public void TestCanLossWater()
{
foreach (char c in new Aminoacids().GetVisibleAminoacids())
{
switch (c)
{
case 'S':
case 'T':
case 'E':
case 'D':
Assert.IsTrue(NeutralLossUtils.CanLossWater(c));
break;
default:
Assert.IsFalse(NeutralLossUtils.CanLossWater(c));
break;
}
}
}
public NeutralLossCandidates(string peptide)
{
canLossWater = true;
canLossAmmonia = false;
string pureSeq = PeptideUtils.GetPureSequence(peptide);
bLossWater = new bool[pureSeq.Length];
bLossAmmonia = new bool[pureSeq.Length];
yLossWater = new bool[pureSeq.Length];
yLossAmmonia = new bool[pureSeq.Length];
for (int i = 0; i < pureSeq.Length; i++)
{
if (NeutralLossUtils.CanLossWater(pureSeq[i]))
{
for (int j = i; j < pureSeq.Length; j++)
{
bLossWater[j] = true;
}
break;
}
bLossWater[i] = false;
}
for (int i = pureSeq.Length - 1; i >= 0; i--)
{
if (NeutralLossUtils.CanLossWater(pureSeq[i]))
{
for (int j = i; j >= 0; j--)
{
yLossWater[pureSeq.Length - 1 - j] = true;
}
break;
}
yLossWater[pureSeq.Length - 1 - i] = false;
}
for (int i = 0; i < pureSeq.Length; i++)
{
if (NeutralLossUtils.CanLossAmmonia(pureSeq[i]))
{
for (int j = i; j < pureSeq.Length; j++)
{
bLossAmmonia[j] = true;
canLossAmmonia = true;
}
break;
}
bLossAmmonia[i] = false;
}
for (int i = pureSeq.Length - 1; i >= 0; i--)
{
if (NeutralLossUtils.CanLossAmmonia(pureSeq[i]))
{
for (int j = i; j >= 0; j--)
{
yLossAmmonia[pureSeq.Length - 1 - j] = true;
}
break;
}
yLossAmmonia[pureSeq.Length - 1 - i] = false;
}
}