internal void FetchGeneDisplay(GeneCollection geneCollection, string[] geneArray, string originSequence)
{
GbkFeatureFetcher fetcher = new GbkFeatureFetcher();
GeneCollection updatedGeneCollection = fetcher.FetchGeneData(geneCollection, geneArray, originSequence);
foreach (Gene gene in updatedGeneCollection.collection)
{
String geneMessage = "";
if (gene.ID != "")
{
geneMessage += ">" + gene.ID + newLine;
}
else
{
geneMessage += ">" + gene.LocusTag + newLine;
} //Print sequence in substrings of 80.
String sequence = gene.Sequence;
int length = sequence.Length;
for (int start = 0; start < length;)
{
int end = start + 80;
if (end < length)
{
geneMessage += sequence.Substring(start, 80) + newLine;
}
else
{
geneMessage += sequence.Substring(start, (length - start));
}
start += 80;
}
Console.WriteLine(geneMessage);
}
Console.WriteLine(newLine);
}
public void FetchCDSs(CodingSequenceCollection cdsCollection, string[] cdsArray)
{
GbkFeatureFetcher fetcher = new GbkFeatureFetcher();
CodingSequenceCollection updatedCodingSequenceCollection = fetcher.FetchCodingSequenceData(cdsCollection, cdsArray);
foreach (CodingSequence codingSequence in updatedCodingSequenceCollection.collection)
{
string cdsMesasge = "";
if (codingSequence.GeneID != "")
{
cdsMesasge += ">CDS " + codingSequence.GeneID + " sequence" + newLine;
}
else
{
cdsMesasge += ">CDS " + codingSequence.LocusTag + " sequence" + newLine;
}
string sequence = codingSequence.TranslatedSequence;
int length = sequence.Length;
for (int start = 0; start < length;)
{
int end = start + 80;
if (end < length)
{
cdsMesasge += sequence.Substring(start, 80) + newLine;
}
else
{
cdsMesasge += sequence.Substring(start, (length - start));
}
start += 80;
}
Console.WriteLine(cdsMesasge);
}
Console.WriteLine(newLine);
}
public void FetchFeatures(GeneCollection geneCollection, CodingSequenceCollection cdsCollection, string[] featureArray)
{
Console.Write("FEATURE;TYPE;START;STOP;ORIENTATION");
GbkFeatureFetcher fetcher = new GbkFeatureFetcher();
SiteFeatureCollection siteFeatureCollection = fetcher.FetchSiteFeatures(geneCollection, cdsCollection, featureArray);
foreach (SiteFeature siteFeature in siteFeatureCollection.collection)
{
Console.WriteLine(siteFeature.GeneID + ";" + siteFeature.Type + ";" + siteFeature.StartCoordinate + ";" + siteFeature.EndCoordinate + ";" + siteFeature.Orientation);
}
Console.WriteLine(newLine);
}
public void FetchSites(GeneCollection geneCollection, string originSequence, string[] siteArray)
{
Console.Write("POSITION;SEQUENCE;GENE");
GbkFeatureFetcher fetcher = new GbkFeatureFetcher();
List <SearchSiteCollection> list = fetcher.FetchSearchSiteData(geneCollection, originSequence, siteArray);
foreach (SearchSiteCollection searchSiteCollection in list)
{
foreach (SearchSite searchSite in searchSiteCollection.collection)
{
Console.WriteLine(searchSite.StartPosition + ";" + searchSite.Site + ";" + searchSite.GeneName);
}
}
Console.WriteLine(newLine);
}