package org.forester.archaeopteryx.phylogeny.data;
+import java.awt.BasicStroke;
import java.awt.Color;
import java.awt.Dimension;
import java.awt.Graphics2D;
+import java.awt.Stroke;
import java.awt.geom.Rectangle2D;
import java.io.IOException;
import java.io.Writer;
import java.util.Map;
import java.util.SortedMap;
-import org.forester.archaeopteryx.Configuration;
+import org.forester.archaeopteryx.AptxUtil;
+import org.forester.archaeopteryx.Constants;
import org.forester.archaeopteryx.TreePanel;
import org.forester.phylogeny.data.DomainArchitecture;
import org.forester.phylogeny.data.PhylogenyData;
-import org.forester.phylogeny.data.PhylogenyDataUtil;
import org.forester.phylogeny.data.ProteinDomain;
import org.forester.util.ForesterUtil;
public final class RenderableDomainArchitecture extends DomainArchitecture implements RenderablePhylogenyData {
- static private Map<String, Color> Domain_colors;
final static private int BRIGHTEN_COLOR_BY = 200;
final static private int E_VALUE_THRESHOLD_EXP_DEFAULT = 0;
- private static int _Next_default_domain_color = 0;
- private final static String[] DEFAULT_DOMAINS_COLORS = { "0xFF0000", "0x0000FF", "0xAAAA00", "0xFF00FF",
- "0x00FFFF", "0x800000", "0x000080", "0x808000", "0x800080", "0x008080", "0xE1B694" };
- private int _e_value_threshold_exp = RenderableDomainArchitecture.E_VALUE_THRESHOLD_EXP_DEFAULT;
- private double _rendering_factor_width = 1.0;
- private double _rendering_height = 0;
+ final static private BasicStroke STROKE_1 = new BasicStroke( 1f );
+ private static Map<String, Color> _domain_colors;
private final DomainArchitecture _domain_structure;
+ private int _e_value_threshold_exp = E_VALUE_THRESHOLD_EXP_DEFAULT;
private final Rectangle2D _rectangle = new Rectangle2D.Float();
- private final Configuration _configuration;
+ private float _rendering_factor_width = 1;
+ private float _rendering_height = 0;
- public RenderableDomainArchitecture( final DomainArchitecture domain_structure, final Configuration configuration ) {
+ public RenderableDomainArchitecture( final DomainArchitecture domain_structure ) {
_domain_structure = domain_structure;
- _configuration = configuration;
}
- private Configuration getConfiguration() {
- return _configuration;
+ public static void setColorMap( final Map<String, Color> domain_colors ) {
+ _domain_colors = domain_colors;
}
@Override
final Color color_two = getColorTwo( color_one );
double step = 1;
if ( to_pdf ) {
- step = 0.1;
+ step = 0.05;
}
for( double i = 0; i < heigth; i += step ) {
g.setColor( org.forester.util.ForesterUtil
}
}
- private Color getColorOne( final String name ) {
- Color c = getConfiguration().getDomainStructureBaseColor();
- if ( RenderableDomainArchitecture.Domain_colors != null ) {
- c = RenderableDomainArchitecture.Domain_colors.get( name );
+ private final Color getColorOne( final String name ) {
+ Color c = _domain_colors.get( name );
+ if ( c == null ) {
+ c = AptxUtil.calculateColorFromString( name, false );
if ( c == null ) {
- if ( RenderableDomainArchitecture._Next_default_domain_color < RenderableDomainArchitecture.DEFAULT_DOMAINS_COLORS.length ) {
- c = Color
- .decode( RenderableDomainArchitecture.DEFAULT_DOMAINS_COLORS[ RenderableDomainArchitecture._Next_default_domain_color++ ] );
- RenderableDomainArchitecture.Domain_colors.put( name, c );
- }
- else {
- c = getConfiguration().getDomainStructureBaseColor();
- }
+ throw new IllegalStateException();
}
+ _domain_colors.put( name, c );
}
return c;
}
return new Integer( _e_value_threshold_exp );
}
- public double getRenderingFactorWidth() {
+ public float getRenderingFactorWidth() {
return _rendering_factor_width;
}
}
@Override
- public void render( final double x1,
- final double y1,
+ public void render( final float x1,
+ final float y1,
final Graphics2D g,
final TreePanel tree_panel,
final boolean to_pdf ) {
- final double f = getRenderingFactorWidth();
- final double y = y1 + ( _rendering_height / 2 );
- final double start = x1 + 20.0;
- g.setColor( getConfiguration().getDomainStructureFontColor() );
+ final float f = getRenderingFactorWidth();
+ final float y = y1 + ( _rendering_height / 2 );
+ final float start = x1 + 20;
+ final Stroke s = g.getStroke();
+ g.setStroke( STROKE_1 );
+ if ( !to_pdf ) {
+ g.setColor( tree_panel.getTreeColorSet().getDomainBaseColor() );
+ }
+ else {
+ g.setColor( Constants.DOMAIN_BASE_COLOR_FOR_PDF );
+ }
_rectangle.setFrame( start, y - 0.5, _domain_structure.getTotalLength() * f, 1 );
g.fill( _rectangle );
for( int i = 0; i < _domain_structure.getDomains().size(); ++i ) {
final ProteinDomain d = _domain_structure.getDomain( i );
if ( d.getConfidence() <= Math.pow( 10, _e_value_threshold_exp ) ) {
- final double xa = start + ( d.getFrom() * f );
- final double xb = xa + ( d.getLength() * f );
- if ( tree_panel.getMainPanel().getOptions().isShowDomainLabels() ) {
+ final float xa = start + ( d.getFrom() * f );
+ final float xb = xa + ( d.getLength() * f );
+ if ( tree_panel.getMainPanel().getOptions().isShowDomainLabels()
+ && ( tree_panel.getMainPanel().getTreeFontSet().getFontMetricsSmall().getHeight() > 4 ) ) {
g.setFont( tree_panel.getMainPanel().getTreeFontSet().getSmallFont() );
- g.setColor( getConfiguration().getDomainStructureFontColor() );
- PhylogenyDataUtil.drawString( d.getName(), xa, y1
- + tree_panel.getMainPanel().getTreeFontSet()._fm_small.getAscent() + 6, g );
+ if ( !to_pdf ) {
+ g.setColor( tree_panel.getTreeColorSet().getDomainLabelColor() );
+ }
+ else {
+ g.setColor( Constants.DOMAIN_LABEL_COLOR_FOR_PDF );
+ }
+ g.drawString( d.getName(), xa, y1
+ + tree_panel.getMainPanel().getTreeFontSet().getFontMetricsSmall().getAscent()
+ + _rendering_height );
}
drawDomain( xa, y1, xb - xa, _rendering_height, d.getName(), g, to_pdf );
}
}
+ g.setStroke( s );
}
@Override
_e_value_threshold_exp = ( int ) e_value_threshold_exp;
}
- public void setRenderingFactorWidth( final double rendering_factor_width ) {
+ public void setRenderingFactorWidth( final float rendering_factor_width ) {
_rendering_factor_width = rendering_factor_width;
}
@Override
- public void setRenderingHeight( final double rendering_height ) {
+ public void setRenderingHeight( final float rendering_height ) {
_rendering_height = rendering_height;
}
public void toPhyloXML( final Writer writer, final int level, final String indentation ) throws IOException {
_domain_structure.toPhyloXML( writer, level, indentation );
}
-
- public static void setColorMap( final Map<String, Color> domain_colors ) {
- RenderableDomainArchitecture.Domain_colors = domain_colors;
- }
}
git://source.jalview.org / jalview.git / blobdiff