private void DrawPdfCoverageMap(ProteinForTreeView protein, Grid mapGrid, string path)
{
// draw coverage map
mapGrid.Width = 1000;
DrawSequenceCoverageMap(protein);
string pathToCoverageMap = Path.Combine(Path.GetDirectoryName(path), "map.png");
CustomPdfWriter.RenderImage((int)mapGrid.Width, (int)mapGrid.Height, pathToCoverageMap, map);
// draw legend
SequenceCoverageMap.drawLegend(legend, proteaseByColor, proteases, legendGrid);
string pathToLegend = Path.Combine(Path.GetDirectoryName(path), "legend.png");
CustomPdfWriter.RenderImage((int)(legend.Width), 50, pathToLegend, legend);
CustomPdfWriter.WriteToPdfMetaDraw(mapGrid.Width, mapGrid.Height, pathToCoverageMap, pathToLegend, path);
}
private void DrawSequenceCoverageMap(ProteinForTreeView protein) //string accession, Dictionary<string, PeptideForTreeView> uniquePeptides, Dictionary<string, PeptideForTreeView> sharedPeptides)
{
string protease = "trypsin"; // only works for single protease for now
string seqCoverage = proteinGroups[protein.Accession];
mapViewer.Visibility = Visibility.Visible;
BaseDraw.clearCanvas(map);
mainViewModel.Model = null; // clear plot
BaseDraw.clearCanvas(canvas);
double spacing = 22;
int height = 10;
int totalHeight = 0;
int accumIndex = 0;
foreach (string seq in seqCoverage.Split('|'))
{
var splitSeq = Split(seq, spacing);
var allPeptides = new List <string>(protein.AllPeptides.Keys);
foreach (var line in splitSeq)
{
List <int> indices = new List <int>();
// draw sequence
for (int r = 0; r < line.Length; r++)
{
SequenceCoverageMap.txtDrawing(map, new Point(r * spacing + 10, height), line[r].ToString().ToUpper(), Brushes.Black);
}
// highlight partial peptide sequences (broken off into multiple lines)
if (partialPeptideMatches.Count > 0)
{
var temp = new Dictionary <string, int>(partialPeptideMatches);
partialPeptideMatches.Clear();
foreach (var peptide in temp)
{
if (MatchPeptideSequence(peptide.Key, line, 0, peptide.Value, accumIndex - peptide.Value == seq.IndexOf(peptide.Key)))
{
int start = 0;
int end = Math.Min(start + peptide.Key.Length - peptide.Value - 1, line.Length - 1);
SequenceCoverageMap.Highlight(start, end, map, indices, height, proteaseByColor[protease], protein.UniquePeptides.Keys.Any(u => u.Contains(peptide.Key))); // draw line for peptide sequence
}
}
}
// highlight full peptide sequences
for (int i = 0; i < line.Length; ++i)
{
var temp = new List <string>(allPeptides);
foreach (string peptide in temp)
{
if (MatchPeptideSequence(peptide, line, i, 0, accumIndex + i == seq.IndexOf(peptide)))
{
int start = i;
int end = Math.Min(start + peptide.Length - 1, line.Length - 1);
SequenceCoverageMap.Highlight(start, end, map, indices, height, proteaseByColor[protease], protein.UniquePeptides.Keys.Any(u => u.Contains(peptide)));
allPeptides.Remove(peptide);
}
}
}
height += 50;
accumIndex += line.Length;
}
totalHeight += splitSeq.Count() * 50;
height += 50;
}
mapGrid.Height = totalHeight + 50 * seqCoverage.Split('|').Count();
SequenceCoverageMap.drawLegend(legend, proteaseByColor, proteases, legendGrid);
}