info.bioinfweb.libralign.actions

Class AlignmentActionProvider<T>

java.lang.Object

info.bioinfweb.libralign.actions.AlignmentActionProvider<T>

public class AlignmentActionProvider<T>
extends java.lang.Object

This class provides the business logic for user actions triggered through the view AlignmentContentArea to manipulate the associated models AlignmentModel and SelectionModel.

Since:

0.3.0

Author:

Ben Stöver

Constructor Summary

Constructors

Constructor and Description
AlignmentActionProvider(AlignmentArea alignmentArea) Creates a new instance of this class that is associated with the specified view and model.

Method Summary

Modifier and Type	Method and Description
boolean	deleteBackwards() Removes the currently selected tokens from the underlying AlignmentModel.
boolean	deleteForward() Removes the currently selected tokens from the underlying AlignmentModel.
void	deleteSelection() Deletes the currently selected tokens.
int	elongateSequence(java.lang.String sequenceID, int newLength) Inserts trailing gaps into a sequence until it has the specified length.
AlignmentArea	getAlignmentArea() Returns the view this instance is associated with.
AlignmentModel<T>	getModel()
boolean	insertToken(T token) Inserts the specified token at the current cursor position specified by selection.
boolean	overwriteWithToken(T token) Overwrites the currently selected token(s) in each selected sequence with the specified token.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

AlignmentActionProvider

public AlignmentActionProvider(AlignmentArea alignmentArea)

Creates a new instance of this class that is associated with the specified view and model.

Note that the token type of the AlignmentModel associated with view and the token type T if this instance must match.

Parameters:

view - the alignment content area from which the user operations will be triggered (The sequence data provider, the selection model and the sequence order this view provides will be used for all operations.)

Method Detail

getAlignmentArea

public AlignmentArea getAlignmentArea()

Returns the view this instance is associated with.

Returns:

the linked view instance

getModel

public AlignmentModel<T> getModel()

deleteSelection

public void deleteSelection()

Deletes the currently selected tokens.

This method is called internally by deleteBackwards() and deleteForward() if the selection is not empty.

deleteForward

public boolean deleteForward()

Removes the currently selected tokens from the underlying AlignmentModel. If no tokens are selected the token right of the cursor is removed from each sequence the cursor spans to.

Most users would probably expect this operation to be executed when the delete button is pressed.

Note that calling this method will have no effect if the underlying AlignmentModel is not writable.

Returns:

true if the underlying data source was changed as a result of this operation, false otherwise

deleteBackwards

public boolean deleteBackwards()

Removes the currently selected tokens from the underlying AlignmentModel. If no tokens are selected the token left of the cursor is removed from each sequence the cursor spans to.

Most users would probably expect this operation to be executed when the backspace button is pressed.

Note that calling this method will have no effect if the underlying AlignmentModel is not writable.

Returns:

true if the underlying data source was changed as a result of this operation, false otherwise

elongateSequence

public int elongateSequence(java.lang.String sequenceID,
                            int newLength)

Inserts trailing gaps into a sequence until it has the specified length.

Parameters:

sequenceID - the ID of the sequence to be elongated

newLength - the new length the sequence shall have

Returns:

the number of trailing gaps that have been inserted

insertToken

public boolean insertToken(T token)

Inserts the specified token at the current cursor position specified by selection. If the cursor spans over multiple rows the token is inserted into each row. If other tokens are currently selected the specified token will be inserted as often as the length of the selection.

Note that no deep copy of the specified token will be used, if it is inserted into several rows. Generally implementations of AlignmentModel do not necessarily store one object per position in a sequence, but equal objects can also be mapped to the token set to save memory.

Note that calling this method will have no effect if the underlying AlignmentModel is not writable.

Parameters:

token - the token to be inserted

Returns:

true if the underlying data source was changed as a result of this operation, false otherwise

overwriteWithToken

public boolean overwriteWithToken(T token)

Overwrites the currently selected token(s) in each selected sequence with the specified token. If no token is selected the token(s) right of the cursor are replaced.

If more than one token in each sequence is selected, the first one will be replaced by AlignmentModel#setTokenAt(int, int, Object) and the other will be deleted using AlignmentModel#removeTokensAt(int, int, int).

Note that calling this method will have no effect if the underlying AlignmentModel is not writable.

Parameters:

token - the new token to replace the other(s)

Returns:

true if the underlying data source was changed as a result of this operation, false otherwise