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/dnaProbe.c src/hg/lib/dnaProbe.c
index 5e7543f..8629643 100644
--- src/hg/lib/dnaProbe.c
+++ src/hg/lib/dnaProbe.c
@@ -1,206 +1,209 @@
 /* dnaProbe.c was originally generated by the autoSql program, which also 
  * generated dnaProbe.h and dnaProbe.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 "dnaProbe.h"
 
 
 void dnaProbeStaticLoad(char **row, struct dnaProbe *ret)
 /* Load a row from dnaProbe table into ret.  The contents of ret will
  * be replaced at the next call to this function. */
 {
 
 ret->name = row[0];
 ret->dna = row[1];
 ret->size = sqlSigned(row[2]);
 ret->chrom = row[3];
 ret->start = sqlSigned(row[4]);
 ret->end = sqlSigned(row[5]);
 strcpy(ret->strand, row[6]);
 ret->tpDist = sqlSigned(row[7]);
 ret->tm = atof(row[8]);
 ret->pGC = atof(row[9]);
 ret->affyHeur = sqlSigned(row[10]);
 ret->secStruct = atof(row[11]);
 ret->blatScore = sqlSigned(row[12]);
 ret->comparison = atof(row[13]);
 }
 
 struct dnaProbe *dnaProbeLoad(char **row)
 /* Load a dnaProbe from row fetched with select * from dnaProbe
  * from database.  Dispose of this with dnaProbeFree(). */
 {
 struct dnaProbe *ret;
 
 AllocVar(ret);
 ret->name = cloneString(row[0]);
 ret->dna = cloneString(row[1]);
 ret->size = sqlSigned(row[2]);
 ret->chrom = cloneString(row[3]);
 ret->start = sqlSigned(row[4]);
 ret->end = sqlSigned(row[5]);
 strcpy(ret->strand, row[6]);
 ret->tpDist = sqlSigned(row[7]);
 ret->tm = atof(row[8]);
 ret->pGC = atof(row[9]);
 ret->affyHeur = sqlSigned(row[10]);
 ret->secStruct = atof(row[11]);
 ret->blatScore = sqlSigned(row[12]);
 ret->comparison = atof(row[13]);
 return ret;
 }
 
 struct dnaProbe *dnaProbeLoadAll(char *fileName) 
 /* Load all dnaProbe from a tab-separated file.
  * Dispose of this with dnaProbeFreeList(). */
 {
 struct dnaProbe *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[14];
 
 while (lineFileRow(lf, row))
     {
     el = dnaProbeLoad(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct dnaProbe *dnaProbeLoadByQuery(struct sqlConnection *conn, char *query)
 /* Load all dnaProbe 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 dnaProbeFreeList(). */
 {
 struct dnaProbe *list = NULL, *el;
 struct sqlResult *sr;
 char **row;
 
 sr = sqlGetResult(conn, query);
 while ((row = sqlNextRow(sr)) != NULL)
     {
     el = dnaProbeLoad(row);
     slAddHead(&list, el);
     }
 slReverse(&list);
 sqlFreeResult(&sr);
 return list;
 }
 
 void dnaProbeSaveToDb(struct sqlConnection *conn, struct dnaProbe *el, char *tableName, int updateSize)
 /* Save dnaProbe 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','%s',%d,'%s',%d,%d,'%s',%d,%f,%f,%d,%f,%d,%f)", 
 	tableName,  el->name,  el->dna,  el->size,  el->chrom,  el->start,  el->end,  el->strand,  el->tpDist,  el->tm,  el->pGC,  el->affyHeur,  el->secStruct,  el->blatScore,  el->comparison);
 sqlUpdate(conn, update->string);
 freeDyString(&update);
 }
 
 struct dnaProbe *dnaProbeCommaIn(char **pS, struct dnaProbe *ret)
 /* Create a dnaProbe out of a comma separated string. 
  * This will fill in ret if non-null, otherwise will
  * return a new dnaProbe */
 {
 char *s = *pS;
 
 if (ret == NULL)
     AllocVar(ret);
 ret->name = sqlStringComma(&s);
 ret->dna = sqlStringComma(&s);
 ret->size = sqlSignedComma(&s);
 ret->chrom = sqlStringComma(&s);
 ret->start = sqlSignedComma(&s);
 ret->end = sqlSignedComma(&s);
 sqlFixedStringComma(&s, ret->strand, sizeof(ret->strand));
 ret->tpDist = sqlSignedComma(&s);
 ret->tm = sqlFloatComma(&s);
 ret->pGC = sqlFloatComma(&s);
 ret->affyHeur = sqlSignedComma(&s);
 ret->secStruct = sqlFloatComma(&s);
 ret->blatScore = sqlSignedComma(&s);
 ret->comparison = sqlFloatComma(&s);
 *pS = s;
 return ret;
 }
 
 void dnaProbeFree(struct dnaProbe **pEl)
 /* Free a single dynamically allocated dnaProbe such as created
  * with dnaProbeLoad(). */
 {
 struct dnaProbe *el;
 
 if ((el = *pEl) == NULL) return;
 freeMem(el->name);
 freeMem(el->dna);
 freeMem(el->chrom);
 freez(pEl);
 }
 
 void dnaProbeFreeList(struct dnaProbe **pList)
 /* Free a list of dynamically allocated dnaProbe's */
 {
 struct dnaProbe *el, *next;
 
 for (el = *pList; el != NULL; el = next)
     {
     next = el->next;
     dnaProbeFree(&el);
     }
 *pList = NULL;
 }
 
 void dnaProbeOutput(struct dnaProbe *el, FILE *f, char sep, char lastSep) 
 /* Print out dnaProbe.  Separate fields with sep. Follow last field with lastSep. */
 {
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->name);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->dna);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 fprintf(f, "%d", el->size);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->chrom);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 fprintf(f, "%d", el->start);
 fputc(sep,f);
 fprintf(f, "%d", el->end);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->strand);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 fprintf(f, "%d", el->tpDist);
 fputc(sep,f);
 fprintf(f, "%f", el->tm);
 fputc(sep,f);
 fprintf(f, "%f", el->pGC);
 fputc(sep,f);
 fprintf(f, "%d", el->affyHeur);
 fputc(sep,f);
 fprintf(f, "%f", el->secStruct);
 fputc(sep,f);
 fprintf(f, "%d", el->blatScore);
 fputc(sep,f);
 fprintf(f, "%f", el->comparison);
 fputc(lastSep,f);
 }
 
 /* -------------------------------- End autoSql Generated Code -------------------------------- */