info.bioinfweb.libralign.model.adapters

Class SingleCharSequenceAdapter<T>

java.lang.Object

info.bioinfweb.libralign.model.adapters.AbstractBasicAlignmentModelView<T>

info.bioinfweb.libralign.model.adapters.AbstractSingleSequenceDataAdapter<T>

info.bioinfweb.libralign.model.adapters.SingleCharSequenceAdapter<T>

Type Parameters:

T - the token type that is used by the underlying alignment model

All Implemented Interfaces:

SingleSequenceDataAdapter<T>, BasicAlignmentModelView<T>, java.lang.CharSequence

public class SingleCharSequenceAdapter<T>
extends AbstractSingleSequenceDataAdapter<T>
implements java.lang.CharSequence, SingleSequenceDataAdapter<T>

An adapter class allowing to view a single sequence provided by an implementation of AlignmentModel as a CharSequence.

Note this implementation directly delegates to the underlying alignment model so that all changes there automatically affect the instance of this class.

Since:

0.1.0

Author:

Ben Stöver

Constructor Summary

Constructors

Constructor and Description
SingleCharSequenceAdapter(AlignmentModel<T> underlyingModel, java.lang.String sequenceID, boolean cutLongRepresentations) Creates a new instance of this class specifying a whole sequence to be viewed.
SingleCharSequenceAdapter(AlignmentModel<T> underlyingModel, java.lang.String sequenceID, int offset, int length, boolean cutLongRepresentations) Creates a new instance of this class specifying a subsequence to be viewed.

Method Summary

Modifier and Type	Method and Description
char	charAt(int index) Returns the character representation of the token in the underlying data source at the specified position.
boolean	isCutLongRepresentations() The return values indicates whether string representations of tokens that are not exactly one character long are allowed.
int	length() This method delegates to AbstractSingleSequenceDataAdapter.getLength().
java.lang.CharSequence	subSequence(int start, int end)
java.lang.String	toString() Returns a copy of this character sequence as a string.

Methods inherited from class info.bioinfweb.libralign.model.adapters.AbstractSingleSequenceDataAdapter

getLength, getOffset, getSequenceID, setLength, setOffset, setSequenceID

Methods inherited from class info.bioinfweb.libralign.model.adapters.AbstractBasicAlignmentModelView

getUnderlyingModel, setUnderlyingModel

Methods inherited from class java.lang.Object

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

Methods inherited from interface java.lang.CharSequence

chars, codePoints

Methods inherited from interface info.bioinfweb.libralign.model.adapters.SingleSequenceDataAdapter

getLength, getOffset, getSequenceID

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

getUnderlyingModel

Constructor Detail

SingleCharSequenceAdapter

public SingleCharSequenceAdapter(AlignmentModel<T> underlyingModel,
                                 java.lang.String sequenceID,
                                 int offset,
                                 int length,
                                 boolean cutLongRepresentations)

Creates a new instance of this class specifying a subsequence to be viewed.

Parameters:

underlyingModel - the alignment model that contains the sequence to be viewed

sequenceID - the ID used in provider of the sequence to be viewed

offset - the start index of the subsequence to be viewed (The first token has the index 0.)

length - the length of the subsequence to be viewed

cutLongRepresentations - Specify true here if tokens that have a string representation that is not exactly one character long shall be exported with the first character of their representation or false if an exception shall be thrown if such a token is found.

SingleCharSequenceAdapter

public SingleCharSequenceAdapter(AlignmentModel<T> underlyingModel,
                                 java.lang.String sequenceID,
                                 boolean cutLongRepresentations)

Creates a new instance of this class specifying a whole sequence to be viewed.

Parameters:

underlyingModel - the alignment model that contains the sequence to be viewed

sequenceID - the ID used in provider of the sequence to be viewed

cutLongRepresentations - Specify true here if tokens that have a string representation that is not exactly one character long shall be exported with the first character of their representation or false if an exception shall be thrown if such a token is found.

Method Detail

isCutLongRepresentations

public boolean isCutLongRepresentations()

The return values indicates whether string representations of tokens that are not exactly one character long are allowed.

Returns:

true if tokens that have a string representation that is not exactly one character long shall be exported with the first character of their representation or false if an exception shall be thrown if such a token is found

charAt

public char charAt(int index)
            throws InvalidUnderlyingTokenException,
                   java.lang.IndexOutOfBoundsException

Returns the character representation of the token in the underlying data source at the specified position.

Specified by:

charAt in interface java.lang.CharSequence

Throws:

InvalidUnderlyingTokenException - if the underlying token has a string representation that is not exactly one character long and isCutLongRepresentations() was set to false

java.lang.IndexOutOfBoundsException - if index was < 0 or >= length()

See Also:

CharSequence.charAt(int)

length

public int length()

This method delegates to AbstractSingleSequenceDataAdapter.getLength().

Specified by:

length in interface java.lang.CharSequence

Returns:

the number of characters in this sequence

subSequence

public java.lang.CharSequence subSequence(int start,
                                          int end)

Specified by:

subSequence in interface java.lang.CharSequence

toString

public java.lang.String toString()

Returns a copy of this character sequence as a string.

Specified by:

toString in interface java.lang.CharSequence

Overrides:

toString in class java.lang.Object

Returns:

the string representation of this object

Throws:

InvalidUnderlyingTokenException - if one token in the underlying data source has a string representation that is not exactly one character long and isCutLongRepresentations() was set to false