Package org.forester.surfacing
Class DomainSimilarity
- java.lang.Object
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- org.forester.surfacing.DomainSimilarity
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- All Implemented Interfaces:
java.lang.Comparable<DomainSimilarity>
public class DomainSimilarity extends java.lang.Object implements java.lang.Comparable<DomainSimilarity>
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Nested Class Summary
Nested Classes Modifier and Type Class Description static class
DomainSimilarity.DomainSimilarityScoring
static class
DomainSimilarity.DomainSimilaritySortField
static class
DomainSimilarity.PRINT_OPTION
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Field Summary
Fields Modifier and Type Field Description static java.lang.String
SPECIES_SEPARATOR
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Constructor Summary
Constructors Constructor Description DomainSimilarity(CombinableDomains combinable_domains, double min, double max, double mean, double median, double sd, int n, int max_difference_in_counts, int max_difference, java.util.SortedMap<Species,org.forester.surfacing.SpeciesSpecificDcData> species_data, boolean sort_by_species_count_first, boolean treat_as_binary_comparison)
DomainSimilarity(CombinableDomains combinable_domains, int max_difference_in_counts, int max_difference, java.util.SortedMap<Species,org.forester.surfacing.SpeciesSpecificDcData> species_data, boolean sort_by_species_count_first, boolean treat_as_binary_comparison)
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description int
compareTo(DomainSimilarity domain_similarity)
java.util.SortedSet<java.lang.String>
getCombinableDomainIds(Species species_of_combinable_domain)
java.lang.String
getDomainId()
int
getMaximalDifference()
For pairwise similarities, this should return the "difference"; for example the difference in counts for copy number based features (the same as getMaximalDifferenceInCounts(), or the number of actually different domain combinations.int
getMaximalDifferenceInCounts()
For pairwise similarities, this should return the difference in counts, while for comparisons of more than two domains, this should return the maximal difference in countsdouble
getMaximalSimilarityScore()
double
getMeanSimilarityScore()
double
getMinimalSimilarityScore()
int
getN()
This should return the number of pairwise distances used to calculate this similarity scorejava.util.SortedSet<Species>
getSpecies()
java.util.List<Species>
getSpeciesCustomOrder()
java.util.SortedMap<Species,org.forester.surfacing.SpeciesSpecificDcData>
getSpeciesData()
This should return a map, which maps species names to SpeciesSpecificDomainSimilariyDatadouble
getStandardDeviationOfSimilarityScore()
void
setDetailedness(DomainSimilarityCalculator.Detailedness detailedness)
void
setSpeciesOrder(java.util.List<Species> species_order)
java.lang.StringBuffer
toStringBuffer(DomainSimilarity.PRINT_OPTION print_option, java.util.Map<java.lang.String,java.lang.Integer> tax_code_to_id_map, Phylogeny phy)
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Field Detail
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SPECIES_SEPARATOR
public static final java.lang.String SPECIES_SEPARATOR
- See Also:
- Constant Field Values
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Constructor Detail
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DomainSimilarity
public DomainSimilarity(CombinableDomains combinable_domains, double min, double max, double mean, double median, double sd, int n, int max_difference_in_counts, int max_difference, java.util.SortedMap<Species,org.forester.surfacing.SpeciesSpecificDcData> species_data, boolean sort_by_species_count_first, boolean treat_as_binary_comparison)
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DomainSimilarity
public DomainSimilarity(CombinableDomains combinable_domains, int max_difference_in_counts, int max_difference, java.util.SortedMap<Species,org.forester.surfacing.SpeciesSpecificDcData> species_data, boolean sort_by_species_count_first, boolean treat_as_binary_comparison)
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Method Detail
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compareTo
public int compareTo(DomainSimilarity domain_similarity)
- Specified by:
compareTo
in interfacejava.lang.Comparable<DomainSimilarity>
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getCombinableDomainIds
public java.util.SortedSet<java.lang.String> getCombinableDomainIds(Species species_of_combinable_domain)
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getDomainId
public java.lang.String getDomainId()
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getMaximalDifference
public int getMaximalDifference()
For pairwise similarities, this should return the "difference"; for example the difference in counts for copy number based features (the same as getMaximalDifferenceInCounts(), or the number of actually different domain combinations. For pairwise similarities, this should return the difference, while for comparisons of more than two domains, this should return the maximal difference
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getMaximalDifferenceInCounts
public int getMaximalDifferenceInCounts()
For pairwise similarities, this should return the difference in counts, while for comparisons of more than two domains, this should return the maximal difference in counts- Returns:
- the (maximal) difference in counts
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getMaximalSimilarityScore
public double getMaximalSimilarityScore()
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getMeanSimilarityScore
public double getMeanSimilarityScore()
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getMinimalSimilarityScore
public double getMinimalSimilarityScore()
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getN
public int getN()
This should return the number of pairwise distances used to calculate this similarity score- Returns:
- the number of pairwise distances
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getSpecies
public java.util.SortedSet<Species> getSpecies()
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getSpeciesCustomOrder
public java.util.List<Species> getSpeciesCustomOrder()
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getSpeciesData
public java.util.SortedMap<Species,org.forester.surfacing.SpeciesSpecificDcData> getSpeciesData()
This should return a map, which maps species names to SpeciesSpecificDomainSimilariyData- Returns:
- SortedMap
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getStandardDeviationOfSimilarityScore
public double getStandardDeviationOfSimilarityScore()
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setDetailedness
public void setDetailedness(DomainSimilarityCalculator.Detailedness detailedness)
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setSpeciesOrder
public void setSpeciesOrder(java.util.List<Species> species_order)
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toStringBuffer
public java.lang.StringBuffer toStringBuffer(DomainSimilarity.PRINT_OPTION print_option, java.util.Map<java.lang.String,java.lang.Integer> tax_code_to_id_map, Phylogeny phy)
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