com.milaboratory.core.alignment.kaligner2

Class OffsetPacksAccumulator

java.lang.Object

com.milaboratory.core.alignment.kaligner2.OffsetPacksAccumulator

public final class OffsetPacksAccumulator
extends Object

Field Summary

Fields

Modifier and Type	Field and Description
static int	DROPPED_CLUSTER
static int	FIRST_RECORD_ID
static int	LAST_INDEX
static int	LAST_RECORD_ID
static int	LAST_VALUE
static int	MAX_VALUE
static int	MIN_VALUE
static int	OUTPUT_RECORD_SIZE
static int	RECORD_SIZE
static int	SCORE
static int	STRETCH_INDEX_MARK
static int	STRETCH_INDEX_MASK

Constructor Summary

Constructors

Constructor and Description
OffsetPacksAccumulator(int slotCount, int maxAllowedDelta, int matchScore, int mismatchScore, int shiftScore, int absoluteMinClusterScore)

Method Summary

Methods

Modifier and Type	Method and Description
void	calculateInitialPartitioning(int[] data)
void	calculateInitialPartitioning(int[] data, int dataFrom, int dataTo) Accepts array with elements in the following format:
void	calculateInitialPartitioning(IntArrayList list)
int	numberOfClusters()
String	toString()
static String	toString(IntArrayList results, IntArrayList seedPositions, int[] data)

Methods inherited from class java.lang.Object

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

Field Detail

DROPPED_CLUSTER

public static final int DROPPED_CLUSTER

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Constant Field Values

FIRST_RECORD_ID

public static final int FIRST_RECORD_ID

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Constant Field Values

LAST_RECORD_ID

public static final int LAST_RECORD_ID

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Constant Field Values

SCORE

public static final int SCORE

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Constant Field Values

MIN_VALUE

public static final int MIN_VALUE

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Constant Field Values

MAX_VALUE

public static final int MAX_VALUE

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Constant Field Values

LAST_VALUE

public static final int LAST_VALUE

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Constant Field Values

LAST_INDEX

public static final int LAST_INDEX

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Constant Field Values

STRETCH_INDEX_MARK

public static final int STRETCH_INDEX_MARK

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Constant Field Values

STRETCH_INDEX_MASK

public static final int STRETCH_INDEX_MASK

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Constant Field Values

RECORD_SIZE

public static final int RECORD_SIZE

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Constant Field Values

OUTPUT_RECORD_SIZE

public static final int OUTPUT_RECORD_SIZE

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Constant Field Values

Constructor Detail

OffsetPacksAccumulator

public OffsetPacksAccumulator(int slotCount,
                      int maxAllowedDelta,
                      int matchScore,
                      int mismatchScore,
                      int shiftScore,
                      int absoluteMinClusterScore)

Method Detail

calculateInitialPartitioning

public void calculateInitialPartitioning(IntArrayList list)

calculateInitialPartitioning

public void calculateInitialPartitioning(int[] data)

calculateInitialPartitioning

public void calculateInitialPartitioning(int[] data,
                                int dataFrom,
                                int dataTo)

Accepts array with elements in the following format:

numberOfClusters

public int numberOfClusters()

toString

public String toString()

Overrides:

toString in class Object

toString

public static String toString(IntArrayList results,
              IntArrayList seedPositions,
              int[] data)