org.forester.surfacing
public class PrintableDomainSimilarity extends java.lang.Object implements DomainSimilarity
Modifier and Type | Class and Description |
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static class |
PrintableDomainSimilarity.PRINT_OPTION |
DomainSimilarity.DomainSimilarityScoring, DomainSimilarity.DomainSimilaritySortField
Modifier and Type | Field and Description |
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static java.lang.String |
SPECIES_SEPARATOR |
Constructor and Description |
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PrintableDomainSimilarity(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.SpeciesSpecificDomainSimilariyData> species_data,
DomainSimilarity.DomainSimilaritySortField sort_field,
boolean sort_by_species_count_first,
boolean treat_as_binary_comparison)
If go_id_to_term_map not null, detailed GO information is written,
only GO ids otherwise.
|
Modifier and Type | Method and Description |
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int |
compareTo(DomainSimilarity domain_similarity) |
java.util.SortedSet<DomainId> |
getCombinableDomainIds(Species species_of_combinable_domain) |
DomainId |
getDomainId() |
GoNameSpace |
getGoNamespaceLimit() |
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.SpeciesSpecificDomainSimilariyData> |
getSpeciesData()
This should return a map, which maps species names to
SpeciesSpecificDomainSimilariyData
|
double |
getStandardDeviationOfSimilarityScore() |
void |
setDetailedness(DomainSimilarityCalculator.Detailedness detailedness) |
void |
setGoAnnotationOutput(DomainSimilarityCalculator.GoAnnotationOutput go_annotation_output) |
void |
setGoIdToTermMap(java.util.Map<GoId,GoTerm> go_id_to_term_map) |
void |
setGoNamespaceLimit(GoNameSpace go_namespace_limit) |
void |
setSpeciesOrder(java.util.List<Species> species_order) |
java.lang.String |
toString() |
java.lang.StringBuffer |
toStringBuffer(PrintableDomainSimilarity.PRINT_OPTION print_option) |
public static final java.lang.String SPECIES_SEPARATOR
public PrintableDomainSimilarity(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.SpeciesSpecificDomainSimilariyData> species_data, DomainSimilarity.DomainSimilaritySortField sort_field, 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<DomainId> getCombinableDomainIds(Species species_of_combinable_domain)
getCombinableDomainIds
in interface DomainSimilarity
public DomainId getDomainId()
getDomainId
in interface DomainSimilarity
public GoNameSpace getGoNamespaceLimit()
public int getMaximalDifference()
DomainSimilarity
getMaximalDifference
in interface DomainSimilarity
public int getMaximalDifferenceInCounts()
DomainSimilarity
getMaximalDifferenceInCounts
in interface DomainSimilarity
public double getMaximalSimilarityScore()
getMaximalSimilarityScore
in interface DomainSimilarity
public double getMeanSimilarityScore()
getMeanSimilarityScore
in interface DomainSimilarity
public double getMinimalSimilarityScore()
getMinimalSimilarityScore
in interface DomainSimilarity
public int getN()
DomainSimilarity
getN
in interface DomainSimilarity
public java.util.SortedSet<Species> getSpecies()
getSpecies
in interface DomainSimilarity
public java.util.List<Species> getSpeciesCustomOrder()
public java.util.SortedMap<Species,org.forester.surfacing.SpeciesSpecificDomainSimilariyData> getSpeciesData()
DomainSimilarity
getSpeciesData
in interface DomainSimilarity
public double getStandardDeviationOfSimilarityScore()
getStandardDeviationOfSimilarityScore
in interface DomainSimilarity
public void setDetailedness(DomainSimilarityCalculator.Detailedness detailedness)
public void setGoAnnotationOutput(DomainSimilarityCalculator.GoAnnotationOutput go_annotation_output)
public void setGoNamespaceLimit(GoNameSpace go_namespace_limit)
public void setSpeciesOrder(java.util.List<Species> species_order)
public java.lang.String toString()
toString
in class java.lang.Object
public java.lang.StringBuffer toStringBuffer(PrintableDomainSimilarity.PRINT_OPTION print_option)
toStringBuffer
in interface DomainSimilarity