/// <summary>
/// This function takes peptide and protein groups and
/// assembles them together. A peptide group contains
/// all peptide identifications that mapped to same
/// protein and a protein group contains all proteins that
/// mapped to same peptides. The function generate clusters
/// and assign the proteins that are connected to the same
/// peptides to a single cluster. The proteins that map to
/// a subset of the peptides in the generated cluster are
/// also assigned to the same cluster in a recursive fashion.
/// </summary>
public void assembleClusters()
{
clusters.Clear();
if (statusOutput == null)
{
// Get each protein
foreach (ProteinGroupInfo proGroup in proteinGroups)
{
foreach (ResultInfo r in proGroup.results)
{
// Assign each peptide to corresponding group
proGroup.peptideGroups.Add(r.peptideGroup);
// Set the peptide to protein group mapping
r.peptideGroup.proteinGroups.Add(proGroup);
}
}
}
else
{
// Do the same as above while reporting the status to the user
ProteinGroupList.Enumerator itr = proteinGroups.GetEnumerator();
for (int i = 0; i < proteinGroups.Count; ++i)
{
itr.MoveNext();
ProteinGroupInfo proGroup = itr.Current;
IEnumerator<ResultInfo> itr2 = proGroup.results.GetEnumerator();
for (int j = 0; j < proGroup.results.Count; ++j)
{
itr2.MoveNext();
ResultInfo r = itr2.Current;
reportStatus("linking peptide group " + (j + 1) + " of " + proGroup.results.Count + " to protein group " + (i + 1) + " of " + proteinGroups.Count, j + 1 == proGroup.results.Count);
proGroup.peptideGroups.Add(r.peptideGroup);
r.peptideGroup.proteinGroups.Add(proGroup);
}
}
}
// Set the protein and peptide group cluster identifications to 0.
foreach (ProteinGroupInfo proGroup in proteinGroups)
{
proGroup.cluster = 0;
}
foreach (PeptideGroupInfo pepGroup in peptideGroups)
{
pepGroup.cluster = 0;
}
// For each protein group
foreach (ProteinGroupInfo proGroup in proteinGroups)
{
if (proGroup.cluster == 0)
{
// Generate a new cluster and assign an incremental ID.
ClusterInfo c = new ClusterInfo();
c.id = clusters.Count + 1;
// Add the protein to the cluster. Also add proteins that
// matched to the peptides of the given protein to the
// cluster
recursivelyAssignProteinGroupsToCluster(proGroup, c);
clusters.Add(c);
}
}
// Sort the clusters
clusters.Sort(ClusterList.SortDescendingBySequencesThenSpectra);
// Assign cluster idenfication numbers. These numbers signify
// how many proteins in a cluster share peptides, and also
// how many protein are identified per peptide cluster.
for (int i = 0; i < clusters.Count; ++i)
{
clusters[i].id = i + 1;
foreach (ProteinGroupInfo proGroup in clusters[i].proteinGroups)
proGroup.cluster = i + 1;
foreach (PeptideGroupInfo pepGroup in clusters[i].peptideGroups)
pepGroup.cluster = i + 1;
}
}
public void assembleMinimumCoveringSet(ClusterInfo c)
{
if (c.proteinGroups.Count == 1) // degenerate case
{
foreach (ProteinGroupInfo proGroup in c.proteinGroups)
proGroup.uniquePeptideCount = int.MaxValue; // value is n/a
return;
}
/*Set<ResultInfo> clusterResults = new Set<ResultInfo>( c.results );
ProteinGroupList clusterGroups = new ProteinGroupList();
foreach( ProteinGroupInfo proGroup in c.proteinGroups )
clusterGroups.Add( proGroup );
//Console.WriteLine();
while( clusterResults.Count > 0 )
{
List<ProteinGroupInfo> minRemainingResults = new List<ProteinGroupInfo>();
int minRemainingResultCount = clusterResults.Count;
//int n = 0;
//Console.WriteLine( "groups: " + clusterGroups.Count + "; results: " + clusterResults.Count );
foreach( ProteinGroupInfo proGroup in clusterGroups )
{
//Console.Write( n++ + " of " + clusterGroups.Count + "\r" );
int count = clusterResults.Count;
foreach( ResultInfo r in proGroup.results )
if( clusterResults.Contains( r ) )
--count;
if( count <= minRemainingResultCount )
{
if( count < minRemainingResultCount )
minRemainingResults.Clear();
minRemainingResults.Add( proGroup );
}
}
ProteinGroupInfo mostGreedyGroup = minRemainingResults[0];
minRemainingResults.Clear();
int oldCount = clusterResults.Count;
clusterResults.Subtract( mostGreedyGroup.results );
if( clusterResults.Count >= oldCount )
{
Console.Error.WriteLine( "Something has gone terribly wrong!" );
System.Diagnostics.Process.GetCurrentProcess().Kill();
}
mostGreedyGroup.minSet = true;
clusterGroups.Remove( mostGreedyGroup );
}*/
// Get the results in the cluster
Set<ResultInfo> clusterResults = new Set<ResultInfo>(c.results);
// Get the protein groups in the cluster
ProteinGroupList clusterGroups = new ProteinGroupList();
foreach (ProteinGroupInfo proGroup in c.proteinGroups)
clusterGroups.Add(proGroup);
//Console.WriteLine();
// while there are results in the cluster
while (clusterResults.Count > 0)
{
// Maps the number of results to a protein group
Map<int, List<ProteinGroupInfo>> remainingResults = new Map<int, List<ProteinGroupInfo>>();
//int n = 0;
//Console.WriteLine( "groups: " + clusterGroups.Count + "; results: " + clusterResults.Count );
// Iterate through protein groups
foreach (ProteinGroupInfo proGroup in clusterGroups)
{
//Console.Write( n++ + " of " + clusterGroups.Count + "\n" );
// Get the number of results in the cluster
int count = clusterResults.Count;
// Iterate over the cluster results and see how
// many cluster group results can be explained
// by that protein group
foreach (ResultInfo r in proGroup.results)
{
if (clusterResults.Contains(r))
--count;
}
// Map the number of remaining results to that
// protein group
remainingResults[count].Add(proGroup);
}
// Take the first protein group that can explain the most results
ProteinGroupInfo mostGreedyGroup = remainingResults.Values[0][0];
// Subtract its results from the cluster results
mostGreedyGroup.uniquePeptideCount = clusterResults.Count - remainingResults.Keys[0];
clusterResults.Subtract(mostGreedyGroup.results);
// Remove the most greedy group from the cluster groups
clusterGroups.Remove(mostGreedyGroup);
}
}
/// <summary>
/// This function takes a protein group, assigns all the peptides and results to the supplied
/// cluster. It then takes all the peptides and the results in the cluster, traces all the
/// proteins mapped to those peptides and the resutls and adds them to the same cluster.
/// </summary>
/// <param name="proGroup">A <see cref="IDPicker.ProteinGroupInfo"/> object containing
/// protein identification results</param>
/// <param name="c">A <see cref="IDPicker.ClusterInfo"/> object</param>
///
private void recursivelyAssignProteinGroupsToCluster(ProteinGroupInfo proGroup, ClusterInfo c)
{
reportStatus("assigning protein group " + proGroup.id + " to cluster " + c.id, true);
if (proGroup.cluster > 0)
{
if (proGroup.cluster != c.id)
throw new InvalidDataException("protein groups that are connected are assigned to different clusters");
return;
}
// Add the protein group to the cluster
proGroup.cluster = c.id;
c.proteinGroups.Add(proGroup);
// For each protein in the group
foreach (ProteinList.MapPair proItr in proGroup.proteins)
{
c.proteins[proItr.Value.locus] = proItr.Value;
// Get the results and assign them to the cluster.
// Also assign the corresponding peptides to the
// same cluster.
foreach (ResultInfo r in proItr.Value.results)
{
c.results.Add(r);
c.peptideGroups.Add(r.peptideGroup);
r.peptideGroup.cluster = c.id;
}
}
// recursively add all "cousin" protein groups to the same cluster
foreach (ResultInfo r in proGroup.results)
foreach (ProteinGroupInfo cousinProGroup in r.peptideGroup.proteinGroups)
{
if (!ReferenceEquals(cousinProGroup, proGroup) && cousinProGroup.cluster == 0)
recursivelyAssignProteinGroupsToCluster(cousinProGroup, c);
else if (cousinProGroup.cluster != c.id)
throw new InvalidDataException("protein groups that are connected are assigned to different clusters");
}
}