public bool InsertPosition(string _position, string _previousPosition, string _nextPosition)
// inserts alignment position object in between noted positions
{
if (alnHash.ContainsKey(_previousPosition) && alnHash.ContainsKey(_nextPosition))
{
if (GetNextPositionKey(_previousPosition) == _nextPosition)
{
AlignmentPosition newPosition = new AlignmentPosition(_previousPosition, _nextPosition);
alnHash.Add(_position, newPosition);
AlignmentPosition prevP = new AlignmentPosition();
AlignmentPosition nextP = new AlignmentPosition();
prevP = (AlignmentPosition)alnHash[_previousPosition];
nextP = (AlignmentPosition)alnHash[_nextPosition];
prevP.SetNextAlignmentPosition(_position); // need to test this! Does this change underlying obj?
nextP.SetPreviousAlignmentPosition(_position); // ditto
numberOfPositions++;
return(true);
}
else
{
return(false);
}
}
else
{
return(false);
}
}
public void AddNewPosition(string _position) // overload to add position to end of alignment
{
// find last position
string currentLastPosition = GetLastPosition();
string endKey = "end";
AlignmentPosition oldLastPosition = new AlignmentPosition();
oldLastPosition = (AlignmentPosition)alnHash[currentLastPosition];
oldLastPosition.SetNextAlignmentPosition(_position);
AlignmentPosition newPosition = new AlignmentPosition();
newPosition.SetPreviousAlignmentPosition(currentLastPosition);
newPosition.SetNextAlignmentPosition(endKey);
alnHash.Add(_position, newPosition);
numberOfPositions++;
return;
}
public bool DeletePosition(string _position) // deletes position, moves Next and Prev keys and returns true if position exists
{
if (alnHash.ContainsKey(_position))
{
string previousPosition = GetPreviousPositionKey(_position);
string nextPosition = GetNextPositionKey(_position);
if (previousPosition != "start")
{
AlignmentPosition prevP = new AlignmentPosition();
prevP = (AlignmentPosition)alnHash[previousPosition];
prevP.SetNextAlignmentPosition(nextPosition);
}
if (nextPosition != "end")
{
AlignmentPosition nextP = new AlignmentPosition();
nextP = (AlignmentPosition)alnHash[nextPosition];
nextP.SetPreviousAlignmentPosition(previousPosition);
}
Hashtable infoFromDeletedPosition = ((AlignmentPosition)alnHash[_position]).GetResidueInfo(); // need to get position info before it's deleted
alnHash.Remove(_position);
// clean up protein list here: if this is the last position containing said protein,
// remove it from the list
string[] allKeys = new string[alnHash.Count];
alnHash.Keys.CopyTo(allKeys, 0);
string[] listOfProteinsInDeletedPosition = new string[infoFromDeletedPosition.Count];
infoFromDeletedPosition.Keys.CopyTo(listOfProteinsInDeletedPosition, 0);
bool[] proteinStillPresent = new bool[listOfProteinsInDeletedPosition.Length];
for (int deletedPositionProteinIndex = 0; deletedPositionProteinIndex < listOfProteinsInDeletedPosition.Length; deletedPositionProteinIndex++)
{
proteinStillPresent[deletedPositionProteinIndex] = false;
for (int alnKeyIndex = 0; alnKeyIndex < allKeys.Length; alnKeyIndex++)
{
if (((AlignmentPosition)alnHash[allKeys[alnKeyIndex]]).IsProteinPresent(listOfProteinsInDeletedPosition[deletedPositionProteinIndex]))
{
proteinStillPresent[deletedPositionProteinIndex] = true;
break;
}
}
}
for (int deletedPositionProteinIndex = 0; deletedPositionProteinIndex < listOfProteinsInDeletedPosition.Length; deletedPositionProteinIndex++)
{
if (!proteinStillPresent[deletedPositionProteinIndex])
{
if (proteinsInAlignment.Contains(listOfProteinsInDeletedPosition[deletedPositionProteinIndex]))
{
proteinsInAlignment.RemoveAt(proteinsInAlignment.IndexOf(listOfProteinsInDeletedPosition[deletedPositionProteinIndex]));
}
}
} // this loop gets rid of proteins that are no longer in alignment after deletion of position
numberOfPositions--;
return(true);
}
else
{
return(false);
}
}