X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Fphylogeny%2Fdata%2FPhylogenyDataUtil.java;h=48da0e01a0bdfaf983a55ac6befd771706d7b4a6;hb=5cad5dbd4f9e8cf09a123d4ee490cf314c05fd2f;hp=f430477aa8598efac8b5be17ca97daf1b245d5e4;hpb=eee996a6476a1e3d84c07f8f690dcde3ff4b2ef5;p=jalview.git

diff --git a/forester/java/src/org/forester/phylogeny/data/PhylogenyDataUtil.java b/forester/java/src/org/forester/phylogeny/data/PhylogenyDataUtil.java
index f430477..48da0e0 100644
--- a/forester/java/src/org/forester/phylogeny/data/PhylogenyDataUtil.java
+++ b/forester/java/src/org/forester/phylogeny/data/PhylogenyDataUtil.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;
 
@@ -35,6 +35,9 @@ import org.forester.util.ForesterUtil;
 
 public final class PhylogenyDataUtil {
 
+    /** Value of -99.0 is used as default value. */
+    public final static double BRANCH_LENGTH_DEFAULT = -1024.0;
+
     public static void appendClose( final Writer w, final String element_name ) throws IOException {
         w.write( "</" );
         w.write( element_name );
@@ -101,6 +104,18 @@ public final class PhylogenyDataUtil {
 
     public static void appendElement( final Writer w,
                                       final String element_name,
+                                      final String value,
+                                      final String attribute1_name,
+                                      final String attribute1_value,
+                                      final String attribute2_name,
+                                      final String attribute2_value ) throws IOException {
+        appendOpen( w, element_name, attribute1_name, attribute1_value, attribute2_name, attribute2_value );
+        w.write( replaceIllegalXmlCharacters( value ) );
+        appendClose( w, element_name );
+    }
+
+    public static void appendElement( final Writer w,
+                                      final String element_name,
                                       final String attribute1_name,
                                       final String attribute1_value,
                                       final String attribute2_name,
@@ -336,7 +351,7 @@ public final class PhylogenyDataUtil {
 
     /**
      * Creates a deep copy of ArrayList of PhylogenyData objects.
-     * 
+     *
      * @param list
      *            an ArrayList of PhylogenyData objects
      * @return a deep copy of ArrayList list
@@ -356,12 +371,6 @@ public final class PhylogenyDataUtil {
                     org.forester.util.ForesterUtil.roundToInt( y2 ) );
     }
 
-    public static void drawString( final String str, final double x, final double y, final Graphics g ) {
-        g.drawString( str,
-                      org.forester.util.ForesterUtil.roundToInt( x ),
-                      org.forester.util.ForesterUtil.roundToInt( y ) );
-    }
-
     public static String replaceIllegalXmlCharacters( final String value ) {
         String v = value.replaceAll( "&", "&amp;" );
         v = v.replaceAll( "<", "&lt;" );