Represents a collection of TreeNode objects. If the full representations of the TreeNode objects reside in memory, this offers the best performance at the expense of memory usage. Alternatively, the trees may be read on demand from a stream in binary format. In this case, accessing any of the trees will require the tree to be parsed. This reduces memory usage, but worsens performance. The internal storage model of the collection is transparent to consumers (except for the difference in performance/memory usage). More...

Inheritance diagram for PhyloTree.TreeCollection:

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Public Member Functions
void	Add (TreeNode item)
	Adds an element to the collection. This is stored in memory, even if the internal storage model of the collection is a Stream. More...

void	AddRange (IEnumerable< TreeNode > items)
	Adds multiple elements to the collection. These are stored in memory, even if the internal storage model of the collection is a Stream. More...

IEnumerator< TreeNode >	GetEnumerator ()
	Get an IEnumerator over the collection. More...

int	IndexOf (TreeNode item)
	Finds the index of the first occurrence of an element in the collection. More...

void	Insert (int index, TreeNode item)
	Inserts an element in the collection at the specified index. More...

void	RemoveAt (int index)
	Removes from the collection the element at the specified index. More...

void	Clear ()
	Removes all elements from the collection. If the internal storage model is a Stream, it is disposed and the internal storage model is converted to a List<TreeNode>. More...

bool	Contains (TreeNode item)
	Determines whether the collection contains the specified element. More...

void	CopyTo (TreeNode[] array, int arrayIndex)
	Copies the collection to an array. More...

bool	Remove (TreeNode item)
	Removes the specified element from the collection. More...

	TreeCollection (List< TreeNode > internalStorage)
	Constructs a TreeCollection object from a List<TreeNode>. More...

	TreeCollection (Stream binaryTreeStream)
	Constructs a TreeCollection object from a stream of trees in binary format. More...

void	Dispose ()
	Disposes the TreeCollection, the underlying Stream and StreamReader, and deletes the TemporaryFile (if applicable). More...

Properties
Stream	UnderlyingStream = null `[get]`
	A stream containing the tree data in binary format, if this is the chosen storage model. This can be either a MemoryStream or a FileStream. More...

string	TemporaryFile = null `[get, set]`
	If the trees are stored on disk in a temporary file, you should assign this property to the full path of the file. The file will be deleted when the TreeCollection is Dispose()d. More...

int	Count `[get]`
	The number of trees in the collection. More...

bool	IsReadOnly `[get]`
	Determine whether the collection is read-only. This is always `false` in the current implementation. More...

TreeNode	this[int index] `[get, set]`
	Obtains an element from the collection. More...

Detailed Description

Represents a collection of TreeNode objects. If the full representations of the TreeNode objects reside in memory, this offers the best performance at the expense of memory usage. Alternatively, the trees may be read on demand from a stream in binary format. In this case, accessing any of the trees will require the tree to be parsed. This reduces memory usage, but worsens performance. The internal storage model of the collection is transparent to consumers (except for the difference in performance/memory usage).

Definition at line 16 of file TreeCollection.cs.

Constructor & Destructor Documentation

◆ TreeCollection() [1/2]

PhyloTree.TreeCollection.TreeCollection ( List< TreeNode > internalStorage )

Constructs a TreeCollection object from a List<TreeNode>.

Parameters

internalStorage The List<TreeNode> containing the trees to store in the collection. Note that this list is not copied, but used as-is.

Definition at line 429 of file TreeCollection.cs.

◆ TreeCollection() [2/2]

PhyloTree.TreeCollection.TreeCollection ( Stream binaryTreeStream )

Constructs a TreeCollection object from a stream of trees in binary format.

Parameters

binaryTreeStream The stream of trees in binary format to use. The stream will be disposed when the TreeCollection is disposed. It should not be disposed earlier by external code.

Definition at line 439 of file TreeCollection.cs.

Member Function Documentation

◆ Add()

void PhyloTree.TreeCollection.Add ( TreeNode item )

Adds an element to the collection. This is stored in memory, even if the internal storage model of the collection is a Stream.

Parameters

item	The element to add.

Definition at line 161 of file TreeCollection.cs.

◆ AddRange()

void PhyloTree.TreeCollection.AddRange ( IEnumerable< TreeNode > items )

Adds multiple elements to the collection. These are stored in memory, even if the internal storage model of the collection is a Stream.

Parameters

items The elements to add.

Definition at line 174 of file TreeCollection.cs.

◆ Clear()

void PhyloTree.TreeCollection.Clear ( )

Removes all elements from the collection. If the internal storage model is a Stream, it is disposed and the internal storage model is converted to a List<TreeNode>.

Definition at line 329 of file TreeCollection.cs.

◆ Contains()

bool PhyloTree.TreeCollection.Contains ( TreeNode item )

Determines whether the collection contains the specified element.

Parameters

item	The element to search for.

Returns: true if the collection contains the specified element, false otherwise.

Definition at line 356 of file TreeCollection.cs.

◆ CopyTo()

void PhyloTree.TreeCollection.CopyTo	(	TreeNode[]	array,
		int	arrayIndex
	)

Copies the collection to an array.

Parameters

array	The array in which to copy the collection.
arrayIndex	The index at which to start the copy.

Definition at line 383 of file TreeCollection.cs.

◆ Dispose()

void PhyloTree.TreeCollection.Dispose ( )

Disposes the TreeCollection, the underlying Stream and StreamReader, and deletes the TemporaryFile (if applicable).

Definition at line 513 of file TreeCollection.cs.

◆ GetEnumerator()

IEnumerator< TreeNode > PhyloTree.TreeCollection.GetEnumerator ( )

Get an IEnumerator over the collection.

Returns: An IEnumerator over the collection.

Definition at line 191 of file TreeCollection.cs.

◆ IndexOf()

int PhyloTree.TreeCollection.IndexOf ( TreeNode item )

Finds the index of the first occurrence of an element in the collection.

Parameters

item	The item to search for.

Returns: The index of the item in the collection.

Definition at line 244 of file TreeCollection.cs.

◆ Insert()

void PhyloTree.TreeCollection.Insert	(	int	index,
		TreeNode	item
	)

Inserts an element in the collection at the specified index.

Parameters

index	The index at which to insert the element.
item	The element to insert.

Definition at line 271 of file TreeCollection.cs.

◆ Remove()

bool PhyloTree.TreeCollection.Remove ( TreeNode item )

Removes the specified element from the collection.

Parameters

item	The element to remove.

Returns: true if the removal was successful (i.e. the list contained the element in the first place), false otherwise.

Definition at line 404 of file TreeCollection.cs.

◆ RemoveAt()

void PhyloTree.TreeCollection.RemoveAt ( int index )

Removes from the collection the element at the specified index.

Parameters

index

Definition at line 298 of file TreeCollection.cs.

Property Documentation

◆ Count

int PhyloTree.TreeCollection.Count

get

The number of trees in the collection.

Definition at line 87 of file TreeCollection.cs.

◆ IsReadOnly

bool PhyloTree.TreeCollection.IsReadOnly

get

Determine whether the collection is read-only. This is always false in the current implementation.

Definition at line 105 of file TreeCollection.cs.

◆ TemporaryFile

string PhyloTree.TreeCollection.TemporaryFile = null

getset

If the trees are stored on disk in a temporary file, you should assign this property to the full path of the file. The file will be deleted when the TreeCollection is Dispose()d.

Definition at line 82 of file TreeCollection.cs.

◆ this[int index]

TreeNode PhyloTree.TreeCollection.this[int index]

getset

Obtains an element from the collection.

Parameters

index The index of the element to extract.

Returns: The requested element from the collection.

Definition at line 112 of file TreeCollection.cs.

◆ UnderlyingStream

Stream PhyloTree.TreeCollection.UnderlyingStream = null

get

A stream containing the tree data in binary format, if this is the chosen storage model. This can be either a MemoryStream or a FileStream.

Definition at line 26 of file TreeCollection.cs.

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

TreeCollection.cs

Public Member Functions

Properties

Detailed Description

Constructor & Destructor Documentation

◆ TreeCollection() [1/2]

◆ TreeCollection() [2/2]

Member Function Documentation

◆ Add()

◆ AddRange()

◆ Clear()

◆ Contains()

◆ CopyTo()

◆ Dispose()

◆ GetEnumerator()

◆ IndexOf()

◆ Insert()

◆ Remove()

◆ RemoveAt()

Property Documentation

◆ Count

◆ IsReadOnly

◆ TemporaryFile

◆ this[int index]

◆ UnderlyingStream