public class DomainSimilarity extends java.lang.Object implements java.lang.Comparable<DomainSimilarity>
Modifier and Type | Class and Description |
---|---|
static class |
DomainSimilarity.DomainSimilarityScoring |
static class |
DomainSimilarity.DomainSimilaritySortField |
static class |
DomainSimilarity.PRINT_OPTION |
Modifier and Type | Field and Description |
---|---|
static java.lang.String |
SPECIES_SEPARATOR |
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,
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) |
Modifier and Type | Method and 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 counts
|
double |
getMaximalSimilarityScore() |
double |
getMeanSimilarityScore() |
double |
getMinimalSimilarityScore() |
int |
getN()
This should return the number of pairwise distances used to calculate
this similarity score
|
java.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
SpeciesSpecificDomainSimilariyData
|
double |
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) |
public static final java.lang.String SPECIES_SEPARATOR
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)
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)
public int compareTo(DomainSimilarity domain_similarity)
compareTo
in interface java.lang.Comparable<DomainSimilarity>
public java.util.SortedSet<java.lang.String> getCombinableDomainIds(Species species_of_combinable_domain)
public java.lang.String getDomainId()
public int getMaximalDifference()
public int getMaximalDifferenceInCounts()
public double getMaximalSimilarityScore()
public double getMeanSimilarityScore()
public double getMinimalSimilarityScore()
public int getN()
public java.util.SortedSet<Species> getSpecies()
public java.util.List<Species> getSpeciesCustomOrder()
public java.util.SortedMap<Species,org.forester.surfacing.SpeciesSpecificDcData> getSpeciesData()
public double getStandardDeviationOfSimilarityScore()
public void setDetailedness(DomainSimilarityCalculator.Detailedness detailedness)
public void setSpeciesOrder(java.util.List<Species> species_order)
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)