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/estOrientInfo.c src/hg/lib/estOrientInfo.c
index e60e926..17e5cb5 100644
--- src/hg/lib/estOrientInfo.c
+++ src/hg/lib/estOrientInfo.c
@@ -1,213 +1,216 @@
 /* estOrientInfo.c was originally generated by the autoSql program, which also 
  * generated estOrientInfo.h and estOrientInfo.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 "localmem.h"
 #include "estOrientInfo.h"
 
 
 static char *createString = 
     "CREATE TABLE %s (\n"
     "    bin smallint unsigned not null,        # Bin for fast index\n"
     "    chrom varchar(255) not null,	        # Human chromosome or FPC contig\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,	        # Accession of EST\n"
     "    intronOrientation smallint not null,	# Orientation of introns with respect to EST\n"
     "    sizePolyA smallint not null,	        # Number of trailing A's\n"
     "    revSizePolyA smallint not null,	# Number of trailing A's on reverse strand\n"
     "    signalPos smallint not null,	        # Position of start of polyA signal relative to end of EST or 0 if no signal\n"
     "    revSignalPos smallint not null,	# PolyA signal position on reverse strand if any\n"
     "              #Indices\n"
     "    INDEX(chrom(%d),bin),\n"
     "    INDEX(chrom(%d),chromStart),\n"
     "    INDEX(chrom(%d),chromEnd),\n"
     "    INDEX(name(20))\n"
     ")\n";
 
 void estOrientInfoStaticLoad(char **row, struct estOrientInfo *ret)
 /* Load a row from estOrientInfo 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->intronOrientation = sqlSigned(row[4]);
 ret->sizePolyA = sqlSigned(row[5]);
 ret->revSizePolyA = sqlSigned(row[6]);
 ret->signalPos = sqlSigned(row[7]);
 ret->revSignalPos = sqlSigned(row[8]);
 }
 
 struct estOrientInfo *estOrientInfoLoad(char **row)
 /* Load a estOrientInfo from row fetched with select * from estOrientInfo
  * from database.  Dispose of this with estOrientInfoFree(). */
 {
 struct estOrientInfo *ret;
 
 AllocVar(ret);
 ret->chrom = cloneString(row[0]);
 ret->chromStart = sqlUnsigned(row[1]);
 ret->chromEnd = sqlUnsigned(row[2]);
 ret->name = cloneString(row[3]);
 ret->intronOrientation = sqlSigned(row[4]);
 ret->sizePolyA = sqlSigned(row[5]);
 ret->revSizePolyA = sqlSigned(row[6]);
 ret->signalPos = sqlSigned(row[7]);
 ret->revSignalPos = sqlSigned(row[8]);
 return ret;
 }
 
 struct estOrientInfo *estOrientInfoLoadLm(char **row, struct lm *lm)
 /* Load a estOrientInfo row into local memory struct. */
 {
 struct estOrientInfo *ret;
 
 lmAllocVar(lm, ret);
 ret->chrom = lmCloneString(lm, row[0]);
 ret->chromStart = sqlUnsigned(row[1]);
 ret->chromEnd = sqlUnsigned(row[2]);
 ret->name = cloneString(row[3]);
 ret->intronOrientation = sqlSigned(row[4]);
 ret->sizePolyA = sqlSigned(row[5]);
 ret->revSizePolyA = sqlSigned(row[6]);
 ret->signalPos = sqlSigned(row[7]);
 ret->revSignalPos = sqlSigned(row[8]);
 return ret;
 }
 
 struct estOrientInfo *estOrientInfoLoadAll(char *fileName) 
 /* Load all estOrientInfo from a tab-separated file.
  * Dispose of this with estOrientInfoFreeList(). */
 {
 struct estOrientInfo *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[9];
 
 while (lineFileRow(lf, row))
     {
     el = estOrientInfoLoad(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct estOrientInfo *estOrientInfoLoadWhere(struct sqlConnection *conn, char *table, char *where)
 /* Load all estOrientInfo from table that satisfy where clause. The
  * where clause may be NULL in which case whole table is loaded
  * Dispose of this with estOrientInfoFreeList(). */
 {
 struct estOrientInfo *list = NULL, *el;
 struct dyString *query = dyStringNew(256);
 struct sqlResult *sr;
 char **row;
 
 sqlDyStringPrintf(query, "select * from %s", table);
 if (where != NULL)
     dyStringPrintf(query, " where %s", where);
 sr = sqlGetResult(conn, query->string);
 while ((row = sqlNextRow(sr)) != NULL)
     {
     el = estOrientInfoLoad(row);
     slAddHead(&list, el);
     }
 slReverse(&list);
 sqlFreeResult(&sr);
 dyStringFree(&query);
 return list;
 }
 
 struct estOrientInfo *estOrientInfoCommaIn(char **pS, struct estOrientInfo *ret)
 /* Create a estOrientInfo out of a comma separated string. 
  * This will fill in ret if non-null, otherwise will
  * return a new estOrientInfo */
 {
 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->intronOrientation = sqlSignedComma(&s);
 ret->sizePolyA = sqlSignedComma(&s);
 ret->revSizePolyA = sqlSignedComma(&s);
 ret->signalPos = sqlSignedComma(&s);
 ret->revSignalPos = sqlSignedComma(&s);
 *pS = s;
 return ret;
 }
 
 void estOrientInfoFree(struct estOrientInfo **pEl)
 /* Free a single dynamically allocated estOrientInfo such as created
  * with estOrientInfoLoad(). */
 {
 struct estOrientInfo *el;
 
 if ((el = *pEl) == NULL) return;
 freeMem(el->chrom);
 freeMem(el->name);
 freez(pEl);
 }
 
 void estOrientInfoFreeList(struct estOrientInfo **pList)
 /* Free a list of dynamically allocated estOrientInfo's */
 {
 struct estOrientInfo *el, *next;
 
 for (el = *pList; el != NULL; el = next)
     {
     next = el->next;
     estOrientInfoFree(&el);
     }
 *pList = NULL;
 }
 
 void estOrientInfoOutput(struct estOrientInfo *el, FILE *f, char sep, char lastSep) 
 /* Print out estOrientInfo.  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, "%d", el->intronOrientation);
 fputc(sep,f);
 fprintf(f, "%d", el->sizePolyA);
 fputc(sep,f);
 fprintf(f, "%d", el->revSizePolyA);
 fputc(sep,f);
 fprintf(f, "%d", el->signalPos);
 fputc(sep,f);
 fprintf(f, "%d", el->revSignalPos);
 fputc(lastSep,f);
 }
 
 char *estOrientInfoGetCreateSql(char *table, int chromIdxLen)
 /* Get SQL to create an estOrientInfo table. chromIdxLen is the number of
  * chars at that start of chrom to use for the index. */
 {
 struct dyString *sqlCmd = newDyString(2048);
 char *sqlCmdStr;
 sqlDyStringPrintf(sqlCmd, createString, table, chromIdxLen, chromIdxLen, chromIdxLen);
 sqlCmdStr = cloneString(sqlCmd->string);
 dyStringFree(&sqlCmd);
 return sqlCmdStr;
 }