandStarts != NULL) - freeMem(el->bandStarts[0]); -freeMem(el->bandStarts); -/* All strings in bandEnds are allocated at once, so only need to free first. */ -if (el->bandEnds != NULL) - freeMem(el->bandEnds[0]); -freeMem(el->bandEnds); -/* All strings in labs are allocated at once, so only need to free first. */ -if (el->labs != NULL) - freeMem(el->labs[0]); -freeMem(el->labs); -freeMem(el->placeType); -/* All strings in accNames are allocated at once, so only need to free first. */ -if (el->accNames != NULL) - freeMem(el->accNames[0]); -freeMem(el->accNames); -/* All strings in stsNames are allocated at once, so only need to free first. */ -if (el->stsNames != NULL) - freeMem(el->stsNames[0]); -freeMem(el->stsNames); -/* All strings in beNames are allocated at once, so only need to free first. */ -if (el->beNames != NULL) - freeMem(el->beNames[0]); -freeMem(el->beNames); -freez(pEl); -} - -void fishClonesFreeList(struct fishClones **pList) -/* Free a list of dynamically allocated fishClones's */ -{ -struct fishClones *el, *next; - -for (el = *pList; el != NULL; el = next) - { - next = el->next; - fishClonesFree(&el); - } -*pList = NULL; -} - -void fishClonesOutput(struct fishClones *el, FILE *f, char sep, char lastSep) -/* Print out fishClones. Separate fields with sep. Follow last field with lastSep. */ -{ -int i; -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); -fprintf(f, "%u", el->placeCount); -fputc(sep,f); -if (sep == ',') fputc('{',f); -for (i=0; i<el->placeCount; ++i) - { - if (sep == ',') fputc('"',f); - fprintf(f, "%s", el->bandStarts[i]); - if (sep == ',') fputc('"',f); - fputc(',', f); - } -if (sep == ',') fputc('}',f); -fputc(sep,f); -if (sep == ',') fputc('{',f); -for (i=0; i<el->placeCount; ++i) - { - if (sep == ',') fputc('"',f); - fprintf(f, "%s", el->bandEnds[i]); - if (sep == ',') fputc('"',f); - fputc(',', f); - } -if (sep == ',') fputc('}',f); -fputc(sep,f); -if (sep == ',') fputc('{',f); -for (i=0; i<el->placeCount; ++i) - { - if (sep == ',') fputc('"',f); - fprintf(f, "%s", el->labs[i]); - if (sep == ',') fputc('"',f); - fputc(',', f); - } -if (sep == ',') fputc('}',f); -fputc(sep,f); -if (sep == ',') fputc('"',f); -fprintf(f, "%s", el->placeType); -if (sep == ',') fputc('"',f); -fputc(sep,f); -fprintf(f, "%u", el->accCount); -fputc(sep,f); -if (sep == ',') fputc('{',f); -for (i=0; i<el->accCount; ++i) - { - if (sep == ',') fputc('"',f); - fprintf(f, "%s", el->accNames[i]); - if (sep == ',') fputc('"',f); - fputc(',', f); - } -if (sep == ',') fputc('}',f); -fputc(sep,f); -fprintf(f, "%u", el->stsCount); -fputc(sep,f); -if (sep == ',') fputc('{',f); -for (i=0; i<el->stsCount; ++i) - { - if (sep == ',') fputc('"',f); - fprintf(f, "%s", el->stsNames[i]); - if (sep == ',') fputc('"',f); - fputc(',', f); - } -if (sep == ',') fputc('}',f); -fputc(sep,f); -fprintf(f, "%u", el->beCount); -fputc(sep,f); -if (sep == ',') fputc('{',f); -for (i=0; i<el->beCount; ++i) - { - if (sep == ',') fputc('"',f); - fprintf(f, "%s", el->beNames[i]); - if (sep == ',') fputc('"',f); - fputc(',', f); - } -if (sep == ',') fputc('}',f); -fputc(lastSep,f); -} -