static public TangriEtAl GetInstance(HowConsevered howConsevered)
{
TangriEtAl aTangriEtAl = new TangriEtAl();
aTangriEtAl.ReadFile();
aTangriEtAl.HowConsevered = howConsevered;
if (howConsevered == HowConsevered.Conserved)
{
aTangriEtAl.Name = string.Format("Con");
//A little unit testing
Debug.Assert(aTangriEtAl.CanGoToSet('G') == "GSATDP");
}
else
{
aTangriEtAl.Name = string.Format("Semi");
//A little unit testing
Debug.Assert(aTangriEtAl.CanComeFromSet('P') == "ACDEGHIKLMNPQRSTVWY");
}
return(aTangriEtAl);
}
private void AddPair(char from, char to, HowConsevered howConsevered)
{
SortedList forward = HowConseveredToForward[(int)howConsevered];
if (!forward.ContainsKey(from))
{
forward.Add(from, new StringBuilder());
}
StringBuilder forwardSB = (StringBuilder)forward[from];
forwardSB.Append(to);
SortedList backward = HowConseveredToBackward[(int)howConsevered];
if (!backward.ContainsKey(to))
{
backward.Add(to, new StringBuilder());
}
StringBuilder backwardSB = (StringBuilder)backward[to];
backwardSB.Append(from);
}
private void ReadFile()
{
for (HowConsevered howConsevered = HowConsevered.Conserved; howConsevered <= HowConsevered.SemiConserved; ++howConsevered)
{
HowConseveredToForward[(int)howConsevered] = new SortedList();
HowConseveredToBackward[(int)howConsevered] = new SortedList();
}
string inputFileName = @"SimilarityOfAminoAcids.txt";
SortedList rgHeadings = new SortedList();
using (StreamReader streamreaderInputFile = Predictor.OpenResource(inputFileName))
{
string sLine;
char cPrevHeading = '\0';
while (null != (sLine = streamreaderInputFile.ReadLine()))
{
if (sLine.StartsWith("//"))
{
continue;
}
//There must be a line for every amino acid and they must be in alpha order
string[] tableParts = sLine.Split(' '); //!!!const
SpecialFunctions.CheckCondition(tableParts.Length == 3); //!!!raise error
Debug.Assert(tableParts[0].Length > 0);
char cHeading = tableParts[0][0];
SpecialFunctions.CheckCondition(cPrevHeading < cHeading); //!!!raise error
cPrevHeading = cHeading;
SpecialFunctions.CheckCondition(Biology.GetInstance().OneLetterAminoAcidAbbrevTo3Letter.ContainsKey(cHeading)); //!!!raise error
SpecialFunctions.CheckCondition(!rgHeadings.ContainsKey(cHeading)); //!!!raise error
rgHeadings.Add(cHeading, null);
//We must see every amino acid in the line;
SortedList rgInLine = new SortedList();
foreach (string part in tableParts)
{
foreach (char cAA in part)
{
SpecialFunctions.CheckCondition(Biology.GetInstance().OneLetterAminoAcidAbbrevTo3Letter.ContainsKey(cAA)); //!!!raise error
SpecialFunctions.CheckCondition(!rgInLine.ContainsKey(cAA)); //!!!raise error
rgInLine.Add(cAA, null);
}
}
SpecialFunctions.CheckCondition(rgInLine.Count == 20); //!!!raise error
foreach (char cAA in tableParts[(int)HowConsevered.Conserved])
{
AddPair(cHeading, cAA, HowConsevered.Conserved);
AddPair(cHeading, cAA, HowConsevered.SemiConserved);
}
foreach (char cAA in tableParts[(int)HowConsevered.SemiConserved])
{
AddPair(cHeading, cAA, HowConsevered.SemiConserved);
}
}
}
SpecialFunctions.CheckCondition(rgHeadings.Count == 20); //!!!raise error
}