PrIMe Data Management Code

// Copyright primekinetics.org  © 2009
using System;
using System.Collections;
using System.Collections.Generic;
using System.Text;
using System.IO;
using System.Xml;
using System.Data;


namespace PrimeKinetics.PrimeHandle.Data
{
    /// <summary>
    /// PrimeModel class gets and manipulates chemical models.
    /// </summary>
    public class PrimeModel
    {
        #region Variables
        private XmlDocument _document;
        #endregion

        #region Constructors
        /// <summary>
        /// Initializes the class components.
        /// </summary>
        public PrimeModel()
        {
            _document = null;
        }

        /// <summary>
        /// Initializes the class components given the input XmlDocument.
        /// </summary>
        /// <param name="xmldoc"> The input XmlDocument</param>
        public PrimeModel(XmlDocument xmldoc)
        {
            _document = xmldoc;
        }
        #endregion Constructors

        #region Properties
        /// <summary>
        /// Gets or sets the Document property as an XmlDocument.
        /// </summary>
        public XmlDocument Document
        {
            get
            {
                return _document;
            }
            set
            {
                _document = value;
            }
        }
        #endregion Properties

        #region Methods
        /// <summary>
        /// Gets the primeID of the document.
        /// </summary>
        /// <returns>
        /// Return the PrimeID string.
        /// </returns>
        public String GetPrimeID()
        {
            return Common.GetPrimeID(Document);
        }

        /// <summary>
        /// Gets the preferred key of the document.
        /// </summary>
        /// <returns>
        /// Return the string of preferred key.
        /// </returns>
        public String GetPreferredKey()
        {
            return Common.GetPreferredKey(Document);
        }

        /// <summary>
        /// Gets the text content of additional data items of the document.
        /// </summary>
        /// <returns>
        /// Return the string array of additional data.
        /// </returns>
        public String[] GetAdditionalDataItems()
        {
            return Common.GetAdditionalDataItems(Document);
        }

        /// <summary>
        /// Gets the bibliography information table of the prime XmlDocument.
        /// </summary>
        /// <returns>
        /// Return the DataTable of bibliography links.
        /// </returns>
        public DataTable GetBibliography()
        {
            return Common.GetBibliography(Document);
        }

        /// <summary>
        /// Gets the species table of the model.
        /// </summary>
        /// <returns>
        /// Return the DataTable of species primeID and preferred keys.
        /// </returns>
        public DataTable GetSpecies()
        {
            DataTable dt = new DataTable();
            dt.Columns.Add("primeID");
            dt.Columns.Add("key");

            XmlNodeList nodelist = Common.GetField(Document, "speciesSet/speciesLink");
            foreach (XmlNode node in nodelist)
            {
                DataRow dbRow = dt.NewRow();
                XmlAttribute xa = node.Attributes["primeID"];
                if (xa != null) dbRow["primeID"] = xa.Value;
                
                xa = node.Attributes["preferredKey"];
                if (xa != null) dbRow["key"] = xa.Value;
                dt.Rows.Add(dbRow);
            }
            return dt;
        }

        /// <summary>
        /// Gets the reaction table of the model.
        /// </summary>
        /// <returns>
        /// Return the DataTable of reaction primeID and preferred keys.
        /// </returns>
        public DataTable GetReactions()
        {
            DataTable dt = new DataTable();
            dt.Columns.Add("primeID");
            dt.Columns.Add("key");

            XmlNodeList nodelist = Common.GetField(Document, "reactionSet/reactionLink");
            foreach (XmlNode node in nodelist)
            {
                DataRow dbRow = dt.NewRow();
                XmlAttribute xa = node.Attributes["primeID"];
                if (xa != null) dbRow["primeID"] = xa.Value;

                xa = node.Attributes["preferredKey"];
                if (xa != null) dbRow["key"] = xa.Value;
                dt.Rows.Add(dbRow);
            }
            return dt;
        }

        /// <summary>
        /// Gets the details of the document
        /// </summary>
        /// <returns>
        /// Return the string of details.
        /// </returns>
        public override String ToString()
        {
            String str = String.Empty;
            //str += "chemicalModel: ";
            str += GetPreferredKey();
            var dt = (DataTable)GetBibliography();
            if (dt.Rows.Count > 0) str += " -- ";
            for (int i = 0; i < dt.Rows.Count; i++)
            {
                str += dt.Rows[i]["key"].ToString() + "; ";
            }
            str = str.TrimEnd("; ".ToCharArray());

            int nSpe = GetSpecies().Rows.Count;
            int nReac = GetReactions().Rows.Count;
            str += " (" + nSpe.ToString() + " species, " + nReac.ToString()
                + " reactions)";

            return str;
        }

        #endregion Methods
    }
}