/// <summary>
/// Add residues with no-coordinates or no-Calpha to the alignment
/// </summary>
/// <param name="alignInfo1"></param>
/// <param name="alignInfo2"></param>
public void AddDisorderResiduesToDomainAlignment(ref DomainAlignSeqInfo alignInfo1, ref DomainAlignSeqInfo alignInfo2)
{
List <string> pdbList = new List <string> ();
pdbList.Add(alignInfo1.pdbId);
if (!pdbList.Contains(alignInfo2.pdbId))
{
pdbList.Add(alignInfo2.pdbId);
}
DataTable seqTable = GetSequenceTable(pdbList, asuSeqInfoTable);
// the sequence in coordinate and sequence from the domain files which are used to FATCAT align
string[] domainSequences1 = GetDomainFileSequences(alignInfo1.pdbId, alignInfo1.domainId, seqTable);
string[] domainSequences2 = GetDomainFileSequences(alignInfo2.pdbId, alignInfo2.domainId, seqTable);
// if there are no disorder residues in the domain sequences, do nothing
if (!IsSequenceWithDisorderResidues(domainSequences1[0]) && !IsSequenceWithDisorderResidues(domainSequences2[0]))
{
return;
}
try
{
if (HasMissingResidues(alignInfo1.alignSequence, alignInfo1.alignStart, alignInfo1.alignEnd))
{
int[] alignXmlSeq1 = ConvertSeqToXmlSeq(ref alignInfo1, domainSequences1[0]);
// from sequence of the domain file
string[] alignSequences = FillMissingResidues(alignInfo1.alignSequence, alignXmlSeq1, domainSequences1[1], alignInfo2.alignSequence);
alignInfo1.alignSequence = alignSequences[0];
alignInfo2.alignSequence = alignSequences[1];
}
}
catch (Exception ex)
{
throw ex;
}
try
{
if (HasMissingResidues(alignInfo2.alignSequence, alignInfo2.alignStart, alignInfo2.alignEnd))
{
int[] alignXmlSeq2 = ConvertSeqToXmlSeq(ref alignInfo2, domainSequences2[0]);
string[] alignSequences = FillMissingResidues(alignInfo2.alignSequence, alignXmlSeq2, domainSequences2[1], alignInfo1.alignSequence);
alignInfo2.alignSequence = alignSequences[0];
alignInfo1.alignSequence = alignSequences[1];
}
}
catch (Exception ex)
{
throw ex;
}
}
/// <summary>
/// residue numbers to xml numbers
/// </summary>
/// <param name="alignInfo"></param>
/// <param name="seqTable"></param>
/// <returns></returns>
private int[] ConvertSeqToXmlSeq(ref DomainAlignSeqInfo alignInfo, string domainSeqInCoord)
{
string nonGapAlignString = GetNonGapSequenceString(alignInfo.alignSequence);
int[] xmlSeqIndexes = GetXmlIndexes(nonGapAlignString, domainSeqInCoord);
/* if (xmlSeqNumbers.Length == 0)
* {
* xmlSeqNumbers = MatchSequencesByBlast(nonGapAlignString, domainSeqInCoord);
* }*/
if (xmlSeqIndexes.Length == 0)
{
return(null);
}
alignInfo.alignStart = xmlSeqIndexes[0] + 1; // added 1 on January 4, 2017
alignInfo.alignEnd = xmlSeqIndexes[xmlSeqIndexes.Length - 1] + 1;
return(xmlSeqIndexes);
}