private void TestNodeBuilder(List <RowEntry> peptideProteinMapList, IReadOnlyList <string> expectedOutput)
{
var nodeBuilder = new NodeBuilder();
var nodeCollapser = new NodeCollapser();
var dfs = new DFS();
var cover = new Cover();
var globalIDTracker = new GlobalIDContainer();
nodeBuilder.RunAlgorithm(peptideProteinMapList, out var proteins, out var peptides);
nodeCollapser.RunAlgorithm(proteins, peptides, globalIDTracker);
var proteinsWithChildren = proteins.Values.ToList();
var clusteredProteinSets = dfs.RunAlgorithm(proteinsWithChildren);
var clusteredProteins = cover.RunAlgorithm(clusteredProteinSets);
var outLines = Utilities.ConvertNodesToStringList(clusteredProteins, globalIDTracker);
foreach (var item in outLines)
{
Console.WriteLine(item);
}
if (expectedOutput == null || expectedOutput.Count == 0)
{
return;
}
for (var i = 0; i < outLines.Count; i++)
{
if (i >= expectedOutput.Count)
{
Assert.Fail("Extra, unexpected output line: " + outLines[i]);
}
Assert.AreEqual(expectedOutput[i], outLines[i], "Mismatch on line {0}", i + 1);
}
if (expectedOutput.Count > outLines.Count)
{
Assert.Fail("Output did not include additional, expected lines, starting with " + expectedOutput[outLines.Count]);
}
}
/// <summary>
/// Group proteins having similar peptides
/// </summary>
/// <returns></returns>
private void PerformParsimonyWork()
{
mProcessingSucceeded = false;
mClusteredProteins = new List <Node>();
mGlobalIDTracker = new GlobalIDContainer();
// Prepare objects and algorithms
var nodeBuilder = new NodeBuilder();
var nodeCollapser = new NodeCollapser();
var dfs = new DFS {
MaxRecursionDepth = mMaxDFSRecursionDepth
};
var cover = new Cover();
RegisterEvents(dfs);
RegisterEvents(cover);
if (ShowProgressAtConsole)
{
Console.WriteLine();
OnStatusEvent("Finding parsimonious protein groups");
}
nodeBuilder.RunAlgorithm(mPeptideProteinMapList, out var proteins, out var peptides);
if (proteins == null || proteins.Count == 0)
{
throw new Exception("Error in PerformParsimony: Protein list is empty");
}
if (peptides == null || peptides.Count == 0)
{
throw new Exception("Error in PerformParsimony: Peptide list is empty");
}
nodeCollapser.RunAlgorithm(proteins, peptides, mGlobalIDTracker);
if (proteins == null || proteins.Count == 0)
{
throw new Exception("Error in PerformParsimony after nodeCollapser.RunAlgorithm: Protein list is empty");
}
if (peptides == null || peptides.Count == 0)
{
throw new Exception("Error in PerformParsimony after nodeCollapser.RunAlgorithm: Peptide list is empty");
}
var proteinsWithChildren = proteins.Values.ToList();
var clusteredProteinSets = dfs.RunAlgorithm(proteinsWithChildren);
if (clusteredProteinSets == null || clusteredProteinSets.Count == 0)
{
throw new Exception("Error in PerformParsimony: DFS returned an empty protein list");
}
mClusteredProteins = cover.RunAlgorithm(clusteredProteinSets);
if (mClusteredProteins == null || mClusteredProteins.Count == 0)
{
throw new Exception("Error in PerformParsimony: cover.RunAlgorithm returned an empty protein list");
}
if (ShowProgressAtConsole)
{
OnStatusEvent("Iteration Complete, found {0} protein groups", mClusteredProteins.Count);
}
mProcessingSucceeded = true;
}
