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=81155ff02d91aac2f55d315b94e9be72924658de;hpb=48f7a89be9d34f1930a1f863e608235cc27184c5;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 81155ff..921ff25 100644
--- a/forester/java/src/org/forester/phylogeny/data/ProteinDomain.java
+++ b/forester/java/src/org/forester/phylogeny/data/ProteinDomain.java
@@ -5,7 +5,7 @@
 // Copyright (C) 2008-2009 Christian M. Zmasek
 // Copyright (C) 2008-2009 Burnham Institute for Medical Research
 // All rights reserved
-// 
+//
 // This library is free software; you can redistribute it and/or
 // modify it under the terms of the GNU Lesser General Public
 // License as published by the Free Software Foundation; either
@@ -15,13 +15,13 @@
 // but WITHOUT ANY WARRANTY; without even the implied warranty of
 // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
 // Lesser General Public License for more details.
-// 
+//
 // You should have received a copy of the GNU Lesser General Public
 // License along with this library; if not, write to the Free Software
 // 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;
@@ -64,10 +64,12 @@ public class ProteinDomain implements PhylogenyData {
         _confidence = confidence;
     }
 
+    @Override
     public StringBuffer asSimpleText() {
         return new StringBuffer( getName() );
     }
 
+    @Override
     public StringBuffer asText() {
         final StringBuffer sb = new StringBuffer( getName() );
         sb.append( " [" );
@@ -76,7 +78,7 @@ public class ProteinDomain implements PhylogenyData {
             sb.append( " " );
             sb.append( getId() );
         }
-        if ( getConfidence() != CONFIDENCE_DEFAULT ) {
+        if ( getConfidence() >= 0 ) {
             sb.append( " " );
             sb.append( getConfidence() );
         }
@@ -84,6 +86,7 @@ public class ProteinDomain implements PhylogenyData {
         return sb;
     }
 
+    @Override
     public PhylogenyData copy() {
         if ( getId() == null ) {
             return new ProteinDomain( getName(), getFrom(), getTo(), getConfidence() );
@@ -104,7 +107,7 @@ public class ProteinDomain implements PhylogenyData {
     }
 
     public int getLength() {
-        return ( getTo() - getFrom() + 1 );
+        return ( ( getTo() - getFrom() ) + 1 );
     }
 
     public String getName() {
@@ -115,6 +118,7 @@ public class ProteinDomain implements PhylogenyData {
         return _to;
     }
 
+    @Override
     public boolean isEqual( final PhylogenyData protein_domain ) {
         if ( protein_domain == null ) {
             return false;
@@ -131,10 +135,12 @@ public class ProteinDomain implements PhylogenyData {
         return true;
     }
 
+    @Override
     public StringBuffer toNHX() {
         throw new UnsupportedOperationException();
     }
 
+    @Override
     public void toPhyloXML( final Writer writer, final int level, final String indentation ) throws IOException {
         writer.write( ForesterUtil.LINE_SEPARATOR );
         writer.write( indentation );