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/ucscRetroInfo.c src/hg/lib/ucscRetroInfo.c
deleted file mode 100644
index f06c452..0000000
--- src/hg/lib/ucscRetroInfo.c
+++ /dev/null
@@ -1,441 +0,0 @@
-/* ucscRetroInfo.c was originally generated by the autoSql program, which also 
- * generated ucscRetroInfo.h and ucscRetroInfo.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 "ucscRetroInfo.h"
-
-
-struct ucscRetroInfo *ucscRetroInfoLoadByQuery(struct sqlConnection *conn, char *query)
-/* Load all ucscRetroInfo 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 ucscRetroInfoFreeList(). */
-{
-struct ucscRetroInfo *list = NULL, *el;
-struct sqlResult *sr;
-char **row;
-
-sr = sqlGetResult(conn, query);
-while ((row = sqlNextRow(sr)) != NULL)
-    {
-    el = ucscRetroInfoLoad(row);
-    slAddHead(&list, el);
-    }
-slReverse(&list);
-sqlFreeResult(&sr);
-return list;
-}
-
-void ucscRetroInfoSaveToDb(struct sqlConnection *conn, struct ucscRetroInfo *el, char *tableName, int updateSize)
-/* Save ucscRetroInfo 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  *blockSizesArray, *chromStartsArray;
-blockSizesArray = sqlSignedArrayToString(el->blockSizes, el->blockCount);
-chromStartsArray = sqlSignedArrayToString(el->chromStarts, el->blockCount);
-sqlDyStringPrintf(update, "insert into %s values ( '%s',%u,%u,'%s',%u,'%s',%u,%u,%u,%d,'%s','%s',%d,%d,'%s','%s',%d,%d,'%s',%u,%u,%u,%d,%d,%u,%u,%u,%u,%u,%u,%u,%d,%u,%d,%d,%d,%d,'%s',%d,%d,'%s',%d,%d,'%s',%d,%d,'%s',%d,%d,'%s',%g,%u)", 
-	tableName,  el->chrom,  el->chromStart,  el->chromEnd,  el->name,  el->score,  el->strand,  el->thickStart,  el->thickEnd,  el->reserved,  el->blockCount,  blockSizesArray ,  chromStartsArray ,  el->retroExonCount,  el->axtScore,  el->type,  el->gChrom,  el->gStart,  el->gEnd,  el->gStrand,  el->parentSpliceCount,  el->geneOverlap,  el->polyA,  el->polyAstart,  el->exonCover,  el->intronCount,  el->bestAliCount,  el->matches,  el->qSize,  el->qEnd,  el->tReps,  el->coverage,  el->label,  el->milliBad, el->alignGapCount,  el->processedIntrons,  el->conservedSpliceSites,  el->maxOverlap,  el->refSeq,  el->rStart,  el->rEnd,  el->mgc,  el->mStart,  el->mEnd,  el->kgName,  el->kStart,  el->kEnd,  el->overName,  el->overStart,  el->overExonCover,  el->overStrand,  el->posConf,  el->polyAlen);
-sqlUpdate(conn, update->string);
-freeDyString(&update);
-freez(&blockSizesArray);
-freez(&chromStartsArray);
-}
-
-
-struct ucscRetroInfo *ucscRetroInfoLoad(char **row)
-/* Load a ucscRetroInfo from row fetched with select * from ucscRetroInfo
- * from database.  Dispose of this with ucscRetroInfoFree(). */
-{
-struct ucscRetroInfo *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->retroExonCount = sqlSigned(row[12]);
-ret->axtScore = sqlSigned(row[13]);
-ret->type = cloneString(row[14]);
-ret->gChrom = cloneString(row[15]);
-ret->gStart = sqlSigned(row[16]);
-ret->gEnd = sqlSigned(row[17]);
-safecpy(ret->gStrand, sizeof(ret->gStrand), row[18]);
-ret->parentSpliceCount = sqlUnsigned(row[19]);
-ret->geneOverlap = sqlUnsigned(row[20]);
-ret->polyA = sqlUnsigned(row[21]);
-ret->polyAstart = sqlSigned(row[22]);
-ret->exonCover = sqlSigned(row[23]);
-ret->intronCount = sqlUnsigned(row[24]);
-ret->bestAliCount = sqlUnsigned(row[25]);
-ret->matches = sqlUnsigned(row[26]);
-ret->qSize = sqlUnsigned(row[27]);
-ret->qEnd = sqlUnsigned(row[28]);
-ret->tReps = sqlUnsigned(row[29]);
-ret->coverage = sqlUnsigned(row[30]);
-ret->label = sqlSigned(row[31]);
-ret->milliBad = sqlUnsigned(row[32]);
-ret->alignGapCount = sqlSigned(row[33]);
-ret->processedIntrons = sqlSigned(row[34]);
-ret->conservedSpliceSites = sqlSigned(row[35]);
-ret->maxOverlap = sqlSigned(row[36]);
-ret->refSeq = cloneString(row[37]);
-ret->rStart = sqlSigned(row[38]);
-ret->rEnd = sqlSigned(row[39]);
-ret->mgc = cloneString(row[40]);
-ret->mStart = sqlSigned(row[41]);
-ret->mEnd = sqlSigned(row[42]);
-ret->kgName = cloneString(row[43]);
-ret->kStart = sqlSigned(row[44]);
-ret->kEnd = sqlSigned(row[45]);
-ret->overName = cloneString(row[46]);
-ret->overStart = sqlSigned(row[47]);
-ret->overExonCover = sqlSigned(row[48]);
-safecpy(ret->overStrand, sizeof(ret->overStrand), row[49]);
-ret->posConf = sqlFloat(row[50]);
-ret->polyAlen = sqlUnsigned(row[51]);
-return ret;
-}
-
-struct ucscRetroInfo *ucscRetroInfoLoadAll(char *fileName) 
-/* Load all ucscRetroInfo from a whitespace-separated file.
- * Dispose of this with ucscRetroInfoFreeList(). */
-{
-struct ucscRetroInfo *list = NULL, *el;
-struct lineFile *lf = lineFileOpen(fileName, TRUE);
-char *row[52];
-
-while (lineFileRow(lf, row))
-    {
-    el = ucscRetroInfoLoad(row);
-    slAddHead(&list, el);
-    }
-lineFileClose(&lf);
-slReverse(&list);
-return list;
-}
-
-struct ucscRetroInfo *ucscRetroInfoLoadAllByChar(char *fileName, char chopper) 
-/* Load all ucscRetroInfo from a chopper separated file.
- * Dispose of this with ucscRetroInfoFreeList(). */
-{
-struct ucscRetroInfo *list = NULL, *el;
-struct lineFile *lf = lineFileOpen(fileName, TRUE);
-char *row[52];
-
-while (lineFileNextCharRow(lf, chopper, row, ArraySize(row)))
-    {
-    el = ucscRetroInfoLoad(row);
-    slAddHead(&list, el);
-    }
-lineFileClose(&lf);
-slReverse(&list);
-return list;
-}
-
-struct ucscRetroInfo *ucscRetroInfoCommaIn(char **pS, struct ucscRetroInfo *ret)
-/* Create a ucscRetroInfo out of a comma separated string. 
- * This will fill in ret if non-null, otherwise will
- * return a new ucscRetroInfo */
-{
-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->retroExonCount = sqlSignedComma(&s);
-ret->axtScore = sqlSignedComma(&s);
-ret->type = sqlStringComma(&s);
-ret->gChrom = sqlStringComma(&s);
-ret->gStart = sqlSignedComma(&s);
-ret->gEnd = sqlSignedComma(&s);
-sqlFixedStringComma(&s, ret->gStrand, sizeof(ret->gStrand));
-ret->parentSpliceCount = sqlUnsignedComma(&s);
-ret->geneOverlap = sqlUnsignedComma(&s);
-ret->polyA = sqlUnsignedComma(&s);
-ret->polyAstart = sqlSignedComma(&s);
-ret->exonCover = sqlSignedComma(&s);
-ret->intronCount = sqlUnsignedComma(&s);
-ret->bestAliCount = sqlUnsignedComma(&s);
-ret->matches = sqlUnsignedComma(&s);
-ret->qSize = sqlUnsignedComma(&s);
-ret->qEnd = sqlUnsignedComma(&s);
-ret->tReps = sqlUnsignedComma(&s);
-ret->coverage = sqlUnsignedComma(&s);
-ret->label = sqlSignedComma(&s);
-ret->milliBad = sqlUnsignedComma(&s);
-ret->alignGapCount = sqlSignedComma(&s);
-ret->processedIntrons = sqlSignedComma(&s);
-ret->conservedSpliceSites = sqlSignedComma(&s);
-ret->maxOverlap = sqlSignedComma(&s);
-ret->refSeq = sqlStringComma(&s);
-ret->rStart = sqlSignedComma(&s);
-ret->rEnd = sqlSignedComma(&s);
-ret->mgc = sqlStringComma(&s);
-ret->mStart = sqlSignedComma(&s);
-ret->mEnd = sqlSignedComma(&s);
-ret->kgName = sqlStringComma(&s);
-ret->kStart = sqlSignedComma(&s);
-ret->kEnd = sqlSignedComma(&s);
-ret->overName = sqlStringComma(&s);
-ret->overStart = sqlSignedComma(&s);
-ret->overExonCover = sqlSignedComma(&s);
-sqlFixedStringComma(&s, ret->overStrand, sizeof(ret->overStrand));
-ret->posConf = sqlFloatComma(&s);
-ret->polyAlen = sqlUnsignedComma(&s);
-*pS = s;
-return ret;
-}
-
-void ucscRetroInfoFree(struct ucscRetroInfo **pEl)
-/* Free a single dynamically allocated ucscRetroInfo such as created
- * with ucscRetroInfoLoad(). */
-{
-struct ucscRetroInfo *el;
-
-if ((el = *pEl) == NULL) return;
-freeMem(el->chrom);
-freeMem(el->name);
-freeMem(el->blockSizes);
-freeMem(el->chromStarts);
-freeMem(el->type);
-freeMem(el->gChrom);
-freeMem(el->refSeq);
-freeMem(el->mgc);
-freeMem(el->kgName);
-freeMem(el->overName);
-freez(pEl);
-}
-
-void ucscRetroInfoFreeList(struct ucscRetroInfo **pList)
-/* Free a list of dynamically allocated ucscRetroInfo's */
-{
-struct ucscRetroInfo *el, *next;
-
-for (el = *pList; el != NULL; el = next)
-    {
-    next = el->next;
-    ucscRetroInfoFree(&el);
-    }
-*pList = NULL;
-}
-
-void ucscRetroInfoOutput(struct ucscRetroInfo *el, FILE *f, char sep, char lastSep) 
-/* Print out ucscRetroInfo.  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, "%d", el->retroExonCount);
-fputc(sep,f);
-fprintf(f, "%d", el->axtScore);
-fputc(sep,f);
-if (sep == ',') fputc('"',f);
-fprintf(f, "%s", el->type);
-if (sep == ',') fputc('"',f);
-fputc(sep,f);
-if (sep == ',') fputc('"',f);
-fprintf(f, "%s", el->gChrom);
-if (sep == ',') fputc('"',f);
-fputc(sep,f);
-fprintf(f, "%d", el->gStart);
-fputc(sep,f);
-fprintf(f, "%d", el->gEnd);
-fputc(sep,f);
-if (sep == ',') fputc('"',f);
-fprintf(f, "%s", el->gStrand);
-if (sep == ',') fputc('"',f);
-fputc(sep,f);
-fprintf(f, "%u", el->parentSpliceCount);
-fputc(sep,f);
-fprintf(f, "%u", el->geneOverlap);
-fputc(sep,f);
-fprintf(f, "%u", el->polyA);
-fputc(sep,f);
-fprintf(f, "%d", el->polyAstart);
-fputc(sep,f);
-fprintf(f, "%d", el->exonCover);
-fputc(sep,f);
-fprintf(f, "%u", el->intronCount);
-fputc(sep,f);
-fprintf(f, "%u", el->bestAliCount);
-fputc(sep,f);
-fprintf(f, "%u", el->matches);
-fputc(sep,f);
-fprintf(f, "%u", el->qSize);
-fputc(sep,f);
-fprintf(f, "%u", el->qEnd);
-fputc(sep,f);
-fprintf(f, "%u", el->tReps);
-fputc(sep,f);
-fprintf(f, "%u", el->coverage);
-fputc(sep,f);
-fprintf(f, "%d", el->label);
-fputc(sep,f);
-fprintf(f, "%u", el->milliBad);
-fputc(sep,f);
-fprintf(f, "%d", el->alignGapCount);
-fputc(sep,f);
-fprintf(f, "%d", el->processedIntrons);
-fputc(sep,f);
-fprintf(f, "%d", el->conservedSpliceSites);
-fputc(sep,f);
-fprintf(f, "%d", el->maxOverlap);
-fputc(sep,f);
-if (sep == ',') fputc('"',f);
-fprintf(f, "%s", el->refSeq);
-if (sep == ',') fputc('"',f);
-fputc(sep,f);
-fprintf(f, "%d", el->rStart);
-fputc(sep,f);
-fprintf(f, "%d", el->rEnd);
-fputc(sep,f);
-if (sep == ',') fputc('"',f);
-fprintf(f, "%s", el->mgc);
-if (sep == ',') fputc('"',f);
-fputc(sep,f);
-fprintf(f, "%d", el->mStart);
-fputc(sep,f);
-fprintf(f, "%d", el->mEnd);
-fputc(sep,f);
-if (sep == ',') fputc('"',f);
-fprintf(f, "%s", el->kgName);
-if (sep == ',') fputc('"',f);
-fputc(sep,f);
-fprintf(f, "%d", el->kStart);
-fputc(sep,f);
-fprintf(f, "%d", el->kEnd);
-fputc(sep,f);
-if (sep == ',') fputc('"',f);
-fprintf(f, "%s", el->overName);
-if (sep == ',') fputc('"',f);
-fputc(sep,f);
-fprintf(f, "%d", el->overStart);
-fputc(sep,f);
-fprintf(f, "%d", el->overExonCover);
-fputc(sep,f);
-if (sep == ',') fputc('"',f);
-fprintf(f, "%s", el->overStrand);
-if (sep == ',') fputc('"',f);
-fputc(sep,f);
-fprintf(f, "%g", el->posConf);
-fputc(sep,f);
-fprintf(f, "%u", el->polyAlen);
-fputc(lastSep,f);
-}
-
-/* -------------------------------- End autoSql Generated Code -------------------------------- */
-
-struct ucscRetroInfo *ucscRetroInfoQuery(struct sqlConnection *conn,
-                                       char *table, char *mappedId)
-/* load a single retro object for an mapped id from a table,
- * or error if not found */
-{
-return sqlQueryObjs(conn, (sqlLoadFunc)ucscRetroInfoLoad,
-                    sqlQuerySingle,
-                    "SELECT * FROM %s WHERE name = \"%s\"",
-                    table, mappedId);
-}