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/protVar.c src/hg/lib/protVar.c
deleted file mode 100644
index 456e1a2..0000000
--- src/hg/lib/protVar.c
+++ /dev/null
@@ -1,695 +0,0 @@
-/* protVar.c was originally generated by the autoSql program, which also 
- * generated protVar.h and protVar.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 "protVar.h"
-
-
-void protVarStaticLoad(char **row, struct protVar *ret)
-/* Load a row from protVar table into ret.  The contents of ret will
- * be replaced at the next call to this function. */
-{
-
-ret->id = row[0];
-ret->name = row[1];
-ret->srcId = row[2];
-ret->baseChangeType = row[3];
-ret->location = row[4];
-ret->coordinateAccuracy = sqlUnsigned(row[5]);
-}
-
-struct protVar *protVarLoad(char **row)
-/* Load a protVar from row fetched with select * from protVar
- * from database.  Dispose of this with protVarFree(). */
-{
-struct protVar *ret;
-
-AllocVar(ret);
-ret->id = cloneString(row[0]);
-ret->name = cloneString(row[1]);
-ret->srcId = cloneString(row[2]);
-ret->baseChangeType = cloneString(row[3]);
-ret->location = cloneString(row[4]);
-ret->coordinateAccuracy = sqlUnsigned(row[5]);
-return ret;
-}
-
-struct protVar *protVarLoadAll(char *fileName) 
-/* Load all protVar from a whitespace-separated file.
- * Dispose of this with protVarFreeList(). */
-{
-struct protVar *list = NULL, *el;
-struct lineFile *lf = lineFileOpen(fileName, TRUE);
-char *row[6];
-
-while (lineFileRow(lf, row))
-    {
-    el = protVarLoad(row);
-    slAddHead(&list, el);
-    }
-lineFileClose(&lf);
-slReverse(&list);
-return list;
-}
-
-struct protVar *protVarLoadAllByChar(char *fileName, char chopper) 
-/* Load all protVar from a chopper separated file.
- * Dispose of this with protVarFreeList(). */
-{
-struct protVar *list = NULL, *el;
-struct lineFile *lf = lineFileOpen(fileName, TRUE);
-char *row[6];
-
-while (lineFileNextCharRow(lf, chopper, row, ArraySize(row)))
-    {
-    el = protVarLoad(row);
-    slAddHead(&list, el);
-    }
-lineFileClose(&lf);
-slReverse(&list);
-return list;
-}
-
-struct protVar *protVarLoadByQuery(struct sqlConnection *conn, char *query)
-/* Load all protVar 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 protVarFreeList(). */
-{
-struct protVar *list = NULL, *el;
-struct sqlResult *sr;
-char **row;
-
-sr = sqlGetResult(conn, query);
-while ((row = sqlNextRow(sr)) != NULL)
-    {
-    el = protVarLoad(row);
-    slAddHead(&list, el);
-    }
-slReverse(&list);
-sqlFreeResult(&sr);
-return list;
-}
-
-void protVarSaveToDb(struct sqlConnection *conn, struct protVar *el, char *tableName, int updateSize)
-/* Save protVar 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','%s','%s','%s','%s',%u)", 
-	tableName,  el->id,  el->name,  el->srcId,  el->baseChangeType,  el->location,  el->coordinateAccuracy);
-sqlUpdate(conn, update->string);
-freeDyString(&update);
-}
-
-
-struct protVar *protVarCommaIn(char **pS, struct protVar *ret)
-/* Create a protVar out of a comma separated string. 
- * This will fill in ret if non-null, otherwise will
- * return a new protVar */
-{
-char *s = *pS;
-
-if (ret == NULL)
-    AllocVar(ret);
-ret->id = sqlStringComma(&s);
-ret->name = sqlStringComma(&s);
-ret->srcId = sqlStringComma(&s);
-ret->baseChangeType = sqlStringComma(&s);
-ret->location = sqlStringComma(&s);
-ret->coordinateAccuracy = sqlUnsignedComma(&s);
-*pS = s;
-return ret;
-}
-
-void protVarFree(struct protVar **pEl)
-/* Free a single dynamically allocated protVar such as created
- * with protVarLoad(). */
-{
-struct protVar *el;
-
-if ((el = *pEl) == NULL) return;
-freeMem(el->id);
-freeMem(el->name);
-freeMem(el->srcId);
-freeMem(el->baseChangeType);
-freeMem(el->location);
-freez(pEl);
-}
-
-void protVarFreeList(struct protVar **pList)
-/* Free a list of dynamically allocated protVar's */
-{
-struct protVar *el, *next;
-
-for (el = *pList; el != NULL; el = next)
-    {
-    next = el->next;
-    protVarFree(&el);
-    }
-*pList = NULL;
-}
-
-void protVarOutput(struct protVar *el, FILE *f, char sep, char lastSep) 
-/* Print out protVar.  Separate fields with sep. Follow last field with lastSep. */
-{
-if (sep == ',') fputc('"',f);
-fprintf(f, "%s", el->id);
-if (sep == ',') fputc('"',f);
-fputc(sep,f);
-if (sep == ',') fputc('"',f);
-fprintf(f, "%s", el->name);
-if (sep == ',') fputc('"',f);
-fputc(sep,f);
-if (sep == ',') fputc('"',f);
-fprintf(f, "%s", el->srcId);
-if (sep == ',') fputc('"',f);
-fputc(sep,f);
-if (sep == ',') fputc('"',f);
-fprintf(f, "%s", el->baseChangeType);
-if (sep == ',') fputc('"',f);
-fputc(sep,f);
-if (sep == ',') fputc('"',f);
-fprintf(f, "%s", el->location);
-if (sep == ',') fputc('"',f);
-fputc(sep,f);
-fprintf(f, "%u", el->coordinateAccuracy);
-fputc(lastSep,f);
-}
-
-void protVarPosStaticLoad(char **row, struct protVarPos *ret)
-/* Load a row from protVarPos table into ret.  The contents of ret will
- * be replaced at the next call to this function. */
-{
-
-ret->bin = sqlUnsigned(row[0]);
-ret->chrom = row[1];
-ret->chromStart = sqlUnsigned(row[2]);
-ret->chromEnd = sqlUnsigned(row[3]);
-ret->name = row[4];
-safecpy(ret->strand, sizeof(ret->strand), row[5]);
-ret->label = row[6];
-}
-
-struct protVarPos *protVarPosLoad(char **row)
-/* Load a protVarPos from row fetched with select * from protVarPos
- * from database.  Dispose of this with protVarPosFree(). */
-{
-struct protVarPos *ret;
-
-AllocVar(ret);
-ret->bin = sqlUnsigned(row[0]);
-ret->chrom = cloneString(row[1]);
-ret->chromStart = sqlUnsigned(row[2]);
-ret->chromEnd = sqlUnsigned(row[3]);
-ret->name = cloneString(row[4]);
-safecpy(ret->strand, sizeof(ret->strand), row[5]);
-ret->label = cloneString(row[6]);
-return ret;
-}
-
-struct protVarPos *protVarPosLoadAll(char *fileName) 
-/* Load all protVarPos from a whitespace-separated file.
- * Dispose of this with protVarPosFreeList(). */
-{
-struct protVarPos *list = NULL, *el;
-struct lineFile *lf = lineFileOpen(fileName, TRUE);
-char *row[7];
-
-while (lineFileRow(lf, row))
-    {
-    el = protVarPosLoad(row);
-    slAddHead(&list, el);
-    }
-lineFileClose(&lf);
-slReverse(&list);
-return list;
-}
-
-struct protVarPos *protVarPosLoadAllByChar(char *fileName, char chopper) 
-/* Load all protVarPos from a chopper separated file.
- * Dispose of this with protVarPosFreeList(). */
-{
-struct protVarPos *list = NULL, *el;
-struct lineFile *lf = lineFileOpen(fileName, TRUE);
-char *row[7];
-
-while (lineFileNextCharRow(lf, chopper, row, ArraySize(row)))
-    {
-    el = protVarPosLoad(row);
-    slAddHead(&list, el);
-    }
-lineFileClose(&lf);
-slReverse(&list);
-return list;
-}
-
-struct protVarPos *protVarPosLoadByQuery(struct sqlConnection *conn, char *query)
-/* Load all protVarPos 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 protVarPosFreeList(). */
-{
-struct protVarPos *list = NULL, *el;
-struct sqlResult *sr;
-char **row;
-
-sr = sqlGetResult(conn, query);
-while ((row = sqlNextRow(sr)) != NULL)
-    {
-    el = protVarPosLoad(row);
-    slAddHead(&list, el);
-    }
-slReverse(&list);
-sqlFreeResult(&sr);
-return list;
-}
-
-void protVarPosSaveToDb(struct sqlConnection *conn, struct protVarPos *el, char *tableName, int updateSize)
-/* Save protVarPos 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 ( %u,'%s',%u,%u,'%s','%s','%s')", 
-	tableName,  el->bin,  el->chrom,  el->chromStart,  el->chromEnd,  el->name,  el->strand,  el->label);
-sqlUpdate(conn, update->string);
-freeDyString(&update);
-}
-
-
-struct protVarPos *protVarPosCommaIn(char **pS, struct protVarPos *ret)
-/* Create a protVarPos out of a comma separated string. 
- * This will fill in ret if non-null, otherwise will
- * return a new protVarPos */
-{
-char *s = *pS;
-
-if (ret == NULL)
-    AllocVar(ret);
-ret->bin = sqlUnsignedComma(&s);
-ret->chrom = sqlStringComma(&s);
-ret->chromStart = sqlUnsignedComma(&s);
-ret->chromEnd = sqlUnsignedComma(&s);
-ret->name = sqlStringComma(&s);
-sqlFixedStringComma(&s, ret->strand, sizeof(ret->strand));
-ret->label = sqlStringComma(&s);
-*pS = s;
-return ret;
-}
-
-void protVarPosFree(struct protVarPos **pEl)
-/* Free a single dynamically allocated protVarPos such as created
- * with protVarPosLoad(). */
-{
-struct protVarPos *el;
-
-if ((el = *pEl) == NULL) return;
-freeMem(el->chrom);
-freeMem(el->name);
-freeMem(el->label);
-freez(pEl);
-}
-
-void protVarPosFreeList(struct protVarPos **pList)
-/* Free a list of dynamically allocated protVarPos's */
-{
-struct protVarPos *el, *next;
-
-for (el = *pList; el != NULL; el = next)
-    {
-    next = el->next;
-    protVarPosFree(&el);
-    }
-*pList = NULL;
-}
-
-void protVarPosOutput(struct protVarPos *el, FILE *f, char sep, char lastSep) 
-/* Print out protVarPos.  Separate fields with sep. Follow last field with lastSep. */
-{
-fprintf(f, "%u", el->bin);
-fputc(sep,f);
-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);
-if (sep == ',') fputc('"',f);
-fprintf(f, "%s", el->strand);
-if (sep == ',') fputc('"',f);
-fputc(sep,f);
-if (sep == ',') fputc('"',f);
-fprintf(f, "%s", el->label);
-if (sep == ',') fputc('"',f);
-fputc(lastSep,f);
-}
-
-void protVarAttrStaticLoad(char **row, struct protVarAttr *ret)
-/* Load a row from protVarAttr table into ret.  The contents of ret will
- * be replaced at the next call to this function. */
-{
-
-ret->id = row[0];
-ret->attrType = row[1];
-ret->attrVal = row[2];
-}
-
-struct protVarAttr *protVarAttrLoad(char **row)
-/* Load a protVarAttr from row fetched with select * from protVarAttr
- * from database.  Dispose of this with protVarAttrFree(). */
-{
-struct protVarAttr *ret;
-
-AllocVar(ret);
-ret->id = cloneString(row[0]);
-ret->attrType = cloneString(row[1]);
-ret->attrVal = cloneString(row[2]);
-return ret;
-}
-
-struct protVarAttr *protVarAttrLoadAll(char *fileName) 
-/* Load all protVarAttr from a whitespace-separated file.
- * Dispose of this with protVarAttrFreeList(). */
-{
-struct protVarAttr *list = NULL, *el;
-struct lineFile *lf = lineFileOpen(fileName, TRUE);
-char *row[3];
-
-while (lineFileRow(lf, row))
-    {
-    el = protVarAttrLoad(row);
-    slAddHead(&list, el);
-    }
-lineFileClose(&lf);
-slReverse(&list);
-return list;
-}
-
-struct protVarAttr *protVarAttrLoadAllByChar(char *fileName, char chopper) 
-/* Load all protVarAttr from a chopper separated file.
- * Dispose of this with protVarAttrFreeList(). */
-{
-struct protVarAttr *list = NULL, *el;
-struct lineFile *lf = lineFileOpen(fileName, TRUE);
-char *row[3];
-
-while (lineFileNextCharRow(lf, chopper, row, ArraySize(row)))
-    {
-    el = protVarAttrLoad(row);
-    slAddHead(&list, el);
-    }
-lineFileClose(&lf);
-slReverse(&list);
-return list;
-}
-
-struct protVarAttr *protVarAttrLoadByQuery(struct sqlConnection *conn, char *query)
-/* Load all protVarAttr 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 protVarAttrFreeList(). */
-{
-struct protVarAttr *list = NULL, *el;
-struct sqlResult *sr;
-char **row;
-
-sr = sqlGetResult(conn, query);
-while ((row = sqlNextRow(sr)) != NULL)
-    {
-    el = protVarAttrLoad(row);
-    slAddHead(&list, el);
-    }
-slReverse(&list);
-sqlFreeResult(&sr);
-return list;
-}
-
-void protVarAttrSaveToDb(struct sqlConnection *conn, struct protVarAttr *el, char *tableName, int updateSize)
-/* Save protVarAttr 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','%s',%s)", 
-	tableName,  el->id,  el->attrType,  el->attrVal);
-sqlUpdate(conn, update->string);
-freeDyString(&update);
-}
-
-
-struct protVarAttr *protVarAttrCommaIn(char **pS, struct protVarAttr *ret)
-/* Create a protVarAttr out of a comma separated string. 
- * This will fill in ret if non-null, otherwise will
- * return a new protVarAttr */
-{
-char *s = *pS;
-
-if (ret == NULL)
-    AllocVar(ret);
-ret->id = sqlStringComma(&s);
-ret->attrType = sqlStringComma(&s);
-ret->attrVal = sqlStringComma(&s);
-*pS = s;
-return ret;
-}
-
-void protVarAttrFree(struct protVarAttr **pEl)
-/* Free a single dynamically allocated protVarAttr such as created
- * with protVarAttrLoad(). */
-{
-struct protVarAttr *el;
-
-if ((el = *pEl) == NULL) return;
-freeMem(el->id);
-freeMem(el->attrType);
-freeMem(el->attrVal);
-freez(pEl);
-}
-
-void protVarAttrFreeList(struct protVarAttr **pList)
-/* Free a list of dynamically allocated protVarAttr's */
-{
-struct protVarAttr *el, *next;
-
-for (el = *pList; el != NULL; el = next)
-    {
-    next = el->next;
-    protVarAttrFree(&el);
-    }
-*pList = NULL;
-}
-
-void protVarAttrOutput(struct protVarAttr *el, FILE *f, char sep, char lastSep) 
-/* Print out protVarAttr.  Separate fields with sep. Follow last field with lastSep. */
-{
-if (sep == ',') fputc('"',f);
-fprintf(f, "%s", el->id);
-if (sep == ',') fputc('"',f);
-fputc(sep,f);
-if (sep == ',') fputc('"',f);
-fprintf(f, "%s", el->attrType);
-if (sep == ',') fputc('"',f);
-fputc(sep,f);
-if (sep == ',') fputc('"',f);
-fprintf(f, "%s", el->attrVal);
-if (sep == ',') fputc('"',f);
-fputc(lastSep,f);
-}
-
-void protVarLinkStaticLoad(char **row, struct protVarLink *ret)
-/* Load a row from protVarLink table into ret.  The contents of ret will
- * be replaced at the next call to this function. */
-{
-
-ret->id = row[0];
-ret->attrType = row[1];
-ret->raKey = row[2];
-ret->acc = row[3];
-ret->displayVal = row[4];
-}
-
-struct protVarLink *protVarLinkLoad(char **row)
-/* Load a protVarLink from row fetched with select * from protVarLink
- * from database.  Dispose of this with protVarLinkFree(). */
-{
-struct protVarLink *ret;
-
-AllocVar(ret);
-ret->id = cloneString(row[0]);
-ret->attrType = cloneString(row[1]);
-ret->raKey = cloneString(row[2]);
-ret->acc = cloneString(row[3]);
-ret->displayVal = cloneString(row[4]);
-return ret;
-}
-
-struct protVarLink *protVarLinkLoadAll(char *fileName) 
-/* Load all protVarLink from a whitespace-separated file.
- * Dispose of this with protVarLinkFreeList(). */
-{
-struct protVarLink *list = NULL, *el;
-struct lineFile *lf = lineFileOpen(fileName, TRUE);
-char *row[5];
-
-while (lineFileRow(lf, row))
-    {
-    el = protVarLinkLoad(row);
-    slAddHead(&list, el);
-    }
-lineFileClose(&lf);
-slReverse(&list);
-return list;
-}
-
-struct protVarLink *protVarLinkLoadAllByChar(char *fileName, char chopper) 
-/* Load all protVarLink from a chopper separated file.
- * Dispose of this with protVarLinkFreeList(). */
-{
-struct protVarLink *list = NULL, *el;
-struct lineFile *lf = lineFileOpen(fileName, TRUE);
-char *row[5];
-
-while (lineFileNextCharRow(lf, chopper, row, ArraySize(row)))
-    {
-    el = protVarLinkLoad(row);
-    slAddHead(&list, el);
-    }
-lineFileClose(&lf);
-slReverse(&list);
-return list;
-}
-
-struct protVarLink *protVarLinkLoadByQuery(struct sqlConnection *conn, char *query)
-/* Load all protVarLink 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 protVarLinkFreeList(). */
-{
-struct protVarLink *list = NULL, *el;
-struct sqlResult *sr;
-char **row;
-
-sr = sqlGetResult(conn, query);
-while ((row = sqlNextRow(sr)) != NULL)
-    {
-    el = protVarLinkLoad(row);
-    slAddHead(&list, el);
-    }
-slReverse(&list);
-sqlFreeResult(&sr);
-return list;
-}
-
-void protVarLinkSaveToDb(struct sqlConnection *conn, struct protVarLink *el, char *tableName, int updateSize)
-/* Save protVarLink 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','%s','%s','%s','%s')", 
-	tableName,  el->id,  el->attrType,  el->raKey,  el->acc,  el->displayVal);
-sqlUpdate(conn, update->string);
-freeDyString(&update);
-}
-
-
-struct protVarLink *protVarLinkCommaIn(char **pS, struct protVarLink *ret)
-/* Create a protVarLink out of a comma separated string. 
- * This will fill in ret if non-null, otherwise will
- * return a new protVarLink */
-{
-char *s = *pS;
-
-if (ret == NULL)
-    AllocVar(ret);
-ret->id = sqlStringComma(&s);
-ret->attrType = sqlStringComma(&s);
-ret->raKey = sqlStringComma(&s);
-ret->acc = sqlStringComma(&s);
-ret->displayVal = sqlStringComma(&s);
-*pS = s;
-return ret;
-}
-
-void protVarLinkFree(struct protVarLink **pEl)
-/* Free a single dynamically allocated protVarLink such as created
- * with protVarLinkLoad(). */
-{
-struct protVarLink *el;
-
-if ((el = *pEl) == NULL) return;
-freeMem(el->id);
-freeMem(el->attrType);
-freeMem(el->raKey);
-freeMem(el->acc);
-freeMem(el->displayVal);
-freez(pEl);
-}
-
-void protVarLinkFreeList(struct protVarLink **pList)
-/* Free a list of dynamically allocated protVarLink's */
-{
-struct protVarLink *el, *next;
-
-for (el = *pList; el != NULL; el = next)
-    {
-    next = el->next;
-    protVarLinkFree(&el);
-    }
-*pList = NULL;
-}
-
-void protVarLinkOutput(struct protVarLink *el, FILE *f, char sep, char lastSep) 
-/* Print out protVarLink.  Separate fields with sep. Follow last field with lastSep. */
-{
-if (sep == ',') fputc('"',f);
-fprintf(f, "%s", el->id);
-if (sep == ',') fputc('"',f);
-fputc(sep,f);
-if (sep == ',') fputc('"',f);
-fprintf(f, "%s", el->attrType);
-if (sep == ',') fputc('"',f);
-fputc(sep,f);
-if (sep == ',') fputc('"',f);
-fprintf(f, "%s", el->raKey);
-if (sep == ',') fputc('"',f);
-fputc(sep,f);
-if (sep == ',') fputc('"',f);
-fprintf(f, "%s", el->acc);
-if (sep == ',') fputc('"',f);
-fputc(sep,f);
-if (sep == ',') fputc('"',f);
-fprintf(f, "%s", el->displayVal);
-if (sep == ',') fputc('"',f);
-fputc(lastSep,f);
-}
-
-/* -------------------------------- End autoSql Generated Code -------------------------------- */
-