inprogress

diff --git a/forester/java/src/org/forester/io/parsers/phyloxml/PhyloXmlHandler.java b/forester/java/src/org/forester/io/parsers/phyloxml/PhyloXmlHandler.java
index ec05952..d33cb74 100644 (file)
--- a/forester/java/src/org/forester/io/parsers/phyloxml/PhyloXmlHandler.java
+++ b/forester/java/src/org/forester/io/parsers/phyloxml/PhyloXmlHandler.java
@@ -55,6 +55,7 @@ import org.forester.phylogeny.data.Date;
 import org.forester.phylogeny.data.Distribution;
 import org.forester.phylogeny.data.Event;
 import org.forester.phylogeny.data.Identifier;
+import org.forester.phylogeny.data.NodeVisualData;
 import org.forester.phylogeny.data.PhylogenyDataUtil;
 import org.forester.phylogeny.data.PropertiesMap;
 import org.forester.phylogeny.data.Property;
@@ -322,11 +323,20 @@ public final class PhyloXmlHandler extends DefaultHandler {
                 node.getNodeData().setEvent( ( Event ) EventParser.getInstance().parse( element ) );
             }
             else if ( qualified_name.equals( PhyloXmlMapping.PROPERTY ) ) {
-                if ( !node.getNodeData().isHasProperties() ) {
-                    node.getNodeData().setProperties( new PropertiesMap() );
+                final Property prop = ( Property ) PropertyParser.getInstance().parse( element );
+                if ( prop.getRef().startsWith( NodeVisualData.APTX_VISUALIZATION_REF ) ) {
+                    if ( node.getNodeData().getNodeVisualData() == null ) {
+                        node.getNodeData().setNodeVisualData( new NodeVisualData() );
+                    }
+                    final NodeVisualData vd = node.getNodeData().getNodeVisualData();
+                    vd.parseProperty( prop );
+                }
+                else {
+                    if ( !node.getNodeData().isHasProperties() ) {
+                        node.getNodeData().setProperties( new PropertiesMap() );
+                    }
+                    node.getNodeData().getProperties().addProperty( prop );
                 }
-                node.getNodeData().getProperties()
-                        .addProperty( ( Property ) PropertyParser.getInstance().parse( element ) );
             }
         }
     }

diff --git a/forester/java/src/org/forester/phylogeny/data/NodeData.java b/forester/java/src/org/forester/phylogeny/data/NodeData.java
index 7e180d4..add11c9 100644 (file)
--- a/forester/java/src/org/forester/phylogeny/data/NodeData.java
+++ b/forester/java/src/org/forester/phylogeny/data/NodeData.java
@@ -488,6 +488,9 @@ public class NodeData implements PhylogenyData {
         if ( isHasProperties() ) {
             getProperties().toPhyloXML( writer, level, indentation.substring( 0, indentation.length() - 2 ) );
         }
+        if ( ( level == 0 ) && ( getNodeVisualData() != null ) && !getNodeVisualData().isEmpty() ) {
+            getNodeVisualData().toPhyloXML( writer, level, indentation.substring( 0, indentation.length() - 2 ) );
+        }
         if ( ( getVector() != null )
                 && !getVector().isEmpty()
                 && ( ( getProperties() == null ) || getProperties()

diff --git a/forester/java/src/org/forester/phylogeny/data/NodeVisualData.java b/forester/java/src/org/forester/phylogeny/data/NodeVisualData.java
index c295a95..79faa7f 100644 (file)
--- a/forester/java/src/org/forester/phylogeny/data/NodeVisualData.java
+++ b/forester/java/src/org/forester/phylogeny/data/NodeVisualData.java
@@ -13,22 +13,31 @@ import org.forester.util.ForesterUtil;
 \r
 public final class NodeVisualData implements PhylogenyData {\r
 \r
-    public static final String SIZE_REF             = "aptx_visualiation:node_size";\r
-    public static final String SIZE_TYPE            = "xsd:decimal";\r
-    private static final byte  DEFAULT_FONT_SIZE    = -1;\r
-    private static final int   DEFAULT_SIZE         = -1;\r
-    private static final int   DEFAULT_TRANSPARANCY = -1;\r
+    public static final String APTX_VISUALIZATION_REF = "aptx_visualization:";\r
+    public static final String FONT_REF               = APTX_VISUALIZATION_REF + "node_font";\r
+    public static final String FONT_SIZE_REF          = APTX_VISUALIZATION_REF + "node_font_size";\r
+    public static final String FONT_SIZE_TYPE         = "xsd:unsignedByte";\r
+    public static final String FONT_STYLE_BOLD        = "bold";\r
+    public static final String FONT_STYLE_BOLD_ITALIC = "bold_italic";\r
+    public static final String FONT_STYLE_ITALIC      = "italic";\r
+    public static final String FONT_STYLE_PLAIN       = "plain";\r
+    public static final String FONT_STYLE_REF         = APTX_VISUALIZATION_REF + "node_font_style";\r
+    public static final String FONT_STYLE_TYPE        = "xsd:token";\r
+    public static final String FONT_TYPE              = "xsd:token";\r
+    private static final byte  DEFAULT_FONT_SIZE      = -1;\r
+    private static final int   DEFAULT_SIZE           = -1;\r
+    private static final int   DEFAULT_TRANSPARANCY   = -1;\r
     private Color              _border_color;\r
     private Color              _fill_color;\r
     private NodeFill           _fill_type;\r
-    private String             _font_name;\r
+    private Font               _font;\r
     private Color              _font_color;\r
+    private String             _font_name;\r
     private byte               _font_size;\r
     private FontType           _font_style;\r
     private NodeShape          _shape;\r
     private float              _size;\r
     private float              _transparancy;\r
-    private Font               _font;\r
 \r
     public NodeVisualData() {\r
         init();\r
@@ -96,14 +105,25 @@ public final class NodeVisualData implements PhylogenyData {
         return _fill_type;\r
     }\r
 \r
-    public final String getFontName() {\r
-        return _font_name;\r
+    public final Font getFont() {\r
+        if ( _font != null ) {\r
+            return _font;\r
+        }\r
+        else if ( !ForesterUtil.isEmpty( getFontName() ) ) {\r
+            _font = new Font( getFontName(), getFontStyleInt(), getFontSize() );\r
+            return _font;\r
+        }\r
+        return null;\r
     }\r
 \r
     public final Color getFontColor() {\r
         return _font_color;\r
     }\r
 \r
+    public final String getFontName() {\r
+        return _font_name;\r
+    }\r
+\r
     public final byte getFontSize() {\r
         return _font_size;\r
     }\r
@@ -112,6 +132,19 @@ public final class NodeVisualData implements PhylogenyData {
         return _font_style;\r
     }\r
 \r
+    public final int getFontStyleInt() {\r
+        if ( getFontStyle() == FontType.BOLD ) {\r
+            return Font.BOLD;\r
+        }\r
+        else if ( getFontStyle() == FontType.ITALIC ) {\r
+            return Font.ITALIC;\r
+        }\r
+        else if ( getFontStyle() == FontType.BOLD_ITALIC ) {\r
+            return Font.BOLD + Font.ITALIC;\r
+        }\r
+        return Font.PLAIN;\r
+    }\r
+\r
     public final NodeShape getShape() {\r
         return _shape;\r
     }\r
@@ -136,6 +169,27 @@ public final class NodeVisualData implements PhylogenyData {
         throw new UnsupportedOperationException();\r
     }\r
 \r
+    public void parseProperty( final Property prop ) {\r
+        if ( prop.getRef().equals( FONT_REF ) ) {\r
+            setFontName( prop.getValue().trim() );\r
+        }\r
+        else if ( prop.getRef().equals( FONT_SIZE_REF ) ) {\r
+            int s = -1;\r
+            try {\r
+                s = Integer.parseInt( prop.getValue() );\r
+            }\r
+            catch ( final NumberFormatException e ) {\r
+                return;\r
+            }\r
+            if ( ( s >= 0 ) && ( s < Byte.MAX_VALUE ) ) {\r
+                setFontSize( s );\r
+            }\r
+        }\r
+        else if ( prop.getRef().equals( FONT_STYLE_REF ) ) {\r
+            setFontStyle( prop.getValue() );\r
+        }\r
+    }\r
+\r
     public final void setBorderColor( final Color border_color ) {\r
         _border_color = border_color;\r
     }\r
@@ -148,6 +202,10 @@ public final class NodeVisualData implements PhylogenyData {
         _fill_type = fill_type;\r
     }\r
 \r
+    public final void setFontColor( final Color font_color ) {\r
+        _font_color = font_color;\r
+    }\r
+\r
     public final void setFontName( final String font_name ) {\r
         if ( !ForesterUtil.isEmpty( font_name ) ) {\r
             _font_name = font_name;\r
@@ -158,10 +216,6 @@ public final class NodeVisualData implements PhylogenyData {
         _font = null;\r
     }\r
 \r
-    public final void setFontColor( final Color font_color ) {\r
-        _font_color = font_color;\r
-    }\r
-\r
     public final void setFontSize( final int font_size ) {\r
         if ( ( font_size != DEFAULT_FONT_SIZE ) && ( font_size < 0 ) ) {\r
             throw new IllegalArgumentException( "negative font size: " + font_size );\r
@@ -193,6 +247,21 @@ public final class NodeVisualData implements PhylogenyData {
         }\r
     }\r
 \r
+    public final void setFontStyle( final String font_style ) {\r
+        if ( font_style.equalsIgnoreCase( FONT_STYLE_BOLD ) ) {\r
+            setFontStyle( FontType.BOLD );\r
+        }\r
+        else if ( font_style.equalsIgnoreCase( FONT_STYLE_ITALIC ) ) {\r
+            setFontStyle( FontType.ITALIC );\r
+        }\r
+        else if ( font_style.equalsIgnoreCase( FONT_STYLE_BOLD_ITALIC ) ) {\r
+            setFontStyle( FontType.BOLD_ITALIC );\r
+        }\r
+        else {\r
+            setFontStyle( FontType.PLAIN );\r
+        }\r
+    }\r
+\r
     public final void setShape( final NodeShape shape ) {\r
         _shape = shape;\r
     }\r
@@ -205,30 +274,6 @@ public final class NodeVisualData implements PhylogenyData {
         _transparancy = transparancy;\r
     }\r
 \r
-    public final int getFontStyleInt() {\r
-        if ( getFontStyle() == FontType.BOLD ) {\r
-            return Font.BOLD;\r
-        }\r
-        else if ( getFontStyle() == FontType.ITALIC ) {\r
-            return Font.ITALIC;\r
-        }\r
-        else if ( getFontStyle() == FontType.BOLD_ITALIC ) {\r
-            return Font.BOLD + Font.ITALIC;\r
-        }\r
-        return Font.PLAIN;\r
-    }\r
-\r
-    public final Font getFont() {\r
-        if ( _font != null ) {\r
-            return _font;\r
-        }\r
-        else if ( !ForesterUtil.isEmpty( getFontName() ) ) {\r
-            _font = new Font( getFontName(), getFontStyleInt(), getFontSize() );\r
-            return _font;\r
-        }\r
-        return null;\r
-    }\r
-\r
     @Override\r
     public final StringBuffer toNHX() {\r
         throw new UnsupportedOperationException();\r
@@ -236,7 +281,9 @@ public final class NodeVisualData implements PhylogenyData {
 \r
     @Override\r
     public final void toPhyloXML( final Writer writer, final int level, final String indentation ) throws IOException {\r
-        throw new UnsupportedOperationException();\r
+        for( final Property p : toProperties() ) {\r
+            p.toPhyloXML( writer, level, indentation );\r
+        }\r
     }\r
 \r
     @Override\r
@@ -260,12 +307,29 @@ public final class NodeVisualData implements PhylogenyData {
 \r
     private final List<Property> toProperties() {\r
         final List<Property> properties = new ArrayList<Property>();\r
-        properties.add( new Property( SIZE_REF, String.valueOf( getSize() ), "", SIZE_TYPE, AppliesTo.NODE ) );\r
-        properties.add( new Property( SIZE_REF, String.valueOf( getShape() ), "", SIZE_TYPE, AppliesTo.NODE ) );\r
-        properties.add( new Property( SIZE_REF, String.valueOf( getFillType() ), "", SIZE_TYPE, AppliesTo.NODE ) );\r
-        properties.add( new Property( SIZE_REF, String.valueOf( getTransparancy() ), "", SIZE_TYPE, AppliesTo.NODE ) );\r
-        properties.add( new Property( SIZE_REF, String.valueOf( getFillColor() ), "", SIZE_TYPE, AppliesTo.NODE ) );\r
-        properties.add( new Property( SIZE_REF, String.valueOf( getBorderColor() ), "", SIZE_TYPE, AppliesTo.NODE ) );\r
+        if ( !ForesterUtil.isEmpty( getFontName() ) ) {\r
+            properties.add( new Property( FONT_REF, getFontName(), "", FONT_TYPE, AppliesTo.NODE ) );\r
+        }\r
+        if ( getFontSize() != DEFAULT_FONT_SIZE ) {\r
+            properties.add( new Property( FONT_SIZE_REF,\r
+                                          String.valueOf( getFontSize() ),\r
+                                          "",\r
+                                          FONT_SIZE_TYPE,\r
+                                          AppliesTo.NODE ) );\r
+        }\r
+        if ( getFontStyle() != FontType.PLAIN ) {\r
+            String font_style = FONT_STYLE_PLAIN;\r
+            if ( getFontStyle() == FontType.ITALIC ) {\r
+                font_style = FONT_STYLE_ITALIC;\r
+            }\r
+            else if ( getFontStyle() == FontType.BOLD ) {\r
+                font_style = FONT_STYLE_BOLD;\r
+            }\r
+            else if ( getFontStyle() == FontType.BOLD_ITALIC ) {\r
+                font_style = FONT_STYLE_BOLD_ITALIC;\r
+            }\r
+            properties.add( new Property( FONT_STYLE_REF, font_style, "", FONT_STYLE_TYPE, AppliesTo.NODE ) );\r
+        }\r
         return properties;\r
     }\r
 \r