/// <summary>
/// Sort the index of SequenceAlignmentMap by QName.
/// Fill the index (sorted by QName) into a list, when the list size reaches
/// the maximum limit, write the list to file and clear the list.
/// </summary>
private IList <string> SortByReadNames()
{
IList <string> files = new List <string>();
var sortedList = new System.Collections.Generic.SortedList <object, string>();
for (int index = 0; index < sequenceAlignMap.QuerySequences.Count; index++)
{
SAMAlignedSequence alignedSeq = sequenceAlignMap.QuerySequences[index];
string indices = string.Empty;
if (!sortedList.TryGetValue(alignedSeq.QName, out indices))
{
sortedList.Add(alignedSeq.QName, index.ToString(CultureInfo.InvariantCulture));
}
else
{
indices = string.Format(CultureInfo.InvariantCulture, "{0},{1}", indices, index.ToString(CultureInfo.InvariantCulture));
sortedList[alignedSeq.QName] = indices;
}
if (sortedList.Count >= SortedListMaxCount)
{
if (files == null)
{
files = new List <string>();
}
files.Add(WriteToFile(sortedList));
sortedList.Clear();
}
}
if (sortedList.Count > 0)
{
files.Add(WriteToFile(sortedList));
sortedList.Clear();
}
return(files);
}
public void Close()
{
adler32 = 0;
header_size = 0;
filetime = 0;
foreach (System.Collections.Generic.KeyValuePair <string, Kom2SubFile> KeyValue in subfiles)
{
KeyValue.Value.Close();
}
subfiles.Clear();
ecb = null;
komtype = EKomType.notkom;
}
public void Clear()
{
items.Clear();
}
/// <summary>
/// Clears the collection, i.e. removes all entries.
/// </summary>
public void Clear()
{
_list.Clear();
}
/// <summary>
/// Sort the index of SequenceAlignmentMap by QName.
/// Fill the index (sorted by QName) into a list, when the list size reaches
/// the maximum limit, write the list to file and clear the list.
/// </summary>
private IList<string> SortByReadNames()
{
IList<string> files = new List<string>();
var sortedList = new System.Collections.Generic.SortedList<object,string>();
for (int index = 0; index < sequenceAlignMap.QuerySequences.Count; index++)
{
SAMAlignedSequence alignedSeq = sequenceAlignMap.QuerySequences[index];
string indices = string.Empty;
if (!sortedList.TryGetValue(alignedSeq.QName, out indices))
{
sortedList.Add(alignedSeq.QName, index.ToString(CultureInfo.InvariantCulture));
}
else
{
indices = string.Format(CultureInfo.InvariantCulture, "{0},{1}", indices, index.ToString(CultureInfo.InvariantCulture));
sortedList[alignedSeq.QName] = indices;
}
if (sortedList.Count >= SortedListMaxCount)
{
if (files == null)
{
files = new List<string>();
}
files.Add(WriteToFile(sortedList));
sortedList.Clear();
}
}
if (sortedList.Count > 0)
{
files.Add(WriteToFile(sortedList));
sortedList.Clear();
}
return files;
}
private ITypedElement GetResourceNavigator(out EvaluationContext evalContext)
{
string parseErrors2;
var inputNavDSTU2 = FhirPathProcessor.GetResourceNavigatorDSTU2(textboxInputXML.Text, out parseErrors2);
string parseErrors3;
var inputNavSTU3 = FhirPathProcessor.GetResourceNavigatorSTU3(textboxInputXML.Text, out parseErrors3);
string parseErrors4;
var inputNavR4 = FhirPathProcessor.GetResourceNavigatorR4(textboxInputXML.Text, out parseErrors4);
if (!string.IsNullOrEmpty(parseErrors2) || !string.IsNullOrEmpty(parseErrors3) || !string.IsNullOrEmpty(parseErrors4))
{
ResetResults();
AppendResults(String.Join("\r\n--------------------\r\n", parseErrors2, parseErrors3, parseErrors4), true);
}
if (inputNavR4 != null || inputNavSTU3 != null || inputNavDSTU2 != null)
{
ISourceNode node;
if (textboxInputXML.Text.StartsWith("{"))
{
node = Hl7.Fhir.Serialization.FhirJsonNode.Parse(textboxInputXML.Text);
}
else
{
node = Hl7.Fhir.Serialization.FhirXmlNode.Parse(textboxInputXML.Text);
}
_locations.Clear();
int lastPos = 0;
IPositionInfo lastNode = null;
AddLocations(node, ref lastNode, ref lastPos, textboxInputXML.Text.ToCharArray());
string t = _locations.LastOrDefault(c => c.Key < textboxInputXML.SelectionStart).Value;
System.Diagnostics.Trace.WriteLine($"Focused: {t}");
}
if (inputNavR4 != null)
{
btnR4.Visibility = Visibility.Visible;
}
else
{
btnR4.Visibility = Visibility.Collapsed;
}
if (inputNavSTU3 != null)
{
btnSTU3.Visibility = Visibility.Visible;
}
else
{
btnSTU3.Visibility = Visibility.Collapsed;
}
if (inputNavDSTU2 != null)
{
btnDSTU2.Visibility = Visibility.Visible;
}
else
{
btnDSTU2.Visibility = Visibility.Collapsed;
}
if (inputNavR4 != null)
{
evalContext = new fp4.FhirEvaluationContext(inputNavR4);
return(inputNavR4);
}
if (inputNavSTU3 != null)
{
evalContext = new fp3.FhirEvaluationContext(inputNavSTU3);
return(inputNavSTU3);
}
evalContext = new fp2.FhirEvaluationContext(inputNavDSTU2);
return(inputNavDSTU2);
}