info.bioinfweb.libralign.pherogram.distortion

Class GapPattern

java.lang.Object

info.bioinfweb.libralign.pherogram.distortion.GapPattern

public class GapPattern
extends java.lang.Object

Represents gaps displayed in a PherogramArea within the area of one base call.

Since:

0.2.0

Author:

Ben Stöver

Constructor Summary

Constructors

Constructor and Description
GapPattern(int size) Creates a new instance of this class initially containing no gaps.

Method Summary

Modifier and Type	Method and Description
int	countGaps(int index) Counts the number of gaps located before the specified position.
int	countGapsBeforeCurveCenter() Calculates the number of gaps that are located before the center of the trace curves belonging to the region this gap pattern belongs to.
int	getGapCount() Returns the number of gaps contained in this pattern
boolean	isGap(int index) Indicates whether a gap is located at the specified position.
void	setGap(int index, boolean gap) This method allows to define whether a gap is located at the specified position or not.
int	size() Returns the length of this pattern.

Methods inherited from class java.lang.Object

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

Constructor Detail

GapPattern

public GapPattern(int size)

Creates a new instance of this class initially containing no gaps.

Parameters:

size - the size the new gap pattern shall have

Method Detail

isGap

public boolean isGap(int index)

Indicates whether a gap is located at the specified position.

Parameters:

index - the index in this pattern (the compound index in the editable sequence relative to the start of this gap pattern)

Returns:

true if a gap is located here, false otherwise

setGap

public void setGap(int index,
                   boolean gap)

This method allows to define whether a gap is located at the specified position or not.

Parameters:

index - the index in this pattern (the compound index in the editable sequence relative to the start of this gap pattern)

gap - Specify true here if a gap shall be located here, false otherwise.

size

public int size()

Returns the length of this pattern.

Returns:

a value >= 0

getGapCount

public int getGapCount()

Returns the number of gaps contained in this pattern

Returns:

a value >= 0

countGaps

public int countGaps(int index)

Counts the number of gaps located before the specified position.

Parameters:

index - the index in this pattern (the compound index in the editable sequence relative to the start of this gap pattern)

Returns:

a value >= 0

countGapsBeforeCurveCenter

public int countGapsBeforeCurveCenter()

Calculates the number of gaps that are located before the center of the trace curves belonging to the region this gap pattern belongs to.

Returns:

a value >= 0