Package com.biomatters.geneious.publicapi.implementations

Class EndGapsHelper

java.lang.Object

com.biomatters.geneious.publicapi.implementations.EndGapsHelper

public class EndGapsHelper
extends Object

Calculates, and provides a method to determine whether residues in a set of sequences are end gaps. End gaps are gaps at either end of the sequence. This is useful in situations where we want to treat end gaps differently from internal gaps.

Field Summary

Fields

Modifier and Type	Field	Description
static final EndGapsHelper	NO_END_GAPS	A EndGaps instance that always returns false from isEndGap(int, int)

Constructor Summary

Constructors

Constructor	Description
EndGapsHelper(CharSequence[] residues, boolean freeEndGaps)	Construct some new end gaps.

Method Summary

Modifier and Type	Method	Description
boolean	isEndGap(int sequenceIndex, int residueIndex)	Is this residue an end gap? End gaps are gaps at either end of the sequence.

Methods inherited from class java.lang.Object

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

Field Details

NO_END_GAPS

public static final EndGapsHelper NO_END_GAPS

A EndGaps instance that always returns false from isEndGap(int, int)

Constructor Details

EndGapsHelper

public EndGapsHelper(CharSequence[] residues,
 boolean freeEndGaps)

Construct some new end gaps.

Parameters:

residues - each CharSequence represents a single sequence. The CharSequences do not have to be all the same length. This parameter is used only for the duration of this method, and is not recorded for future use.

freeEndGaps - if this is false, then all calls to isEndGap(int, int) will return false. Useful in situations where we do not have free end gaps.

Method Details

isEndGap

public boolean isEndGap(int sequenceIndex,
 int residueIndex)

Is this residue an end gap? End gaps are gaps at either end of the sequence.

Parameters:

sequenceIndex - the index of the sequence in the range [0,n-1]

residueIndex - the index of the residue in the range [0,n-1]

Returns:

true if this residue an end gap.