e70152e44cc66cc599ff6b699eb8adc07f3e656a
kent
  Sat May 24 21:09:34 2014 -0700
Adding Copyright NNNN Regents of the University of California to all files I believe with reasonable certainty were developed under UCSC employ or as part of Genome Browser copyright assignment.
diff --git src/hg/lib/rnaHybridization.c src/hg/lib/rnaHybridization.c
index 9cd5cae..fbf52c8 100644
--- src/hg/lib/rnaHybridization.c
+++ src/hg/lib/rnaHybridization.c
@@ -1,278 +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 -------------------------------- */