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more test for isDuplication() and isSpecation() added (phyloXML encoded
[jalview.git]
/
forester
/
java
/
src
/
org
/
forester
/
protein
/
BinaryDomainCombination.java
diff --git
a/forester/java/src/org/forester/protein/BinaryDomainCombination.java
b/forester/java/src/org/forester/protein/BinaryDomainCombination.java
index
02bd7f8
..
4013904
100644
(file)
--- a/
forester/java/src/org/forester/protein/BinaryDomainCombination.java
+++ b/
forester/java/src/org/forester/protein/BinaryDomainCombination.java
@@
-21,7
+21,7
@@
// 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.protein;
package org.forester.protein;
@@
-29,23
+29,17
@@
public interface BinaryDomainCombination extends Comparable<BinaryDomainCombinat
public static final String SEPARATOR = "=";
public static final String SEPARATOR = "=";
- public DomainId getId0();
+ public String getId0();
- public DomainId getId1();
+ public String getId1();
- public abstract StringBuffer toGraphDescribingLanguage( final OutputFormat format,
- final String node_attribute,
- String edge_attribute );
+ short getId0Code();
- /**
- * This has to return a String representation
- * in the following format:
- * id0 - id1
- *
- * @return a String representation in the form id0 - id1
- */
- @Override
- public String toString();
+ short getId1Code();
+
+ public StringBuffer toGraphDescribingLanguage( final OutputFormat format,
+ final String node_attribute,
+ String edge_attribute );
public static enum DomainCombinationType {
BASIC, DIRECTED, DIRECTED_ADJACTANT;
public static enum DomainCombinationType {
BASIC, DIRECTED, DIRECTED_ADJACTANT;