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version 0.9910 beta
[jalview.git]
/
forester
/
java
/
src
/
org
/
forester
/
phylogeny
/
data
/
ProteinDomain.java
diff --git
a/forester/java/src/org/forester/phylogeny/data/ProteinDomain.java
b/forester/java/src/org/forester/phylogeny/data/ProteinDomain.java
index
5bb947a
..
921ff25
100644
(file)
--- a/
forester/java/src/org/forester/phylogeny/data/ProteinDomain.java
+++ b/
forester/java/src/org/forester/phylogeny/data/ProteinDomain.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.phylogeny.data;
package org.forester.phylogeny.data;
@@
-33,7
+33,7
@@
import org.forester.util.ForesterUtil;
public class ProteinDomain implements PhylogenyData {
public class ProteinDomain implements PhylogenyData {
- final public static double CONFIDENCE_DEFAULT = 0.0;
+ final public static double CONFIDENCE_DEFAULT = -1;
final public static String IDENTIFIER_DEFAULT = "";
final private String _name;
final private int _from;
final public static String IDENTIFIER_DEFAULT = "";
final private String _name;
final private int _from;
@@
-78,7
+78,7
@@
public class ProteinDomain implements PhylogenyData {
sb.append( " " );
sb.append( getId() );
}
sb.append( " " );
sb.append( getId() );
}
- if ( getConfidence() != CONFIDENCE_DEFAULT ) {
+ if ( getConfidence() >= 0 ) {
sb.append( " " );
sb.append( getConfidence() );
}
sb.append( " " );
sb.append( getConfidence() );
}
@@
-107,7
+107,7
@@
public class ProteinDomain implements PhylogenyData {
}
public int getLength() {
}
public int getLength() {
- return ( getTo() - getFrom() + 1 );
+ return ( ( getTo() - getFrom() ) + 1 );
}
public String getName() {
}
public String getName() {