info.bioinfweb.libralign.model.concatenated

Interface ConcatenatedAlignmentModel

All Superinterfaces:

AlignmentModel<java.lang.Object>

public interface ConcatenatedAlignmentModel
extends AlignmentModel<java.lang.Object>

Warning: This interface is currently a placeholder. Current versions of LibrAlign contain no implementations of it and a number of LibrAlign classes do not yet support concatenated alignment models and would throw exceptions if such an implementation would be used together with them. Support for concatenated models is planned for the future. If you are interested in using this functionality or want to contribute to implementing it, contact support@bioinfweb.info or ask a question on our ResearchGate project page.

This interface allows to concatenate multiple instances of AlignmentModel implementations. It extends AlignmentModel by additional methods allowing to add and remove underlying models which provide the contents a sets of subsequent columns of the concatenated alignment.

Each contained model may provide a different token set valid for the part of the alignment it models. To allow combining any different token sets this interface does not have a generic token type but uses Object as the token type instead. Implementing classes should return a global token set containing all tokens if the different submodels with the according inherited method.

Since:

0.4.0

Author:

Ben Stöver

Method Summary

Modifier and Type	Method and Description
void	appendPartModel(AlignmentModel<?> model) Appends an additional part model at the end of this concatenated alignment.
int	columnOffsetForPartModel(AlignmentModel<?> partModel) Returns the global index of the first column provided by the specified part model.
int	columnOffsetForPartModel(int partIndex) Returns the global index of the first column provided by the part model with the specified index.
boolean	containsPartModel(AlignmentModel<?> partModel) Checks if the specified model is contained in this concatenated model.
AlignmentModel<?>	getLastPartModel() Returns the right most part model contained in this alignment.
AlignmentModel<?>	getPartModel(int index) Returns the part model at the specified position.
int	getPartModelCount() Returns the number of part models contained in this alignment.
void	insertPartModel(int modelIndex, AlignmentModel<?> model) Inserts an additional part model at the specified position.
int	parentIDByPartID(int partID, int partIndex) Translates the sequence ID used in an underlying part model to the according sequence ID in this concatenated model.
int	partIDByParentID(int parentID, int partIndex) Translates the sequence ID used in this concatenated model to the according sequence ID in an underlying part model.
AlignmentModel<?>	partModelByColumn(int columnIndex) Returns the part model currently responsible for providing the contents of the specified column.
int	partModelIndex(AlignmentModel<?> partModel) Returns the index of the specified part model in this concatenated alignment model.
AlignmentModel<?>	removePartModel(int index) Removes the part model at the specified index from this concatenated alignment model.

Methods inherited from interface info.bioinfweb.libralign.model.AlignmentModel

addSequence, addSequence, appendToken, appendTokens, containsSequence, getChangeListeners, getID, getLabel, getMaxSequenceLength, getSequenceCount, getSequenceLength, getTokenAt, getTokenSet, getWriteType, insertTokenAt, insertTokensAt, isSequencesReadOnly, isTokensReadOnly, removeSequence, removeTokenAt, removeTokensAt, renameSequence, sequenceIDIterator, sequenceIDsByName, sequenceNameByID, setID, setLabel, setTokenAt, setTokensAt, setTokenSet

Method Detail

appendPartModel

void appendPartModel(AlignmentModel<?> model)

Appends an additional part model at the end of this concatenated alignment.

Parameters:

model - the model to be added

Throws:

java.lang.IllegalArgumentException - if this instance is not the owner of model or the IDs of the sequences contained in model do not match the sequence IDs of this instance

java.lang.NullPointerException - if model is null

insertPartModel

void insertPartModel(int modelIndex,
                     AlignmentModel<?> model)

Inserts an additional part model at the specified position.

Parameters:

modelIndex - the index where the new model shall be inserted (The index in the list of models is meant here, which is different from the global index the first alignment column of the new model will have.)

model - the new model to be inserted

Throws:

java.lang.IllegalArgumentException - if this instance is not the owner of model or the IDs of the sequences contained in model do not match the sequence IDs of this instance

java.lang.NullPointerException - if model is null

java.lang.IndexOutOfBoundsException - if the index is out of range (index < 0 || index > getPartModelCount())

removePartModel

AlignmentModel<?> removePartModel(int index)

Removes the part model at the specified index from this concatenated alignment model.

Parameters:

index - the index of the part model to be removed

Returns:

the part model that has been removed

Throws:

java.lang.IndexOutOfBoundsException - if index is below 0 or >= getPartModelCount()

getPartModel

AlignmentModel<?> getPartModel(int index)

Returns the part model at the specified position.

Parameters:

index - the index of the part model to be returned

Returns:

the part model at the specified position

Throws:

java.lang.IndexOutOfBoundsException - if index is below 0 or >= getPartModelCount()

getLastPartModel

AlignmentModel<?> getLastPartModel()

Returns the right most part model contained in this alignment.

Returns:

the right most model or null if no part models are contained in this alignment

getPartModelCount

int getPartModelCount()

Returns the number of part models contained in this alignment.

Returns:

the number of contained models

partModelIndex

int partModelIndex(AlignmentModel<?> partModel)

Returns the index of the specified part model in this concatenated alignment model.

Parameters:

partModel - the sought-after part model

Returns:

the index or -1 of the specified model is not part of this instance

containsPartModel

boolean containsPartModel(AlignmentModel<?> partModel)

Checks if the specified model is contained in this concatenated model.

Parameters:

partModel - the sought-after part model

Returns:

true if the specified model was found, false otherwise

columnOffsetForPartModel

int columnOffsetForPartModel(int partIndex)

Returns the global index of the first column provided by the part model with the specified index.

Parameters:

partIndex - the index of the part model

Returns:

an integer value >= 0

Throws:

java.lang.IndexOutOfBoundsException - if partIndex is below zero or >= getPartModelCount()

columnOffsetForPartModel

int columnOffsetForPartModel(AlignmentModel<?> partModel)

Returns the global index of the first column provided by the specified part model.

Parameters:

partModel - the part model that has the returned offset

Returns:

an integer value >= 0

Throws:

java.lang.IllegalArgumentException - if partModel is not contained in this concatenated model

partModelByColumn

AlignmentModel<?> partModelByColumn(int columnIndex)

Returns the part model currently responsible for providing the contents of the specified column.

Parameters:

columnIndex - the global column index (The first column has the index 0.)

Returns:

the according part model

Throws:

java.lang.IndexOutOfBoundsException - if columnIndex is below zero or greater than the index of the right most column in this model

parentIDByPartID

int parentIDByPartID(int partID,
                     int partIndex)
              throws java.lang.IllegalArgumentException,
                     java.lang.IndexOutOfBoundsException

Translates the sequence ID used in an underlying part model to the according sequence ID in this concatenated model.

Parameters:

partID - the ID used in the part model

partIndex - the index of the part model

Returns:

the according sequence ID in the parent model

Throws:

java.lang.IllegalArgumentException - if the specified ID is not contained in the specified part model

java.lang.IndexOutOfBoundsException - if the index of the part model is not valid

partIDByParentID

int partIDByParentID(int parentID,
                     int partIndex)
              throws java.lang.IllegalArgumentException,
                     java.lang.IndexOutOfBoundsException

Translates the sequence ID used in this concatenated model to the according sequence ID in an underlying part model.

Note that not all part models need to contain all sequences represented by the concatenated model.

Parameters:

parentID - the ID used in this model

partIndex - the index of the part model

Returns:

the according sequence ID in the specified part model or -1 if the specified part model does not contain a sequence according to the parent ID (although other part models do)

Throws:

java.lang.IllegalArgumentException - if the specified ID is not contained in this model (i.e. no part model contains an according sequence)

java.lang.IndexOutOfBoundsException - if the index of the part model is not valid