public class SequenceMatchingParameters extends Object implements Serializable
Modifier and Type | Class and Description |
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static class |
SequenceMatchingParameters.MatchingType
The different types of amino acid matching.
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Modifier and Type | Field and Description |
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static SequenceMatchingParameters |
defaultStringMatching
Default string matching.
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Constructor and Description |
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SequenceMatchingParameters()
Constructor for empty preferences.
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Modifier and Type | Method and Description |
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static SequenceMatchingParameters |
getDefaultSequenceMatching()
Returns default preferences from amino acid matching.
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double |
getLimitX()
Returns the maximal share of X's a match can contain, range [0.0-1.0].
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SequenceMatchingParameters.MatchingType |
getSequenceMatchingType()
Returns the sequence matching type.
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String |
getShortDescription()
Returns a short description of the parameters.
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static SequenceMatchingParameters |
getStringMatching()
Returns preferences for simple string matching.
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boolean |
isSameAs(SequenceMatchingParameters sequenceMatchingPreferences)
Indicates whether another sequence matching preferences is the same as
this one.
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void |
setLimitX(double limitX)
Sets the maximal share of X's a match can contain, range [0.0-1.0].
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void |
setSequenceMatchingType(SequenceMatchingParameters.MatchingType sequenceMatchingType)
Sets the sequence matching type.
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public static final SequenceMatchingParameters defaultStringMatching
public SequenceMatchingParameters()
public static SequenceMatchingParameters getStringMatching()
public static SequenceMatchingParameters getDefaultSequenceMatching()
public SequenceMatchingParameters.MatchingType getSequenceMatchingType()
public void setSequenceMatchingType(SequenceMatchingParameters.MatchingType sequenceMatchingType)
sequenceMatchingType
- the sequence matching typepublic double getLimitX()
public void setLimitX(double limitX)
limitX
- the maximal share of X's a match can containpublic boolean isSameAs(SequenceMatchingParameters sequenceMatchingPreferences)
sequenceMatchingPreferences
- the other sequence matching
preferencespublic String getShortDescription()
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