/// <summary>
///
/// </summary>
/// <param name="LocusName"></param>
/// <param name="fastaSequence"></param>
/// <param name="peptides">PeptidesWithPTMs</param>
/// <param name="hmmResults"></param>
public void Plot(string LocusName, string fastaSequence, List <string> peptides, List <HMMResult> hmmResults = null)
{
chartCoverage.Series[0].Points.Clear();
chartCoverage.Series[1].Points.Clear();
chartCoverage.Series[2].Points.Clear();
//To Fix
cacheProtein = new ProteinData(LocusName, fastaSequence, peptides);
//Get the locations
List <PeptidePositionMatch> theMatches = new List <PeptidePositionMatch>();
foreach (string peptide in peptides)
{
//Make sure the peptide is clean
string cleanedPep = CleanPeptide(peptide, true);
string pepWithPTM = CleanPeptide(peptide, false);
MatchCollection location = Regex.Matches(fastaSequence, cleanedPep);
List <int> thepos = new List <int>();
foreach (Match m in location)
{
thepos.Add(m.Index);
}
thepos = thepos.Distinct().ToList();
theMatches.Add(new PeptidePositionMatch(thepos, pepWithPTM, cleanedPep.Length));
}
theMatches = theMatches.OrderBy(a => a.Position[0]).ThenBy(a => a.Length).ToList();
// Populate series data
//First, the protein
chartCoverage.Series[0].Points.AddXY(0, 0, fastaSequence.Length);
chartCoverage.Series[0].Points[0].AxisLabel = LocusName;
//And add a blank petide
chartCoverage.Series[1].Points.AddXY(0, 0, 0);
//And add a blank peptide
//And now the rest
for (int i = 0; i < theMatches.Count; i++)
{
int startPos = theMatches[i].Position[0];
int length = theMatches[i].Length;
if (hmmResults == null)
{
//Prints peptides in the protein stripe
chartCoverage.Series[1].Points.AddXY(i + 1, startPos, startPos + length);
chartCoverage.Series[1].Points.Last().AxisLabel = theMatches[i].Sequence;
}
if (true)
{
//Prints in a new layer
chartCoverage.Series[1].Points.AddXY(0, startPos, startPos + length);
}
}
if (hmmResults != null)
{
for (int i = 0; i < hmmResults.Count; i++)
{
chartCoverage.Series[2].Points.AddXY(i + 1, hmmResults[i].AFromk__BackingField, hmmResults[i].ATok__BackingField);
chartCoverage.Series[2].Points.Last().AxisLabel = hmmResults[i].Descriptionk__BackingField;
}
}
//Scroll bar
chartCoverage.ChartAreas[0].AxisX.ScrollBar.Size = 10;
chartCoverage.ChartAreas[0].AxisY.Interval = 100;
chartCoverage.ChartAreas[0].AxisX.ScrollBar.IsPositionedInside = true;
//For some unknown reasons, Y is X and X is Y
chartCoverage.ChartAreas[0].AxisY.Maximum = fastaSequence.Length + (int)fastaSequence.Length * 0.05;
chartCoverage.ChartAreas[0].AxisY.Minimum = 0;
chartCoverage.ChartAreas[0].AxisY.Title = "Amino Acid Number";
if (checkBoxAllPeptideLabels.Checked)
{
chartCoverage.ChartAreas[0].AxisX.Interval = 1;
}
else
{
chartCoverage.ChartAreas[0].AxisX.Interval = 0;
}
}
private void Plot(ProteinData pd, List <HMMResult> hmmResults = null)
{
Plot(pd.Locus, pd.FastaSequence, pd.Peptides, hmmResults);
}
