com.milaboratory.core.tree

Class TreeSearchParameters

java.lang.Object

com.milaboratory.core.tree.TreeSearchParameters

All Implemented Interfaces:

Serializable

public final class TreeSearchParameters
extends Object
implements Serializable

See Also:

Serialized Form

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	TreeSearchParameters.Deserializer
static class	TreeSearchParameters.Serializer

Field Summary

Fields

Modifier and Type	Field and Description
static double[]	DEFAULT_PENALTY
static TreeSearchParameters	FOUR_INDELS
static TreeSearchParameters	FOUR_MISMATCHES
static TreeSearchParameters	FOUR_MISMATCHES_OR_INDELS
static TreeSearchParameters	ONE_INDEL
static TreeSearchParameters	ONE_MISMATCH
static TreeSearchParameters	ONE_MISMATCH_OR_INDEL
static TreeSearchParameters	THREE_INDELS
static TreeSearchParameters	THREE_MISMATCHES
static TreeSearchParameters	THREE_MISMATCHES_OR_INDELS
static TreeSearchParameters	TWO_INDELS
static TreeSearchParameters	TWO_MISMATCHES
static TreeSearchParameters	TWO_MISMATCHES_OR_INDELS

Constructor Summary

Constructors

Constructor and Description
TreeSearchParameters(int[] maxErrors, double[] penalty, double maxPenalty)
TreeSearchParameters(int[] maxErrors, double[] penalty, double maxPenalty, boolean greedy)
TreeSearchParameters(int mismatches, int deletions, int insertions) Parameters to search with limited number of each mutation type.
TreeSearchParameters(int mismatches, int deletions, int insertions, boolean greedy) Parameters to search with limited number of each mutation type.
TreeSearchParameters(int maxSubstitutions, int maxDeletions, int maxInsertions, double substitutionPenalty, double deletionPenalty, double insertionPenalty, double maxPenalty)
TreeSearchParameters(int maxSubstitutions, int maxDeletions, int maxInsertions, double substitutionPenalty, double deletionPenalty, double insertionPenalty, double maxPenalty, boolean greedy)
TreeSearchParameters(int mismatches, int deletions, int insertions, int totalMutations)
TreeSearchParameters(int mismatches, int deletions, int insertions, int totalMutations, boolean greedy)

Method Summary

Methods

Modifier and Type	Method and Description
boolean	equals(Object o)
double	getDeletionPenalty()
double	getInsertionPenalty()
int	getMaxDeletions()
int	getMaxErrors(int errorType)
int	getMaxInsertions()
double	getMaxPenalty()
int	getMaxSubstitutions()
double	getPenalty(int errorType)
double	getSubstitutionPenalty()
int	hashCode()
boolean	isGreedy()

Methods inherited from class java.lang.Object

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

Field Detail

DEFAULT_PENALTY

public static final double[] DEFAULT_PENALTY

ONE_MISMATCH

public static final TreeSearchParameters ONE_MISMATCH

ONE_INDEL

public static final TreeSearchParameters ONE_INDEL

ONE_MISMATCH_OR_INDEL

public static final TreeSearchParameters ONE_MISMATCH_OR_INDEL

TWO_MISMATCHES

public static final TreeSearchParameters TWO_MISMATCHES

TWO_INDELS

public static final TreeSearchParameters TWO_INDELS

TWO_MISMATCHES_OR_INDELS

public static final TreeSearchParameters TWO_MISMATCHES_OR_INDELS

THREE_MISMATCHES

public static final TreeSearchParameters THREE_MISMATCHES

THREE_INDELS

public static final TreeSearchParameters THREE_INDELS

THREE_MISMATCHES_OR_INDELS

public static final TreeSearchParameters THREE_MISMATCHES_OR_INDELS

FOUR_MISMATCHES

public static final TreeSearchParameters FOUR_MISMATCHES

FOUR_INDELS

public static final TreeSearchParameters FOUR_INDELS

FOUR_MISMATCHES_OR_INDELS

public static final TreeSearchParameters FOUR_MISMATCHES_OR_INDELS

Constructor Detail

TreeSearchParameters

public TreeSearchParameters(int[] maxErrors,
                    double[] penalty,
                    double maxPenalty)

TreeSearchParameters

public TreeSearchParameters(int[] maxErrors,
                    double[] penalty,
                    double maxPenalty,
                    boolean greedy)

TreeSearchParameters

public TreeSearchParameters(int mismatches,
                    int deletions,
                    int insertions)

Parameters to search with limited number of each mutation type.

Ordering of search is according to DEFAULT_PENALTY.

Parameters:

mismatches - maximum number of mismatches

deletions - maximum number of deletions

insertions - maximum number of insertions

TreeSearchParameters

public TreeSearchParameters(int mismatches,
                    int deletions,
                    int insertions,
                    boolean greedy)

Parameters to search with limited number of each mutation type.

Ordering of search is according to DEFAULT_PENALTY.

Parameters:

mismatches - maximum number of mismatches

deletions - maximum number of deletions

insertions - maximum number of insertions

greedy - speed up search by not considering substitutions right after indels (forcing them to be before indels)

TreeSearchParameters

public TreeSearchParameters(int mismatches,
                    int deletions,
                    int insertions,
                    int totalMutations,
                    boolean greedy)

TreeSearchParameters

public TreeSearchParameters(int mismatches,
                    int deletions,
                    int insertions,
                    int totalMutations)

TreeSearchParameters

public TreeSearchParameters(int maxSubstitutions,
                    int maxDeletions,
                    int maxInsertions,
                    double substitutionPenalty,
                    double deletionPenalty,
                    double insertionPenalty,
                    double maxPenalty,
                    boolean greedy)

TreeSearchParameters

public TreeSearchParameters(int maxSubstitutions,
                    int maxDeletions,
                    int maxInsertions,
                    double substitutionPenalty,
                    double deletionPenalty,
                    double insertionPenalty,
                    double maxPenalty)

Method Detail

getMaxErrors

public int getMaxErrors(int errorType)

getPenalty

public double getPenalty(int errorType)

getMaxSubstitutions

public int getMaxSubstitutions()

getMaxDeletions

public int getMaxDeletions()

getMaxInsertions

public int getMaxInsertions()

getSubstitutionPenalty

public double getSubstitutionPenalty()

getDeletionPenalty

public double getDeletionPenalty()

getInsertionPenalty

public double getInsertionPenalty()

getMaxPenalty

public double getMaxPenalty()

isGreedy

public boolean isGreedy()

equals

public boolean equals(Object o)

Overrides:

equals in class Object

hashCode

public int hashCode()

Overrides:

hashCode in class Object