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fixed issue with cutting off of long names in pdf export + minor changes
[jalview.git]
/
forester
/
java
/
src
/
org
/
forester
/
surfacing
/
DirectedCombinableDomains.java
diff --git
a/forester/java/src/org/forester/surfacing/DirectedCombinableDomains.java
b/forester/java/src/org/forester/surfacing/DirectedCombinableDomains.java
index
24943a1
..
35f73f8
100644
(file)
--- a/
forester/java/src/org/forester/surfacing/DirectedCombinableDomains.java
+++ b/
forester/java/src/org/forester/surfacing/DirectedCombinableDomains.java
@@
-22,26
+22,29
@@
// 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.ArrayList;
import java.util.List;
package org.forester.surfacing;
import java.util.ArrayList;
import java.util.List;
+import org.forester.protein.BinaryDomainCombination;
+import org.forester.species.Species;
+
public class DirectedCombinableDomains extends BasicCombinableDomains {
public class DirectedCombinableDomains extends BasicCombinableDomains {
- public DirectedCombinableDomains( final DomainId n_terminal_key_domain, final Species species ) {
+ public DirectedCombinableDomains( final String n_terminal_key_domain, final Species species ) {
super( n_terminal_key_domain, species );
}
@Override
public List<BinaryDomainCombination> toBinaryDomainCombinations() {
final List<BinaryDomainCombination> binary_combinations = new ArrayList<BinaryDomainCombination>( getNumberOfCombinableDomains() );
super( n_terminal_key_domain, species );
}
@Override
public List<BinaryDomainCombination> toBinaryDomainCombinations() {
final List<BinaryDomainCombination> binary_combinations = new ArrayList<BinaryDomainCombination>( getNumberOfCombinableDomains() );
- for( final DomainId domain : getCombiningDomains().keySet() ) {
+ for( final String domain : getCombiningDomains().keySet() ) {
// Precondition (!): key domain is most upstream domain.
//TODO ensure this is true.
// Precondition (!): key domain is most upstream domain.
//TODO ensure this is true.
- binary_combinations.add( new DirectedBinaryDomainCombination( getKeyDomain(), domain ) );
+ binary_combinations.add( DirectedBinaryDomainCombination.obtainInstance( getKeyDomain(), domain ) );
}
return binary_combinations;
}
}
return binary_combinations;
}