Contains methods to read and write trees in the NCBI ASN.1 binary format.
Note: this is a hackish reverse-engineering of the NCBI binary ASN format. A lot of this is derived by assumptions and observations. More...

Static Public Member Functions
static IEnumerable< TreeNode >	ParseTrees (string inputFile)
	Parses a tree from an NCBI ASN.1 binary 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 binary 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 binary 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 binary 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 (BinaryReader reader)
	Parses a tree from a BinaryReader reading a stream in NCBI ASN.1 binary format 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 binary 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 binary 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 binary 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 binary 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 binary 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 binary 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 void	WriteTree (TreeNode tree, BinaryWriter writer, string treeType=null, string label=null)
	Writes a TreeNode to a BinaryWriter in NCBI ASN.1 binary format. More...

Detailed Description

Contains methods to read and write trees in the NCBI ASN.1 binary format.
Note: this is a hackish reverse-engineering of the NCBI binary ASN format. A lot of this is derived by assumptions and observations.

Definition at line 13 of file NcbiAsnBer.cs.

Member Function Documentation

◆ ParseAllTrees() [1/2]

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

static

Parses a tree from an NCBI ASN.1 binary 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 145 of file NcbiAsnBer.cs.

◆ ParseAllTrees() [2/2]

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

static

Parses a tree from an NCBI ASN.1 binary 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 132 of file NcbiAsnBer.cs.

◆ ParseTree()

static TreeNode PhyloTree.Formats.NcbiAsnBer.ParseTree ( BinaryReader reader )

static

Parses a tree from a BinaryReader reading a stream in NCBI ASN.1 binary format into a TreeNode object.

Parameters

reader The BinaryReader that reads a stream in NCBI ASN.1 binary format.

Returns: The parsed TreeNode object.

Definition at line 156 of file NcbiAsnBer.cs.

◆ ParseTrees() [1/2]

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

static

Parses a tree from an NCBI ASN.1 binary 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 122 of file NcbiAsnBer.cs.

◆ ParseTrees() [2/2]

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

static

Parses a tree from an NCBI ASN.1 binary 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 111 of file NcbiAsnBer.cs.

◆ WriteAllTrees() [1/4]

static void PhyloTree.Formats.NcbiAsnBer.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 binary 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 550 of file NcbiAsnBer.cs.

◆ WriteAllTrees() [2/4]

static void PhyloTree.Formats.NcbiAsnBer.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 binary 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 577 of file NcbiAsnBer.cs.

◆ WriteAllTrees() [3/4]

static void PhyloTree.Formats.NcbiAsnBer.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 binary 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 605 of file NcbiAsnBer.cs.

◆ WriteAllTrees() [4/4]

static void PhyloTree.Formats.NcbiAsnBer.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 binary 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 624 of file NcbiAsnBer.cs.

◆ WriteTree() [1/3]

static void PhyloTree.Formats.NcbiAsnBer.WriteTree	(	TreeNode	tree,
		BinaryWriter	writer,
		string	treeType = `null`,
		string	label = `null`
	)

static

Writes a TreeNode to a BinaryWriter in NCBI ASN.1 binary format.

Parameters

tree	The tree to write.
writer	The BinaryWriter on which the tree will be written..
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 643 of file NcbiAsnBer.cs.

◆ WriteTree() [2/3]

static void PhyloTree.Formats.NcbiAsnBer.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 binary 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 536 of file NcbiAsnBer.cs.

◆ WriteTree() [3/3]

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

static

Writes a TreeNode to a file in NCBI ASN.1 binary 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 522 of file NcbiAsnBer.cs.

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

NcbiAsnBer.cs

Static Public Member Functions

Detailed Description

Member Function Documentation

◆ ParseAllTrees() [1/2]

◆ ParseAllTrees() [2/2]

◆ ParseTree()

◆ 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]