// 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;
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;
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
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() );
}
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 ) {
}
@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;
+ }
}
git://source.jalview.org / jalview.git / blobdiff