/// <summary>
/// Writes a PhylogeneticTree to the writer.
/// </summary>
/// <param name="stream">The Stream used to write the formatted Phylogenetic tree text, it will remain open.</param>
/// <param name="tree">PhylogeneticTree to format.</param>
public void Format(Stream stream, Tree tree)
{
if (tree == null)
{
throw new ArgumentNullException(string.Format
(CultureInfo.CurrentCulture, Resource.IOFormatErrorMessage, Name,
"Tree object is null"));
}
if (stream == null)
{
throw new ArgumentNullException("stream");
}
var stringBuilder = new StringBuilder();
this.Write(tree.Root, null, ref stringBuilder);
// Append end char ";"
stringBuilder.Append(";");
using (var writer = stream.OpenWrite())
{
writer.Write(stringBuilder.ToString());
writer.Flush();
}
}
/// <summary>
/// Writes a single data element to the formatter.
/// </summary>
/// <param name="formatter">Formatter</param>
/// <param name="data">Tree Data</param>
public static void Format(this IPhylogeneticTreeFormatter formatter, Tree data)
{
var fs = ParserFormatterExtensions<IPhylogeneticTreeFormatter>.GetOpenStream(formatter, true);
if (fs != null)
formatter.Format(fs, data);
else
throw new Exception("You must open a formatter before calling Write.");
}
/// <summary>
/// Writes a single sequence to the formatter.
/// </summary>
/// <param name="formatter">Formatter</param>
/// <param name="data">Tree data</param>
/// <param name="filename">Filename</param>
public static void Format(this IPhylogeneticTreeFormatter formatter, Tree data, string filename)
{
if (formatter == null)
{
throw new ArgumentNullException("formatter");
}
if (data == null)
{
throw new ArgumentNullException("data");
}
if (string.IsNullOrWhiteSpace(filename))
{
throw new ArgumentNullException("filename");
}
using (var fs = File.Create(filename))
formatter.Format(fs, data);
}
/// <summary>
/// Internal parse method used to parse out the data from a low-level TextReader.
/// </summary>
/// <param name="reader">Reader</param>
/// <returns>Parsed Tree</returns>
protected Tree InternalParse(TextReader reader)
{
string treeName = TreeName;
if (string.IsNullOrWhiteSpace(treeName))
treeName = DefaultTreeName;
Tree tree = new Tree { Name = treeName };
Node rootNode = GetNode(reader, true).Key;
if (Peek(reader) != ';')
{
if (Peek(reader) == ':')
{
ReadChar(reader);
}
}
// move to next char after ";"
char semicolon = ReadChar(reader);
if (semicolon != ';')
{
throw new FormatException(string.Format
(CultureInfo.CurrentCulture, Resource.IOFormatErrorMessage, Name,
"Missing [;] at the end of tree text"));
}
tree.Root = rootNode;
return tree;
}
/// <summary>
/// Gets the formatted object which is used for formatting
/// </summary>
/// <returns>Formatter tree.</returns>
private static Tree GetFormattedObject()
{
// Tree with three nodes are created
Node nd1 = new Node();
nd1.Name = "a";
Edge ed1 = new Edge();
ed1.Distance = 0.1;
Node nd2 = new Node();
nd2.Name = "b";
Edge ed2 = new Edge();
ed2.Distance = 0.2;
Node nd3 = new Node();
nd3.Name = "c";
Edge ed3 = new Edge();
ed3.Distance = 0.3;
Node nd4 = new Node();
nd4.Children.Add(nd1, ed1);
Edge ed4 = new Edge();
ed4.Distance = 0.4;
Node nd5 = new Node();
nd5.Children.Add(nd2, ed2);
nd5.Children.Add(nd3, ed3);
Edge ed5 = new Edge();
ed5.Distance = 0.5;
Node ndRoot = new Node();
ndRoot.Children.Add(nd4, ed4);
ndRoot.Children.Add(nd5, ed5);
// All the Node and Edges are combined to form a tree
Tree baseTree = new Tree();
baseTree.Root = ndRoot;
return baseTree;
}