/// <summary>
/// Determine equality (by Id) of two ILinearDomain objects.
/// </summary>
/// <param name="other">
/// An object that implements ILinearDomain against which this object is to be
/// compared.
/// </param>
/// <returns>
/// Returns true if and only if the respective Id fields of this object and the
/// comparison object are equal.
/// </returns>
public bool Equals(ILinearDomain other)
{
return(CompareTo(other) == 0);
}
/// <summary>
/// Loads the contents of a list of blast result collator objects into the model.
/// <para>
/// When finished, fires the LoadComplete event to notify listeners.
/// </para>
/// </summary>
public void Load(IList <BlastResultCollator> blastResults)
{
StringWriter errorLog = new StringWriter();
featureCollection.features.Clear();
featureCollection.hits.Clear();
featureCollection.sequences.Clear();
featureCollection.initialQuerySequence = null;
foreach (BlastResultCollator blastResult in blastResults)
{
try
{
ILinearDomain querySequence = null;
ILinearDomain hitSequence = null;
string queryId = blastResult.QueryId == null
? String.Format(Resource.SILVERMAP_UNKNOWN_QUERY_ID, unknownQuerySerialNumber ++)
: blastResult.QueryId;
string subjectId = blastResult.SubjectId == null ? blastResult.Accession : blastResult.SubjectId;
if (featureCollection.sequences.ContainsKey(queryId))
{
querySequence = featureCollection.sequences[queryId];
}
else
{
querySequence = new SilverMapSequence(
queryId,
Resource.SILVERMAP_QUERY_SEQUENCE,
queryId,
blastResult.Length
);
featureCollection.sequences.Add(queryId, querySequence);
}
if (featureCollection.initialQuerySequence == null)
{
featureCollection.initialQuerySequence = querySequence;
}
featureCollection.querySequences.Add(querySequence);
if (featureCollection.sequences.ContainsKey(subjectId))
{
hitSequence = featureCollection.sequences[subjectId];
}
else
{
hitSequence = new SilverMapSequence(
subjectId,
blastResult.Description,
subjectId,
blastResult.Length
);
featureCollection.sequences.Add(subjectId, hitSequence);
}
long queryStart = Math.Min(blastResult.QStart, blastResult.QEnd);
long queryEnd = Math.Max(blastResult.QStart, blastResult.QEnd);
DefaultFeature queryFeature = new DefaultFeature(
querySequence,
queryStart,
queryEnd,
blastResult.QueryString
);
long subjectStart = Math.Min(blastResult.SStart, blastResult.SEnd);
long subjectEnd = Math.Max(blastResult.SStart, blastResult.SEnd);
DefaultFeature hitFeature = new DefaultFeature(
hitSequence,
subjectStart,
subjectEnd,
blastResult.SubjectString
);
featureCollection.features.Add(queryFeature);
featureCollection.features.Add(hitFeature);
featureCollection.hits.Add(new Hit(queryFeature, hitFeature)
{
EValue = blastResult.EValue,
Identities = blastResult.Identity,
Midline = Hit.SEQUENCE_DATA_UNAVAILABLE,
Positives = blastResult.Positives
});
}
catch (Exception e)
{
errorLog.WriteLine(String.Format(Resource.SILVERMAP_ERROR_PROCESSING_BLAST_RESULT, e));
}
}
if (errorLog.GetStringBuilder().Length > 0)
{
MessageDialogBox.Show(errorLog.ToString(), Resource.CAPTION, MessageDialogButton.OK);
}
SignalLoadComplete();
}
/// <summary>
/// Compare this sequence to another, based on Id.
/// </summary>
/// <param name="other">
/// An object that implements ILinearDomain against which this object is to be
/// compared.
/// </param>
/// <returns>
/// Returns the result obtained by comparing the Id of this sequence with that of
/// the comparison sequence.
/// </returns>
public int CompareTo(ILinearDomain other)
{
return(id.CompareTo(other.Id));
}
