void TestAlign()
{
Alignment x = new Alignment();
Macromolecule y1 = new Macromolecule();
y1.Sequence = "ACTGGGTAGA";
y1.Name = "TestSeq1";
y1.identifier = 1;
int[] y11 = new int[10] {
0, 1, 2, 3, 4, 5, 6, 7, 8, 9
};
//Macromolecule y2 = new Macromolecule();
//y2.Sequence = "CTGGTAG";
//y2.Name = "TestSeq1";
//y2.identifier = 1;
//int[] y22 = new int[7] { 1, 2, 4, 5, 6, 7, 8 };
x.AlignmentLength = 10; // Need to set up Alignment to do this automatically when a sequence is added.
//x.AddAlignedMacromolecule(Tuple.Create(y1, y11));
x.AddAlignedMacromolecule(new AlignedMacromolecule(y1, y11));
//x.AddAlignedMacromolecule(Tuple.Create(y2, y22));
//.NudgeSequences(new List<int>{1}, 6, 6, 4);
DataContext = x;
}
public AlignedMacromolecule(Macromolecule newMacromolecule, int[] newAlignedPositions)
: base(newMacromolecule)
{
alignedPositions = newAlignedPositions;
sequenceWeight = 0;
newGaps = new List <int>();
}
public AlignedMacromolecule(Macromolecule newMacromolecule)
: base(newMacromolecule)
{
alignedPositions = new int[newMacromolecule.Sequence.Length];
for (int i = 0; i < newMacromolecule.Sequence.Length; i++)
{
alignedPositions[i] = i;
}
sequenceWeight = 0;
}
//internal void AddAlignedMacromolecule(Tuple<Macromolecule, int[]> newAlignedMacromolecule, bool doAdjustments = true)
internal void AddAlignedMacromolecule(AlignedMacromolecule newAlignedMacromolecule, bool doAdjustments = true)
// Provides an interface to add an aligned macromolecule to the list.
// Adjust the name if it is not unique, adjust the alignmentLength, and add it to the list.
{
//Macromolecule newMacromolecule = newAlignedMacromolecule.Item1;
Macromolecule newMacromolecule = newAlignedMacromolecule;
// Rename the macromolecule if another with the same name is already loaded.
// Appends a "1" if already exists; then if this new name matches another, add "2", etc.
// Could lead to some weirdness if the loaded sequences were "seq1" "seq4" "seq4", which would
// become "seq1", "seq4", "seq4 1", but this is tolerable.
int nameInteger = 1;
for (int i = 0; i < alignedMacromolecules.Count; i++)
{
//Macromolecule testMacromolecule = alignedMacromolecules[i].Item1;
Macromolecule testMacromolecule = alignedMacromolecules[i];
if (newMacromolecule.Name == testMacromolecule.Name) // same name
{
newMacromolecule.Name += " " + nameInteger.ToString();
nameInteger++;
}
}
alignedMacromolecules.Add(newAlignedMacromolecule);
if (doAdjustments)
{ // Make into another sub so the Add routines can be synced?
NormalizeAlignedPositions();
CalculateAlignmentLength();
NotifyPropertyChanged("AlignedMacromolecules");
//isNucleicAcid = newAlignedMacromolecule.Item1.IsNucleicAcid;
isNucleicAcid = newAlignedMacromolecule.IsNucleicAcid;
NotifyPropertyChanged("IsNucleicAcid");
RecalculateMaximumLength();
}
}
protected Macromolecule(Macromolecule newMacromolecule)
{
sequence = newMacromolecule.Sequence;
name = newMacromolecule.Name;
isNucleicAcid = newMacromolecule.IsNucleicAcid;
}