public static void testLevenshteinDistanceCalculatorForNonAlpha() //tests to see that calculator can handle non-alpha values
{
int actualDistance = 3; // the peptides below have an edit distance of three
string stringOne = "LKAEEQAADQVA*QQAVQAIKDKQFVLEADQVI!FKR";
string stringTwo = "LKAEEQAADQVAYQQAVQAIKDKQFVLEADAVIKFKR";
int distanceCalculated = ComputeLevenshteinDistance.LevenshteinDistance(stringOne, stringTwo);
Assert.That(distanceCalculated, Is.EqualTo(actualDistance));
}
public static void testLevenshteinDistanceCalculator() // tests to see that calculator is giving correct values
{
int actualDistance = 1; // the peptides below are one edit distance apart
string stringOne = "LKAEEQAADQVAYQQAVQAIKDKQFVLEADQVIFKR";
string stringTwo = "LKAEEQAADQVAYQQAVQAIKDKQFVLEADAVIFKR";
int distanceCalculated = ComputeLevenshteinDistance.LevenshteinDistance(stringOne, stringTwo);
Assert.That(distanceCalculated, Is.EqualTo(actualDistance));
}
public static void testLevenshteinDistanceCalculatorForAsterick() // tests to see that calculator can handle asterisk
{
int actualDistance = 2; // the peptides below have an edit distance of two
string stringOne = "LKAEEQAADQVAYQQAVQAIKDKQFVLEADQVI*FKR";
string stringTwo = "LKAEEQAADQVAYQQAVQAIKDKQFVLEADAVIKFKR";
int distanceCalculated = ComputeLevenshteinDistance.LevenshteinDistance(stringOne, stringTwo);
Assert.That(distanceCalculated, Is.EqualTo(actualDistance));
}
public void MakeAllCombinations()
{
Stopwatch time = new Stopwatch();
time.Start();
ulong count = 0;
for (int i = 0; i < inputs.Count - 1; i++)// prsmFile used to be a List<PrSmAndFile>
{
for (int j = i + 1; j < inputs.Count; j++)
{
count++;
if (count % 100000000 == 0) // only output every 100 million lines
{
Console.WriteLine("Processed: " + count + ", Elapsed Time: " + time.ElapsedMilliseconds);
}
var left = inputs[i]; // this is one object
var right = inputs[j]; // this is the second object for comparison
if (filterForPeptideLength(left.peptide, right.peptide) != true)
{
continue;
}
if (filterForSameCharge(left.charge, right.charge) != true)
{
continue;
}
if (filterForBeginningOrEndMatch(left.peptide, right.peptide) != true)
{
continue;
}
if (filterForOrganismMatch(left.organismName, right.organismName) != true)
{
continue;
} //later use actual org name, not codex
var tableAppendix = ComputeLevenshteinDistance.LevenshteinDistance(left.peptide, right.peptide);
string valuesForPairsTable = "('" + left.id + "','" + right.id + "','" + tableAppendix + "')";
if (tableAppendix < 3)
{
aggregateValuesForPairsTable.Add(valuesForPairsTable);
}
if (aggregateValuesForPairsTable.Count >= 800 && aggregateValuesForPairsTable.Count > 0)
{
SQLiteConnector.FillDatabase(string.Join(",", aggregateValuesForPairsTable.ToArray()));
aggregateValuesForPairsTable = new List <string>();
}
}
}
}
