public void SetUp()
{
this.list = new AnnotationList();
}
/// <summary>
/// Adds a list of annotations to the already existing annotations of the
/// sequence.
/// </summary>
/// <param name="annotationList"> List of annotations to add. </param>
public void AddAnnotations(AnnotationList annotationList)
{
if (annotationList != null)
{
AnnotationList a = Annotations();
for (int i = 0; i < annotationList.Count; i++)
a.Add(annotationList[i]);
}
}
public void TestAddGetAnnotations () {
Sequence seq = new Sequence( AlphabetType.DNA, "ACTG" );
AnnotationList a1 = seq.Annotations;
Assert.AreEqual( 0, a1.Count );
AnnotationList a2 = new AnnotationList();
a2.Add( new Annotation( "name1", "value1" ) );
a2.Add( new Annotation( "name2", "value2" ) );
seq.Annotations.AddRange( a2 );
Assert.AreEqual( "name1", seq.Annotations[0].Name );
Assert.AreEqual( "value2", seq.Annotations[1].Value );
Assert.AreEqual( "name1", seq.Annotations[ "name1" ].Name );
Assert.AreEqual( "value2", seq.Annotations.Value( "name2" ) );
Assert.AreEqual( null, seq.Annotations.Value( "name3" ) );
Assert.AreEqual( null, seq.Annotations[ "name3" ] );
}
/// <summary>
/// This method takes in a MBF sequence and converts it to BioPatML sequence.
/// </summary>
/// <param name="mbfseq">The MBF sequence one is interested in.</param>
/// <returns>Returns the converted BioPatML sequence.</returns>
public QUT.Bio.BioPatML.Sequences.Sequence ParseMBFSequence
(Sequence mbfseq)
{
GenBankMetadata metaData;
#region If sequence is complex type e.g. Genbank file with features
if (mbfseq.Metadata.ContainsKey(Helper.GenBankMetadataKey))
{
//Retrieves our meta data out
metaData = (GenBankMetadata)mbfseq.Metadata[Helper.GenBankMetadataKey];
//Create our BioPatML sequence
QUT.Bio.BioPatML.Sequences.Sequence bioSequence = new QUT.Bio.BioPatML.Sequences.Sequence
(ParseAlphabet(mbfseq), mbfseq.ToString(),
IsCircularStrand(metaData.Locus));
#region Top the BioPatML Sequence with Feature data and sequence name
//Add features to sequence
bioSequence.AddFeatures(ExtractFeatures(metaData));
//Add mbf sequence name to BioPatML sequence
//Create annotation to put in our sequence data like name
AnnotationList jacobiMeta = new AnnotationList();
jacobiMeta.Add("SequenceName", metaData.Locus.Name);
bioSequence.AddAnnotations(jacobiMeta);
#endregion
return bioSequence;
}
#endregion
#region Else we assume it is a simple type e.g. Fasta files
else
{
QUT.Bio.BioPatML.Sequences.Sequence bioSequence = new QUT.Bio.BioPatML.Sequences.Sequence
(ParseAlphabet(mbfseq), mbfseq.ToString(),
false);
AnnotationList jacobiMeta = new AnnotationList();
jacobiMeta.Add("SequenceName", mbfseq.DisplayID);
bioSequence.AddAnnotations(jacobiMeta);
return bioSequence;
}
#endregion
}
/// <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>
/// Gets all annotations which name matches the given regular expression.
/// </summary>
/// <param name="regExp">
/// Regular expression, <see> Pattern package </see>
/// </param>
/// <returns>
/// Returns an annotation list with all annotations matching the given name.
/// </returns>
public AnnotationList GetAll(Regex regExp)
{
AnnotationList aList = new AnnotationList();
foreach (Annotation a in ListAnnotation)
if (regExp.IsMatch(a.Name))
aList.Add(a);
return (aList);
}
/// <summary>
/// Get all annotations with a given name.
/// </summary>
/// <param name="name"> Name of the annotations to retrieve. </param>
/// <returns>
/// Returns a of list annotations that matches the
/// specified name.
/// </returns>
public AnnotationList GetAll(String name)
{
AnnotationList aList = new AnnotationList();
foreach (Annotation a in ListAnnotation)
if(a.Name.Equals(name))
aList.Add(a);
return aList;
}
/// <summary>
/// Getter for the list of annotations attached to the sequence. As soon as
/// this method is called an empty annotation list will be attached to the
/// sequence if none is existing before.
/// </summary>
/// <returns></returns>
public AnnotationList Annotations()
{
if (ListAnnotations == null)
ListAnnotations = new AnnotationList();;
return (ListAnnotations);
}
