public OriginalData(string name, string fileName, IntensityMatrix intentisyMatrix)
{
this.OverrideDisplayName = name;
this._fileName = fileName;
this._intentisyMatrix = intentisyMatrix;
}
public VectorCollection(IntensityMatrix intensityMatrix)
{
this._owner = intensityMatrix;
}
/// <summary>
/// Creates a StylisedCluster for plotting from this cluster.
/// </summary>
/// <param name="core">Core</param>
/// <param name="highlight">What to highlight in the result</param>
/// <returns>A StylisedCluster</returns>
internal StylisedCluster CreateStylisedCluster(Core core, IntensityMatrix source, Associational highlight)
{
Cluster fakeCluster = new Cluster(this.DefaultDisplayName, null);
Dictionary <Peak, LineInfo> colourInfo = new Dictionary <Peak, LineInfo>();
string caption = "Plot of peaks potentially representing {0}.";
// Compound --> Peaks in compound
// Adduct: NA
// Peak: Peak
// Cluster: Peaks in cluster
// Pathway: None
StylisedCluster.HighlightElement[] toHighlight = null;
if (highlight != null)
{
switch (highlight.AssociationalClass)
{
case EVisualClass.Peak:
toHighlight = new StylisedCluster.HighlightElement[] { new StylisedCluster.HighlightElement((Peak)highlight, null) };
caption += " {1} is shown in red.";
break;
case EVisualClass.Cluster:
Cluster highlightCluster = (Cluster)highlight;
toHighlight = highlightCluster.Assignments.Vectors.Select(StylisedCluster.HighlightElement.FromVector).ToArray();
caption += " Peaks in {1} are shown in red.";
break;
}
}
HashSet <Peak> peaks = this.Annotations.Select(z => z.Peak).Unique();
IntensityMatrix vm = source.Subset(z => peaks.Contains(z), null, ESubsetFlags.None);
for (int index = 0; index < vm.NumVectors; index++)
{
Vector vec = vm.Vectors[index];
Peak peak = vec.Peak;
fakeCluster.Assignments.Add(new Assignment(vec, fakeCluster, double.NaN));
StringBuilder sb = new StringBuilder();
if (peak.Annotations.Count > 5)
{
sb.Append(this.DefaultDisplayName + " OR " + (peak.Annotations.Count - 1) + " others");
}
else
{
sb.Append(this.DefaultDisplayName);
foreach (Annotation c2 in peak.Annotations)
{
if (c2.Compound != this)
{
sb.Append(" OR ");
sb.Append(c2.Compound.DefaultDisplayName + " (" + c2.Adduct.DefaultDisplayName + ")");
}
}
}
colourInfo.Add(peak, new LineInfo(peak.DisplayName + ": " + sb.ToString(), Color.Black, DashStyle.Solid));
}
StylisedCluster r = new StylisedCluster(fakeCluster, this, colourInfo);
r.IsFake = true;
r.CaptionFormat = caption;
r.WhatIsHighlighted = highlight;
r.Highlight = toHighlight;
return(r);
}
/// <summary>
/// Creates a StylisedCluster for plotting from this pathway.
/// </summary>
/// <param name="core">Core</param>
/// <param name="highlightContents">What to highlight in the plot</param>
/// <returns>A StylisedCluster</returns>
internal StylisedCluster CreateStylisedCluster(Core core, IntensityMatrix source, Associational highlightContents)
{
var colours = new Dictionary <Peak, LineInfo>();
// Adduct: NA
// Peak: Pathways for peak -> Peaks (THIS PEAK)
// Cluster: Pathways for cluster -> Peaks (PEAKS IN CLUSTER)
// Compound: Pathway for compound -> Peaks (PEAKS IN COMPOUND)
// Pathway: NA
const string caption1 = "Plot of peaks potentially representing compounds implicated in {0}.";
string caption2 = " Colours represent peaks that share the same cluster(s).";
string caption3;
// Find out the peaks that we are supposed to highlight
StylisedCluster.HighlightElement[] toHighlight = null;
if (highlightContents != null)
{
switch (highlightContents.AssociationalClass)
{
case EVisualClass.Compound:
Compound highlightCompound = (Compound)highlightContents;
toHighlight = highlightCompound.Annotations.Select(z => new StylisedCluster.HighlightElement(z, null)).ToArray();
caption3 = " Peaks potentially representing {1} are {HIGHLIGHTED}.";
break;
case EVisualClass.Cluster:
Cluster highlightCluster = (Cluster)highlightContents;
toHighlight = highlightCluster.Assignments.Vectors.Select(StylisedCluster.HighlightElement.FromVector).ToArray();
caption3 = " Peaks potentially representing compounds in {1} are {HIGHLIGHTED}.";
break;
case EVisualClass.Peak:
toHighlight = new StylisedCluster.HighlightElement[] { new StylisedCluster.HighlightElement((Peak)highlightContents, null) };
caption3 = " {1} is {HIGHLIGHTED}.";
break;
default:
caption3 = "";
break;
}
}
else
{
caption3 = "";
}
bool highlightByCompound = false;
// Make a list of the peaks in this pathway
Dictionary <Peak, List <Compound> > peaks = new Dictionary <Peak, List <Compound> >();
foreach (Compound compound in this.Compounds)
{
foreach (Annotation annotation in compound.Annotations)
{
Peak peak = annotation.Peak;
if (peaks.ContainsKey(peak))
{
peaks[peak].Add(compound);
}
else
{
peaks[peak] = new List <Compound>();
peaks[peak].Add(compound);
}
}
}
// Depending on the mode assign either each combination of compounds OR clusters a unique colour
Cluster fakeCluster = new Cluster(this.DisplayName, null);
List <List <Compound> > uniqueCompoundCombinations = new List <List <Compound> >();
List <List <Cluster> > uniqueClusterCombinations = new List <List <Cluster> >();
int cindex = -1;
IntensityMatrix vm = source.Subset(z => peaks.ContainsKey(z), null, ESubsetFlags.None);
for (int vIndex = 0; vIndex < vm.NumVectors; vIndex++)
{
var vec = vm.Vectors[vIndex];
Peak peak = vec.Peak;
var asses = vec.Peak.FindAssignments(core).ToArray();
List <Compound> compounds = peaks[peak];
Color col;
// Find or create peak in list
if (highlightByCompound)
{
int uniqueIndex = Maths.FindMatch(uniqueCompoundCombinations, compounds);
if (uniqueIndex == -1)
{
uniqueIndex = uniqueCompoundCombinations.Count;
uniqueCompoundCombinations.Add(compounds); // add list of peaks for this peak
}
if (uniqueCompoundCombinations[uniqueIndex].Count == 1)
{
col = Color.Black;
}
else
{
cindex++;
if (cindex == UiControls.BrightColours.Length)
{
// If there are too many don't bother
col = Color.Black;
caption2 = "";
foreach (var lii in colours)
{
lii.Value.Colour = Color.Black;
}
}
else
{
col = UiControls.BrightColours[cindex % UiControls.BrightColours.Length];
}
}
}
else
{
var l = asses.Select(z => z.Cluster).ToList();
int uniqueIndex = Maths.FindMatch(uniqueClusterCombinations, l);
if (uniqueIndex == -1)
{
uniqueIndex = uniqueClusterCombinations.Count;
uniqueClusterCombinations.Add(l); // add list of peaks for this peak
}
col = UiControls.BrightColours[uniqueIndex % UiControls.BrightColours.Length];
}
StringBuilder legend = new StringBuilder();
int xCount = 0;
foreach (Annotation potential in peak.Annotations)
{
if (this.Compounds.Contains(potential.Compound))
{
if (legend.Length != 0)
{
legend.Append(" OR ");
}
legend.Append(potential.Compound.DefaultDisplayName);
}
else
{
xCount++;
}
}
if (xCount != 0)
{
legend.Append(" OR " + xCount + " others not in this pathway");
}
fakeCluster.Assignments.Add(new Assignment(vec, fakeCluster, double.NaN));
string seriesName = peak.DisplayName + (!asses.IsEmpty() ? (" (" + StringHelper.ArrayToString(asses.Select(z => z.Cluster)) + ")") : "") + ": " + legend.ToString();
var li = new LineInfo(seriesName, col, DashStyle.Solid);
colours.Add(peak, li);
}
var r = new StylisedCluster(fakeCluster, this, colours);
r.IsFake = true;
r.Highlight = toHighlight;
r.CaptionFormat = (caption1 + caption2 + caption3);
r.WhatIsHighlighted = highlightContents;
return(r);
}