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/rnaHybridization.c src/hg/cgilib/rnaHybridization.c
new file mode 100644
index 0000000..fbf52c8
--- /dev/null
+++ src/hg/cgilib/rnaHybridization.c
@@ -0,0 +1,281 @@
+/* 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 -------------------------------- */
+