private void LoadAndFindTaxonomy()
{
var dc = RcadSequenceProvider.CreateDbContext(ConnectionString);
_rootTaxonomy = new TaxonomyEntry(dc, true);
// Get a list of the taxids leading up to the selected one.
string sql = @"with cte as (select ParentTaxID from Taxonomy where TaxID={0} " +
@"union all select t.ParentTaxID from Taxonomy t join cte tp on t.TaxID = tp.ParentTaxID) " +
@"select * from cte";
var taxIds = dc.ExecuteQuery <int>(sql, ParentTaxId).Reverse().ToList();
taxIds.RemoveAt(0); // Remove root entry
taxIds.Add(ParentTaxId);
TaxonomyEntry current = _rootTaxonomy;
foreach (int tid in taxIds)
{
// Skip root (level 0)
if (tid <= 1)
{
continue;
}
current.IsExpanded = true;
foreach (var child in current.Children)
{
if (child.Id == tid)
{
current = child;
break;
}
}
}
if (current.Id == ParentTaxId)
{
current.IsSelected = true;
}
else
{
_rootTaxonomy = null;
dc.Dispose();
}
}
public IEnumerable <IBioSymbol> LoadRange(int startIndex, int count)
{
using (var dc = RcadSequenceProvider.CreateDbContext(_connectionString))
{
startIndex++;
// select ColumnNumber, Base from sequence
// where seqid = @id and ColumnNumber >= @startIndex
// order by columnNumber
//KJD (10/21/2009) - Change query to use vAlignmentGridUngapped which takes into account column indirection supported by the rCAD schema
//we use the ungapped view to avoid transmitting gap characters from the db to the view (which would happen with vAlignmentGrid).
var data = (from seq in dc.vAlignmentGridUngappeds
where seq.SeqID == _id && seq.AlnID == _aid && seq.LogicalColumnNumber >= startIndex
orderby seq.LogicalColumnNumber
select new { seq.LogicalColumnNumber, seq.BioSymbol }).Take(count);
// Push back the requested count, fill in gaps in the sequence
int i = 0;
var ie = data.GetEnumerator();
if (ie.MoveNext())
{
var entry = ie.Current;
for (; i < count; i++)
{
int currentIndex = i + startIndex;
Debug.Assert(entry.LogicalColumnNumber >= currentIndex);
if (entry.LogicalColumnNumber == currentIndex)
{
Debug.Assert(_startingSequenceColumn <= currentIndex);
yield return(new BioSymbol(BioSymbolType.Nucleotide, entry.BioSymbol));
if (!ie.MoveNext())
{
break;
}
entry = ie.Current;
}
else
{
if (_startingSequenceColumn > currentIndex)
{
yield return(BioSymbol.None);
}
else
{
yield return(BioSymbol.Gap);
}
}
}
}
// Pad to end
for (; i < count; i++)
{
yield return(BioSymbol.None);
}
}
}
