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/putaInfo.c src/hg/lib/putaInfo.c
deleted file mode 100644
index 0ee0709..0000000
--- src/hg/lib/putaInfo.c
+++ /dev/null
@@ -1,347 +0,0 @@
-/* putaInfo.c was originally generated by the autoSql program, which also 
- * generated putaInfo.h and putaInfo.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 "putaInfo.h"
-
-
-struct putaInfo *putaInfoLoad(char **row)
-/* Load a putaInfo from row fetched with select * from putaInfo
- * from database.  Dispose of this with putaInfoFree(). */
-{
-struct putaInfo *ret;
-
-AllocVar(ret);
-ret->blockCount = sqlUnsigned(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]);
-ret->strand = cloneString(row[5]);
-ret->oChrom = cloneString(row[6]);
-ret->oChromStart = sqlUnsigned(row[7]);
-ret->oChromEnd = sqlUnsigned(row[8]);
-ret->stop = sqlUnsigned(row[10]);
-sqlUnsignedArray(row[11], ret->tExons, 2);
-sqlUnsignedArray(row[12], ret->qExons, 4);
-sqlUnsignedArray(row[13], ret->qBases, 4);
-sqlUnsignedArray(row[14], ret->repeats, 2);
-{
-int sizeOne;
-sqlUnsignedDynamicArray(row[15], &ret->stops, &sizeOne);
-assert(sizeOne == ret->blockCount);
-}
-sqlDoubleArray(row[16], ret->id, 2);
-return ret;
-}
-
-struct putaInfo *putaInfoLoadAll(char *fileName) 
-/* Load all putaInfo from a whitespace-separated file.
- * Dispose of this with putaInfoFreeList(). */
-{
-struct putaInfo *list = NULL, *el;
-struct lineFile *lf = lineFileOpen(fileName, TRUE);
-char *row[17];
-
-while (lineFileRow(lf, row))
-    {
-    el = putaInfoLoad(row);
-    slAddHead(&list, el);
-    }
-lineFileClose(&lf);
-slReverse(&list);
-return list;
-}
-
-struct putaInfo *putaInfoLoadAllByChar(char *fileName, char chopper) 
-/* Load all putaInfo from a chopper separated file.
- * Dispose of this with putaInfoFreeList(). */
-{
-struct putaInfo *list = NULL, *el;
-struct lineFile *lf = lineFileOpen(fileName, TRUE);
-char *row[17];
-
-while (lineFileNextCharRow(lf, chopper, row, ArraySize(row)))
-    {
-    el = putaInfoLoad(row);
-    slAddHead(&list, el);
-    }
-lineFileClose(&lf);
-slReverse(&list);
-return list;
-}
-
-struct putaInfo *putaInfoLoadByQuery(struct sqlConnection *conn, char *query)
-/* Load all putaInfo 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 putaInfoFreeList(). */
-{
-struct putaInfo *list = NULL, *el;
-struct sqlResult *sr;
-char **row;
-
-sr = sqlGetResult(conn, query);
-while ((row = sqlNextRow(sr)) != NULL)
-    {
-    el = putaInfoLoad(row);
-    slAddHead(&list, el);
-    }
-slReverse(&list);
-sqlFreeResult(&sr);
-return list;
-}
-
-void putaInfoSaveToDb(struct sqlConnection *conn, struct putaInfo *el, char *tableName, int updateSize)
-/* Save putaInfo 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);
-char  *tExonsArray, *qExonsArray, *qBasesArray, *repeatsArray, *stopsArray, *idArray;
-tExonsArray = sqlUnsignedArrayToString(el->tExons, 2);
-qExonsArray = sqlUnsignedArrayToString(el->qExons, 4);
-qBasesArray = sqlUnsignedArrayToString(el->qBases, 4);
-repeatsArray = sqlUnsignedArrayToString(el->repeats, 2);
-stopsArray = sqlUnsignedArrayToString(el->stops, el->blockCount);
-idArray = sqlDoubleArrayToString(el->id, 2);
-sqlDyStringPrintf(update, "insert into %s values ( '%s',%u,%u,'%s',%u,'%s','%s',%u,%u,%u,%u,'%s','%s','%s','%s','%s','%s')", 
-	tableName,  el->chrom,  el->chromStart,  el->chromEnd,  el->name,  el->score,  el->strand,  el->oChrom,  el->oChromStart,  el->oChromEnd,  el->blockCount,  el->stop,  tExonsArray ,  qExonsArray ,  qBasesArray ,  repeatsArray ,  stopsArray ,  idArray );
-sqlUpdate(conn, update->string);
-freeDyString(&update);
-freez(&tExonsArray);
-freez(&qExonsArray);
-freez(&qBasesArray);
-freez(&repeatsArray);
-freez(&stopsArray);
-freez(&idArray);
-}
-
-
-struct putaInfo *putaInfoCommaIn(char **pS, struct putaInfo *ret)
-/* Create a putaInfo out of a comma separated string. 
- * This will fill in ret if non-null, otherwise will
- * return a new putaInfo */
-{
-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);
-ret->strand = sqlStringComma(&s);
-ret->oChrom = sqlStringComma(&s);
-ret->oChromStart = sqlUnsignedComma(&s);
-ret->oChromEnd = sqlUnsignedComma(&s);
-ret->blockCount = sqlUnsignedComma(&s);
-ret->stop = sqlUnsignedComma(&s);
-{
-int i;
-s = sqlEatChar(s, '{');
-for (i=0; i<2; ++i)
-    {
-    ret->tExons[i] = sqlUnsignedComma(&s);
-    }
-s = sqlEatChar(s, '}');
-s = sqlEatChar(s, ',');
-}
-{
-int i;
-s = sqlEatChar(s, '{');
-for (i=0; i<4; ++i)
-    {
-    ret->qExons[i] = sqlUnsignedComma(&s);
-    }
-s = sqlEatChar(s, '}');
-s = sqlEatChar(s, ',');
-}
-{
-int i;
-s = sqlEatChar(s, '{');
-for (i=0; i<4; ++i)
-    {
-    ret->qBases[i] = sqlUnsignedComma(&s);
-    }
-s = sqlEatChar(s, '}');
-s = sqlEatChar(s, ',');
-}
-{
-int i;
-s = sqlEatChar(s, '{');
-for (i=0; i<2; ++i)
-    {
-    ret->repeats[i] = sqlUnsignedComma(&s);
-    }
-s = sqlEatChar(s, '}');
-s = sqlEatChar(s, ',');
-}
-{
-int i;
-s = sqlEatChar(s, '{');
-AllocArray(ret->stops, ret->blockCount);
-for (i=0; i<ret->blockCount; ++i)
-    {
-    ret->stops[i] = sqlUnsignedComma(&s);
-    }
-s = sqlEatChar(s, '}');
-s = sqlEatChar(s, ',');
-}
-{
-int i;
-s = sqlEatChar(s, '{');
-for (i=0; i<2; ++i)
-    {
-    ret->id[i] = sqlDoubleComma(&s);
-    }
-s = sqlEatChar(s, '}');
-s = sqlEatChar(s, ',');
-}
-*pS = s;
-return ret;
-}
-
-void putaInfoFree(struct putaInfo **pEl)
-/* Free a single dynamically allocated putaInfo such as created
- * with putaInfoLoad(). */
-{
-struct putaInfo *el;
-
-if ((el = *pEl) == NULL) return;
-freeMem(el->chrom);
-freeMem(el->name);
-freeMem(el->strand);
-freeMem(el->oChrom);
-freeMem(el->stops);
-freez(pEl);
-}
-
-void putaInfoFreeList(struct putaInfo **pList)
-/* Free a list of dynamically allocated putaInfo's */
-{
-struct putaInfo *el, *next;
-
-for (el = *pList; el != NULL; el = next)
-    {
-    next = el->next;
-    putaInfoFree(&el);
-    }
-*pList = NULL;
-}
-
-void putaInfoOutput(struct putaInfo *el, FILE *f, char sep, char lastSep) 
-/* Print out putaInfo.  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);
-if (sep == ',') fputc('"',f);
-fprintf(f, "%s", el->oChrom);
-if (sep == ',') fputc('"',f);
-fputc(sep,f);
-fprintf(f, "%u", el->oChromStart);
-fputc(sep,f);
-fprintf(f, "%u", el->oChromEnd);
-fputc(sep,f);
-fprintf(f, "%u", el->blockCount);
-fputc(sep,f);
-fprintf(f, "%u", el->stop);
-fputc(sep,f);
-{
-int i;
-if (sep == ',') fputc('{',f);
-for (i=0; i<2; ++i)
-    {
-    fprintf(f, "%u", el->tExons[i]);
-    fputc(',', f);
-    }
-if (sep == ',') fputc('}',f);
-}
-fputc(sep,f);
-{
-int i;
-if (sep == ',') fputc('{',f);
-for (i=0; i<4; ++i)
-    {
-    fprintf(f, "%u", el->qExons[i]);
-    fputc(',', f);
-    }
-if (sep == ',') fputc('}',f);
-}
-fputc(sep,f);
-{
-int i;
-if (sep == ',') fputc('{',f);
-for (i=0; i<4; ++i)
-    {
-    fprintf(f, "%u", el->qBases[i]);
-    fputc(',', f);
-    }
-if (sep == ',') fputc('}',f);
-}
-fputc(sep,f);
-{
-int i;
-if (sep == ',') fputc('{',f);
-for (i=0; i<2; ++i)
-    {
-    fprintf(f, "%u", el->repeats[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, "%u", el->stops[i]);
-    fputc(',', f);
-    }
-if (sep == ',') fputc('}',f);
-}
-fputc(sep,f);
-{
-int i;
-if (sep == ',') fputc('{',f);
-for (i=0; i<2; ++i)
-    {
-    fprintf(f, "%g", el->id[i]);
-    fputc(',', f);
-    }
-if (sep == ',') fputc('}',f);
-}
-fputc(lastSep,f);
-}
-
-/* -------------------------------- End autoSql Generated Code -------------------------------- */
-