public void TestScanRegularCase()
{
InitVals();
Nucleobase[] seq1 = FrameshiftUtil.StringSeq("CGAUGCC");
// start codon found at index 2
Assert.AreEqual(2, Ribosome.Scan(seq1, start));
}
//initializes the 'default' ribosome to be used in testing
// might have to change based on actual syntax
public void Init()
{
start = AACodon.AUG;
stops = new List <AACodon>
{
AACodon.UGA,
AACodon.UAA,
AACodon.UAG
};
seq = FrameshiftUtil.StringSeq("AUGCCCUAA");
r = new Ribosome(start, stops, new AAFactory(), 3);
}
public void TestBuildAAFailStopIndexOOB2()
{
var seq = FrameshiftUtil.StringSeq("UGCACC");
AACodonExtension.BuildAACodon(seq, 0, 13);
}
public void TestBuildAAFailInvalidSequence()
{
var seq = FrameshiftUtil.StringSeq("GAT");
AACodonExtension.BuildAACodon(seq, 0, 3);
}
public void TestBuildAAFailTooShort()
{
var seq = FrameshiftUtil.StringSeq("GA");
AACodonExtension.BuildAACodon(seq, 0, 3);
}
public void TestBuildAAMiddle()
{
var seq = FrameshiftUtil.StringSeq("UGGAGUCCCGA");
Assert.AreEqual(AACodon.CCC, AACodonExtension.BuildAACodon(seq, 6, 9));
}
public void TestBuildAAStop()
{
var seq = FrameshiftUtil.StringSeq("UAG");
Assert.AreEqual(AACodon.UAG, AACodonExtension.BuildAACodon(seq, 0, 3));
}
public void TestScanShortSequence()
{
InitVals();
Nucleobase[] seq1 = FrameshiftUtil.StringSeq("CG");
Ribosome.Scan(seq1, start);
}
public void TestScanNoStart()
{
InitVals();
Nucleobase[] seq1 = FrameshiftUtil.StringSeq("CGAUCUAGUCGUAGCGU");
Ribosome.Scan(seq1, start);
}
public void TestScanLast()
{
InitVals();
Nucleobase[] seq1 = FrameshiftUtil.StringSeq("CCGAUG");
Assert.AreEqual(3, Ribosome.Scan(seq1, start));
}
private void InitVals()
{
seq = FrameshiftUtil.GenerateRNASequence(length);
start = FrameshiftUtil.StringSeq("AUG");
}
