6031d05b102c1cb34c9e8394a8acf5809a8eca8f
angie
  Mon Jan 31 16:19:37 2011 -0800
Track #34 (dbVar for human): Added new track type gvf with basichandlers in hgTracks and hgc.  dbVar's GVF attributes are recognized,
esp. var_type is used to color items, and items are sorted using
the Parent keyword so that parents appear immediately before their
children, and children are sorted by var_type.  Attributes are
displayed in hgc; need to do a bit better for the Start_range and
End_range (e.g. translate "." to "inner start unknown" etc.).

diff --git src/hg/lib/bed8Attrs.c src/hg/lib/bed8Attrs.c
new file mode 100644
index 0000000..7a72f1e
--- /dev/null
+++ src/hg/lib/bed8Attrs.c
@@ -0,0 +1,211 @@
+/* bed8Attrs.c was originally generated by the autoSql program, which also 
+ * generated bed8Attrs.h and bed8Attrs.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 "bed8Attrs.h"
+
+static char const rcsid[] = "$Id:$";
+
+struct bed8Attrs *bed8AttrsLoad(char **row)
+/* Load a bed8Attrs from row fetched with select * from bed8Attrs
+ * from database.  Dispose of this with bed8AttrsFree(). */
+{
+struct bed8Attrs *ret;
+
+AllocVar(ret);
+ret->attrCount = sqlSigned(row[8]);
+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->thickStart = sqlUnsigned(row[6]);
+ret->thickEnd = sqlUnsigned(row[7]);
+{
+int sizeOne;
+sqlStringDynamicArray(row[9], &ret->attrTags, &sizeOne);
+assert(sizeOne == ret->attrCount);
+}
+{
+int sizeOne;
+sqlStringDynamicArray(row[10], &ret->attrVals, &sizeOne);
+assert(sizeOne == ret->attrCount);
+}
+return ret;
+}
+
+struct bed8Attrs *bed8AttrsLoadAll(char *fileName) 
+/* Load all bed8Attrs from a whitespace-separated file.
+ * Dispose of this with bed8AttrsFreeList(). */
+{
+struct bed8Attrs *list = NULL, *el;
+struct lineFile *lf = lineFileOpen(fileName, TRUE);
+char *row[11];
+
+while (lineFileRow(lf, row))
+    {
+    el = bed8AttrsLoad(row);
+    slAddHead(&list, el);
+    }
+lineFileClose(&lf);
+slReverse(&list);
+return list;
+}
+
+struct bed8Attrs *bed8AttrsLoadAllByChar(char *fileName, char chopper) 
+/* Load all bed8Attrs from a chopper separated file.
+ * Dispose of this with bed8AttrsFreeList(). */
+{
+struct bed8Attrs *list = NULL, *el;
+struct lineFile *lf = lineFileOpen(fileName, TRUE);
+char *row[11];
+
+while (lineFileNextCharRow(lf, chopper, row, ArraySize(row)))
+    {
+    el = bed8AttrsLoad(row);
+    slAddHead(&list, el);
+    }
+lineFileClose(&lf);
+slReverse(&list);
+return list;
+}
+
+struct bed8Attrs *bed8AttrsCommaIn(char **pS, struct bed8Attrs *ret)
+/* Create a bed8Attrs out of a comma separated string. 
+ * This will fill in ret if non-null, otherwise will
+ * return a new bed8Attrs */
+{
+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->thickStart = sqlUnsignedComma(&s);
+ret->thickEnd = sqlUnsignedComma(&s);
+ret->attrCount = sqlSignedComma(&s);
+{
+int i;
+s = sqlEatChar(s, '{');
+AllocArray(ret->attrTags, ret->attrCount);
+for (i=0; i<ret->attrCount; ++i)
+    {
+    ret->attrTags[i] = sqlStringComma(&s);
+    }
+s = sqlEatChar(s, '}');
+s = sqlEatChar(s, ',');
+}
+{
+int i;
+s = sqlEatChar(s, '{');
+AllocArray(ret->attrVals, ret->attrCount);
+for (i=0; i<ret->attrCount; ++i)
+    {
+    ret->attrVals[i] = sqlStringComma(&s);
+    }
+s = sqlEatChar(s, '}');
+s = sqlEatChar(s, ',');
+}
+*pS = s;
+return ret;
+}
+
+void bed8AttrsFree(struct bed8Attrs **pEl)
+/* Free a single dynamically allocated bed8Attrs such as created
+ * with bed8AttrsLoad(). */
+{
+struct bed8Attrs *el;
+
+if ((el = *pEl) == NULL) return;
+freeMem(el->chrom);
+freeMem(el->name);
+/* All strings in attrTags are allocated at once, so only need to free first. */
+if (el->attrTags != NULL)
+    freeMem(el->attrTags[0]);
+freeMem(el->attrTags);
+/* All strings in attrVals are allocated at once, so only need to free first. */
+if (el->attrVals != NULL)
+    freeMem(el->attrVals[0]);
+freeMem(el->attrVals);
+freez(pEl);
+}
+
+void bed8AttrsFreeList(struct bed8Attrs **pList)
+/* Free a list of dynamically allocated bed8Attrs's */
+{
+struct bed8Attrs *el, *next;
+
+for (el = *pList; el != NULL; el = next)
+    {
+    next = el->next;
+    bed8AttrsFree(&el);
+    }
+*pList = NULL;
+}
+
+void bed8AttrsOutput(struct bed8Attrs *el, FILE *f, char sep, char lastSep) 
+/* Print out bed8Attrs.  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->thickStart);
+fputc(sep,f);
+fprintf(f, "%u", el->thickEnd);
+fputc(sep,f);
+fprintf(f, "%d", el->attrCount);
+fputc(sep,f);
+{
+int i;
+if (sep == ',') fputc('{',f);
+for (i=0; i<el->attrCount; ++i)
+    {
+    if (sep == ',') fputc('"',f);
+    fprintf(f, "%s", el->attrTags[i]);
+    if (sep == ',') fputc('"',f);
+    fputc(',', f);
+    }
+if (sep == ',') fputc('}',f);
+}
+fputc(sep,f);
+{
+int i;
+if (sep == ',') fputc('{',f);
+for (i=0; i<el->attrCount; ++i)
+    {
+    if (sep == ',') fputc('"',f);
+    fprintf(f, "%s", el->attrVals[i]);
+    if (sep == ',') fputc('"',f);
+    fputc(',', f);
+    }
+if (sep == ',') fputc('}',f);
+}
+fputc(lastSep,f);
+}
+
+/* -------------------------------- End autoSql Generated Code -------------------------------- */
+