381dc1cd9197dc1d8a4fe910b962104092d2896e
kate
  Thu Jan 26 14:29:21 2017 -0800
Initial cut of hgTracks and hgTrackUi for new barchart type track (generalization of GTEx gene expression display). refs #18736

diff --git src/hg/lib/barChartBed.c src/hg/lib/barChartBed.c
new file mode 100644
index 0000000..a71e98a
--- /dev/null
+++ src/hg/lib/barChartBed.c
@@ -0,0 +1,255 @@
+/* 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);
+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);
+    slAddHead(&list, el);
+    }
+lineFileClose(&lf);
+slReverse(&list);
+return list;
+}
+
+struct barChartBed *barChartBedLoadAllByChar(char *fileName, char chopper) 
+/* Load all barChartBed from a chopper separated file.
+ * Dispose of this with barChartBedFreeList(). */
+{
+struct barChartBed *list = NULL, *el;
+struct lineFile *lf = lineFileOpen(fileName, TRUE);
+char *row[8];
+
+while (lineFileNextCharRow(lf, chopper, row, ArraySize(row)))
+    {
+    el = barChartBedLoad(row);
+    slAddHead(&list, el);
+    }
+lineFileClose(&lf);
+slReverse(&list);
+return list;
+}
+
+struct barChartBed *barChartBedCommaIn(char **pS, struct barChartBed *ret)
+/* Create a barChartBed out of a comma separated string. 
+ * This will fill in ret if non-null, otherwise will
+ * return a new barChartBed */
+{
+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->score = sqlUnsignedComma(&s);
+sqlFixedStringComma(&s, ret->strand, sizeof(ret->strand));
+ret->expCount = sqlUnsignedComma(&s);
+{
+int i;
+s = sqlEatChar(s, '{');
+AllocArray(ret->expScores, ret->expCount);
+for (i=0; i<ret->expCount; ++i)
+    {
+    ret->expScores[i] = sqlFloatComma(&s);
+    }
+s = sqlEatChar(s, '}');
+s = sqlEatChar(s, ',');
+}
+*pS = s;
+return ret;
+}
+
+void barChartBedFree(struct barChartBed **pEl)
+/* Free a single dynamically allocated barChartBed such as created
+ * with barChartBedLoad(). */
+{
+struct barChartBed *el;
+
+if ((el = *pEl) == NULL) return;
+freeMem(el->chrom);
+freeMem(el->name);
+freeMem(el->expScores);
+freez(pEl);
+}
+
+void barChartBedFreeList(struct barChartBed **pList)
+/* Free a list of dynamically allocated barChartBed's */
+{
+struct barChartBed *el, *next;
+
+for (el = *pList; el != NULL; el = next)
+    {
+    next = el->next;
+    barChartBedFree(&el);
+    }
+*pList = NULL;
+}
+
+void barChartBedOutput(struct barChartBed *el, FILE *f, char sep, char lastSep) 
+/* Print out barChartBed.  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->score);
+fputc(sep,f);
+if (sep == ',') fputc('"',f);
+fprintf(f, "%s", el->strand);
+if (sep == ',') fputc('"',f);
+fputc(sep,f);
+fprintf(f, "%u", el->expCount);
+fputc(sep,f);
+{
+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 -------------------------------- */
+
+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)
+/* 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)
+/* 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;
+}