Contains methods to read and write trees in the NCBI ASN.1 text format. More...

Static Public Member Functions
static IEnumerable< TreeNode >	ParseTrees (string inputFile)
	Parses a tree from an NCBI ASN.1 text format file. Note that the tree can only contain a single file, and this method will always return a collection with a single element. More...

static IEnumerable< TreeNode >	ParseTrees (Stream inputStream, bool keepOpen=false)
	Parses a tree from an NCBI ASN.1 text format file. Note that the tree can only contain a single file, and this method will always return a collection with a single element. More...

static List< TreeNode >	ParseAllTrees (string inputFile)
	Parses a tree from an NCBI ASN.1 text format file. Note that the tree can only contain a single file, and this method will always return a list with a single element. More...

static List< TreeNode >	ParseAllTrees (Stream inputStream, bool keepOpen=false)
	Parses a tree from an NCBI ASN.1 text format file. Note that the tree can only contain a single file, and this method will always return a list with a single element. More...

static TreeNode	ParseTree (string source)
	Parses a tree from an NCBI ASN.1 format string into a TreeNode object. More...

static TreeNode	ParseTree (TextReader reader)
	Parses a tree from a TextReader that reads an NCBI ASN.1 format string into a TreeNode object. More...

static void	WriteTree (TreeNode tree, string outputFile, string treeType=null, string label=null)
	Writes a TreeNode to a file in NCBI ASN.1 text format. More...

static void	WriteTree (TreeNode tree, Stream outputStream, bool keepOpen=false, string treeType=null, string label=null)
	Writes a TreeNode to a file in NCBI ASN.1 text format. More...

static void	WriteAllTrees (IEnumerable< TreeNode > trees, Stream outputStream, bool keepOpen=false, string treeType=null, string label=null)
	Writes a collection of TreeNodes to a file in NCBI ASN.1 text format. Note that only one tree can be saved in each file; if the collection contains more than one tree an exception will be thrown. More...

static void	WriteAllTrees (IEnumerable< TreeNode > trees, string outputFile, string treeType=null, string label=null)
	Writes a collection of TreeNodes to a file in NCBI ASN.1 text format. Note that only one tree can be saved in each file; if the collection contains more than one tree an exception will be thrown. More...

static void	WriteAllTrees (List< TreeNode > trees, Stream outputStream, bool keepOpen=false, string treeType=null, string label=null)
	Writes a list of TreeNodes to a file in NCBI ASN.1 text format. Note that only one tree can be saved in each file; if the tree contains more than one tree an exception will be thrown. More...

static void	WriteAllTrees (List< TreeNode > trees, string outputFile, string treeType=null, string label=null)
	Writes a list of TreeNodes to a file in NCBI ASN.1 text format. Note that only one tree can be saved in each file; if the list contains more than one tree an exception will be thrown. More...

static string	WriteTree (TreeNode tree, string treeType=null, string label=null)
	Writes a TreeNode to a string in NCBI ASN.1 text format. More...

Detailed Description

Contains methods to read and write trees in the NCBI ASN.1 text format.

Definition at line 12 of file NcbiAsnText.cs.

Member Function Documentation

◆ ParseAllTrees() [1/2]

static List< TreeNode > PhyloTree.Formats.NcbiAsnText.ParseAllTrees	(	Stream	inputStream,
		bool	keepOpen = `false`
	)

static

Parses a tree from an NCBI ASN.1 text format file. Note that the tree can only contain a single file, and this method will always return a list with a single element.

Parameters

inputStream	The Stream from which the file should be read.
keepOpen	Determines whether the stream should be disposed at the end of this method or not.

Returns: A List<T> containing the tree defined in the file. This will always consist of a single element.

Definition at line 52 of file NcbiAsnText.cs.

◆ ParseAllTrees() [2/2]

static List< TreeNode > PhyloTree.Formats.NcbiAsnText.ParseAllTrees ( string inputFile )

static

Parses a tree from an NCBI ASN.1 text format file. Note that the tree can only contain a single file, and this method will always return a list with a single element.

Parameters

inputFile The path to the input file.

Returns: A List<T> containing the tree defined in the file. This will always consist of a single element.

Definition at line 40 of file NcbiAsnText.cs.

◆ ParseTree() [1/2]

static TreeNode PhyloTree.Formats.NcbiAsnText.ParseTree ( string source )

static

Parses a tree from an NCBI ASN.1 format string into a TreeNode object.

Parameters

source The NCBI ASN.1 format tree string.

Returns: The parsed TreeNode object.

Definition at line 63 of file NcbiAsnText.cs.

◆ ParseTree() [2/2]

static TreeNode PhyloTree.Formats.NcbiAsnText.ParseTree ( TextReader reader )

static

Parses a tree from a TextReader that reads an NCBI ASN.1 format string into a TreeNode object.

Parameters

reader The TextReader that reads the NCBI ASN.1 format string.

Returns: The parsed TreeNode object.

Definition at line 74 of file NcbiAsnText.cs.

◆ ParseTrees() [1/2]

static IEnumerable< TreeNode > PhyloTree.Formats.NcbiAsnText.ParseTrees	(	Stream	inputStream,
		bool	keepOpen = `false`
	)

static

Parses a tree from an NCBI ASN.1 text format file. Note that the tree can only contain a single file, and this method will always return a collection with a single element.

Parameters

inputStream	The Stream from which the file should be read.
keepOpen	Determines whether the stream should be disposed at the end of this method or not.

Returns: A IEnumerable<T> containing the tree defined in the file. This will always consist of a single element.

Definition at line 30 of file NcbiAsnText.cs.

◆ ParseTrees() [2/2]

static IEnumerable< TreeNode > PhyloTree.Formats.NcbiAsnText.ParseTrees ( string inputFile )

static

Parses a tree from an NCBI ASN.1 text format file. Note that the tree can only contain a single file, and this method will always return a collection with a single element.

Parameters

inputFile The path to the input file.

Returns: A IEnumerable<T> containing the tree defined in the file. This will always consist of a single element.

Definition at line 19 of file NcbiAsnText.cs.

◆ WriteAllTrees() [1/4]

static void PhyloTree.Formats.NcbiAsnText.WriteAllTrees	(	IEnumerable< TreeNode >	trees,
		Stream	outputStream,
		bool	keepOpen = `false`,
		string	treeType = `null`,
		string	label = `null`
	)

static

Writes a collection of TreeNodes to a file in NCBI ASN.1 text format. Note that only one tree can be saved in each file; if the collection contains more than one tree an exception will be thrown.

Parameters

trees	The collection of trees to write. If this contains more than one tree, an exception will be thrown.
outputStream	The Stream on which the tree should be written.
keepOpen	Determines whether the outputStream should be kept open after the end of this method.
treeType	An optional value for the `treetype` property defined in the NCBI ASN.1 tree format.
label	An optional value for the `label` property defined in the NCBI ASN.1 tree format.

Definition at line 359 of file NcbiAsnText.cs.

◆ WriteAllTrees() [2/4]

static void PhyloTree.Formats.NcbiAsnText.WriteAllTrees	(	IEnumerable< TreeNode >	trees,
		string	outputFile,
		string	treeType = `null`,
		string	label = `null`
	)

static

Writes a collection of TreeNodes to a file in NCBI ASN.1 text format. Note that only one tree can be saved in each file; if the collection contains more than one tree an exception will be thrown.

Parameters

trees	The collection of trees to write. If this contains more than one tree, an exception will be thrown.
outputFile	The path to the output file.
treeType	An optional value for the `treetype` property defined in the NCBI ASN.1 tree format.
label	An optional value for the `label` property defined in the NCBI ASN.1 tree format.

Definition at line 386 of file NcbiAsnText.cs.

◆ WriteAllTrees() [3/4]

static void PhyloTree.Formats.NcbiAsnText.WriteAllTrees	(	List< TreeNode >	trees,
		Stream	outputStream,
		bool	keepOpen = `false`,
		string	treeType = `null`,
		string	label = `null`
	)

static

Writes a list of TreeNodes to a file in NCBI ASN.1 text format. Note that only one tree can be saved in each file; if the tree contains more than one tree an exception will be thrown.

Parameters

trees	The list of trees to write. If this contains more than one tree, an exception will be thrown.
outputStream	The Stream on which the tree should be written.
keepOpen	Determines whether the outputStream should be kept open after the end of this method.
treeType	An optional value for the `treetype` property defined in the NCBI ASN.1 tree format.
label	An optional value for the `label` property defined in the NCBI ASN.1 tree format.

Definition at line 414 of file NcbiAsnText.cs.

◆ WriteAllTrees() [4/4]

static void PhyloTree.Formats.NcbiAsnText.WriteAllTrees	(	List< TreeNode >	trees,
		string	outputFile,
		string	treeType = `null`,
		string	label = `null`
	)

static

Writes a list of TreeNodes to a file in NCBI ASN.1 text format. Note that only one tree can be saved in each file; if the list contains more than one tree an exception will be thrown.

Parameters

trees	The list of trees to write. If this contains more than one tree, an exception will be thrown.
outputFile	The path to the output file.
treeType	An optional value for the `treetype` property defined in the NCBI ASN.1 tree format.
label	An optional value for the `label` property defined in the NCBI ASN.1 tree format.

Definition at line 433 of file NcbiAsnText.cs.

◆ WriteTree() [1/3]

static void PhyloTree.Formats.NcbiAsnText.WriteTree	(	TreeNode	tree,
		Stream	outputStream,
		bool	keepOpen = `false`,
		string	treeType = `null`,
		string	label = `null`
	)

static

Writes a TreeNode to a file in NCBI ASN.1 text format.

Parameters

tree	The tree to write.
outputStream	The Stream on which the tree should be written.
keepOpen	Determines whether the outputStream should be kept open after the end of this method.
treeType	An optional value for the `treetype` property defined in the NCBI ASN.1 tree format.
label	An optional value for the `label` property defined in the NCBI ASN.1 tree format.

Definition at line 345 of file NcbiAsnText.cs.

◆ WriteTree() [2/3]

static void PhyloTree.Formats.NcbiAsnText.WriteTree	(	TreeNode	tree,
		string	outputFile,
		string	treeType = `null`,
		string	label = `null`
	)

static

Writes a TreeNode to a file in NCBI ASN.1 text format.

Parameters

tree	The tree to write.
outputFile	The path to the output file.
treeType	An optional value for the `treetype` property defined in the NCBI ASN.1 tree format.
label	An optional value for the `label` property defined in the NCBI ASN.1 tree format.

Definition at line 332 of file NcbiAsnText.cs.

◆ WriteTree() [3/3]

static string PhyloTree.Formats.NcbiAsnText.WriteTree	(	TreeNode	tree,
		string	treeType = `null`,
		string	label = `null`
	)

static

Writes a TreeNode to a string in NCBI ASN.1 text format.

Parameters

tree	The tree to write.
treeType	An optional value for the `treetype` property defined in the NCBI ASN.1 tree format.
label	An optional value for the `label` property defined in the NCBI ASN.1 tree format.

Returns: A string containing the NCBI ASN.1 representation of the TreeNode.

Definition at line 452 of file NcbiAsnText.cs.

The documentation for this class was generated from the following file:

NcbiAsnText.cs

Static Public Member Functions

Detailed Description

Member Function Documentation

◆ ParseAllTrees() [1/2]

◆ ParseAllTrees() [2/2]

◆ ParseTree() [1/2]

◆ ParseTree() [2/2]

◆ ParseTrees() [1/2]

◆ ParseTrees() [2/2]

◆ WriteAllTrees() [1/4]

◆ WriteAllTrees() [2/4]

◆ WriteAllTrees() [3/4]

◆ WriteAllTrees() [4/4]

◆ WriteTree() [1/3]

◆ WriteTree() [2/3]

◆ WriteTree() [3/3]