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/gencodeIntron.c src/hg/lib/gencodeIntron.c
index 2e98e9c..34ba349 100644
--- src/hg/lib/gencodeIntron.c
+++ src/hg/lib/gencodeIntron.c
@@ -1,223 +1,226 @@
 /* gencodeIntron.c was originally generated by the autoSql program, which also 
  * generated gencodeIntron.h and gencodeIntron.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 "gencodeIntron.h"
 
 
 void gencodeIntronStaticLoad(char **row, struct gencodeIntron *ret)
 /* Load a row from gencodeIntron 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->status = row[4];
 strcpy(ret->strand, row[5]);
 ret->transcript = row[6];
 ret->geneId = row[7];
 }
 
 struct gencodeIntron *gencodeIntronLoad(char **row)
 /* Load a gencodeIntron from row fetched with select * from gencodeIntron
  * from database.  Dispose of this with gencodeIntronFree(). */
 {
 struct gencodeIntron *ret;
 
 AllocVar(ret);
 ret->chrom = cloneString(row[0]);
 ret->chromStart = sqlUnsigned(row[1]);
 ret->chromEnd = sqlUnsigned(row[2]);
 ret->name = cloneString(row[3]);
 ret->status = cloneString(row[4]);
 strcpy(ret->strand, row[5]);
 ret->transcript = cloneString(row[6]);
 ret->geneId = cloneString(row[7]);
 return ret;
 }
 
 struct gencodeIntron *gencodeIntronLoadAll(char *fileName) 
 /* Load all gencodeIntron from a whitespace-separated file.
  * Dispose of this with gencodeIntronFreeList(). */
 {
 struct gencodeIntron *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[8];
 
 while (lineFileRow(lf, row))
     {
     el = gencodeIntronLoad(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct gencodeIntron *gencodeIntronLoadAllByChar(char *fileName, char chopper) 
 /* Load all gencodeIntron from a chopper separated file.
  * Dispose of this with gencodeIntronFreeList(). */
 {
 struct gencodeIntron *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[8];
 
 while (lineFileNextCharRow(lf, chopper, row, ArraySize(row)))
     {
     el = gencodeIntronLoad(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct gencodeIntron *gencodeIntronLoadByQuery(struct sqlConnection *conn, char *query, int rowOffset)
 /* Load all gencodeIntron 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 gencodeIntronFreeList(). */
 {
 struct gencodeIntron *list = NULL, *el;
 struct sqlResult *sr;
 char **row;
 
 sr = sqlGetResult(conn, query);
 while ((row = sqlNextRow(sr)) != NULL)
     {
     el = gencodeIntronLoad(row+rowOffset);
     slAddHead(&list, el);
     }
 slReverse(&list);
 sqlFreeResult(&sr);
 return list;
 }
 
 void gencodeIntronSaveToDb(struct sqlConnection *conn, struct gencodeIntron *el, char *tableName, int updateSize)
 /* Save gencodeIntron 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','%s','%s','%s','%s')", 
 	tableName,  el->chrom,  el->chromStart,  el->chromEnd,  el->name,  el->status,  el->strand,  el->transcript,  el->geneId);
 sqlUpdate(conn, update->string);
 freeDyString(&update);
 }
 
 
 struct gencodeIntron *gencodeIntronCommaIn(char **pS, struct gencodeIntron *ret)
 /* Create a gencodeIntron out of a comma separated string. 
  * This will fill in ret if non-null, otherwise will
  * return a new gencodeIntron */
 {
 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->status = sqlStringComma(&s);
 sqlFixedStringComma(&s, ret->strand, sizeof(ret->strand));
 ret->transcript = sqlStringComma(&s);
 ret->geneId = sqlStringComma(&s);
 *pS = s;
 return ret;
 }
 
 void gencodeIntronFree(struct gencodeIntron **pEl)
 /* Free a single dynamically allocated gencodeIntron such as created
  * with gencodeIntronLoad(). */
 {
 struct gencodeIntron *el;
 
 if ((el = *pEl) == NULL) return;
 freeMem(el->chrom);
 freeMem(el->name);
 freeMem(el->status);
 freeMem(el->transcript);
 freeMem(el->geneId);
 freez(pEl);
 }
 
 void gencodeIntronFreeList(struct gencodeIntron **pList)
 /* Free a list of dynamically allocated gencodeIntron's */
 {
 struct gencodeIntron *el, *next;
 
 for (el = *pList; el != NULL; el = next)
     {
     next = el->next;
     gencodeIntronFree(&el);
     }
 *pList = NULL;
 }
 
 void gencodeIntronOutput(struct gencodeIntron *el, FILE *f, char sep, char lastSep) 
 /* Print out gencodeIntron.  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);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->status);
 if (sep == ',') fputc('"',f);
 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->transcript);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->geneId);
 if (sep == ',') fputc('"',f);
 fputc(lastSep,f);
 }
 
 /* -------------------------------- End autoSql Generated Code -------------------------------- */
 
 void gencodeIntronTableCreate(struct sqlConnection *conn, char *tableName, int indexSize)
 /* Create a gencodeIntron table with the given name */
 {
 char *createString =
 "CREATE TABLE %s (\n"
 "       chrom varchar(255) not null,	# Chromosome\n"
 "       chromStart int unsigned not null,	# Start position in chromosome\n"
 "       chromEnd int unsigned not null,	# End position in chromosome\n"
 "       name varchar(255) not null,	# Intron ID\n"
 "       status enum('not_tested', 'RT_positive','RT_negative','RT_wrong_junction','RT_submitted', 'RACE_validated'),      # Status\n"
 "       strand char(1) not null,	# + or -\n"
 "       transcript varchar(255) not null,	# Transcript ID from GTF\n"
 "       geneId varchar(255) not null,	# Gene ID from GTF\n"
 "    INDEX(chrom(%d),chromStart),\n"
 "    INDEX(chrom(%d),chromEnd)\n"
 ")\n";
 struct dyString *dy = newDyString(1024);
 sqlDyStringPrintf(dy, createString, tableName, indexSize, indexSize, indexSize);
 sqlRemakeTable(conn, tableName, dy->string);
 dyStringFree(&dy);
 }