org.forester.surfacing

Class PrintableDomainSimilarity

java.lang.Object

org.forester.surfacing.PrintableDomainSimilarity

All Implemented Interfaces:

java.lang.Comparable<DomainSimilarity>, DomainSimilarity

public class PrintableDomainSimilarity
extends java.lang.Object
implements DomainSimilarity

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	PrintableDomainSimilarity.PRINT_OPTION

Nested classes/interfaces inherited from interface org.forester.surfacing.DomainSimilarity

DomainSimilarity.DomainSimilarityScoring, DomainSimilarity.DomainSimilaritySortField

Field Summary

Fields

Modifier and Type	Field and Description
static java.lang.String	SPECIES_SEPARATOR

Constructor Summary

Constructors

Constructor and Description

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.

Method Summary

Methods

Modifier and Type	Method and Description
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)

Methods inherited from class java.lang.Object

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

Field Detail

SPECIES_SEPARATOR

public static final java.lang.String SPECIES_SEPARATOR

See Also:

Constant Field Values

Constructor Detail

PrintableDomainSimilarity

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)

If go_id_to_term_map not null, detailed GO information is written, only GO ids otherwise.

Method Detail

compareTo

public int compareTo(DomainSimilarity domain_similarity)

Specified by:

compareTo in interface java.lang.Comparable<DomainSimilarity>

getCombinableDomainIds

public java.util.SortedSet<DomainId> getCombinableDomainIds(Species species_of_combinable_domain)

Specified by:

getCombinableDomainIds in interface DomainSimilarity

getDomainId

public DomainId getDomainId()

Specified by:

getDomainId in interface DomainSimilarity

getGoNamespaceLimit

public GoNameSpace getGoNamespaceLimit()

getMaximalDifference

public int getMaximalDifference()

Description copied from interface: DomainSimilarity

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

Specified by:

getMaximalDifference in interface DomainSimilarity

Returns:

getMaximalDifferenceInCounts

public int getMaximalDifferenceInCounts()

Description copied from interface: DomainSimilarity

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

Specified by:

getMaximalDifferenceInCounts in interface DomainSimilarity

Returns:

the (maximal) difference in counts

getMaximalSimilarityScore

public double getMaximalSimilarityScore()

Specified by:

getMaximalSimilarityScore in interface DomainSimilarity

getMeanSimilarityScore

public double getMeanSimilarityScore()

Specified by:

getMeanSimilarityScore in interface DomainSimilarity

getMinimalSimilarityScore

public double getMinimalSimilarityScore()

Specified by:

getMinimalSimilarityScore in interface DomainSimilarity

getN

public int getN()

Description copied from interface: DomainSimilarity

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

Specified by:

getN in interface DomainSimilarity

Returns:

the number of pairwise distances

getSpecies

public java.util.SortedSet<Species> getSpecies()

Specified by:

getSpecies in interface DomainSimilarity

getSpeciesCustomOrder

public java.util.List<Species> getSpeciesCustomOrder()

getSpeciesData

public java.util.SortedMap<Species,org.forester.surfacing.SpeciesSpecificDomainSimilariyData> getSpeciesData()

Description copied from interface: DomainSimilarity

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

Specified by:

getSpeciesData in interface DomainSimilarity

Returns:

SortedMap

getStandardDeviationOfSimilarityScore

public double getStandardDeviationOfSimilarityScore()

Specified by:

getStandardDeviationOfSimilarityScore in interface DomainSimilarity

setDetailedness

public void setDetailedness(DomainSimilarityCalculator.Detailedness detailedness)

setGoAnnotationOutput

public void setGoAnnotationOutput(DomainSimilarityCalculator.GoAnnotationOutput go_annotation_output)

setGoIdToTermMap

public void setGoIdToTermMap(java.util.Map<GoId,GoTerm> go_id_to_term_map)

setGoNamespaceLimit

public void setGoNamespaceLimit(GoNameSpace go_namespace_limit)

setSpeciesOrder

public void setSpeciesOrder(java.util.List<Species> species_order)

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object

toStringBuffer

public java.lang.StringBuffer toStringBuffer(PrintableDomainSimilarity.PRINT_OPTION print_option)

Specified by:

toStringBuffer in interface DomainSimilarity