/// <summary>
/// Given a set of structure and alignments between chains, and directionality to identify which structure contributes the N and C-terminus,
/// return selections corresponding to each block of structure that is left remaining between fusion regions, and selections constituting the fusion
/// regions themselves.
/// </summary>
/// <param name="structures"></param>
/// <param name="alignments"></param>
/// <param name="ncDirections"></param>
/// <param name="blocks"></param>
/// <param name="junctions"></param>
public static void GetSelections(IStructure[] structures, SequenceAlignment[] alignments, bool[] ncDirections, out Selection[] blocks, out Selection[] junctions, out Selection[] removed)
{
junctions = new Selection[alignments.Length];
blocks = new Selection[structures.Length];
removed = new Selection[structures.Length];
// Mark which aas to remove without actually removing them at first, so that their indices remain unchanged while
// those to be removed are being computed
Selection remove = new Selection();
// Determine junction residues and residues that are removed due to splicing
for (int alignmentIndex = 0; alignmentIndex < alignments.Length; alignmentIndex++)
{
Selection junction = new Selection();
bool ncDirection = ncDirections[alignmentIndex];
SequenceAlignment alignment = ncDirection ? alignments[alignmentIndex] : SequenceAlignment.Reversed(alignments[alignmentIndex]); // N as chain1
IStructure structureN = ncDirection ? structures[alignmentIndex] : structures[alignmentIndex + 1];
IStructure structureC = ncDirection ? structures[alignmentIndex + 1] : structures[alignmentIndex];
IChain chainN = structureN[alignment.ChainIndex1];
IChain chainC = structureC[alignment.ChainIndex2];
remove.Aas.UnionWith(chainN[alignment.Range1.Middle + 1, chainN.Count - 1]);
remove.Aas.UnionWith(chainC[0, alignment.Range2.Middle]);
junction.Aas.UnionWith(chainN[alignment.Range1.Start, alignment.Range1.Middle]);
junction.Aas.UnionWith(chainC[alignment.Range2.Middle + 1, alignment.Range2.End]);
junctions[alignmentIndex] = junction;
}
// Determine blocks as the set of aas in the original structure, minus junction residues and residues that are lost from fusion
for (int structureIndex = 0; structureIndex < structures.Length; structureIndex++)
{
IStructure structure = structures[structureIndex];
Selection block = new Selection(structure.SelectMany(chain => chain));
removed[structureIndex] = Selection.Intersect(block, remove);
block.ExceptWith(remove);
if (structureIndex > 0)
{
block.ExceptWith(junctions[structureIndex - 1]);
}
if (structureIndex < junctions.Length)
{
block.ExceptWith(junctions[structureIndex]);
}
blocks[structureIndex] = block;
}
}
protected virtual IndexInsertAction[] CreateGroupedIndexInsertActions(IStructureSchema structureSchema, IStructure[] structures)
{
var indexesTableNames = structureSchema.GetIndexesTableNames();
var insertActions = new Dictionary<DataTypeCode, IndexInsertAction>(indexesTableNames.All.Length);
foreach (var group in structures.SelectMany(s => s.Indexes).GroupBy(i => i.DataTypeCode))
{
var insertAction = CreateIndexInsertActionGroup(structureSchema, indexesTableNames, group.Key, group.ToArray());
if (insertAction.HasData)
insertActions.Add(group.Key, insertAction);
}
var mergeStringsAndEnums = insertActions.ContainsKey(DataTypeCode.String) && insertActions.ContainsKey(DataTypeCode.Enum);
if (mergeStringsAndEnums)
{
var strings = insertActions[DataTypeCode.String];
var enums = insertActions[DataTypeCode.Enum];
insertActions.Remove(DataTypeCode.Enum);
insertActions[DataTypeCode.String] = CreateIndexInsertActionGroup(structureSchema, indexesTableNames, DataTypeCode.String, strings.Data.MergeWith(enums.Data).ToArray());
}
return insertActions.Values.ToArray();
}
protected virtual void InsertUniques(IStructureSchema structureSchema, IStructure[] structures)
{
if (!structures.Any())
return;
var uniques = structures.SelectMany(s => s.Uniques).ToArray();
if (!uniques.Any())
return;
if (uniques.Length == 1)
MainDbClient.SingleInsertOfUniqueIndex(uniques[0], structureSchema);
else
MainDbClient.BulkInsertUniques(structureSchema, uniques);
}
