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[jalview.git]
/
forester
/
java
/
src
/
org
/
forester
/
surfacing
/
CombinationsBasedPairwiseDomainSimilarityCalculator.java
diff --git
a/forester/java/src/org/forester/surfacing/CombinationsBasedPairwiseDomainSimilarityCalculator.java
b/forester/java/src/org/forester/surfacing/CombinationsBasedPairwiseDomainSimilarityCalculator.java
index
965f595
..
feda0bc
100644
(file)
--- a/
forester/java/src/org/forester/surfacing/CombinationsBasedPairwiseDomainSimilarityCalculator.java
+++ b/
forester/java/src/org/forester/surfacing/CombinationsBasedPairwiseDomainSimilarityCalculator.java
@@
-23,14
+23,12
@@
// Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
//
// Contact: phylosoft @ gmail . com
// Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
//
// Contact: phylosoft @ gmail . com
-// WWW: www.phylosoft.org/forester
+// WWW: https://sites.google.com/site/cmzmasek/home/software/forester
package org.forester.surfacing;
import java.util.List;
package org.forester.surfacing;
import java.util.List;
-import org.forester.protein.DomainId;
-
public class CombinationsBasedPairwiseDomainSimilarityCalculator implements PairwiseDomainSimilarityCalculator {
@Override
public class CombinationsBasedPairwiseDomainSimilarityCalculator implements PairwiseDomainSimilarityCalculator {
@Override
@@
-39,11
+37,11
@@
public class CombinationsBasedPairwiseDomainSimilarityCalculator implements Pair
if ( !domains_1.getKeyDomain().equals( domains_2.getKeyDomain() ) ) {
throw new IllegalArgumentException( "attempt to calculate similarity between domain collection with different keys" );
}
if ( !domains_1.getKeyDomain().equals( domains_2.getKeyDomain() ) ) {
throw new IllegalArgumentException( "attempt to calculate similarity between domain collection with different keys" );
}
- final List<DomainId> d1 = domains_1.getCombinableDomains();
- final List<DomainId> d2 = domains_2.getCombinableDomains();
+ final List<String> d1 = domains_1.getCombinableDomains();
+ final List<String> d2 = domains_2.getCombinableDomains();
int same = 0;
int different = 0;
int same = 0;
int different = 0;
- for( final DomainId domain : d1 ) {
+ for( final String domain : d1 ) {
if ( d2.contains( domain ) ) {
same++;
}
if ( d2.contains( domain ) ) {
same++;
}
@@
-51,7
+49,7
@@
public class CombinationsBasedPairwiseDomainSimilarityCalculator implements Pair
different++;
}
}
different++;
}
}
- for( final DomainId domain : d2 ) {
+ for( final String domain : d2 ) {
if ( !( d1.contains( domain ) ) ) {
different++;
}
if ( !( d1.contains( domain ) ) ) {
different++;
}