public override IEnumerable <Selection> Select(IStructure structure)
{
List <Selection> results = new List <Selection>();
for (int chainIndex = 0; chainIndex < structure.Count; chainIndex++)
{
if (chainIndex == ChainIndex)
{
continue;
}
IChain chain = structure[chainIndex];
List <SSBlock> chainSelections = SecondaryStructure.GetPhiPsiSSBlocks(chain, MinLength);
if (IncludeAdjacentLoops)
{
// Extend the SSBlock ranges to include everything up to the neighboring blocks
List <SSBlock> extendedChainSelections = new List <SSBlock>();
for (int selectionIndex = 0; selectionIndex < chainSelections.Count; selectionIndex++)
{
int start = selectionIndex == 0 ? 0 : chainSelections[selectionIndex - 1].End + 1;
int end = selectionIndex == chainSelections.Count - 1 ? chain.Count - 1 : chainSelections[selectionIndex + 1].Start - 1;
extendedChainSelections.Add(new SSBlock(chainSelections[selectionIndex].SS, start, end));
}
chainSelections = extendedChainSelections;
}
if (SkipCountC != null && SkipCountC > 0)
{
int firstSkipIndex = Math.Max(0, chainSelections.Count - (int)SkipCountC);
chainSelections.RemoveRange(firstSkipIndex, chainSelections.Count - firstSkipIndex);
}
if (SkipCountN != null && SkipCountN > 0)
{
int skipCount = Math.Min((int)SkipCountN, chainSelections.Count);
chainSelections.RemoveRange(0, skipCount);
}
// Convert the computed SS block ranges to an AA selection and add that to list
results.AddRange(chainSelections.Select(block => new Selection(chain[block.Start, block.End])));
}
return(results);
}
