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/cgilib/putaInfo.c src/hg/cgilib/putaInfo.c
new file mode 100644
index 0000000..0ee0709
--- /dev/null
+++ src/hg/cgilib/putaInfo.c
@@ -0,0 +1,347 @@
+/* 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 -------------------------------- */
+