cleanup

diff --git a/forester/java/src/org/forester/archaeopteryx/MainFrame.java b/forester/java/src/org/forester/archaeopteryx/MainFrame.java
index 0820cbf..7ef6dd6 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/MainFrame.java
+++ b/forester/java/src/org/forester/archaeopteryx/MainFrame.java
@@ -65,7 +65,6 @@ import org.forester.phylogeny.PhylogenyMethods.DESCENDANT_SORT_PRIORITY;
 import org.forester.phylogeny.PhylogenyNode;
 import org.forester.phylogeny.PhylogenyNode.NH_CONVERSION_SUPPORT_VALUE_STYLE;
 import org.forester.phylogeny.data.Annotation;
-
 import org.forester.phylogeny.data.NodeVisualData.NodeFill;
 import org.forester.phylogeny.data.NodeVisualData.NodeShape;
 import org.forester.sdi.GSDI;

diff --git a/forester/java/src/org/forester/archaeopteryx/Options.java b/forester/java/src/org/forester/archaeopteryx/Options.java
index 3a10245..fdaeacb 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/Options.java
+++ b/forester/java/src/org/forester/archaeopteryx/Options.java
@@ -51,8 +51,8 @@ final public class Options {
     private CLADOGRAM_TYPE                    _cladogram_type;
     private boolean                           _color_by_taxonomic_group;
     private boolean                           _color_labels_same_as_parent_branch;
-    private NodeVisualData.NodeFill        _default_node_fill;
-    private NodeVisualData.NodeShape       _default_node_shape;
+    private NodeVisualData.NodeFill           _default_node_fill;
+    private NodeVisualData.NodeShape          _default_node_shape;
     private short                             _default_node_shape_size;
     private boolean                           _editable;
     private NODE_DATA                         _ext_desc_data_to_return;

diff --git a/forester/java/src/org/forester/phylogeny/data/NodeData.java b/forester/java/src/org/forester/phylogeny/data/NodeData.java
index 609b203..7e180d4 100644 (file)
--- a/forester/java/src/org/forester/phylogeny/data/NodeData.java
+++ b/forester/java/src/org/forester/phylogeny/data/NodeData.java
@@ -52,17 +52,17 @@ public class NodeData implements PhylogenyData {
         TAXONOMY_CODE,
         UNKNOWN;
     }
-    private String                  _node_name;
-    private Event                   _event;
-    private List<Sequence>          _sequences;
-    private List<Taxonomy>          _taxonomies;
-    private List<Distribution>      _distributions;
-    private Date                    _date;
-    private BinaryCharacters        _binary_characters;
-    private PropertiesMap           _properties;
-    private List<Reference>         _references;
-    private List<Double>            _vector;
-    private NodeVisualData          _node_visual_data;
+    private String             _node_name;
+    private Event              _event;
+    private List<Sequence>     _sequences;
+    private List<Taxonomy>     _taxonomies;
+    private List<Distribution> _distributions;
+    private Date               _date;
+    private BinaryCharacters   _binary_characters;
+    private PropertiesMap      _properties;
+    private List<Reference>    _references;
+    private List<Double>       _vector;
+    private NodeVisualData     _node_visual_data;
 
     public NodeData() {
         init();
@@ -71,15 +71,15 @@ public class NodeData implements PhylogenyData {
     private void init() {
         _node_name = "";
         _event = null;
-        _sequences= null;
-         _taxonomies= null;
-            _distributions= null;
-                    _date= null;
-           _binary_characters= null;
-                 _properties= null;
-               _references= null;
-                   _vector= null;
-                 _node_visual_data= null;
+        _sequences = null;
+        _taxonomies = null;
+        _distributions = null;
+        _date = null;
+        _binary_characters = null;
+        _properties = null;
+        _references = null;
+        _vector = null;
+        _node_visual_data = null;
     }
 
     public void addDistribution( final Distribution distribution ) {
@@ -162,7 +162,7 @@ public class NodeData implements PhylogenyData {
                 }
             }
         }
-        if ( getNodeVisualData() != null && !getNodeVisualData().isEmpty() ) {
+        if ( ( getNodeVisualData() != null ) && !getNodeVisualData().isEmpty() ) {
             new_data.setNodeVisualData( ( NodeVisualData ) getNodeVisualData().copy() );
         }
         if ( isHasDate() ) {

diff --git a/forester/java/src/org/forester/phylogeny/data/NodeVisualData.java b/forester/java/src/org/forester/phylogeny/data/NodeVisualData.java
index e77016f..e3b19a4 100644 (file)
--- a/forester/java/src/org/forester/phylogeny/data/NodeVisualData.java
+++ b/forester/java/src/org/forester/phylogeny/data/NodeVisualData.java
@@ -1,3 +1,4 @@
+\r
 package org.forester.phylogeny.data;\r
 \r
 import java.awt.Color;\r
@@ -6,45 +7,43 @@ import java.io.Writer;
 import java.util.ArrayList;\r
 import java.util.List;\r
 \r
-\r
 import org.forester.phylogeny.data.Property.AppliesTo;\r
 import org.forester.util.ForesterUtil;\r
 \r
-\r
 public final class NodeVisualData implements PhylogenyData {\r
-    \r
-    private static final int DEFAULT_SIZE = -1;\r
-    private static final int DEFAULT_TRANSPARANCY = -1;\r
-    private static final byte DEFAULT_FONT_SIZE = -1;\r
-    private NodeShape _shape;\r
-    private NodeFill  _fill_type;\r
-    private Color     _border_color;\r
-    private Color     _fill_color;\r
-    \r
-    private String    _font;\r
-    private FontType    _font_type;\r
-    private byte    _font_size;\r
-    private Color    _font_color;\r
-    \r
-    private float    _size;\r
-    private float    _transparancy;\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
+    private Color              _border_color;\r
+    private Color              _fill_color;\r
+    private NodeFill           _fill_type;\r
+    private String             _font;\r
+    private Color              _font_color;\r
+    private byte               _font_size;\r
+    private FontType           _font_type;\r
+    private NodeShape          _shape;\r
+    private float              _size;\r
+    private float              _transparancy;\r
 \r
     public NodeVisualData() {\r
         init();\r
     }\r
 \r
-    public NodeVisualData(    final String font,\r
-                              final FontType    font_type,\r
-                              byte    font_size,\r
-                              Color    font_color,\r
-                              final NodeShape shape,\r
-                              final NodeFill fill_type,\r
-                              final Color border_color,\r
-                              final Color fill_color,\r
-                              final float size,\r
-                              final float transparancy ) {\r
+    public NodeVisualData( final String font,\r
+                           final FontType font_type,\r
+                           final byte font_size,\r
+                           final Color font_color,\r
+                           final NodeShape shape,\r
+                           final NodeFill fill_type,\r
+                           final Color border_color,\r
+                           final Color fill_color,\r
+                           final float size,\r
+                           final float transparancy ) {\r
         setFont( font );\r
-        setFontType(font_type );\r
+        setFontType( font_type );\r
         setFontSize( font_size );\r
         setFontColor( font_color );\r
         setShape( shape );\r
@@ -67,20 +66,20 @@ public final class NodeVisualData implements PhylogenyData {
     }\r
 \r
     @Override\r
-    public final  PhylogenyData copy() {\r
-        return new NodeVisualData(  ForesterUtil.isEmpty( getFont() ) ? new String( getFont()) : null  ,\r
+    public final PhylogenyData copy() {\r
+        return new NodeVisualData( !ForesterUtil.isEmpty( getFont() ) ? new String( getFont() ) : null,\r
                                    getFontType(),\r
                                    getFontSize(),\r
                                    getFontColor() != null ? new Color( getFontColor().getRed(), getFontColor()\r
-                                      .getGreen(), getFontColor().getBlue() ) : null,     \r
+                                           .getGreen(), getFontColor().getBlue() ) : null,\r
                                    getShape(),\r
-                                      getFillType(),\r
-                                      getBorderColor() != null ? new Color( getBorderColor().getRed(), getBorderColor()\r
-                                              .getGreen(), getBorderColor().getBlue() ) : null,\r
-                                      getFillColor() != null ? new Color( getFillColor().getRed(), getFillColor()\r
-                                              .getGreen(), getFillColor().getBlue() ) : null,\r
-                                      getSize(),\r
-                                      getTransparancy() );\r
+                                   getFillType(),\r
+                                   getBorderColor() != null ? new Color( getBorderColor().getRed(), getBorderColor()\r
+                                           .getGreen(), getBorderColor().getBlue() ) : null,\r
+                                   getFillColor() != null ? new Color( getFillColor().getRed(), getFillColor()\r
+                                           .getGreen(), getFillColor().getBlue() ) : null,\r
+                                   getSize(),\r
+                                   getTransparancy() );\r
     }\r
 \r
     public final Color getBorderColor() {\r
@@ -95,6 +94,22 @@ public final class NodeVisualData implements PhylogenyData {
         return _fill_type;\r
     }\r
 \r
+    public final String getFont() {\r
+        return _font;\r
+    }\r
+\r
+    public final Color getFontColor() {\r
+        return _font_color;\r
+    }\r
+\r
+    public final byte getFontSize() {\r
+        return _font_size;\r
+    }\r
+\r
+    public final FontType getFontType() {\r
+        return _font_type;\r
+    }\r
+\r
     public final NodeShape getShape() {\r
         return _shape;\r
     }\r
@@ -107,17 +122,11 @@ public final class NodeVisualData implements PhylogenyData {
         return _transparancy;\r
     }\r
 \r
-    private final  void init() {\r
-        setFont( null );\r
-        setFontType( FontType.NORMAL );\r
-        setFontSize( DEFAULT_FONT_SIZE );\r
-        setFontColor( null );\r
-        setShape( NodeShape.DEFAULT );\r
-        setFillType( NodeFill.DEFAULT );\r
-        setBorderColor( null );\r
-        setFillColor( null );\r
-        setSize( DEFAULT_SIZE );\r
-        setTransparancy( DEFAULT_TRANSPARANCY );\r
+    public final boolean isEmpty() {\r
+        return ( ForesterUtil.isEmpty( getFont() ) && ( getFontType() == FontType.NORMAL )\r
+                && ( getFontSize() == DEFAULT_FONT_SIZE ) && ( getFontColor() == null )\r
+                && ( getShape() == NodeShape.DEFAULT ) && ( getFillType() == NodeFill.DEFAULT )\r
+                && ( getBorderColor() == null ) && ( getFillColor() == null ) && ( getSize() == DEFAULT_SIZE ) && ( getTransparancy() == DEFAULT_TRANSPARANCY ) );\r
     }\r
 \r
     @Override\r
@@ -137,6 +146,27 @@ public final class NodeVisualData implements PhylogenyData {
         _fill_type = fill_type;\r
     }\r
 \r
+    public final void setFont( final String font ) {\r
+        if ( !ForesterUtil.isEmpty( font ) ) {\r
+            _font = font;\r
+        }\r
+        else {\r
+            _font = null;\r
+        }\r
+    }\r
+\r
+    public final void setFontColor( final Color font_color ) {\r
+        _font_color = font_color;\r
+    }\r
+\r
+    public final void setFontSize( final byte font_size ) {\r
+        _font_size = font_size;\r
+    }\r
+\r
+    public final void setFontType( final FontType font_type ) {\r
+        _font_type = font_type;\r
+    }\r
+\r
     public final void setShape( final NodeShape shape ) {\r
         _shape = shape;\r
     }\r
@@ -164,16 +194,17 @@ public final class NodeVisualData implements PhylogenyData {
         return asText().toString();\r
     }\r
 \r
-    public enum NodeFill {\r
-        NONE, GRADIENT, SOLID, DEFAULT\r
-    }\r
-\r
-    public enum NodeShape {\r
-        CIRCLE, RECTANGLE, DEFAULT\r
-    }\r
-    \r
-    public enum FontType {\r
-        NORMAL, BOLD, ITALIC, BOLD_ITALIC\r
+    private final void init() {\r
+        setFont( null );\r
+        setFontType( FontType.NORMAL );\r
+        setFontSize( DEFAULT_FONT_SIZE );\r
+        setFontColor( null );\r
+        setShape( NodeShape.DEFAULT );\r
+        setFillType( NodeFill.DEFAULT );\r
+        setBorderColor( null );\r
+        setFillColor( null );\r
+        setSize( DEFAULT_SIZE );\r
+        setTransparancy( DEFAULT_TRANSPARANCY );\r
     }\r
 \r
     private final List<Property> toProperties() {\r
@@ -186,56 +217,16 @@ public final class NodeVisualData implements PhylogenyData {
         properties.add( new Property( SIZE_REF, String.valueOf( getBorderColor() ), "", SIZE_TYPE, AppliesTo.NODE ) );\r
         return properties;\r
     }\r
-    public static final String SIZE_REF  = "aptx_visualiation:node_sise";\r
-    public static final String SIZE_TYPE = "xsd:decimal";\r
-\r
-    public final boolean isEmpty() {\r
-        return ( ForesterUtil.isEmpty( getFont() ) &&\r
-                getFontType() == FontType.NORMAL && \r
-                getFontSize() == DEFAULT_FONT_SIZE &&\r
-                getFontColor() == null &&\r
-                getShape() == NodeShape.DEFAULT &&\r
-        getFillType() == NodeFill.DEFAULT &&\r
-        getBorderColor() == null &&\r
-        getFillColor() == null &&\r
-        getSize() == DEFAULT_SIZE &&\r
-        getTransparancy() == DEFAULT_TRANSPARANCY );\r
-    }\r
-\r
-    public final String getFont() {\r
-        return _font;\r
-    }\r
 \r
-    public final void setFont( final String font ) {\r
-        if ( !ForesterUtil.isEmpty( font ) ) {\r
-            _font = font;\r
-        }\r
-        else {\r
-            _font = null;\r
-        }\r
-    }\r
-\r
-    public final FontType getFontType() {\r
-        return _font_type;\r
-    }\r
-\r
-    public final void setFontType( FontType font_type ) {\r
-        _font_type = font_type;\r
-    }\r
-\r
-    public final byte getFontSize() {\r
-        return _font_size;\r
-    }\r
-\r
-    public final void setFontSize( byte font_size ) {\r
-        _font_size = font_size;\r
+    public enum FontType {\r
+        BOLD, BOLD_ITALIC, ITALIC, NORMAL\r
     }\r
 \r
-    public final Color getFontColor() {\r
-        return _font_color;\r
+    public enum NodeFill {\r
+        DEFAULT, GRADIENT, NONE, SOLID\r
     }\r
 \r
-    public final void setFontColor( Color font_color ) {\r
-        _font_color = font_color;\r
+    public enum NodeShape {\r
+        CIRCLE, DEFAULT, RECTANGLE\r
     }\r
 }\r