inprogress

[jalview.git] / forester / java / src / org / forester / archaeopteryx / phylogeny / data / RenderableVector.java

diff --git a/forester/java/src/org/forester/archaeopteryx/phylogeny/data/RenderableVector.java b/forester/java/src/org/forester/archaeopteryx/phylogeny/data/RenderableVector.java
index 2785daf..cc0d772 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/phylogeny/data/RenderableVector.java
+++ b/forester/java/src/org/forester/archaeopteryx/phylogeny/data/RenderableVector.java
@@ -22,7 +22,7 @@
 // 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.archaeopteryx.phylogeny.data;
 
@@ -34,6 +34,7 @@ import java.io.IOException;
 import java.io.Writer;
 import java.util.List;
 
+import org.forester.archaeopteryx.AptxUtil;
 import org.forester.archaeopteryx.Configuration;
 import org.forester.archaeopteryx.TreePanel;
 import org.forester.phylogeny.data.PhylogenyData;
@@ -54,26 +55,6 @@ public final class RenderableVector implements RenderablePhylogenyData {
     private double                  _mean;
     private static RenderableVector _instance               = null;
 
-    public static RenderableVector createInstance( final List<Double> values,
-                                                   final DescriptiveStatistics stats,
-                                                   final Configuration configuration ) {
-        if ( _instance == null ) {
-            _instance = new RenderableVector();
-        }
-        _instance.setRenderingHeight( DEFAULT_HEIGHT );
-        _instance._values = values;
-        _instance._configuration = configuration;
-        _instance._min = stats.getMin();
-        _instance._max = stats.getMax();
-        _instance._mean = stats.arithmeticMean();
-        return _instance;
-    }
-
-    @Override
-    public Object clone() {
-        throw new NoSuchMethodError();
-    }
-
     private RenderableVector() {
         _values = null;
         _configuration = null;
@@ -89,10 +70,35 @@ public final class RenderableVector implements RenderablePhylogenyData {
         return asSimpleText();
     }
 
+    @Override
+    public Object clone() {
+        throw new NoSuchMethodError();
+    }
+
+    @Override
+    public PhylogenyData copy() {
+        throw new NoSuchMethodError();
+    }
+
+    @Override
+    public Dimension getOriginalSize() {
+        return new Dimension( getTotalLength(), ( int ) getRenderingHeight() );
+    }
+
+    @Override
+    public Object getParameter() {
+        return null;
+    }
+
     public double getRenderingFactorWidth() {
         return _rendering_factor_width;
     }
 
+    @Override
+    public Dimension getRenderingSize() {
+        return getOriginalSize();
+    }
+
     public int getTotalLength() {
         return ( int ) ( _values.size() * getRenderingHeight() );
     }
@@ -113,13 +119,14 @@ public final class RenderableVector implements RenderablePhylogenyData {
         final double width = ( double ) DEFAULT_WIDTH / _values.size();
         for( int i = 0; i < _values.size(); ++i ) {
             g.setColor( calculateColor( _values.get( i ) ) );
-            _rectangle.setFrame( start + i * width, y - 0.5, width, getRenderingHeight() );
+            _rectangle.setFrame( start + ( i * width ), y - 0.5, width, getRenderingHeight() );
             g.fill( _rectangle );
         }
     }
 
-    private Color calculateColor( final double v ) {
-        return ForesterUtil.calcColor( v, _min, _max, _mean, Color.MAGENTA, Color.GREEN, Color.WHITE );
+    @Override
+    public void setParameter( final double parameter ) {
+        throw new NoSuchMethodError();
     }
 
     public void setRenderingFactorWidth( final double rendering_factor_width ) {
@@ -127,46 +134,48 @@ public final class RenderableVector implements RenderablePhylogenyData {
     }
 
     @Override
-    public StringBuffer toNHX() {
-        throw new NoSuchMethodError();
-    }
-
-    @Override
-    public void toPhyloXML( final Writer writer, final int level, final String indentation ) throws IOException {
-        throw new NoSuchMethodError();
+    public void setRenderingHeight( final double height ) {
+        _height = height;
     }
 
     @Override
-    public PhylogenyData copy() {
+    public StringBuffer toNHX() {
         throw new NoSuchMethodError();
     }
 
     @Override
-    public Dimension getOriginalSize() {
-        return new Dimension( getTotalLength(), ( int ) getRenderingHeight() );
-    }
-
-    @Override
-    public Object getParameter() {
-        return null;
-    }
-
-    @Override
-    public Dimension getRenderingSize() {
-        return getOriginalSize();
-    }
-
-    @Override
-    public void setParameter( final double parameter ) {
+    public void toPhyloXML( final Writer writer, final int level, final String indentation ) throws IOException {
         throw new NoSuchMethodError();
     }
 
-    @Override
-    public void setRenderingHeight( final double height ) {
-        _height = height;
+    private Color calculateColor( final double v ) {
+        return ForesterUtil.calcColor( v, _min, _max, _mean, Color.MAGENTA, Color.GREEN, Color.WHITE );
     }
 
     private double getRenderingHeight() {
         return _height;
     }
+
+    public static RenderableVector createInstance( final List<Double> values,
+                                                   final DescriptiveStatistics stats,
+                                                   final Configuration configuration ) {
+        if ( _instance == null ) {
+            _instance = new RenderableVector();
+        }
+        _instance.setRenderingHeight( DEFAULT_HEIGHT );
+        _instance._values = values;
+        _instance._configuration = configuration;
+        if ( stats.getN() > 0 ) {
+            _instance._min = stats.getMin();
+            _instance._max = stats.getMax();
+            _instance._mean = stats.arithmeticMean();
+        }
+        else {
+            _instance._min = 0;
+            _instance._max = 0;
+            _instance._mean = 0;
+            AptxUtil.printWarningMessage( "Archaeopteryx", "creating renderable vector with empty statistics" );
+        }
+        return _instance;
+    }
 }