private void Instance_SequenceParseCompleted(iDnaSequence sender, int nodeCount)
{
if (sender != null)
{
textBlockNodeCount.Text = sender.Count.ToString();
}
}
public static async Task <iDnaSequence> FromString(string str)
{
iDnaSequence sequence = new iDnaSequence();
await sequence.ParseString(str);
return(sequence);
}
private void _sequence_SequenceParseCompleted(iDnaSequence sender, int nodeCount)
{
if (_sequence == null)
{
return;
}
// assign repeats and hairpins only after parse string process is complete
_sequence.RepeatsRegionIndex = _deserializedRepeatIndexes;
_sequence.HairpinsRegionIndex = _deserializedHairPinIndexes;
_sequence.NotifySequenceLoaded();
}
public iDnaRegionIndex(iDnaSequence sequence, string regionName) : base()
{
_name = regionName;
if (sequence == null)
{
return;
}
int min = sequence.Min(i => i.Index),
max = sequence.Max(i => i.Index);
_limitMin = min;
_limitMax = max;
_minValue = min;
_maxValue = max;
}
/// <summary>
/// rebuild sequence basket (repeats and hairpins) from region indexes
/// </summary>
/// <param name="sourceSequence">the parent sequence to which the basket should be attached</param>
/// <param name="sourceList">the region index list</param>
/// <returns>the list of sequence basket</returns>
protected static List <iDnaSequence> RegionListToSequenceList(iDnaSequence sourceSequence, iDnaRegionIndexList sourceList)
{
List <iDnaSequence> list = new List <iDnaSequence>();
if (sourceList == null || sourceList.Count() <= 0 || sourceSequence == null)
{
return(list);
}
foreach (var region in sourceList)
{
var nodes = sourceSequence.Where(i => i.Index >= region.MinValue && i.Index <= region.MaxValue);
if (nodes == null || nodes.Count() <= 0)
{
continue;
}
list.Add(new iDnaSequence(region.Name, nodes, refOnly: true, nOccurrences: region.Occurrences));
}
return(list);
}
protected override void OnStartup(StartupEventArgs e)
{
if (e == null)
{
base.OnStartup(e);
return;
}
string[] args = e.Args;
iDnaSequence seq = iDnaSequence.Instance;
if (args != null && args.Length > 0)
{
_startupFileName = args[0];
}
if (seq != null)
{
seq.SequenceParseCompleted += Seq_SequenceParseCompleted;
}
base.OnStartup(e);
}
/// <summary>
/// for deserialzation !
/// </summary>
/// <param name="seq"></param>
internal void SetParentSequenceNoCheck(iDnaSequence seq)
{
_parentSequence = seq;
}
public iDnaRegionIndexList(iDnaSequence sequence, string regionName)
{
_parentSequence = sequence;
}
private void Seq_SequenceParseCompleted(iDnaSequence sender, int nodeCount)
{
SetMainWindowTitle(iDnaSequence.Instance.Name);
}
void InitialzeRootSequence()
{
_sequence = iDnaSequence.Instance;
_sequence.SequenceParseCompleted += _sequence_SequenceParseCompleted;
}
public iDnaSequenceContract(iDnaSequence sequence) : base()
{
_sequence = sequence;
}
public iDnaSequenceContract() : base()
{
_sequence = iDnaSequence.Instance;
}
public iDnaNode(iDnaSequence parentSequence, iDnaBase rootBase, int index) : base()
{
_parentSequence = parentSequence;
_base = rootBase;
_index = index;
}