X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Fphylogeny%2Fdata%2FProteinDomain.java;h=921ff2577fb5d32f3ab7bae1b14e741661183683;hb=5cad5dbd4f9e8cf09a123d4ee490cf314c05fd2f;hp=5bb947a98235080cf5ae83e27d96cdfa08dbc82f;hpb=eee996a6476a1e3d84c07f8f690dcde3ff4b2ef5;p=jalview.git

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
--- 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
-// WWW: www.phylosoft.org/forester
+// WWW: https://sites.google.com/site/cmzmasek/home/software/forester
 
 package org.forester.phylogeny.data;
 
@@ -33,7 +33,7 @@ import org.forester.util.ForesterUtil;
 
 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;
@@ -78,7 +78,7 @@ public class ProteinDomain implements PhylogenyData {
             sb.append( " " );
             sb.append( getId() );
         }
-        if ( getConfidence() != CONFIDENCE_DEFAULT ) {
+        if ( getConfidence() >= 0 ) {
             sb.append( " " );
             sb.append( getConfidence() );
         }
@@ -107,7 +107,7 @@ public class ProteinDomain implements PhylogenyData {
     }
 
     public int getLength() {
-        return ( getTo() - getFrom() + 1 );
+        return ( ( getTo() - getFrom() ) + 1 );
     }
 
     public String getName() {