private IEnumerable <AnnotationAndOffset> AnnotationsAndOffsetsParallelInternal(int minLength, int numTolerableTermini,
int numMissedCleavages, IEnumerable <char> enzymaticResidues, bool isNTermEnzyme, SequenceLcpAndOffset seqAndLcp, bool[] isCleavable, bool[] isStandardAminoAcid
)
{
var seqArr = Encoding.GetString(seqAndLcp.Sequence);
//var seqArr = seqAndLcp.Sequence;
var lcp = seqAndLcp.Lcp;
var offset = seqAndLcp.Offset;
var seqBuild = new StringBuilder(seqArr.Length + 3);
seqBuild.Append(seqArr[0] + ".");
if (enzymaticResidues != null)
{
var ntt = 0;
var nmc = 0;
if (!isNTermEnzyme) // C-term enzyme
{
if (isCleavable[seqArr[0]])
{
++ntt;
}
if (!(ntt < numTolerableTermini - 1))
{
// Could be run in parallel, but probably not worth the cost.
for (var i = 1; i < seqArr.Length - 1; i++)
{
var code = seqArr[i];
if (!isStandardAminoAcid[code])
{
break;
}
if (isCleavable[code])
{
++nmc;
}
seqBuild.Append(code);
if (i >= minLength && i >= lcp)
{
if (ntt + (isCleavable[code] || seqArr[i + 1] == FastaDatabaseConstants.Delimiter ? 1 : 0) >= numTolerableTermini)
{
yield return(new AnnotationAndOffset(offset, seqBuild + "." + seqArr[i + 1]));
}
}
if (nmc > numMissedCleavages)
{
break;
}
}
}
}
else // N-term enzyme
{
if (seqArr[0] == FastaDatabaseConstants.Delimiter || isCleavable[seqArr[1]])
{
++ntt;
}
if (!(ntt < numTolerableTermini - 1))
{
// Could be run in parallel, but probably not worth the cost.
for (var i = 2; i < seqArr.Length - 1; i++)
{
var code = seqArr[i];
if (!isStandardAminoAcid[code])
{
break;
}
if (isCleavable[code])
{
++nmc;
}
if (nmc > numMissedCleavages)
{
break;
}
seqBuild.Append(code);
if (i >= minLength && i >= lcp)
{
if (ntt + (isCleavable[seqArr[i + 1]] ? 1 : 0) >= numTolerableTermini)
{
yield return(new AnnotationAndOffset(offset, seqBuild + "." + seqArr[i + 1]));
}
}
}
}
}
}
else // No enzyme
{
// Could be run in parallel, but probably not worth the cost.
for (var i = 1; i < seqArr.Length - 1; i++)
{
var code = seqArr[i];
if (!isStandardAminoAcid[code])
{
break;
}
seqBuild.Append(code);
if (i >= minLength && i >= lcp)
{
yield return(new AnnotationAndOffset(offset, seqBuild + "." + seqArr[i + 1]));
}
}
}
}
private IEnumerable<AnnotationAndOffset> AnnotationsAndOffsetsParallelInternal(int minLength, int numTolerableTermini,
int numMissedCleavages, IEnumerable<char> enzymaticResidues, bool isNTermEnzyme, SequenceLcpAndOffset seqAndLcp, bool[] isCleavable, bool[] isStandardAminoAcid
)
{
var seqArr = Encoding.GetString(seqAndLcp.Sequence);
//var seqArr = seqAndLcp.Sequence;
var lcp = seqAndLcp.Lcp;
var offset = seqAndLcp.Offset;
var seqBuild = new StringBuilder(seqArr.Length + 3);
seqBuild.Append(seqArr[0] + ".");
if (enzymaticResidues != null)
{
var ntt = 0;
var nmc = 0;
if (!isNTermEnzyme) // C-term enzyme
{
if (isCleavable[seqArr[0]]) ++ntt;
if (!(ntt < numTolerableTermini-1))
{
// Could be run in parallel, but probably not worth the cost.
for (var i = 1; i < seqArr.Length-1; i++)
{
var code = seqArr[i];
if (!isStandardAminoAcid[code]) break;
if (isCleavable[code]) ++nmc;
seqBuild.Append(code);
if (i >= minLength && i >= lcp)
{
if (ntt + (isCleavable[code] || seqArr[i+1] == FastaDatabase.Delimiter ? 1 : 0) >= numTolerableTermini)
{
yield return new AnnotationAndOffset(offset, seqBuild + "." + seqArr[i + 1]);
}
}
if (nmc > numMissedCleavages) break;
}
}
}
else // N-term enzyme
{
if (seqArr[0] == FastaDatabase.Delimiter || isCleavable[seqArr[1]]) ++ntt;
if (!(ntt < numTolerableTermini - 1))
{
// Could be run in parallel, but probably not worth the cost.
for (var i = 2; i < seqArr.Length - 1; i++)
{
var code = seqArr[i];
if (!isStandardAminoAcid[code]) break;
if (isCleavable[code]) ++nmc;
if (nmc > numMissedCleavages) break;
seqBuild.Append(code);
if (i >= minLength && i >= lcp)
{
if (ntt + (isCleavable[seqArr[i + 1]] ? 1 : 0) >= numTolerableTermini)
{
yield return new AnnotationAndOffset(offset, seqBuild + "." + seqArr[i + 1]);
}
}
}
}
}
}
else // No enzyme
{
// Could be run in parallel, but probably not worth the cost.
for (var i = 1; i < seqArr.Length-1; i++)
{
var code = seqArr[i];
if (!isStandardAminoAcid[code]) break;
seqBuild.Append(code);
if (i >= minLength && i >= lcp)
{
yield return new AnnotationAndOffset(offset, seqBuild + "." + seqArr[i + 1]);
}
}
}
}
