/// <summary>
/// Generate profiles from one single sequence
/// The set of sequence items of the seq should be the same as
/// 'static ItemSet' of this class.
/// </summary>
/// <param name="seq">an input sequence</param>
public static IProfiles GenerateProfiles(ISequence seq)
{
IProfiles profiles;
int sequenceLength = seq.Count;
int colSize = ItemSet.Count;
profiles = new Profiles(sequenceLength, colSize);
for (int i = 0; i < sequenceLength; ++i)
{
try
{
if (seq[i].IsAmbiguous)
{
//Console.WriteLine("residue {0} is {1}, ambiguous? {2}", i, seq[i].Symbol, seq[i].IsAmbiguous);
for (int b = 0; b < AmbiguousCharactersMap[seq[i]].Count; ++b)
{
++(profiles[i][ItemSet[AmbiguousCharactersMap[seq[i]][b]]]);
}
}
else
{
++(profiles[i][ItemSet[seq[i]]]);
}
}
catch (IndexOutOfRangeException ex)
{
throw new Exception("Invalid alphabet", ex.InnerException);
}
//MsaUtils.Normalize(profiles[i]);
}
profiles.ColumnSize = colSize;
profiles.RowSize = sequenceLength;
return(profiles);
}
/// <summary>
/// Generate IProfiles from a subset of aligned sequences.
/// In the subset of sequences, those columns containing no residues,
/// i.e. indels only, are discarded.
/// </summary>
/// <param name="sequences">a set of aligned sequences</param>
/// <param name="sequenceIndices">the subset indices of the aligned sequences</param>
/// <param name="allIndelPositions">the list of all-indel positions that have been removed when constructing</param>
/// <param name="weights">sequence weights</param>
public static IProfiles GenerateProfiles(List <ISequence> sequences, List <int> sequenceIndices, out List <int> allIndelPositions, float[] weights)
{
IProfiles profiles;
if (sequences.Count <= 0)
{
throw new ArgumentException("Empty input sequences");
}
if (sequenceIndices.Count > sequences.Count)
{
throw new ArgumentException("Invalid subset indices");
}
MsaUtils.Normalize(weights);
try
{
int sequenceLength = sequences[sequenceIndices[0]].Count;
IAlphabet alphabet = sequences[sequenceIndices[0]].Alphabet;
foreach (int i in sequenceIndices)
{
if (sequences[i].Count != sequenceLength)
{
throw new ArgumentException("Input sequences are not aligned");
}
if (sequences[i].Alphabet != alphabet)
{
throw new ArgumentException("Input sequences use different alphabets");
}
}
allIndelPositions = new List <int>();
profiles = new Profiles();
int colSize = ItemSet.Count;
// Discard all indels columns.
for (int col = 0; col < sequenceLength; ++col)
{
float[] vector = new float[colSize];
bool isAllIndels = true;
foreach (int i in sequenceIndices)
{
if (!sequences[i][col].IsGap)
{
isAllIndels = false;
}
if (sequences[i][col].IsAmbiguous)
{
//Console.WriteLine("residue {0} is {1}, ambiguous? {2}", i, seq[i].Symbol, seq[i].IsAmbiguous);
for (int b = 0; b < AmbiguousCharactersMap[sequences[i][col]].Count; ++b)
{
vector[ItemSet[AmbiguousCharactersMap[sequences[i][col]][b]]] += weights[i];
}
}
else
{
vector[ItemSet[sequences[i][col]]] += weights[i];
}
}
if (!isAllIndels)
{
MsaUtils.Normalize(vector);
profiles.ProfilesMatrix.Add(vector);
}
else
{
allIndelPositions.Add(col);
}
}
profiles.ColumnSize = colSize;
profiles.RowSize = profiles.ProfilesMatrix.Count;
}
catch (IndexOutOfRangeException ex)
{
throw new Exception("Invalid index", ex.InnerException);
}
return(profiles);
}
