protected static Alignment <string, char> CreateAlignment(params string[] alignment)
{
var sequences = new Tuple <string, AlignmentCell <char>, IEnumerable <AlignmentCell <char> >, AlignmentCell <char> > [alignment.GetLength(0)];
for (int i = 0; i < alignment.Length; i++)
{
var sb = new StringBuilder();
string[] split = alignment[i].Split('|');
string prefix = split[0].Trim();
sb.Append(prefix);
string[] cellStrs = split[1].Trim().Split(new[] { ' ' }, StringSplitOptions.RemoveEmptyEntries);
var cells = new AlignmentCell <char> [cellStrs.Length];
for (int j = 0; j < cellStrs.Length; j++)
{
if (cellStrs[j] == "-")
{
cells[j] = new AlignmentCell <char>();
}
else
{
sb.Append(cellStrs[j]);
cells[j] = new AlignmentCell <char>(cellStrs[j]);
}
}
string suffix = split[2].Trim();
sb.Append(suffix);
sequences[i] = Tuple.Create(sb.ToString(), new AlignmentCell <char>(prefix), (IEnumerable <AlignmentCell <char> >)cells, new AlignmentCell <char>(suffix));
}
return(new Alignment <string, char>(0, 0, sequences));
}
public AlignedNodeViewModel(int column, AlignmentCell<ShapeNode> cell1, AlignmentCell<ShapeNode> cell2, string note)
{
_column = column;
_cell1 = cell1;
_cell2 = cell2;
_note = note;
}
public AlignedNodeViewModel(int column, AlignmentCell <ShapeNode> cell1, AlignmentCell <ShapeNode> cell2, string note)
{
_column = column;
_cell1 = cell1;
_cell2 = cell2;
_note = note;
}
public static ShapeNode GetRightNode(this Alignment <Word, ShapeNode> alignment, int seq, int col)
{
AlignmentCell <ShapeNode> cell = alignment[seq, col];
ShapeNode rightNode;
if (cell.IsNull)
{
int index = col + 1;
while (index < alignment.ColumnCount && alignment[seq, index].Count == 0)
{
index++;
}
if (index < alignment.ColumnCount)
{
rightNode = alignment[seq, index].First;
if (!NodeFilter(rightNode))
{
rightNode = rightNode.GetNext(NodeFilter);
}
}
else
{
rightNode = alignment.Sequences[seq].Shape.End;
}
}
else
{
rightNode = cell.Last.GetNext(NodeFilter);
}
return(rightNode);
}
public static ShapeNode GetLeftNode(this Alignment <Word, ShapeNode> alignment, int seq, int col)
{
AlignmentCell <ShapeNode> cell = alignment[seq, col];
ShapeNode leftNode;
if (cell.IsNull)
{
int index = col - 1;
while (index >= 0 && alignment[seq, index].Count == 0)
{
index--;
}
if (index >= 0)
{
leftNode = alignment[seq, index].Last;
if (!NodeFilter(leftNode))
{
leftNode = leftNode.GetPrev(NodeFilter);
}
}
else
{
leftNode = alignment.Sequences[seq].Shape.Begin;
}
}
else
{
leftNode = cell.First.GetPrev(NodeFilter);
}
return(leftNode);
}
public void UpdateCognicity(WordPair wordPair, IWordAlignerResult alignerResult)
{
wordPair.AlignmentNotes.Clear();
Alignment <Word, ShapeNode> alignment = alignerResult.GetAlignments().First();
int initialEquivalentClasses = 0;
bool mismatchFound = false;
for (int column = 0; column < alignment.ColumnCount; column++)
{
AlignmentCell <ShapeNode> cell1 = alignment[0, column];
AlignmentCell <ShapeNode> cell2 = alignment[1, column];
if ((cell1.Count > 0 && cell1[0].Type() == CogFeatureSystem.VowelType) || (cell2.Count > 0 && cell2[0].Type() == CogFeatureSystem.VowelType))
{
wordPair.AlignmentNotes.Add("X");
}
else
{
if (cell1.StrRep() == cell2.StrRep())
{
wordPair.AlignmentNotes.Add("1");
if (!mismatchFound)
{
initialEquivalentClasses++;
}
}
else
{
SoundClass sc1;
if (!_soundClasses.TryGetMatchingSoundClass(_segmentPool, alignment, 0, column, out sc1))
{
sc1 = null;
}
SoundClass sc2;
if (!_soundClasses.TryGetMatchingSoundClass(_segmentPool, alignment, 1, column, out sc2))
{
sc2 = null;
}
if (sc1 != null && sc2 != null && sc1 == sc2)
{
wordPair.AlignmentNotes.Add("1");
if (!mismatchFound)
{
initialEquivalentClasses++;
}
}
else
{
wordPair.AlignmentNotes.Add("0");
mismatchFound = true;
}
}
}
}
wordPair.AreCognatePredicted = !mismatchFound || initialEquivalentClasses >= _initialEquivalenceThreshold;
wordPair.CognicityScore = (double)initialEquivalentClasses / alignment.ColumnCount;
}
public MultipleWordAlignmentWordViewModel(Word word, AlignmentCell <ShapeNode> prefix, IEnumerable <AlignmentCell <ShapeNode> > columns, AlignmentCell <ShapeNode> suffix, int cognateSetIndex)
{
_word = word;
_variety = new VarietyViewModel(word.Variety);
_prefix = prefix.StrRep();
_columns = new ReadOnlyList <string>(columns.Select(cell => cell.IsNull ? "-" : cell.StrRep()).ToArray());
_suffix = suffix.StrRep();
_cognateSetIndex = cognateSetIndex;
}
public MultipleWordAlignmentWordViewModel(MultipleWordAlignmentViewModel parent, Word word, AlignmentCell<ShapeNode> prefix, IEnumerable<AlignmentCell<ShapeNode>> columns, AlignmentCell<ShapeNode> suffix, int cognateSetIndex)
{
_word = word;
ReadOnlyCollection<Word> words = word.Variety.Words[word.Meaning];
_variety = new MultipleWordAlignmentVarietyViewModel(word.Variety, words.Count == 1 ? 0 : IndexOf(words, word));
_prefix = prefix.StrRep();
_columns = new ReadOnlyList<string>(columns.Select(cell => cell.IsNull ? "-" : cell.StrRep()).ToArray());
_suffix = suffix.StrRep();
_cognateSetIndex = cognateSetIndex;
_parent = parent;
}
public void Process(VarietyPair data)
{
IWordAligner aligner = _project.WordAligners[_alignerId];
var correspondenceColls = new Dictionary <FeatureSymbol, SoundCorrespondenceCollection>
{
{ CogFeatureSystem.Onset, new SoundCorrespondenceCollection() },
{ CogFeatureSystem.Nucleus, new SoundCorrespondenceCollection() },
{ CogFeatureSystem.Coda, new SoundCorrespondenceCollection() }
};
foreach (WordPair wordPair in data.WordPairs.Where(wp => wp.Cognacy))
{
Alignment <Word, ShapeNode> alignment = aligner.Compute(wordPair).GetAlignments().First();
for (int i = 0; i < alignment.ColumnCount; i++)
{
AlignmentCell <ShapeNode> cell1 = alignment[0, i];
AlignmentCell <ShapeNode> cell2 = alignment[1, i];
if (!cell1.IsNull && !cell2.IsNull && cell1.Count == 1 && cell2.Count == 1)
{
SymbolicFeatureValue pos1, pos2;
if (cell1.First.Annotation.FeatureStruct.TryGetValue(CogFeatureSystem.SyllablePosition, out pos1) &&
cell2.First.Annotation.FeatureStruct.TryGetValue(CogFeatureSystem.SyllablePosition, out pos2) &&
(FeatureSymbol)pos1 == (FeatureSymbol)pos2)
{
Ngram <Segment> ngram1 = cell1.ToNgram(_segmentPool);
Ngram <Segment> ngram2 = cell2.ToNgram(_segmentPool);
Segment seg1 = ngram1.First;
Segment seg2 = ngram2.First;
if (!seg1.Equals(seg2))
{
SoundCorrespondenceCollection correspondences = correspondenceColls[(FeatureSymbol)pos1];
SoundCorrespondence corr;
if (!correspondences.TryGet(seg1, seg2, out corr))
{
corr = new SoundCorrespondence(seg1, seg2);
correspondences.Add(corr);
}
corr.Frequency++;
corr.WordPairs.Add(wordPair);
}
}
}
}
}
foreach (KeyValuePair <FeatureSymbol, SoundCorrespondenceCollection> kvp in correspondenceColls)
{
data.CognateSoundCorrespondencesByPosition[kvp.Key].ReplaceAll(kvp.Value);
}
}
public MultipleWordAlignmentWordViewModel(MultipleWordAlignmentViewModel parent, Word word, AlignmentCell <ShapeNode> prefix, IEnumerable <AlignmentCell <ShapeNode> > columns, AlignmentCell <ShapeNode> suffix, int cognateSetIndex)
{
_word = word;
ReadOnlyCollection <Word> words = word.Variety.Words[word.Meaning];
_variety = new MultipleWordAlignmentVarietyViewModel(word.Variety, words.Count == 1 ? 0 : IndexOf(words, word));
_prefix = prefix.StrRep();
_columns = new ReadOnlyList <string>(columns.Select(cell => cell.IsNull ? "-" : cell.StrRep()).ToArray());
_suffix = suffix.StrRep();
_cognateSetIndex = cognateSetIndex;
_parent = parent;
}
private void AlignWords()
{
if (_selectedMeaning == null)
{
return;
}
_busyService.ShowBusyIndicatorUntilFinishDrawing();
var words = new HashSet <Word>();
foreach (VarietyPair vp in _projectService.Project.VarietyPairs)
{
WordPair wp;
if (vp.WordPairs.TryGetValue(_selectedMeaning.DomainMeaning, out wp))
{
words.Add(wp.Word1);
words.Add(wp.Word2);
}
}
if (words.Count == 0)
{
_words.Clear();
return;
}
IWordAligner aligner = _projectService.Project.WordAligners[ComponentIdentifiers.PrimaryWordAligner];
Alignment <Word, ShapeNode> alignment;
if (words.Count == 1)
{
Word word = words.First();
Annotation <ShapeNode> prefixAnn = word.Prefix;
var prefix = new AlignmentCell <ShapeNode>(prefixAnn != null ? word.Shape.GetNodes(prefixAnn.Span).Where(NodeFilter) : Enumerable.Empty <ShapeNode>());
IEnumerable <AlignmentCell <ShapeNode> > columns = word.Shape.GetNodes(word.Stem.Span).Where(NodeFilter).Select(n => new AlignmentCell <ShapeNode>(n));
Annotation <ShapeNode> suffixAnn = word.Suffix;
var suffix = new AlignmentCell <ShapeNode>(suffixAnn != null ? word.Shape.GetNodes(suffixAnn.Span).Where(NodeFilter) : Enumerable.Empty <ShapeNode>());
alignment = new Alignment <Word, ShapeNode>(0, 0, Tuple.Create(word, prefix, columns, suffix));
}
else
{
IWordAlignerResult result = aligner.Compute(words);
alignment = result.GetAlignments().First();
}
List <Cluster <Word> > cognateSets = _projectService.Project.GenerateCognateSets(_selectedMeaning.DomainMeaning).OrderBy(c => c.Noise).ThenByDescending(c => c.DataObjects.Count).ToList();
ColumnCount = alignment.ColumnCount;
using (_words.BulkUpdate())
{
_words.Clear();
for (int i = 0; i < alignment.SequenceCount; i++)
{
AlignmentCell <ShapeNode> prefix = alignment.Prefixes[i];
Word word = alignment.Sequences[i];
IEnumerable <AlignmentCell <ShapeNode> > columns = Enumerable.Range(0, alignment.ColumnCount).Select(col => alignment[i, col]);
AlignmentCell <ShapeNode> suffix = alignment.Suffixes[i];
int cognateSetIndex = cognateSets.FindIndex(set => set.DataObjects.Contains(word));
_words.Add(new MultipleWordAlignmentWordViewModel(word, prefix, columns, suffix, cognateSetIndex == cognateSets.Count - 1 ? int.MaxValue : cognateSetIndex + 1));
}
}
}
private void AlignWords()
{
if (_selectedMeaning == null || !_projectService.AreAllVarietiesCompared)
return;
_busyService.ShowBusyIndicatorUntilFinishDrawing();
var words = new HashSet<Word>();
foreach (VarietyPair vp in _projectService.Project.VarietyPairs)
{
WordPair wp;
if (vp.WordPairs.TryGetValue(_selectedMeaning.DomainMeaning, out wp))
{
words.Add(wp.Word1);
words.Add(wp.Word2);
}
}
if (words.Count == 0)
{
_words.Clear();
return;
}
IWordAligner aligner = _projectService.Project.WordAligners[ComponentIdentifiers.PrimaryWordAligner];
Alignment<Word, ShapeNode> alignment;
if (words.Count == 1)
{
Word word = words.First();
Annotation<ShapeNode> prefixAnn = word.Prefix;
var prefix = new AlignmentCell<ShapeNode>(prefixAnn != null ? word.Shape.GetNodes(prefixAnn.Span).Where(NodeFilter) : Enumerable.Empty<ShapeNode>());
IEnumerable<AlignmentCell<ShapeNode>> columns = word.Shape.GetNodes(word.Stem.Span).Where(NodeFilter).Select(n => new AlignmentCell<ShapeNode>(n));
Annotation<ShapeNode> suffixAnn = word.Suffix;
var suffix = new AlignmentCell<ShapeNode>(suffixAnn != null ? word.Shape.GetNodes(suffixAnn.Span).Where(NodeFilter) : Enumerable.Empty<ShapeNode>());
alignment = new Alignment<Word, ShapeNode>(0, 0, Tuple.Create(word, prefix, columns, suffix));
}
else
{
IWordAlignerResult result = aligner.Compute(words);
alignment = result.GetAlignments().First();
}
List<Cluster<Word>> cognateSets = _projectService.Project.GenerateCognateSets(_selectedMeaning.DomainMeaning).OrderBy(c => c.Noise).ThenByDescending(c => c.DataObjects.Count).ToList();
ColumnCount = alignment.ColumnCount;
using (_words.BulkUpdate())
{
_words.Clear();
for (int i = 0; i < alignment.SequenceCount; i++)
{
AlignmentCell<ShapeNode> prefix = alignment.Prefixes[i];
Word word = alignment.Sequences[i];
IEnumerable<AlignmentCell<ShapeNode>> columns = Enumerable.Range(0, alignment.ColumnCount).Select(col => alignment[i, col]);
AlignmentCell<ShapeNode> suffix = alignment.Suffixes[i];
int cognateSetIndex = cognateSets.FindIndex(set => set.DataObjects.Contains(word));
_words.Add(new MultipleWordAlignmentWordViewModel(this, word, prefix, columns, suffix, cognateSetIndex == cognateSets.Count - 1 ? int.MaxValue : cognateSetIndex + 1));
}
}
IsEmpty = false;
}
internal HeadCell(string text, AlignmentCell align)
{
Text = text;
Align = align;
}
public AlignedNodeViewModel(AlignmentCell<ShapeNode> cell1, AlignmentCell<ShapeNode> cell2)
: this(-1, cell1, cell2, null)
{
}
public AlignedNodeViewModel(AlignmentCell <ShapeNode> cell1, AlignmentCell <ShapeNode> cell2)
: this(-1, cell1, cell2, null)
{
}
