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further reduction of NHX fields
[jalview.git]
/
forester
/
java
/
src
/
org
/
forester
/
phylogeny
/
data
/
NodeData.java
diff --git
a/forester/java/src/org/forester/phylogeny/data/NodeData.java
b/forester/java/src/org/forester/phylogeny/data/NodeData.java
index
d0a7fc2
..
fd8e460
100644
(file)
--- a/
forester/java/src/org/forester/phylogeny/data/NodeData.java
+++ b/
forester/java/src/org/forester/phylogeny/data/NodeData.java
@@
-23,7
+23,7
@@
// 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;
@@
-38,6
+38,17
@@
import org.forester.util.ForesterUtil;
public class NodeData implements PhylogenyData {
public class NodeData implements PhylogenyData {
+ public enum NODE_DATA {
+ NODE_NAME,
+ EVENT,
+ SEQUENCE_NAME,
+ SEQUENCE_SYMBOL,
+ SEQUENCE_MOL_SEQ,
+ SEQUENCE_ACC,
+ TAXONOMY_SCIENTIFIC_NAME,
+ TAXONOMY_CODE,
+ UNKNOWN;
+ }
private String _node_name;
private Event _event;
private List<Sequence> _sequences;
private String _node_name;
private Event _event;
private List<Sequence> _sequences;
@@
-281,7
+292,7
@@
public class NodeData implements PhylogenyData {
}
public boolean isHasProperties() {
}
public boolean isHasProperties() {
- return getProperties() != null;
+ return ( getProperties() != null ) && ( getProperties().size() > 0 );
}
public boolean isHasReference() {
}
public boolean isHasReference() {
@@
-429,9
+440,6
@@
public class NodeData implements PhylogenyData {
@Override
public StringBuffer toNHX() {
final StringBuffer sb = new StringBuffer();
@Override
public StringBuffer toNHX() {
final StringBuffer sb = new StringBuffer();
- if ( isHasNodeIdentifier() ) {
- sb.append( getNodeIdentifier().toNHX() );
- }
if ( isHasTaxonomy() ) {
sb.append( getTaxonomy().toNHX() );
}
if ( isHasTaxonomy() ) {
sb.append( getTaxonomy().toNHX() );
}
@@
-441,9
+449,6
@@
public class NodeData implements PhylogenyData {
if ( isHasEvent() ) {
sb.append( getEvent().toNHX() );
}
if ( isHasEvent() ) {
sb.append( getEvent().toNHX() );
}
- if ( isHasProperties() ) {
- sb.append( getProperties().toNHX() );
- }
return sb;
}
return sb;
}