public final class TreeSearchParameters extends Object implements Serializable
| Modifier and Type | Class and Description |
|---|---|
static class |
TreeSearchParameters.Deserializer |
static class |
TreeSearchParameters.Serializer |
| 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 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) |
| 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() |
public static final double[] DEFAULT_PENALTY
public static final TreeSearchParameters ONE_MISMATCH
public static final TreeSearchParameters ONE_INDEL
public static final TreeSearchParameters ONE_MISMATCH_OR_INDEL
public static final TreeSearchParameters TWO_MISMATCHES
public static final TreeSearchParameters TWO_INDELS
public static final TreeSearchParameters TWO_MISMATCHES_OR_INDELS
public static final TreeSearchParameters THREE_MISMATCHES
public static final TreeSearchParameters THREE_INDELS
public static final TreeSearchParameters THREE_MISMATCHES_OR_INDELS
public static final TreeSearchParameters FOUR_MISMATCHES
public static final TreeSearchParameters FOUR_INDELS
public static final TreeSearchParameters FOUR_MISMATCHES_OR_INDELS
public TreeSearchParameters(int[] maxErrors,
double[] penalty,
double maxPenalty)
public TreeSearchParameters(int[] maxErrors,
double[] penalty,
double maxPenalty,
boolean greedy)
public TreeSearchParameters(int mismatches,
int deletions,
int insertions)
Ordering of search is according to
DEFAULT_PENALTY.
mismatches - maximum number of mismatchesdeletions - maximum number of deletionsinsertions - maximum number of insertionspublic TreeSearchParameters(int mismatches,
int deletions,
int insertions,
boolean greedy)
Ordering of search is according to
DEFAULT_PENALTY.
mismatches - maximum number of mismatchesdeletions - maximum number of deletionsinsertions - maximum number of insertionsgreedy - speed up search by not considering substitutions right after indels (forcing them to be before indels)public TreeSearchParameters(int mismatches,
int deletions,
int insertions,
int totalMutations,
boolean greedy)
public TreeSearchParameters(int mismatches,
int deletions,
int insertions,
int totalMutations)
public TreeSearchParameters(int maxSubstitutions,
int maxDeletions,
int maxInsertions,
double substitutionPenalty,
double deletionPenalty,
double insertionPenalty,
double maxPenalty,
boolean greedy)
public TreeSearchParameters(int maxSubstitutions,
int maxDeletions,
int maxInsertions,
double substitutionPenalty,
double deletionPenalty,
double insertionPenalty,
double maxPenalty)
public int getMaxErrors(int errorType)
public double getPenalty(int errorType)
public int getMaxSubstitutions()
public int getMaxDeletions()
public int getMaxInsertions()
public double getSubstitutionPenalty()
public double getDeletionPenalty()
public double getInsertionPenalty()
public double getMaxPenalty()
public boolean isGreedy()
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