/** Tests the construction of a feature list */
public void TestConstructor () {
Sequence seq = new Sequence( AlphabetType.DNA, "acgt" );
FeatureList featureList = new FeatureList( "Test" );
seq.AddFeatures( featureList );
Assert.AreEqual( 1, seq.FeatureLists.Count );
Assert.AreEqual( "Test", featureList.Name );
// Assert.AreEqual(seq, featureList.GetSequence());
}
public void TestGetFeatureSequence()
{
Sequence seq = new Sequence(AlphabetType.DNA, "acgta");
FeatureList featureList = new FeatureList("test");
Feature feature = new Feature("feature1", 2, 4, +1);
featureList.Add(feature);
seq.AddFeatures(featureList);
Assert.AreEqual("cgt", feature.Letters());
}
/** Tests the adding of features */
public void TestAdd () {
Sequence seq = new Sequence( AlphabetType.DNA, "acgt" );
FeatureList featureList = new FeatureList( "Test" );
seq.AddFeatures( featureList );
Feature feature1 = new Feature( "Test1", 1, 3, +1 );
Feature feature2 = new Feature( "Test2", 1, 3, +1 );
featureList.Add( feature1, false );
featureList.Add( feature2, true );
Assert.AreEqual( 2, featureList.Count );
Assert.AreEqual( null, feature1.BaseSequence );
Assert.AreEqual( seq, feature2.BaseSequence );
}
/** Tests the adding of feature lists */
public void TestAddList () {
FeatureList featureList1 = new FeatureList( "Test" );
featureList1.Add( new Feature( "Test1", 1, 3, +1 ) );
featureList1.Add( new Feature( "Test2", 1, 3, +1 ) );
FeatureList featureList2 = new FeatureList( "Test" );
featureList2.Add( new Feature( "Test3", 1, 3, +1 ) );
featureList2.Add( new Feature( "Test4", 1, 3, +1 ) );
featureList1.Append( featureList2, true );
Assert.AreEqual( "Test1", featureList1[0].Name );
Assert.AreEqual( "Test2", featureList1[1].Name );
Assert.AreEqual( "Test3", featureList1[2].Name );
Assert.AreEqual( "Test4", featureList1[3].Name );
}
public List<Matched> PerformSearch(string BioPatMLContent, SequenceContract sequence)
{
List<Matched> matchedList = new List<Matched>();
StringReader sr = new StringReader(BioPatMLContent);
Definition MyPatterns = null;
using (BioPatMLPatternReader reader = new BioPatMLPatternReader())
{
MyPatterns = reader.ReadBioPatML(sr);
}
Sequence targetSequence = new Sequence(sequence.AlphabetName, sequence.Characters);
SequenceList matches = new FeatureList();
IPattern MatchingPattern = MyPatterns.MainPattern;
#region If bioPatML pattern is SeriesBest OR SetBest : Search by best
if (MatchingPattern is SeriesBest
|| MatchingPattern is SetBest)
{
Match match = targetSequence.SearchBest(0, 0, MatchingPattern);
matches.Add(match);
}
#endregion
#region Else, pattern is Motif, Any, Anchor, Prosite, RegularEx : Search by normal
else
//The rest
{
matches = targetSequence.Search(1, targetSequence.Length, MatchingPattern);
}
#endregion
for (int i = 0; i < matches.Count; i++)
{
Match matched = matches[i] as Match;
matchedList.Add(new Matched
(matched.Similarity,
matched.Start, matched.End,
matched.Length, matched.Letters(), sequence.Name));
}
return matchedList;
}
/** Tests the getter of features */
public void TestFeature () {
FeatureList featureList = new FeatureList( "Test" );
Feature feature1 = new Feature( "Test1", 1, 3, +1 );
Feature feature2 = new Feature( "Test2", 1, 3, +1 );
featureList.Add( feature1, false );
featureList.Add( feature2, true );
var t = featureList[ 0 ];
bool ans = feature1.Equals( featureList[0] );
Assert.IsTrue( feature1.Equals( featureList[0] ) );
Assert.IsTrue( feature2.Equals( featureList[1] ) );
Assert.IsTrue( feature2.Equals( featureList[-1] ) );
Assert.IsTrue( feature1.Equals( featureList[2] ) );
Assert.IsTrue( feature2.Equals( featureList[-3] ) );
Assert.IsTrue( feature1.Equals( featureList[4] ) );
Assert.IsTrue( feature1.Equals( featureList["Test1"] ) );
Assert.IsTrue( feature2.Equals( featureList["Test2"] ) );
}
/// <summary>
/// Adds the features of the given list to the list.
/// </summary>
/// <param name="featureList"> A feature list.</param>
/// <param name="setSequence"> <see> #add(Feature, boolean </see></param>
public void Append(FeatureList featureList, bool setSequence)
{
for (int i = 0; i < featureList.Count; i++)
Add(featureList.Feature(i), setSequence);
}
/// <summary>
/// Creates a feature list with all features of the sequences of the list
/// which match the given feature name .
/// </summary>
/// <param name="featureListName">
/// Name of the feature lists which contain the features to extract.
/// </param>
/// <param name="featureName">Feature name.</param>
/// <returns>
/// Returns a feature list with all features which name matches the
/// given feature name over all sequences of the sequence list.
///
/// </returns>
public FeatureList Features(String featureListName, String featureName)
{
FeatureList featureList = new FeatureList(featureListName);
for (int i = 0; i < Count; i++)
{
FeatureList list = this[i].Features(featureListName);
if (list != null)
{
for (int j = 0; j < list.Count; j++)
{
Feature feature = list.Feature(j);
if (feature.AnnotationValue("Name").Equals(featureName))
featureList.Add(feature);
}
}
}
return (featureList);
}
/// <summary>
/// Setter for a match object on base of another match object.
/// </summary>
/// <param name="match">Match object with initial values.</param>
public void Set(Match match)
{
Set(match.BaseSequence, match.Start, match.Length,
match.Strand, match.Similarity);
this.MatchPattern = match.MatchPattern;
//this.Name = match.MatchPattern.PatternName;
this.impact = match.impact;
FeatureList subMatchList = match.SubMatchedList;
if (subMatchList != null)
{
if (MatchedList == null)
{
FeatureList matchList = new FeatureList("SubMatches");
for (int i = 0; i < subMatchList.Count; i++)
matchList.Add(Clone((Match)subMatchList.Feature(i)));
MatchedList = matchList;
}
else
{
for (int i = 0; i < subMatchList.Count; i++)
((Match)MatchedList.Feature(i)).Set((Match)subMatchList.Feature(i));
}
}
else
MatchedList = null;
}
/** Tests the search for a feature which covers a given position */
public void TestInside () {
Sequence seq = new Sequence( AlphabetType.DNA, "acgtactgactg" );
FeatureList featureList = new FeatureList( "Test" );
Feature feature1 = new Feature( "Test1", 2, 4, +1 );
Feature feature2 = new Feature( "Test2", 7, 10, +1 );
featureList.Add( feature1 );
featureList.Add( feature2 );
featureList.AttachSequence( seq );
Assert.AreEqual( feature1, featureList.Inside( seq, 2 ) );
Assert.AreEqual( feature1, featureList.Inside( seq, 4 ) );
Assert.AreEqual( null, featureList.Inside( seq, 1 ) );
Assert.AreEqual( null, featureList.Inside( seq, 5 ) );
Assert.AreEqual( feature2, featureList.Inside( seq, 7 ) );
Assert.AreEqual( feature2, featureList.Inside( seq, 10 ) );
Assert.AreEqual( null, featureList.Inside( seq, 6 ) );
Assert.AreEqual( null, featureList.Inside( seq, 11 ) );
}
/** Test getter for feature list name */
public void TestSetGetName () {
FeatureList featureList = new FeatureList( "Test" );
Assert.AreEqual( "Test", featureList.Name );
}
public void TestAddGetFeature () {
Sequence seq = new Sequence( AlphabetType.DNA, "ACTG" );
FeatureList flist1 = new FeatureList( "test1" );
FeatureList flist2 = new FeatureList( "test2" );
Assert.AreEqual( 0, seq.FeatureLists.Count );
seq.AddFeatures( flist1 );
seq.AddFeatures( flist2 );
Assert.AreEqual( 2, seq.FeatureLists.Count );
Assert.AreEqual( flist1, seq.FeatureLists[ 0 ] );
Assert.AreEqual( flist1, seq.FeatureLists[ "test1" ] );
Assert.AreEqual( flist2, seq.FeatureLists[ 1 ] );
Assert.AreEqual( flist2, seq.FeatureLists[ "test2" ] );
}
public void TestAddFeatureLists () {
Sequence seq = new Sequence( AlphabetType.DNA, "ACTG" );
FeatureList flist1 = new FeatureList( "test1" );
FeatureList flist2 = new FeatureList( "test2" );
AnnotatedList<FeatureList> flists = new AnnotatedList<FeatureList>();
flists.Add( flist1 );
flists.Add( flist2 );
seq.AddFeatures( flists );
Assert.AreEqual( 2, seq.FeatureLists.Count );
}
/// <summary>
/// This method transfers all available features from the MBF sequence and
/// populate them into biopatml features data type.
/// In this version only its name, start and end location is populated.
/// </summary>
/// <param name="metadata"></param>
/// <returns></returns>
private FeatureList ExtractFeatures(GenBankMetadata metadata)
{
List<FeatureItem> mbfFeatures = metadata.Features.All;
FeatureList bioFeatureList = new FeatureList();
foreach (FeatureItem item in mbfFeatures)
{
#region Constructs the feature outline first
//Strand is always assumed to be forward +1
QUT.Bio.BioPatML.Sequences.Feature bioFeature = new QUT.Bio.BioPatML.Sequences.Feature
(item.Key, item.Location.Start, item.Location.End, 1);
bioFeatureList.Add(bioFeature);
#endregion
#region Adds the qualifier key and values to Feature using AnnotationList
AnnotationList annList = new AnnotationList();
foreach (KeyValuePair<string, List<string>> qualitfier in item.Qualifiers)
annList.Add(qualitfier.Key, qualitfier.Value[0]);
bioFeature.AddAnnotations(annList);
#endregion
}
return bioFeatureList;
}
/// <summary>
/// Adds a feature list to the sequence. This attaches the feature list and
/// all it's features to the sequence. Features which were attached to a
/// different sequence before are then attached to the current sequence!
/// </summary>
/// <param name="featureList"> Feature list. </param>
public void AddFeatures(FeatureList featureList)
{
Features().Add(featureList);
featureList.AttachSequence(this);
}
