/eLMM/CodePlex/MBF/IO/GenBank/RepeatRegion.cs

//*********************************************************

//

// Copyright (c) Microsoft Corporation. All rights reserved.

//

//

//

//

//

//

//*********************************************************







using System;

using System.Collections.Generic;



namespace Bio.IO.GenBank

{

    /// <summary>

    ///  Region of genome containing repeating units.

    /// </summary>

    [Serializable]

    public class RepeatRegion : FeatureItem

    {

        #region Constructors

        /// <summary>

        /// Creates new RepeatRegion feature item from the specified location.

        /// </summary>

        /// <param name="location">Location of the RepeatRegion.</param>

        public RepeatRegion(ILocation location)

            : base(StandardFeatureKeys.RepeatRegion, location) { }



        /// <summary>

        /// Creates new RepeatRegion feature item with the specified location.

        /// Note that this constructor uses LocationBuilder to construct location object from the specified 

        /// location string.

        /// </summary>

        /// <param name="location">Location of the RepeatRegion.</param>

        public RepeatRegion(string location)

            : base(StandardFeatureKeys.RepeatRegion, location) { }



        /// <summary>

        /// Private constructor for clone method.

        /// </summary>

        /// <param name="other">Other RepeatRegion instance.</param>

        private RepeatRegion(RepeatRegion other)

            : base(other) { }

        #endregion Constructors



        #region Properties



        /// <summary>

        /// Name of the allele for the given gene.

        /// All gene-related features (exon, CDS etc) for a given gene should share the same Allele qualifier value; 

        /// the Allele qualifier value must, by definition, be different from the Gene qualifier value; when used with 

        /// the variation feature key, the Allele qualifier value should be that of the variant.

        /// </summary>

        public string Allele

        {

            get

            {

                return GetSingleTextQualifier(StandardQualifierNames.Allele);

            }



            set

            {

                SetSingleTextQualifier(StandardQualifierNames.Allele, value);

            }

        }



        /// <summary>

        /// Reference to a citation listed in the entry reference field.

        /// </summary>

        public List<string> Citation

        {

            get

            {

                return GetQualifier(StandardQualifierNames.Citation);

            }

        }



        /// <summary>

        /// Database cross-reference: pointer to related information in another database.

        /// </summary>

        public List<string> DatabaseCrossReference

        {

            get

            {

                return GetQualifier(StandardQualifierNames.DatabaseCrossReference);

            }

        }



        /// <summary>

        /// A brief description of the nature of the experimental evidence that supports the feature 

        /// identification or assignment.

        /// </summary>

        public List<string> Experiment

        {

            get

            {

                return GetQualifier(StandardQualifierNames.Experiment);

            }

        }



        /// <summary>

        /// Function attributed to a sequence.

        /// </summary>

        public List<string> Function

        {

            get

            {

                return GetQualifier(StandardQualifierNames.Function);

            }

        }



        /// <summary>

        /// Symbol of the gene corresponding to a sequence region.

        /// </summary>

        public string GeneSymbol

        {

            get

            {

                return GetSingleTextQualifier(StandardQualifierNames.GeneSymbol);

            }



            set

            {

                SetSingleTextQualifier(StandardQualifierNames.GeneSymbol, value);

            }

        }



        /// <summary>

        /// Synonymous, replaced, obsolete or former gene symbol.

        /// </summary>

        public List<string> GeneSynonym

        {

            get

            {

                return GetQualifier(StandardQualifierNames.GeneSynonym);

            }

        }



        /// <summary>

        /// Genomic map position of feature.

        /// </summary>

        public string GenomicMapPosition

        {

            get

            {

                return GetSingleTextQualifier(StandardQualifierNames.GenomicMapPosition);

            }



            set

            {

                SetSingleTextQualifier(StandardQualifierNames.GenomicMapPosition, value);

            }

        }



        /// <summary>

        /// A structured description of non-experimental evidence that supports the feature 

        /// identification or assignment.

        /// </summary>

        public List<string> Inference

        {

            get

            {

                return GetQualifier(StandardQualifierNames.Inference);

            }

        }



        /// <summary>

        /// A submitter-supplied, systematic, stable identifier for a gene and its associated 

        /// features, used for tracking purposes.

        /// </summary>

        public List<string> LocusTag

        {

            get

            {

                return GetQualifier(StandardQualifierNames.LocusTag);

            }

        }



        /// <summary>

        /// Type and name or identifier of the mobile element which is described by the parent feature.

        /// </summary>

        public List<string> MobileElement

        {

            get

            {

                return GetQualifier(StandardQualifierNames.MobileElement);

            }

        }



        /// <summary>

        /// Any comment or additional information.

        /// </summary>

        public List<string> Note

        {

            get

            {

                return GetQualifier(StandardQualifierNames.Note);

            }

        }



        /// <summary>

        /// Feature tag assigned for tracking purposes.

        /// </summary>

        public List<string> OldLocusTag

        {

            get

            {

                return GetQualifier(StandardQualifierNames.OldLocusTag);

            }

        }



        /// <summary>

        /// rpt_unit_range; Identity of a repeat range.

        /// </summary>

        public List<string> RepeatedRange

        {

            get

            {

                return GetQualifier(StandardQualifierNames.RepeatedRange);

            }

        }



        /// <summary>

        /// rpt_unit_seq; Identity of a repeat sequence.

        /// </summary>

        public List<string> RepeatedSequence

        {

            get

            {

                return GetQualifier(StandardQualifierNames.RepeatedSequence);

            }

        }



        /// <summary>

        /// rpt_family; Type of repeated sequence; ""Alu"" or ""Kpn"", for example.

        /// </summary>

        public List<string> RepeatedSequenceFamily

        {

            get

            {

                return GetQualifier(StandardQualifierNames.RepeatedSequenceFamily);

            }

        }



        /// <summary>

        /// rpt_type; Organization of repeated sequence.

        /// </summary>

        public List<string> RepeatedSequenceType

        {

            get

            {

                return GetQualifier(StandardQualifierNames.RepeatedSequenceType);

            }

        }



        /// <summary>

        /// Identifier for a satellite DNA marker, compose of many tandem repeats 

        /// (identical or related) of a short basic repeated unit.

        /// </summary>

        public string Satellite

        {

            get

            {

                return GetSingleTextQualifier(StandardQualifierNames.Satellite);

            }



            set

            {

                SetSingleTextQualifier(StandardQualifierNames.Satellite, value);

            }

        }



        /// <summary>

        /// Accepted standard name for this feature.

        /// </summary>

        public string StandardName

        {

            get

            {

                return GetSingleTextQualifier(StandardQualifierNames.StandardName);

            }



            set

            {

                SetSingleTextQualifier(StandardQualifierNames.StandardName, value);

            }

        }

        #endregion Properties



        #region Methods

        /// <summary>

        /// Creates a new RepeatRegion that is a copy of the current RepeatRegion.

        /// </summary>

        /// <returns>A new RepeatRegion that is a copy of this RepeatRegion.</returns>

        public new RepeatRegion Clone()

        {

            return new RepeatRegion(this);

        }

        #endregion Methods

    }

}