X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Farchaeopteryx%2Fphylogeny%2Fdata%2FRenderableVector.java;h=02782ffb441b5d6847abe84038396a5f3e8d95b0;hb=9673231c870387fffa4516124d802ee47bbdaf45;hp=2785daf23f0d47cffa5dcbd01f6b28edf4505782;hpb=eee996a6476a1e3d84c07f8f690dcde3ff4b2ef5;p=jalview.git

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..02782ff 100644
--- 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;
@@ -42,31 +43,36 @@ import org.forester.util.ForesterUtil;
 
 public final class RenderableVector implements RenderablePhylogenyData {
 
-    final static public int         DEFAULT_HEIGHT          = 12;
-    final static public int         DEFAULT_WIDTH           = 120;
+    final static int         VECTOR_DEFAULT_HEIGHT          = 12;
+    public final static  int         VECTOR_DEFAULT_WIDTH           = 120;
     private double                  _rendering_factor_width = 1.0;
     private List<Double>            _values;
     private final Rectangle2D       _rectangle              = new Rectangle2D.Float();
-    private Configuration           _configuration;
-    private double                  _height;
+   
+    private double                  _height =  VECTOR_DEFAULT_HEIGHT;
     private double                  _min;
     private double                  _max;
     private double                  _mean;
+    private  Color _min_color = Color.BLUE;
+    private  Color _max_color = Color.YELLOW;
+    private  Color _mean_color = Color.WHITE;
+    private  int _width = VECTOR_DEFAULT_WIDTH;
+    
+    
     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;
+    private RenderableVector() {
+        _values = null;
+    }
+
+    @Override
+    public StringBuffer asSimpleText() {
+        return new StringBuffer( _values.toString() );
+    }
+
+    @Override
+    public StringBuffer asText() {
+        return asSimpleText();
     }
 
     @Override
@@ -74,25 +80,30 @@ public final class RenderableVector implements RenderablePhylogenyData {
         throw new NoSuchMethodError();
     }
 
-    private RenderableVector() {
-        _values = null;
-        _configuration = null;
+    @Override
+    public PhylogenyData copy() {
+        throw new NoSuchMethodError();
     }
 
     @Override
-    public StringBuffer asSimpleText() {
-        return new StringBuffer( _values.toString() );
+    public Dimension getOriginalSize() {
+        return new Dimension( getTotalLength(), ( int ) getRenderingHeight() );
     }
 
     @Override
-    public StringBuffer asText() {
-        return asSimpleText();
+    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() );
     }
@@ -110,16 +121,17 @@ public final class RenderableVector implements RenderablePhylogenyData {
                         final boolean to_pdf ) {
         final double y = y1;
         final double start = x1 + 20.0;
-        final double width = ( double ) DEFAULT_WIDTH / _values.size();
+        final double width = ( double ) _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 +139,57 @@ 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, _min_color, _max_color, _mean_color );
     }
 
     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._values = values;
+        
+        if ( configuration != null ) {
+            _instance._min_color =configuration.getVectorDataMinColor();
+            _instance._max_color = configuration.getVectorDataMaxColor();
+            _instance._mean_color = configuration.getVectorDataMeanColor();
+            _instance._width = configuration.getVectorDataWidth();
+            _instance._height = configuration.getVectorDataHeight();
+        }
+        
+        
+        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;
+    }
 }