// $Id: // $ // FORESTER -- software libraries and applications // for evolutionary biology research and applications. // // Copyright (C) 2008-2009 Christian M. Zmasek // Copyright (C) 2008-2009 Burnham Institute for Medical Research // All rights reserved // // This library is free software; you can redistribute it and/or // modify it under the terms of the GNU Lesser General Public // License as published by the Free Software Foundation; either // version 2.1 of the License, or (at your option) any later version. // // This library is distributed in the hope that it will be useful, // but WITHOUT ANY WARRANTY; without even the implied warranty of // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU // Lesser General Public License for more details. // // You should have received a copy of the GNU Lesser General Public // License along with this library; if not, write to the Free Software // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com // WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.archaeopteryx.phylogeny.data; import java.awt.Color; import java.awt.Dimension; import java.awt.Graphics2D; import java.awt.geom.Rectangle2D; import java.io.IOException; import java.io.Writer; import java.math.BigDecimal; import java.util.Map; import java.util.SortedMap; import org.forester.archaeopteryx.Configuration; 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 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; private final DomainArchitecture _domain_structure; private final Rectangle2D _rectangle = new Rectangle2D.Float(); private final Configuration _configuration; public RenderableDomainArchitecture( final DomainArchitecture domain_structure, final Configuration configuration ) { _domain_structure = domain_structure; _configuration = configuration; } private Configuration getConfiguration() { return _configuration; } @Override public StringBuffer asSimpleText() { return _domain_structure.asSimpleText(); } @Override public StringBuffer asText() { return _domain_structure.asText(); } @Override public PhylogenyData copy() { return _domain_structure.copy(); } private final void drawDomain( final double x, final double y, final double width, final double heigth, final String name, final Graphics2D g, final boolean to_pdf ) { final double h2 = heigth / 2.0; final Color color_one = getColorOne( name ); final Color color_two = getColorTwo( color_one ); double step = 1; if ( to_pdf ) { step = 0.1; } for( double i = 0; i < heigth; i += step ) { g.setColor( org.forester.util.ForesterUtil .calcColor( i >= h2 ? heigth - i : i, 0, h2, color_one, color_two ) ); _rectangle.setFrame( x, i + y, width, step ); g.fill( _rectangle ); } } private Color getColorOne( final String name ) { Color c = getConfiguration().getDomainStructureBaseColor(); if ( RenderableDomainArchitecture.Domain_colors != null ) { c = RenderableDomainArchitecture.Domain_colors.get( name ); 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(); } } } return c; } private Color getColorTwo( final Color color_one ) { final int red = color_one.getRed() + RenderableDomainArchitecture.BRIGHTEN_COLOR_BY; final int green = color_one.getGreen() + RenderableDomainArchitecture.BRIGHTEN_COLOR_BY; final int blue = color_one.getBlue() + RenderableDomainArchitecture.BRIGHTEN_COLOR_BY; return new Color( red > 255 ? 255 : red, green > 255 ? 255 : green, blue > 255 ? 255 : blue ); } @Override public ProteinDomain getDomain( final int i ) { return _domain_structure.getDomain( i ); } @Override public SortedMap getDomains() { return _domain_structure.getDomains(); } @Override public int getNumberOfDomains() { return _domain_structure.getNumberOfDomains(); } @Override public Dimension getOriginalSize() { return new Dimension( _domain_structure.getTotalLength(), ForesterUtil.roundToInt( _rendering_height ) ); } @Override public Object getParameter() { return new Integer( _e_value_threshold_exp ); } public double getRenderingFactorWidth() { return _rendering_factor_width; } @Override public Dimension getRenderingSize() { return new Dimension( ForesterUtil.roundToInt( _domain_structure.getTotalLength() * getRenderingFactorWidth() ), ForesterUtil.roundToInt( _rendering_height ) ); } @Override public int getTotalLength() { return _domain_structure.getTotalLength(); } @Override public boolean isEqual( final PhylogenyData data ) { return _domain_structure.isEqual( data ); } @Override public void render( final double x1, final double 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() ); _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() ) { 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 ); } drawDomain( xa, y1, xb - xa, _rendering_height, d.getName(), g, to_pdf ); } } } @Override public void setParameter( final double e_value_threshold_exp ) { _e_value_threshold_exp = ( int ) e_value_threshold_exp; } public void setRenderingFactorWidth( final double rendering_factor_width ) { _rendering_factor_width = rendering_factor_width; } @Override public void setRenderingHeight( final double rendering_height ) { _rendering_height = rendering_height; } @Override public StringBuffer toNHX() { return _domain_structure.toNHX(); } @Override 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 domain_colors ) { RenderableDomainArchitecture.Domain_colors = domain_colors; } }