e2e920776dddac39896fdb4aebae84a12bcb52b1
kate
  Tue May 9 11:06:33 2017 -0700
Add table browwser support for barChart custom tracks. refs #18736

diff --git src/hg/lib/barChartBed.c src/hg/lib/barChartBed.c
index 97b470b..9784bc0 100644
--- src/hg/lib/barChartBed.c
+++ src/hg/lib/barChartBed.c
@@ -1,328 +1,352 @@
 /* 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,name2,expCount,expScores,_dataOffset,_dataLen";
 
 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','%s',%u,'%s',%lld,%d)", 
 	tableName,  el->chrom,  el->chromStart,  el->chromEnd,  el->name,  el->score,  el->strand,  el->name2,  el->expCount,  expScoresArray ,  el->_dataOffset,  el->_dataLen);
 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[7]);
 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]);
 ret->name2 = cloneString(row[6]);
 {
 int sizeOne;
 sqlFloatDynamicArray(row[8], &ret->expScores, &sizeOne);
 assert(sizeOne == ret->expCount);
 }
 ret->_dataOffset = sqlLongLong(row[9]);
 ret->_dataLen = sqlSigned(row[10]);
 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[11];
 
 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[11];
 
 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->name2 = sqlStringComma(&s);
 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, ',');
 }
 ret->_dataOffset = sqlLongLongComma(&s);
 ret->_dataLen = sqlSignedComma(&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->name2);
 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);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->name2);
 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(sep,f);
 fprintf(f, "%lld", el->_dataOffset);
 fputc(sep,f);
 fprintf(f, "%d", el->_dataLen);
 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,         # Identifier\n"
 "   score int unsigned not null,        # Score from 0-1000\n"
 "   strand char(1) not null,            # + or - for strand\n"
 "   name2 varchar(255) not null,        # Alternative name for item\n"
 "   expCount int unsigned not null,     # Number of experiment values\n"
 "   expScores longblob not null,        # Comma separated list of experiment scores\n"
 "   _dataOffset bigint not null,        # Offset of sample data in data matrix file, for boxplot on details page\n"
 "   _dataLen int not null,              # Length of sample data row in data matrix file\n"
 "   INDEX(name),\n"
 "   INDEX(chrom(20), chromStart)\n"
 ")\n",
     table);
 sqlRemakeTable(conn, table, query);
 }
 
+static char *barChartAutoSqlString =
+"table barChartBed"
+"\"BED6+5 with additional fields for category count and median values, and sample matrix fields\""
+"    ("
+"   string chrom;       \"Reference sequence chromosome or scaffold\""
+"   uint   chromStart;  \"Start position in chromosome\""
+"   uint   chromEnd;    \"End position in chromosome\""
+"   string name;        \"Name or ID of item, ideally both human readable and unique\""
+"   uint   score;       \"Score from 0-1000, typically derived from total of median value from all categories\""
+"   char[1] strand;     \"+ or - for strand. Use . if not applicable\""
+"   string name2;       \"Alternative name for item\""
+"   uint expCount;      \"Number of categories\""
+"   float[expCount] expScores; \"Comma separated list of category values\""
+"   bigint _dataOffset; \"Offset of sample data in data matrix file, for boxplot on details page\""
+"   int _dataLen;       \"Length of sample data row in data matrix file\""
+"   )"
+;
+
+struct asObject *barChartAsObj()
+/* Return asObject describing fields of barChart database table (includes bin) */
+{
+return asParseText(barChartAutoSqlString);
+}
+
+
 struct bed *barChartSimpleBedLoad(char **row)
 /* Load a bed from row containing barChart bed fields. 
  * This reuses autoSql barChartBedLoad, but with a full-size bed.
  Dispose of this with bedFree() */
 {
 struct bed *ret;
 AllocVar(ret);
 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]);
 // name2 is in row[6]
 ret->expCount = sqlUnsigned(row[7]);
 {
 int sizeOne;
 sqlFloatDynamicArray(row[8], &ret->expScores, &sizeOne);
 assert(sizeOne == ret->expCount);
 }
 return ret;
 }
 
 struct barChartBed *barChartBedLoadOptionalOffsets(char **row, boolean hasOffsets)
 /* Load a barChartBed from row fetched with select * from barChartBed
  * from database or file.  Also supports schema lacking file offet and length for details.
 .  Dispose of this with barChartBedFree(). */
 {
 struct barChartBed *ret;
 
 AllocVar(ret);
 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]);
 ret->name2 = cloneString(row[6]);
 ret->expCount = sqlUnsigned(row[7]);
 {
 int sizeOne;
 sqlFloatDynamicArray(row[8], &ret->expScores, &sizeOne);
 assert(sizeOne == ret->expCount);
 }
 if (hasOffsets)
     {
     ret->_dataOffset = sqlLongLong(row[9]);
     ret->_dataLen = sqlSigned(row[10]);
     }
 return ret;
 }
 
 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 barChartMaxValue(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;
 }
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