public class AlignmentSpecification extends IndexingScheme
Constructor and Description |
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AlignmentSpecification(NodeSpecification nodeSpecification)
Initializes an alignment specification from a given node specification.
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AlignmentSpecification(NodeSpecification nodeSpecification,
String[] keywords,
Comparator[] comparators) |
AlignmentSpecification(NodeSpecification nodeSpecification,
String[] keywords,
Comparator[] comparators,
double[] weighting) |
AlignmentSpecification(Sequence sequence)
Initializes an alignment specification using the node specification
inside.
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Modifier and Type | Method and Description |
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boolean |
equals(Object obj) |
Comparator |
getComparator(int index)
Returns the Comparator that is currently set for the given keyword.
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Comparator |
getComparator(String keyword)
Returns the Comparator that is currently set for the given keyword.
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NodeSpecification |
getNodeSpecification() |
int |
getOriginalIndex(int index)
This is semantically equivalent to
getNodeSpecification().getKeywordIndex(getKeyword(index)) but this is
preprocessed here for better performance.
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double[] |
getWeighting()
Returns the current keyword weighting.
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int |
hashCode() |
static boolean |
isValidWeighting(double[] weighting)
This checks whether the given weighting is a valid one.
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void |
setComparator(int index,
Comparator comparator)
Sets the comparator for a given keyword.
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void |
setComparator(String keyword,
Comparator comparator)
Sets the comparator for a given keyword.
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void |
setWeighting(double[] weighting)
This sets the current weighting of keywords.
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String |
toString() |
getKeyword, getKeywordIndex, getKeywords, hasKeyword, size
public AlignmentSpecification(NodeSpecification nodeSpecification)
nodeSpecification
- The node specification that is the basis for all
sequences that will be aligned.public AlignmentSpecification(Sequence sequence)
sequence
- a sequence that has a representative NodeSpecification
for all Sequences that are going to be aligned.public AlignmentSpecification(NodeSpecification nodeSpecification, String[] keywords, Comparator[] comparators)
nodeSpecification
- The node specification that is the basis of all
sequences for this alignment.keywords
- The keywords that shall be used in this alignment. This
has to be a subset of the keywords in the node specification.comparators
- the comparators that shall be used for the keywords.
Please note that these have to match the types of the keywords.public AlignmentSpecification(NodeSpecification nodeSpecification, String[] keywords, Comparator[] comparators, double[] weighting)
nodeSpecification
- The node specification that is the basis of all
sequences for this alignment.keywords
- The keywords that shall be used in this alignment. This
has to be a subset of the keywords in the node specification.comparators
- the comparators that shall be used for the keywords.
Please note that these have to match the types of the keywords.weighting
- the weights that highlight the importance of certain
keywords/features. These have to be double values between 0 and 1 that
add up to 1.public NodeSpecification getNodeSpecification()
public void setComparator(String keyword, Comparator comparator)
keyword
- a keyword that is used in this Alignment.comparator
- a fitting Comparator that defines a local normalized
distance on the values for the given keyword.public void setComparator(int index, Comparator comparator)
index
- a keyword index that is used in this Alignment.comparator
- a fitting Comparator that defines a local normalized
distance on the values for the given keyword.public Comparator getComparator(String keyword)
keyword
- a keyword that is used in this Alignment.public Comparator getComparator(int index)
index
- a keyword index that is used in this Alignment.public int getOriginalIndex(int index)
index
- a keyword index in this AlignmentSpecification.public void setWeighting(double[] weighting)
weighting
- a double vector fulfilling the criteria given above.public double[] getWeighting()
public static boolean isValidWeighting(double[] weighting)
weighting
- a double array that might be a weighting.public int hashCode()
hashCode
in class IndexingScheme
public boolean equals(Object obj)
equals
in class IndexingScheme
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