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[jalview.git]
/
forester
/
java
/
src
/
org
/
forester
/
surfacing
/
DomainSimilarity.java
diff --git
a/forester/java/src/org/forester/surfacing/DomainSimilarity.java
b/forester/java/src/org/forester/surfacing/DomainSimilarity.java
index
be7273e
..
5a0735e
100644
(file)
--- a/
forester/java/src/org/forester/surfacing/DomainSimilarity.java
+++ b/
forester/java/src/org/forester/surfacing/DomainSimilarity.java
@@
-30,6
+30,7
@@
import java.util.Map;
import java.util.SortedMap;
import java.util.SortedSet;
import java.util.SortedMap;
import java.util.SortedSet;
+import org.forester.phylogeny.Phylogeny;
import org.forester.species.Species;
import org.forester.surfacing.PrintableDomainSimilarity.PRINT_OPTION;
import org.forester.species.Species;
import org.forester.surfacing.PrintableDomainSimilarity.PRINT_OPTION;
@@
-97,9
+98,11
@@
public interface DomainSimilarity extends Comparable<DomainSimilarity> {
*
* @return SortedMap<String, SpeciesSpecificDomainSimilariyData>
*/
*
* @return SortedMap<String, SpeciesSpecificDomainSimilariyData>
*/
- public SortedMap<Species, SpeciesSpecificDomainSimilariyData> getSpeciesData();
+ public SortedMap<Species, SpeciesSpecificDcData> getSpeciesData();
public double getStandardDeviationOfSimilarityScore();
public double getStandardDeviationOfSimilarityScore();
- public StringBuffer toStringBuffer( PRINT_OPTION print_option, Map<String, Integer> tax_code_to_id_map );
+ public StringBuffer toStringBuffer( PRINT_OPTION print_option,
+ Map<String, Integer> tax_code_to_id_map,
+ Phylogeny phy );
}
}