/// <summary>
/// Sort the index of SequenceAlignmentMap by RName then by Pos.
/// Fill the index (sorted by RName then by Pos) into a list, when the list size reaches
/// the maximum limit, write the list to file and clear the list.
/// </summary>
private SortedDictionary <string, IList <string> > SortByChromosomeCoordinates()
{
SortedDictionary <string, IList <string> > sortedFiles = new SortedDictionary <string, IList <string> >();
IList <string> files = null;
var groups = new System.Collections.Generic.SortedList <string, System.Collections.Generic.SortedList <object, string> >();
System.Collections.Generic.SortedList <object, string> sortedList = null;
for (int index = 0; index < sequenceAlignMap.QuerySequences.Count; index++)
{
SAMAlignedSequence alignedSeq = sequenceAlignMap.QuerySequences[index];
if (!groups.TryGetValue(alignedSeq.RName, out sortedList))
{
sortedList = new System.Collections.Generic.SortedList <object, string>();
groups.Add(alignedSeq.RName, sortedList);
}
string indices = string.Empty;
if (!sortedList.TryGetValue(alignedSeq.Pos, out indices))
{
sortedList.Add(alignedSeq.Pos, index.ToString(CultureInfo.InvariantCulture));
}
else
{
indices = string.Format(CultureInfo.InvariantCulture, "{0},{1}", indices, index.ToString(CultureInfo.InvariantCulture));
sortedList[alignedSeq.Pos] = indices;
}
if (sortedList.Count >= SortedListMaxCount)
{
if (!sortedFiles.TryGetValue(alignedSeq.RName, out files))
{
files = new List <string>();
sortedFiles.Add(alignedSeq.RName, files);
}
files.Add(WriteToFile(sortedList));
sortedList.Clear();
}
}
foreach (KeyValuePair <string, System.Collections.Generic.SortedList <object, string> > group in groups)
{
if (group.Value.Count > 0)
{
if (!sortedFiles.TryGetValue(group.Key, out files))
{
files = new List <string>();
sortedFiles.Add(group.Key, files);
}
files.Add(WriteToFile(group.Value));
group.Value.Clear();
}
}
return(sortedFiles);
}
private void btnRunSearch_Click(object sender, EventArgs e)
{
UInt32 id = 0;
try
{
id = UInt32.Parse(txtSearchID.Text);
}
catch (Exception)
{
MessageBox.Show(this,
"Error parsing search id.", "Invalid ID");
lvResults.Clear();
return;
}
lvResults.Clear();
ContentObject o = null; //ContentManager.Instance.FindEntry(id);
if (o != null)
{
ListViewItem item = new ListViewItem(o.Name);
item.Tag = o.Object;
lvResults.Items.Add(item);
}
if (m_CRCList != null)
{
string val;
if (m_CRCList.TryGetValue(id, out val))
{
ListViewItem item =
new ListViewItem("CRC Match: \"" + val + "\"");
lvResults.Items.Add(item);
}
}
}
/// <summary>
/// Sort the index of SequenceAlignmentMap by RName then by Pos.
/// Fill the index (sorted by RName then by Pos) into a list, when the list size reaches
/// the maximum limit, write the list to file and clear the list.
/// </summary>
private SortedDictionary<string, IList<string>> SortByChromosomeCoordinates()
{
SortedDictionary<string, IList<string>> sortedFiles = new SortedDictionary<string, IList<string>>();
IList<string> files = null;
var groups = new System.Collections.Generic.SortedList<string, System.Collections.Generic.SortedList<object, string>>();
System.Collections.Generic.SortedList<object, string> sortedList = null;
for (int index = 0; index < sequenceAlignMap.QuerySequences.Count; index++)
{
SAMAlignedSequence alignedSeq = sequenceAlignMap.QuerySequences[index];
if (!groups.TryGetValue(alignedSeq.RName, out sortedList))
{
sortedList = new System.Collections.Generic.SortedList<object, string>();
groups.Add(alignedSeq.RName, sortedList);
}
string indices = string.Empty;
if (!sortedList.TryGetValue(alignedSeq.Pos, out indices))
{
sortedList.Add(alignedSeq.Pos, index.ToString(CultureInfo.InvariantCulture));
}
else
{
indices = string.Format(CultureInfo.InvariantCulture, "{0},{1}", indices, index.ToString(CultureInfo.InvariantCulture));
sortedList[alignedSeq.Pos] = indices;
}
if (sortedList.Count >= SortedListMaxCount)
{
if (!sortedFiles.TryGetValue(alignedSeq.RName, out files))
{
files = new List<string>();
sortedFiles.Add(alignedSeq.RName, files);
}
files.Add(WriteToFile(sortedList));
sortedList.Clear();
}
}
foreach (KeyValuePair<string, System.Collections.Generic.SortedList<object, string>> group in groups)
{
if (group.Value.Count > 0)
{
if (!sortedFiles.TryGetValue(group.Key, out files))
{
files = new List<string>();
sortedFiles.Add(group.Key, files);
}
files.Add(WriteToFile(group.Value));
group.Value.Clear();
}
}
return sortedFiles;
}