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/rnaHybridization.c src/hg/lib/rnaHybridization.c
deleted file mode 100644
index fbf52c8..0000000
--- src/hg/lib/rnaHybridization.c
+++ /dev/null
@@ -1,281 +0,0 @@
-/* rnaHybridization.c was originally generated by the autoSql program, which also 
- * generated rnaHybridization.h and rnaHybridization.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 "rnaHybridization.h"
-
-
-void rnaHybridizationStaticLoad(char **row, struct rnaHybridization *ret)
-/* Load a row from rnaHybridization 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->dummy = sqlUnsigned(row[4]);
-safecpy(ret->strand, sizeof(ret->strand), row[5]);
-ret->chromTarget = row[6];
-ret->chromStartTarget = sqlUnsigned(row[7]);
-ret->chromEndTarget = sqlUnsigned(row[8]);
-safecpy(ret->strandTarget, sizeof(ret->strandTarget), row[9]);
-ret->refSeqTarget = row[10];
-ret->aorfTarget = row[11];
-ret->igenicsTarget = row[12];
-ret->trnaTarget = row[13];
-ret->JGITarget = row[14];
-ret->patternSeq = row[15];
-ret->targetSeq = row[16];
-ret->gcContent = sqlFloat(row[17]);
-ret->matchLength = sqlUnsigned(row[18]);
-ret->targetAnnotation = sqlUnsigned(row[19]);
-}
-
-struct rnaHybridization *rnaHybridizationLoad(char **row)
-/* Load a rnaHybridization from row fetched with select * from rnaHybridization
- * from database.  Dispose of this with rnaHybridizationFree(). */
-{
-struct rnaHybridization *ret;
-
-AllocVar(ret);
-ret->chrom = cloneString(row[0]);
-ret->chromStart = sqlUnsigned(row[1]);
-ret->chromEnd = sqlUnsigned(row[2]);
-ret->name = cloneString(row[3]);
-ret->dummy = sqlUnsigned(row[4]);
-safecpy(ret->strand, sizeof(ret->strand), row[5]);
-ret->chromTarget = cloneString(row[6]);
-ret->chromStartTarget = sqlUnsigned(row[7]);
-ret->chromEndTarget = sqlUnsigned(row[8]);
-safecpy(ret->strandTarget, sizeof(ret->strandTarget), row[9]);
-ret->refSeqTarget = cloneString(row[10]);
-ret->aorfTarget = cloneString(row[11]);
-ret->igenicsTarget = cloneString(row[12]);
-ret->trnaTarget = cloneString(row[13]);
-ret->JGITarget = cloneString(row[14]);
-ret->patternSeq = cloneString(row[15]);
-ret->targetSeq = cloneString(row[16]);
-ret->gcContent = sqlFloat(row[17]);
-ret->matchLength = sqlUnsigned(row[18]);
-ret->targetAnnotation = sqlUnsigned(row[19]);
-return ret;
-}
-
-struct rnaHybridization *rnaHybridizationLoadAll(char *fileName) 
-/* Load all rnaHybridization from a whitespace-separated file.
- * Dispose of this with rnaHybridizationFreeList(). */
-{
-struct rnaHybridization *list = NULL, *el;
-struct lineFile *lf = lineFileOpen(fileName, TRUE);
-char *row[20];
-
-while (lineFileRow(lf, row))
-    {
-    el = rnaHybridizationLoad(row);
-    slAddHead(&list, el);
-    }
-lineFileClose(&lf);
-slReverse(&list);
-return list;
-}
-
-struct rnaHybridization *rnaHybridizationLoadAllByChar(char *fileName, char chopper) 
-/* Load all rnaHybridization from a chopper separated file.
- * Dispose of this with rnaHybridizationFreeList(). */
-{
-struct rnaHybridization *list = NULL, *el;
-struct lineFile *lf = lineFileOpen(fileName, TRUE);
-char *row[20];
-
-while (lineFileNextCharRow(lf, chopper, row, ArraySize(row)))
-    {
-    el = rnaHybridizationLoad(row);
-    slAddHead(&list, el);
-    }
-lineFileClose(&lf);
-slReverse(&list);
-return list;
-}
-
-struct rnaHybridization *rnaHybridizationLoadByQuery(struct sqlConnection *conn, char *query)
-/* Load all rnaHybridization 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 rnaHybridizationFreeList(). */
-{
-struct rnaHybridization *list = NULL, *el;
-struct sqlResult *sr;
-char **row;
-
-sr = sqlGetResult(conn, query);
-while ((row = sqlNextRow(sr)) != NULL)
-    {
-    el = rnaHybridizationLoad(row);
-    slAddHead(&list, el);
-    }
-slReverse(&list);
-sqlFreeResult(&sr);
-return list;
-}
-
-void rnaHybridizationSaveToDb(struct sqlConnection *conn, struct rnaHybridization *el, char *tableName, int updateSize)
-/* Save rnaHybridization 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);
-sqlDyStringPrintf(update, "insert into %s values ( '%s',%u,%u,'%s',%u,'%s','%s',%u,%u,'%s','%s','%s','%s','%s','%s','%s','%s',%g,%u,%u)", 
-	tableName,  el->chrom,  el->chromStart,  el->chromEnd,  el->name,  el->dummy,  el->strand,  el->chromTarget,  el->chromStartTarget,  el->chromEndTarget,  el->strandTarget,  el->refSeqTarget,  el->aorfTarget,  el->igenicsTarget,  el->trnaTarget,  el->JGITarget,  el->patternSeq,  el->targetSeq,  el->gcContent,  el->matchLength,  el->targetAnnotation);
-sqlUpdate(conn, update->string);
-freeDyString(&update);
-}
-
-
-struct rnaHybridization *rnaHybridizationCommaIn(char **pS, struct rnaHybridization *ret)
-/* Create a rnaHybridization out of a comma separated string. 
- * This will fill in ret if non-null, otherwise will
- * return a new rnaHybridization */
-{
-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->dummy = sqlUnsignedComma(&s);
-sqlFixedStringComma(&s, ret->strand, sizeof(ret->strand));
-ret->chromTarget = sqlStringComma(&s);
-ret->chromStartTarget = sqlUnsignedComma(&s);
-ret->chromEndTarget = sqlUnsignedComma(&s);
-sqlFixedStringComma(&s, ret->strandTarget, sizeof(ret->strandTarget));
-ret->refSeqTarget = sqlStringComma(&s);
-ret->aorfTarget = sqlStringComma(&s);
-ret->igenicsTarget = sqlStringComma(&s);
-ret->trnaTarget = sqlStringComma(&s);
-ret->JGITarget = sqlStringComma(&s);
-ret->patternSeq = sqlStringComma(&s);
-ret->targetSeq = sqlStringComma(&s);
-ret->gcContent = sqlFloatComma(&s);
-ret->matchLength = sqlUnsignedComma(&s);
-ret->targetAnnotation = sqlUnsignedComma(&s);
-*pS = s;
-return ret;
-}
-
-void rnaHybridizationFree(struct rnaHybridization **pEl)
-/* Free a single dynamically allocated rnaHybridization such as created
- * with rnaHybridizationLoad(). */
-{
-struct rnaHybridization *el;
-
-if ((el = *pEl) == NULL) return;
-freeMem(el->chrom);
-freeMem(el->name);
-freeMem(el->chromTarget);
-freeMem(el->refSeqTarget);
-freeMem(el->aorfTarget);
-freeMem(el->igenicsTarget);
-freeMem(el->trnaTarget);
-freeMem(el->JGITarget);
-freeMem(el->patternSeq);
-freeMem(el->targetSeq);
-freez(pEl);
-}
-
-void rnaHybridizationFreeList(struct rnaHybridization **pList)
-/* Free a list of dynamically allocated rnaHybridization's */
-{
-struct rnaHybridization *el, *next;
-
-for (el = *pList; el != NULL; el = next)
-    {
-    next = el->next;
-    rnaHybridizationFree(&el);
-    }
-*pList = NULL;
-}
-
-void rnaHybridizationOutput(struct rnaHybridization *el, FILE *f, char sep, char lastSep) 
-/* Print out rnaHybridization.  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->dummy);
-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->chromTarget);
-if (sep == ',') fputc('"',f);
-fputc(sep,f);
-fprintf(f, "%u", el->chromStartTarget);
-fputc(sep,f);
-fprintf(f, "%u", el->chromEndTarget);
-fputc(sep,f);
-if (sep == ',') fputc('"',f);
-fprintf(f, "%s", el->strandTarget);
-if (sep == ',') fputc('"',f);
-fputc(sep,f);
-if (sep == ',') fputc('"',f);
-fprintf(f, "%s", el->refSeqTarget);
-if (sep == ',') fputc('"',f);
-fputc(sep,f);
-if (sep == ',') fputc('"',f);
-fprintf(f, "%s", el->aorfTarget);
-if (sep == ',') fputc('"',f);
-fputc(sep,f);
-if (sep == ',') fputc('"',f);
-fprintf(f, "%s", el->igenicsTarget);
-if (sep == ',') fputc('"',f);
-fputc(sep,f);
-if (sep == ',') fputc('"',f);
-fprintf(f, "%s", el->trnaTarget);
-if (sep == ',') fputc('"',f);
-fputc(sep,f);
-if (sep == ',') fputc('"',f);
-fprintf(f, "%s", el->JGITarget);
-if (sep == ',') fputc('"',f);
-fputc(sep,f);
-if (sep == ',') fputc('"',f);
-fprintf(f, "%s", el->patternSeq);
-if (sep == ',') fputc('"',f);
-fputc(sep,f);
-if (sep == ',') fputc('"',f);
-fprintf(f, "%s", el->targetSeq);
-if (sep == ',') fputc('"',f);
-fputc(sep,f);
-fprintf(f, "%g", el->gcContent);
-fputc(sep,f);
-fprintf(f, "%u", el->matchLength);
-fputc(sep,f);
-fprintf(f, "%u", el->targetAnnotation);
-fputc(lastSep,f);
-}
-
-/* -------------------------------- End autoSql Generated Code -------------------------------- */
-