public IChromosomeStream GetChromosome(string chromosomeId)
{
IList<IGene> genes = new List<IGene>();
string prefix = chromosomeId.Substring(chromosomeId.Length > 3 ? chromosomeId.Length - 3 : 0);
int totalGenes = 100;
int namedGeneInterval = 10;
int geneLength = 800;
int geneMargin = 200;
string sequence = "gattacagattacagattacagattacagattacagattacagattacagattacagattacagattacagattacagattacagattacagattacagattacagattaca";
string translation = "LSASTDUGQWEJHRHWGESBDFKJGHSUIDTDHFGJWHEGRTWEHJDGVFJHSDGBFNMWEBRIYTQTWUWERUOUSDPFSYOZSDJKFHOIUER";
for (int i = 0; i < totalGenes; i++)
{
String name = (i % namedGeneInterval == 0) ? ("kR" + i.ToString()) : null;
IGene gene = new GeneImplementation();
gene.LocusTag = prefix + i.ToString();
gene.LeftBasePair = (geneLength + geneMargin) * i + geneMargin;
gene.RightBasePair = gene.LeftBasePair + geneLength;
gene.Sequence = sequence;
gene.Name = name;
gene.Translation = translation;
genes.Add(gene);
IGene reverseGene = new GeneImplementation();
reverseGene.LocusTag = prefix + i.ToString();
reverseGene.LeftBasePair = (geneLength + geneMargin) * i + geneMargin;
reverseGene.RightBasePair = gene.LeftBasePair + geneLength;
reverseGene.IsForward = false;
reverseGene.Sequence = sequence;
reverseGene.Name = name;
reverseGene.Translation = translation;
genes.Add(reverseGene);
}
IChromosomeStream stream = new ChromosomeStreamImplementation();
stream.GeneList = genes;
stream.TotalBasePairs = totalGenes * (geneLength + geneMargin) + geneMargin;
return stream;
}
private void addGene()
{
IGene gene = new GeneImplementation();
state = 2;
#region Start, Stop, and Direction
words = words[1].Split(' ');
gene.LeftBasePair = Int32.Parse(words[0]);
gene.RightBasePair = Int32.Parse(words[1]);
index++;
line = features[index];
words = line.Split('=');
gene.IsForward = !Boolean.Parse(words[1].ToLower());
#endregion
index++;
while (state == 2 && index < features.Length)
{
line = features[index];
words = line.Split(delimiters, StringSplitOptions.RemoveEmptyEntries);
switch (words[0])
{
case "DNA":
gene.Sequence = words[1];
break;
case "GENE":
gene.Name = words[1];
break;
case "LOCUS_TAG":
gene.LocusTag = words[1];
break;
case "NOTE":
gene.Note = words[1];
break;
case "PRODUCT":
gene.Product = words[1];
if (gene.Product == "hypothetical protein")
{
gene.IsHypothetical = true;
}
break;
case "PROTEIN_ID":
gene.ProteinID = words[1];
break;
case "TRANSLATION":
gene.Translation = words[1];
state = 1;
break;
default:
state = 1;
break;
}
index++;
}
_chromosome.GeneList.Add(gene);
}
