org.forester.surfacing
Class PrintableDomainSimilarity
java.lang.Object
org.forester.surfacing.PrintableDomainSimilarity
- All Implemented Interfaces:
- Comparable<DomainSimilarity>, DomainSimilarity
public class PrintableDomainSimilarity
- extends Object
- implements DomainSimilarity
Constructor Summary |
PrintableDomainSimilarity(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.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. |
SPECIES_SEPARATOR
public static final String SPECIES_SEPARATOR
- See Also:
- Constant Field Values
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,
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.
compareTo
public int compareTo(DomainSimilarity domain_similarity)
- Specified by:
compareTo
in interface Comparable<DomainSimilarity>
getCombinableDomainIds
public 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 SortedSet<Species> getSpecies()
- Specified by:
getSpecies
in interface DomainSimilarity
getSpeciesCustomOrder
public List<Species> getSpeciesCustomOrder()
getSpeciesData
public 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(Map<GoId,GoTerm> go_id_to_term_map)
setGoNamespaceLimit
public void setGoNamespaceLimit(GoNameSpace go_namespace_limit)
setSpeciesOrder
public void setSpeciesOrder(List<Species> species_order)
toString
public String toString()
- Overrides:
toString
in class Object
toStringBuffer
public StringBuffer toStringBuffer(PrintableDomainSimilarity.PRINT_OPTION print_option)
- Specified by:
toStringBuffer
in interface DomainSimilarity