info.bioinfweb.libralign.model.utils.indextranslation

Class IndexRelation

java.lang.Object

info.bioinfweb.libralign.model.utils.indextranslation.IndexRelation

Direct Known Subclasses:

PherogramAlignmentRelation

public class IndexRelation
extends java.lang.Object

Bean class that models the result of an index translation between an aligned and an unaligned sequence.

Since:

0.5.0

Author:

Ben Stöver

Field Summary

Fields

Modifier and Type	Field and Description
static int	GAP This value returned as an index indicates that there is a gap in the associated sequence.
static int	OUT_OF_RANGE This value returned as an index indicates that the position specified to obtain lies outside the parts of the two sequences that are aligned with each other.

Constructor Summary

Constructors

Constructor and Description
IndexRelation(int before, int corresponding, int after)

Method Summary

Modifier and Type	Method and Description
int	getAfter() This value is only needed if getCorresponding() returns GAP or OUT_OF_RANGE.
int	getAfterValidIndex() Returns any index that is not GAP or OUT_OF_RANGE and first tries getCorresponding() than getAfter() and finally getBefore().
int	getBefore() This value is only needed if getCorresponding() returns GAP or OUT_OF_RANGE.
int	getBeforeValidIndex() Returns any index that is not GAP or OUT_OF_RANGE and first tries getCorresponding() than getBefore() and finally getAfter().
int	getCorresponding() Returns the position corresponding to the one specified to obtain this result object.
java.lang.String	indexToString(int index)
java.lang.String	toString()

Methods inherited from class java.lang.Object

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

Field Detail

GAP

public static final int GAP

This value returned as an index indicates that there is a gap in the associated sequence.

See Also:

Constant Field Values

OUT_OF_RANGE

public static final int OUT_OF_RANGE

This value returned as an index indicates that the position specified to obtain lies outside the parts of the two sequences that are aligned with each other.

See Also:

Constant Field Values

Constructor Detail

IndexRelation

public IndexRelation(int before,
                     int corresponding,
                     int after)

Method Detail

getBefore

public int getBefore()

This value is only needed if getCorresponding() returns GAP or OUT_OF_RANGE. In that case it returns the first index in the corresponding sequence that is aligned with a position in the original sequence, that is located before the specified position of the original sequence that produced this result.

Returns:

a valid index or OUT_OF_RANGE but never GAP

getCorresponding

public int getCorresponding()

Returns the position corresponding to the one specified to obtain this result object.

Returns:

a valid index or GAP if the specified index producing this result object is aligned with a gap in the other sequence or OUT_OF_RANGE if the specified index lies outside the aligned area

getAfter

public int getAfter()

This value is only needed if getCorresponding() returns GAP or OUT_OF_RANGE. In that case it returns the first index in the corresponding sequence that is aligned with a position in the original sequence, that is located after the specified position of the original sequence that produced this result.

Returns:

a valid index or OUT_OF_RANGE but never GAP

getBeforeValidIndex

public int getBeforeValidIndex()

Returns any index that is not GAP or OUT_OF_RANGE and first tries getCorresponding() than getBefore() and finally getAfter().

Returns:

the first valid index that is found in the algorithm above or the same as getAfter() if all indices should be invalid

getAfterValidIndex

public int getAfterValidIndex()

Returns any index that is not GAP or OUT_OF_RANGE and first tries getCorresponding() than getAfter() and finally getBefore().

Returns:

the first valid index that is found in the algorithm above or the same as getBefore() if all indices should be invalid

indexToString

public java.lang.String indexToString(int index)

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object