public void AddSiteFeature(SiteFeature feature)
{
collection.Add(feature);
}
/**
* Fetches data from GeneCollection and CodingSequenceCollection.
* @returns siteFeatureCollection containing SiteFeature objects.
*/
public SiteFeatureCollection FetchSiteFeatures(GeneCollection geneCollection, CodingSequenceCollection cdsCollection, string[] featureCoordinateArray)
{
SiteFeatureCollection siteFeatureCollection = new SiteFeatureCollection();
List <string> nonMatchedFeatures = new List <string>();
foreach (string coordinate in featureCoordinateArray)
{
bool isMatch = false;
if (Regex.IsMatch(coordinate, "\\d*\\.\\.\\d*"))
{
string[] split = Regex.Split(coordinate, "\\.\\.");
int startCoordinate = Int32.Parse(split[0]);
int endCoordinate = Int32.Parse(split[1]);
for (int i = 0; i < geneCollection.collection.Count; i++)
{
string geneId = "";
string type = "";
string orientation = "";
Gene gene = geneCollection.collection[i];
CodingSequence cds = cdsCollection.collection[i];
if (gene.StartCoordinate >= startCoordinate && gene.EndCoordinate <= endCoordinate)
{
if (gene.ID != "")
{
geneId = gene.ID;
}
else
{
geneId = gene.LocusTag;
}
type = "gene";
int geneStartCoordinate = gene.StartCoordinate;
int geneStopCoordinate = gene.EndCoordinate;
if (gene.IsReverse)
{
orientation = "R";
}
else
{
orientation = "F";
}
SiteFeature feature = new SiteFeature(geneId, type, geneStartCoordinate, geneStopCoordinate, orientation);
siteFeatureCollection.AddSiteFeature(feature);
//Change type and change geneId to geneProduct for a CDS entry. Other values are similar to Gene values.
string product = cds.GeneProduct;
type = "CDS";
feature = new SiteFeature(product, type, geneStartCoordinate, geneStopCoordinate, orientation);
siteFeatureCollection.AddSiteFeature(feature);
isMatch = true;
}
}
if (!isMatch)
{
nonMatchedFeatures.Add(coordinate);
}
}
}
if (!siteFeatureCollection.collection.Any() || !nonMatchedFeatures.Any())
{
//Display list of site entries that did not match.
String message = "";
foreach (String feature in nonMatchedFeatures)
{
if (message != "")
{
message += "Some of the provided enrties could not be found. Here is the list of sites; ";
message += feature;
}
else
{
message += ", " + feature;
}
}
Console.WriteLine("\n" + message);
}
siteFeatureCollection.Sort();
return(siteFeatureCollection);
}