/// <summary>
/// IMPLEMENTS IVisualisable
/// </summary>
protected override void OnFindAssociations(ContentsRequest request)
{
switch (request.Type)
{
case EVisualClass.Peak:
request.Text = "Peak using {0}.";
request.AddRange(this.Annotations.Select(z => z.Peak));
break;
case EVisualClass.Cluster:
break;
case EVisualClass.Compound:
request.Text = "Compounds using {0}.";
request.AddRange(this.Annotations.Select(z => z.Compound));
break;
case EVisualClass.Adduct:
break;
case EVisualClass.Pathway:
break;
case EVisualClass.Annotation:
request.Text = "Annotations using {0}.";
request.AddRange(this.Annotations);
break;
default:
break;
}
}
internal static void AddHeaders(ContentsRequest request)
{
request.AddExtraColumn("Score", "The score for the assignment of {0} to this cluster.");
request.AddExtraColumn("Group", "The group to which the cluster is assigned (only visible for individual group clustering).");
//request.AddHeader("Next Nearest Cluster", "The next nearest cluster.");
//request.AddHeader("Silhouette width", "The silhouette width.");
}
public static ContentsRequest FindAssociations(object target, ContentsRequest request)
{
switch (request.Type)
{
case EVisualClass.SpecialAdvanced:
case EVisualClass.SpecialMeta:
case EVisualClass.SpecialAll:
case EVisualClass.SpecialStatistic:
IEnumerable <Column> cols = ColumnManager.GetColumns(request.Core, target).OrderBy(z => z.Special.Has(EColumn.Visible));
bool shortName;
switch (request.Type)
{
case EVisualClass.SpecialAll:
request.Text = "All data fields for {0}";
cols = cols.Where(z => !z.Special.Has(EColumn.Advanced));
shortName = false;
break;
case EVisualClass.SpecialStatistic:
request.Text = "Statistics fields for {0}";
cols = cols.Where(z => !z.Special.Has(EColumn.Advanced) && z.Special.Has(EColumn.IsStatistic));
shortName = true;
break;
case EVisualClass.SpecialMeta:
request.Text = "Meta-data fields for {0}";
cols = cols.Where(z => !z.Special.Has(EColumn.Advanced) && z.Special.Has(EColumn.IsMeta));
shortName = true;
break;
default:
case EVisualClass.SpecialAdvanced:
request.Text = "Internal data for {0}";
shortName = false;
break;
}
foreach (var c in cols)
{
request.Add(new ColumnValuePair(c, target, ColumnManager.GetColumnColour(c), Resources.ListIconInformation, shortName));
}
break;
default:
if (target is Associational)
{
((Associational)target).OnFindAssociations(request);
}
break;
}
return(request);
}
/// <summary>
/// IMPELEMENTS IVisualisable
/// </summary>
protected override void OnFindAssociations(ContentsRequest request)
{
switch (request.Type)
{
case EVisualClass.Peak:
request.Text = "Potential peaks for {0}";
foreach (var pp in this.Annotations)
{
request.Add(pp.Peak);
}
break;
case EVisualClass.Cluster:
request.Text = "Clusters representing potential peaks of {0}";
request.AddExtraColumn("Num. in compound", "Number of peaks in {0} in this cluster");
Counter <Cluster> counts = new Counter <Cluster>();
foreach (Annotation p in this.Annotations)
{
foreach (Cluster pat in p.Peak.FindAssignments(request.Core).Select(z => z.Cluster))
{
counts.Increment(pat); // assume there is only one of each cluster per peak so the count holds
}
}
request.AddRangeWithCounts(counts);
break;
case EVisualClass.Annotation:
request.Text = "Annotations using {0}";
request.AddRange(this.Annotations);
break;
case EVisualClass.Compound:
break;
case EVisualClass.Adduct:
break;
case EVisualClass.Pathway:
request.Text = "List of pathways implicating {0}";
request.AddRange(this.Pathways);
break;
default:
break;
}
}
protected override void OnFindAssociations(ContentsRequest list)
{
switch (list.Type)
{
case EVisualClass.Adduct:
list.Text = "Adduct for annotation {0}";
list.Add(this.Adduct);
break;
case EVisualClass.Annotation:
((Associational)this.Peak).FindAssociations(list);
((Associational)this.Compound).FindAssociations(list);
list.Text = "Annotations with same peaks/compounds to {0}";
break;
case EVisualClass.Assignment:
((Associational)this.Peak).FindAssociations(list);
break;
case EVisualClass.Cluster:
((Associational)this.Peak).FindAssociations(list);
break;
case EVisualClass.Compound:
list.Text = "Compound for annotation {0}";
list.Add(this.Compound);
break;
case EVisualClass.Pathway:
((Associational)this.Peak).FindAssociations(list);
((Associational)this.Compound).FindAssociations(list);
break;
case EVisualClass.Peak:
list.Text = "Peak for annotation {0}";
list.Add(this.Peak);
break;
}
}
protected override void OnFindAssociations(ContentsRequest request)
{
switch (request.Type)
{
case EVisualClass.Peak:
request.Add(this.Peak);
request.Text = "Peak for {0}";
break;
case EVisualClass.Cluster:
request.Add(this.Cluster);
request.Text = "Clusters for {0}";
break;
case EVisualClass.Assignment:
case EVisualClass.Compound:
case EVisualClass.Adduct:
case EVisualClass.Pathway:
case EVisualClass.Annotation:
default:
break;
}
}
/// <summary>
/// IMPLEMENTS IVisualisable
/// </summary>
protected override void OnFindAssociations(ContentsRequest request)
{
switch (request.Type)
{
case EVisualClass.Peak:
request.Text = "Peaks with similar m/z to {0} (" + Maths.SignificantDigits((double)this.Mz, 5) + ")";
request.AddRange(this.SimilarPeaks);
break;
case EVisualClass.Cluster:
request.Text = "Assigned clusters for {0}";
Assignment.AddHeaders(request);
foreach (var ass in this.FindAssignments(request.Core))
{
request.Add(ass.Cluster, ass.GetHeaders());
}
break;
case EVisualClass.Assignment:
request.Text = "Assignments for {0}";
request.AddRange(this.FindAssignments(request.Core));
break;
case EVisualClass.Compound:
request.Text = "Potential compounds of {0}";
foreach (var annotation in this.Annotations)
{
request.Add(annotation.Compound);
}
break;
case EVisualClass.Annotation:
request.Text = "Annotations for {0}";
foreach (var annotation in this.Annotations)
{
request.Add(annotation);
}
break;
case EVisualClass.Adduct:
{
request.Text = "Adducts of potential compounds for {0}";
HashSet <Adduct> counter = new HashSet <Adduct>();
foreach (var c in this.Annotations)
{
counter.Add(c.Adduct);
}
foreach (var kvp in counter)
{
request.Add(kvp);
}
}
break;
case EVisualClass.Pathway:
{
request.Text = "Pathways of potential compounds for {0}";
request.AddExtraColumn("Compounds", "Compounds in this pathway potentially represented by {0}.");
Dictionary <Pathway, List <Compound> > counter = new Dictionary <Pathway, List <Compound> >();
foreach (var pc in this.Annotations)
{
foreach (var p in pc.Compound.Pathways)
{
counter.GetOrNew(p).Add(pc.Compound);
}
}
foreach (var kvp in counter)
{
request.Add(kvp.Key, kvp.Value);
}
}
break;
default:
break;
}
}
/// <summary>
/// IMPLEMENTS Associational
/// </summary>
protected override void OnFindAssociations(ContentsRequest request)
{
switch (request.Type)
{
case EVisualClass.Peak:
request.Text = "Peaks assigned to {0}";
Assignment.AddHeaders(request);
foreach (Assignment assignment in this.Assignments.List)
{
request.Add(assignment.Peak, assignment.GetHeaders());
}
break;
case EVisualClass.Assignment:
request.Text = "Assignments to {0}";
request.AddRange(this.Assignments.List);
break;
case EVisualClass.Cluster:
request.Text = "Clusters with peaks also in {0}";
foreach (Cluster c in request.Core.Clusters.Where(c => c != this).Where(c => c.Assignments.Peaks.Any(this.Assignments.Peaks.Contains)))
{
request.Add(c);
}
break;
case EVisualClass.Compound:
{
request.Text = "Potential compounds of peaks assigned to {0}";
request.AddExtraColumn("Overlapping Peaks", "Peaks potentially representing this compound also in {0}");
Dictionary <Compound, List <Peak> > counter = new Dictionary <Compound, List <Peak> >();
foreach (var peak in this.Assignments.Peaks)
{
foreach (var c in peak.Annotations)
{
counter.GetOrNew(c.Compound).Add(peak);
}
}
foreach (var kvp in counter)
{
request.Add(kvp.Key, kvp.Value);
}
}
break;
case EVisualClass.Adduct:
{
request.Text = "Adducts of potential compounds of peaks assigned to {0}";
request.AddExtraColumn("Overlapping Compounds", "Compounds potentially representing {0} with this adduct");
Dictionary <Adduct, List <Compound> > counter = new Dictionary <Adduct, List <Compound> >();
foreach (Annotation c in this.Assignments.Peaks.SelectMany(p => p.Annotations))
{
counter.GetOrNew(c.Adduct).Add(c.Compound);
}
foreach (var kvp in counter)
{
request.Add(kvp.Key, kvp.Value);
}
}
break;
case EVisualClass.Pathway:
{
request.Text = "Pathways of potential compounds of peaks assigned to {0}";
request.AddExtraColumn("Overlapping Compounds", "Compounds in this pathway with peaks in {0}");
request.AddExtraColumn("Overlapping Peaks", "Peaks potentially representing compounds in this pathway in {0}");
Dictionary <Pathway, HashSet <Compound> > compounds = new Dictionary <Pathway, HashSet <Compound> >();
Dictionary <Pathway, HashSet <Peak> > peaks = new Dictionary <Pathway, HashSet <Peak> >();
foreach (Peak peak in this.Assignments.Peaks) // peaks in cluster
{
foreach (Annotation annotation in peak.Annotations) // compounds in peak
{
foreach (Pathway pathway in annotation.Compound.Pathways) // pathways in compound
{
compounds.GetOrNew(pathway).Add(annotation.Compound); // pathway += compound
peaks.GetOrNew(pathway).Add(peak); // pathway += peak
}
}
}
foreach (var kvp in compounds)
{
// Pathway, compound, peaks
request.Add(kvp.Key, kvp.Value.ToArray(), peaks[kvp.Key].ToArray());
}
}
break;
case EVisualClass.Annotation:
request.Text = "Annotations for peaks in {0}";
request.AddRange(this.Assignments.Peaks.SelectMany(z => z.Annotations));
break;
default:
break;
}
}
/// <summary>
/// IMPLEMENTS IVisualisable.
/// </summary>
protected override void OnFindAssociations(ContentsRequest list)
{
switch (list.Type)
{
case EVisualClass.Peak:
list.Text = "Peaks marked with {0}";
list.AddRange(list.Core.Peaks.Where(z => z.UserFlags.Contains(this)));
break;
case EVisualClass.Cluster:
list.Text = "Clusters containing peaks marked with {0}";
list.AddExtraColumn("Flag count", "Number of peaks in this cluster with the comment flag " + this.ToString());
foreach (Cluster c in list.Core.Clusters)
{
if (c.CommentFlags.ContainsKey(this))
{
list.Add(c, c.CommentFlags[this]);
}
}
break;
case EVisualClass.Pathway:
list.Text = "Pathways containing compounds annotated with peaks marked with {0}";
foreach (Pathway c in list.Core.Pathways)
{
if (c.Compounds.Any(z => z.Annotations.Any(zz => zz.Peak.UserFlags.Contains(this))))
{
list.Add(c);
}
}
break;
case EVisualClass.Annotation:
list.Text = "Annotations for peaks peaks marked with {0}";
foreach (Annotation c in list.Core.Annotations)
{
if (c.Peak.UserFlags.Contains(this))
{
list.Add(c);
}
}
break;
case EVisualClass.Assignment:
list.Text = "Assignments for peaks peaks marked with {0}";
foreach (Assignment c in list.Core.Assignments)
{
if (c.Peak.UserFlags.Contains(this))
{
list.Add(c);
}
}
break;
case EVisualClass.Compound:
list.Text = "Compounds with annotations for peaks peaks marked with {0}";
foreach (Compound c in list.Core.Compounds)
{
if (c.Annotations.Any(z => z.Peak.UserFlags.Contains(this)))
{
list.Add(c);
}
}
break;
}
}
/// <summary>
/// IMPLEMENTS IVisualisable
/// </summary>
protected override void OnFindAssociations(ContentsRequest request)
{
switch (request.Type)
{
case EVisualClass.Peak:
{
request.Text = "Potential peaks of compounds in {0}";
request.AddExtraColumn("Compounds", "Compounds potentially representing this peak in {0}.");
Dictionary <Peak, List <Compound> > dict = new Dictionary <Peak, List <Compound> >();
foreach (Compound c in this.Compounds)
{
foreach (Annotation p in c.Annotations)
{
dict.GetOrNew(p.Peak).Add(c);
}
}
foreach (var kvp in dict)
{
request.Add(kvp.Key, kvp.Value);
}
}
break;
case EVisualClass.Annotation:
request.Text = "Annotations with compounds in {0}";
foreach (Compound c in this.Compounds)
{
request.AddRange(c.Annotations);
}
break;
case EVisualClass.Cluster:
{
request.Text = "Clusters representing potential peaks of compounds in {0}";
request.AddExtraColumn("Overlapping Peaks", "Number of peaks in this cluster in with compounds in {0}");
request.AddExtraColumn("Overlapping Compounds", "Number of compounds with peaks in this cluster with peaks also in {0}");
foreach (Cluster cluster in request.Core.Clusters)
{
var peaks = new HashSet <Peak>();
var comps = new HashSet <Compound>();
foreach (Peak peak in cluster.Assignments.Peaks)
{
foreach (Annotation comp in peak.Annotations)
{
comps.Add(comp.Compound);
if (comp.Compound.Pathways.Contains(this))
{
peaks.Add(peak);
}
}
}
if (peaks.Count != 0)
{
request.Add(cluster, peaks.ToArray(), comps.ToArray());
}
}
}
break;
case EVisualClass.Compound:
{
request.Text = "Compounds in {0}";
request.AddExtraColumn("Clusters", "Clusters"); // TODO: This is actually generic to all compounds and not related to this Pathway class
foreach (Compound c in this.Compounds)
{
HashSet <Cluster> pats = new HashSet <Cluster>();
foreach (Annotation p in c.Annotations)
{
foreach (Cluster pat in p.Peak.FindAssignments(request.Core).Select(z => z.Cluster))
{
pats.Add(pat);
}
}
request.Add(c, (object)pats.ToArray());
}
}
break;
case EVisualClass.Adduct:
break;
case EVisualClass.Pathway:
{
request.Text = "Pathways related to {0}";
request.AddRange(this.RelatedPathways);
}
break;
default:
break;
}
}
public ContentsRequest FindAssociations(ContentsRequest request)
{
return(FindAssociations(this, request));
}
/// <summary> /// Gets related items. /// </summary> protected abstract void OnFindAssociations(ContentsRequest request);