void UpdateFront() {
var newFrontEdges = new Set<CdtEdge>();
foreach (var t in addedTriangles)
foreach (var e in t.Edges)
if (e.CwTriangle == null || e.CcwTriangle == null)
newFrontEdges.Insert(e);
foreach (var e in newFrontEdges)
AddEdgeToFront(e);
}
private static bool SetOfActiveNodesIsLargerThanThreshold(Cluster ancestor, Node node, Set<Node> usedNodeSet, int threshold) {
Cluster parent = Parent(node);
do {
foreach (var n in Children(parent)) {
usedNodeSet.Insert(n);
if (usedNodeSet.Count > threshold)
return true;
}
if (parent == ancestor)
break;
parent = Parent(parent);
} while (true);
usedNodeSet.Insert(parent);
return usedNodeSet.Count > threshold;
}
Set<Tuple<int, int, int>> GetVisibleTilesSet() {
int iLevel = GetBackgroundTileLevel();
GridTraversal grid = new GridTraversal(GeomGraph.BoundingBox, iLevel);
var tiles = new Set<Triple>();
var visibleRectangle = GetVisibleRectangleInGraph();
var t1 = grid.PointToTuple(visibleRectangle.LeftBottom);
var t2 = grid.PointToTuple(visibleRectangle.RightTop);
for (int ix = t1.Item1; ix <= t2.Item1; ix++)
for (int iy = t1.Item2; iy <= t2.Item2; iy++) {
var t = new Triple(iLevel, ix, iy);
TileType tileType;
if (!_tileDictionary.TryGetValue(t, out tileType)) continue;
if (tileType == TileType.Image) tiles.Insert(t);
}
return tiles;
}
void FillExistingNodesEdges(Set<Node> existindNodes, Set<DrawingEdge> existingEdges) {
foreach (var dro in _drawingObjectsToIViewerObjects.Keys) {
var n = dro as Node;
if (n != null && dro.IsVisible) //added: visibility
existindNodes.Insert(n);
else {
var edge = dro as DrawingEdge;
if (edge != null && dro.IsVisible)
existingEdges.Insert((DrawingEdge) dro);
}
}
}
private Set<Node> GetIntersectingVisibleRectangle(Set<Node> fakeTileNodes)
{
var rect = GetVisibleRectangleInGraph();
var nodes = new Set<Node>();
foreach (var node in fakeTileNodes)
{
IViewerObject o;
if (!_drawingObjectsToIViewerObjects.TryGetValue(node, out o)) continue;
var vnode = ((GraphmapsNode)o);
if (NodeDotRect(vnode.LgNodeInfo).Intersects(rect))
{
nodes.Insert(node);
}
}
return nodes;
}
void treeDataGridView_PreviewKeyDown(object sender, PreviewKeyDownEventArgs e)
{
if (e.KeyCode == Keys.Escape)
treeDataGridView.ClearSelection();
if (e.KeyCode != Keys.Enter)
return;
var newDataFilter = new DataFilter { FilterSource = this, Analysis = new List<Analysis>() };
if (treeDataGridView.SelectedCells.Count == 0)
return;
var processedRows = new Set<int>();
foreach (DataGridViewCell cell in treeDataGridView.SelectedCells)
{
if (!processedRows.Insert(cell.RowIndex).WasInserted)
continue;
var rowIndexHierarchy = treeDataGridView.GetRowHierarchyForRowIndex(cell.RowIndex);
var row = GetRowFromRowHierarchy(rowIndexHierarchy) as AnalysisRow;
if (row != null) newDataFilter.Analysis.Add(row.Analysis);
}
if (AnalysisViewFilter != null)
AnalysisViewFilter(this, new ViewFilterEventArgs(newDataFilter));
}
private List<SpectrumSourceGroup> applyAssemblyText(ISession session, string filepath)
{
var spectrumSources = session.Query<SpectrumSource>().ToList();
var sourcesByGroup = new Map<string, List<SpectrumSource>>();
var alreadyGroupedSources = new Set<string>();
var sourceGroups = new List<SpectrumSourceGroup>();
// open the assembly.txt file
using (var assembleTxtFile = File.OpenText(filepath))
{
string line;
while ((line = assembleTxtFile.ReadLine()) != null)
{
if (line.Length == 0)
continue;
try
{
Regex groupFilemaskPair = new Regex("((\"(.+)\")|(\\S+))\\s+((\"(.+)\")|(\\S+))");
Match lineMatch = groupFilemaskPair.Match(line);
string group = lineMatch.Groups[3].ToString() + lineMatch.Groups[4].ToString();
string filemask = lineMatch.Groups[7].ToString() + lineMatch.Groups[8].ToString();
// for wildcards, use old style behavior
if (filemask.IndexOfAny("*?".ToCharArray()) > -1)
{
if (!Path.IsPathRooted(filemask))
filemask = Path.Combine(Path.GetDirectoryName(filepath), filemask);
if (!sourcesByGroup.Contains(group))
sourcesByGroup[group] = new List<SpectrumSource>();
if (!Directory.Exists(Path.GetDirectoryName(filemask)))
continue;
var files = Directory.GetFiles(Path.GetDirectoryName(filemask), Path.GetFileName(filemask));
var sourceNames = files.Select(o => Path.GetFileNameWithoutExtension(o));
foreach (string sourceName in sourceNames)
{
var spectrumSource = spectrumSources.SingleOrDefault(o => o.Name == sourceName);
if (spectrumSource == null)
continue;
var insertResult = alreadyGroupedSources.Insert(sourceName);
if (insertResult.WasInserted)
sourcesByGroup[group].Add(spectrumSource);
}
}
else
{
// otherwise, match directly to source names
string sourceName = Path.GetFileNameWithoutExtension(filemask);
var spectrumSource = spectrumSources.SingleOrDefault(o => o.Name == sourceName);
if (spectrumSource == null)
continue;
var insertResult = alreadyGroupedSources.Insert(sourceName);
if (insertResult.WasInserted)
sourcesByGroup[group].Add(spectrumSource);
}
}
catch (Exception ex)
{
Program.HandleException(new Exception("Error reading assembly text from \"" + filepath + "\": " + ex.Message, ex));
}
}
}
// remove existing groups
RemoveGroupNode(_rootNode, false);
sourceGroups.Add(new SpectrumSourceGroup { Name = "/" });
// build new group hierarchy
foreach (var itr in sourcesByGroup)
{
if (itr.Value.IsNullOrEmpty())
continue;
var ssg = new SpectrumSourceGroup { Name = itr.Key };
if (!alreadyGroupedSources.Contains(ssg.Name))
sourceGroups.Add(ssg);
// decompose group path into segments, e.g. /foo/bar/ -> {foo, bar}
IEnumerable<string> segments = ssg.Name.Split("/".ToCharArray(), StringSplitOptions.RemoveEmptyEntries);
segments = segments.Take(segments.Count() - 1); // ignore the last segment
var parentNode = _rootNode;
foreach(string segment in segments)
{
var segmentNode = parentNode.Children.FirstOrDefault(o => o.Text == segment);
if (segmentNode == null)
{
var segmentGroup = new SpectrumSourceGroup { Name = (parentNode.Text + "/").Replace("//", "/") + segment };
if (!alreadyGroupedSources.Contains(segmentGroup.Name))
sourceGroups.Add(segmentGroup);
segmentNode = new tlvBranch
{
Text = segment,
cms = cmRightClickGroupNode,
Parent = parentNode,
Children = new List<tlvBranch>(),
Data = segmentGroup
};
parentNode.Children.Add(segmentNode);
}
parentNode = segmentNode;
}
// parentNode is now the immediate parent of the current group
var groupNode = new tlvBranch
{
Text = Path.GetFileName(ssg.Name),
cms = cmRightClickGroupNode,
Parent = parentNode,
Children = new List<tlvBranch>(),
Data = ssg
};
foreach (var source in itr.Value)
{
var sourceNode = new tlvBranch
{
Text = Path.GetFileName(source.Name),
Parent = groupNode,
Data = source,
cms = cmRightClickFileNode
};
groupNode.Children.Add(sourceNode);
lvNonGroupedFiles.Items.RemoveByKey(sourceNode.Text);
}
parentNode.Children.Add(groupNode);
}
tlvGroupedFiles.RefreshObject(_rootNode);
tlvGroupedFiles.ExpandAll();
return sourceGroups.ToList();
}
void treeDataGridView_PreviewKeyDown (object sender, PreviewKeyDownEventArgs e)
{
if (e.KeyCode == Keys.Escape)
treeDataGridView.ClearSelection();
if (e.KeyCode != Keys.Enter)
return;
var newDataFilter = new DataFilter { FilterSource = this };
if (treeDataGridView.SelectedCells.Count == 0)
return;
var processedRows = new Set<int>();
var selectedSourceGroups = new List<SpectrumSourceGroup>();
var selectedSources = new List<SpectrumSource>();
var selectedSpectra = new List<Spectrum>();
var selectedAnalyses = new List<Analysis>();
var selectedPeptides = new List<Peptide>();
var selectedCharges = new List<int>();
var selectedMatches = new List<PeptideSpectrumMatchRow>();
foreach (DataGridViewCell cell in treeDataGridView.SelectedCells)
{
if (!processedRows.Insert(cell.RowIndex).WasInserted)
continue;
var rowIndexHierarchy = treeDataGridView.GetRowHierarchyForRowIndex(cell.RowIndex);
Row row = GetRowFromRowHierarchy(rowIndexHierarchy);
if (row is SpectrumSourceGroupRow)
selectedSourceGroups.Add((row as SpectrumSourceGroupRow).SpectrumSourceGroup);
else if (row is SpectrumSourceRow)
selectedSources.Add((row as SpectrumSourceRow).SpectrumSource);
else if (row is SpectrumRow)
selectedSpectra.Add((row as SpectrumRow).Spectrum);
else if (row is AnalysisRow)
selectedAnalyses.Add((row as AnalysisRow).Analysis);
else if (row is PeptideRow)
selectedPeptides.Add((row as PeptideRow).Peptide);
else if (row is ChargeRow)
selectedCharges.Add((row as ChargeRow).Charge);
else if (row is PeptideSpectrumMatchRow)
selectedMatches.Add(row as PeptideSpectrumMatchRow);
}
if (selectedSourceGroups.Count > 0) newDataFilter.SpectrumSourceGroup = selectedSourceGroups;
if (selectedSources.Count > 0) newDataFilter.SpectrumSource = selectedSources;
if (selectedSpectra.Count > 0) newDataFilter.Spectrum = selectedSpectra;
if (selectedAnalyses.Count > 0) newDataFilter.Analysis = selectedAnalyses;
if (selectedPeptides.Count > 0) newDataFilter.Peptide = selectedPeptides;
if (selectedCharges.Count > 0) newDataFilter.Charge = selectedCharges;
// TODO: visualize multiple PSMs?
//if (selectedMatches.Count > 0)
if (SpectrumViewFilter != null)
SpectrumViewFilter(this, new ViewFilterEventArgs(newDataFilter));
}
