org.forester.surfacing

Class DomainSimilarity

java.lang.Object

org.forester.surfacing.DomainSimilarity

All Implemented Interfaces:

Comparable<DomainSimilarity>

public class DomainSimilarity
extends Object
implements Comparable<DomainSimilarity>

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	DomainSimilarity.DomainSimilarityScoring
static class	DomainSimilarity.DomainSimilaritySortField
static class	DomainSimilarity.PRINT_OPTION

Field Summary

Fields

Modifier and Type	Field and Description
static String	SPECIES_SEPARATOR

Constructor Summary

Constructors

Constructor and 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, 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, SortedMap<Species,org.forester.surfacing.SpeciesSpecificDcData> species_data, boolean sort_by_species_count_first, boolean treat_as_binary_comparison)

Method Summary

Modifier and Type	Method and Description
int	compareTo(DomainSimilarity domain_similarity)
SortedSet<String>	getCombinableDomainIds(Species species_of_combinable_domain)
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 counts
double	getMaximalSimilarityScore()
double	getMeanSimilarityScore()
double	getMinimalSimilarityScore()
int	getN() This should return the number of pairwise distances used to calculate this similarity score
SortedSet<Species>	getSpecies()
List<Species>	getSpeciesCustomOrder()
SortedMap<Species,org.forester.surfacing.SpeciesSpecificDcData>	getSpeciesData() This should return a map, which maps species names to SpeciesSpecificDomainSimilariyData
double	getStandardDeviationOfSimilarityScore()
void	setDetailedness(DomainSimilarityCalculator.Detailedness detailedness)
void	setSpeciesOrder(List<Species> species_order)
StringBuffer	toStringBuffer(DomainSimilarity.PRINT_OPTION print_option, Map<String,Integer> tax_code_to_id_map, Phylogeny phy)

Methods inherited from class java.lang.Object

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

Field Detail

SPECIES_SEPARATOR

public static final String SPECIES_SEPARATOR

See Also:

Constant Field Values

Constructor Detail

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,
                        SortedMap<Species,org.forester.surfacing.SpeciesSpecificDcData> species_data,
                        boolean sort_by_species_count_first,
                        boolean treat_as_binary_comparison)

DomainSimilarity

public DomainSimilarity(CombinableDomains combinable_domains,
                        int max_difference_in_counts,
                        int max_difference,
                        SortedMap<Species,org.forester.surfacing.SpeciesSpecificDcData> species_data,
                        boolean sort_by_species_count_first,
                        boolean treat_as_binary_comparison)

Method Detail

compareTo

public int compareTo(DomainSimilarity domain_similarity)

Specified by:

compareTo in interface Comparable<DomainSimilarity>

getCombinableDomainIds

public SortedSet<String> getCombinableDomainIds(Species species_of_combinable_domain)

getDomainId

public String getDomainId()

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

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

getMaximalSimilarityScore

public double getMaximalSimilarityScore()

getMeanSimilarityScore

public double getMeanSimilarityScore()

getMinimalSimilarityScore

public double getMinimalSimilarityScore()

getN

public int getN()

This should return the number of pairwise distances used to calculate this similarity score

Returns:

the number of pairwise distances

getSpecies

public SortedSet<Species> getSpecies()

getSpeciesCustomOrder

public List<Species> getSpeciesCustomOrder()

getSpeciesData

public SortedMap<Species,org.forester.surfacing.SpeciesSpecificDcData> getSpeciesData()

This should return a map, which maps species names to SpeciesSpecificDomainSimilariyData

Returns:

SortedMap

getStandardDeviationOfSimilarityScore

public double getStandardDeviationOfSimilarityScore()

setDetailedness

public void setDetailedness(DomainSimilarityCalculator.Detailedness detailedness)

setSpeciesOrder

public void setSpeciesOrder(List<Species> species_order)

toStringBuffer

public StringBuffer toStringBuffer(DomainSimilarity.PRINT_OPTION print_option,
                                   Map<String,Integer> tax_code_to_id_map,
                                   Phylogeny phy)