549dcd456f5d557e15426176e487f91246363548
kate
  Mon Apr 10 17:21:22 2017 -0700
Better integration with bigBed cod. Fixes loading problem and allows labelFields code to operate (not yet tested). refs #18736

diff --git src/hg/lib/barChartBed.c src/hg/lib/barChartBed.c
index 2ad58a9..027904a 100644
--- src/hg/lib/barChartBed.c
+++ src/hg/lib/barChartBed.c
@@ -1,87 +1,47 @@
 /* barChartBed.c was originally generated by the autoSql program, which also 
  * generated barChartBed.h and barChartBed.sql.  This module links the database and
  * the RAM representation of objects. */
 
 #include "common.h"
 #include "linefile.h"
 #include "dystring.h"
 #include "jksql.h"
 #include "barChartBed.h"
 
 
 
 char *barChartBedCommaSepFieldNames = "chrom,chromStart,chromEnd,name,score,strand,expCount,expScores";
 
-struct barChartBed *barChartBedLoadByQuery(struct sqlConnection *conn, char *query)
-/* Load all barChartBed 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 barChartBedFreeList(). */
-{
-struct barChartBed *list = NULL, *el;
-struct sqlResult *sr;
-char **row;
-
-sr = sqlGetResult(conn, query);
-while ((row = sqlNextRow(sr)) != NULL)
-    {
-    el = barChartBedLoad(row);
-    slAddHead(&list, el);
-    }
-slReverse(&list);
-sqlFreeResult(&sr);
-return list;
-}
-
-void barChartBedSaveToDb(struct sqlConnection *conn, struct barChartBed *el, char *tableName, int updateSize)
-/* Save barChartBed 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. This function automatically escapes quoted strings for mysql. */
-{
-struct dyString *update = newDyString(updateSize);
-char  *expScoresArray;
-expScoresArray = sqlFloatArrayToString(el->expScores, el->expCount);
-sqlDyStringPrintf(update, "insert into %s values ( '%s',%u,%u,'%s',%u,'%s',%u,'%s')", 
-	tableName,  el->chrom,  el->chromStart,  el->chromEnd,  el->name,  el->score,  el->strand,  el->expCount,  expScoresArray );
-sqlUpdate(conn, update->string);
-freeDyString(&update);
-freez(&expScoresArray);
-}
-
 struct barChartBed *barChartBedLoad(char **row)
 /* Load a barChartBed from row fetched with select * from barChartBed
  * from database.  Dispose of this with barChartBedFree(). */
 {
 struct barChartBed *ret;
 
 AllocVar(ret);
 ret->expCount = sqlUnsigned(row[6]);
 ret->chrom = cloneString(row[0]);
 ret->chromStart = sqlUnsigned(row[1]);
 ret->chromEnd = sqlUnsigned(row[2]);
 ret->name = cloneString(row[3]);
 ret->score = sqlUnsigned(row[4]);
 safecpy(ret->strand, sizeof(ret->strand), row[5]);
 {
 int sizeOne;
 sqlFloatDynamicArray(row[7], &ret->expScores, &sizeOne);
-if (sizeOne != ret->expCount)
-    errAbort("Bad record in barChart track: '%s' has missing category values", ret->name);
+assert(sizeOne == ret->expCount);
 }
 return ret;
 }
 
 struct barChartBed *barChartBedLoadAll(char *fileName) 
 /* Load all barChartBed from a whitespace-separated file.
  * Dispose of this with barChartBedFreeList(). */
 {
 struct barChartBed *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[8];
 
 while (lineFileRow(lf, row))
     {
     el = barChartBedLoad(row);
@@ -193,64 +153,89 @@
 {
 int i;
 if (sep == ',') fputc('{',f);
 for (i=0; i<el->expCount; ++i)
     {
     fprintf(f, "%g", el->expScores[i]);
     fputc(',', f);
     }
 if (sep == ',') fputc('}',f);
 }
 fputc(lastSep,f);
 }
 
 /* -------------------------------- End autoSql Generated Code -------------------------------- */
 
+#include "basicBed.h"
+
 void barChartBedCreateTable(struct sqlConnection *conn, char *table)
 /* Create barChart format table of given name. */
 {
 char query[1024];
 
 sqlSafef(query, sizeof(query),
 "CREATE TABLE %s (\n"
 "   chrom varchar(255) not null,	# Reference sequence chromosome or scaffold\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,	# Unique identifier\n"
 "   score int unsigned not null,	# Score from 0-1000\n"
 "   strand char(1) not null,	# + or - for strand\n"
 "   expCount int unsigned not null,	# Number of experiment values\n"
 "   expScores longblob not null,	# Comma separated list of experiment scores\n"
           "#Indices\n"
 "   PRIMARY KEY(name)\n"
 ")\n",
     table);
 sqlRemakeTable(conn, table, query);
 }
 
-float barChartTotalValue(struct barChartBed *bed)
+struct bed *barChartSimpleBedLoad(char **row)
+/* Load a bed from row containing barChart bed fields. 
+ * This is reuses autoSql barChartBedLoad, but with a full-size bed.
+ Dispose of this with bedFree() */
+{
+struct bed *ret;
+AllocVar(ret);
+ret->expCount = sqlUnsigned(row[6]);
+ret->chrom = cloneString(row[0]);
+ret->chromStart = sqlUnsigned(row[1]);
+ret->chromEnd = sqlUnsigned(row[2]);
+ret->name = cloneString(row[3]);
+ret->score = sqlUnsigned(row[4]);
+safecpy(ret->strand, sizeof(ret->strand), row[5]);
+{
+int sizeOne;
+sqlFloatDynamicArray(row[7], &ret->expScores, &sizeOne);
+assert(sizeOne == ret->expCount);
+}
+return ret;
+}
+
+float barChartTotalValue(struct bed *bed)
 /* Return total of all category values */
 {
 int i;
 float sum = 0.0;
 for (i=0; i<bed->expCount; i++)
     sum += bed->expScores[i];
 return sum;
 }
 
-float barChartHighestValue(struct barChartBed *bed, int *categIdRet)
+float barChartMaxValue(struct bed *bed, int *categIdRet)
 /* Return value and id of category with highest value for this item */
 {
 int i;
 float maxScore = 0.0;
 assert(categIdRet);
 for (i=0; i<bed->expCount; i++)
     {
     float score = bed->expScores[i];
     if (score > maxScore)
         {
         maxScore = score;
         *categIdRet = i;
         }
     }
 return maxScore;
 }
+