3 // FORESTER -- software libraries and applications
4 // for evolutionary biology research and applications.
6 // Copyright (C) 2008-2009 Christian M. Zmasek
7 // Copyright (C) 2008-2009 Burnham Institute for Medical Research
10 // This library is free software; you can redistribute it and/or
11 // modify it under the terms of the GNU Lesser General Public
12 // License as published by the Free Software Foundation; either
13 // version 2.1 of the License, or (at your option) any later version.
15 // This library is distributed in the hope that it will be useful,
16 // but WITHOUT ANY WARRANTY; without even the implied warranty of
17 // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
18 // Lesser General Public License for more details.
20 // You should have received a copy of the GNU Lesser General Public
21 // License along with this library; if not, write to the Free Software
22 // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
24 // Contact: phylosoft @ gmail . com
25 // WWW: https://sites.google.com/site/cmzmasek/home/software/forester
27 package org.forester.archaeopteryx.phylogeny.data;
29 import java.awt.BasicStroke;
30 import java.awt.Color;
31 import java.awt.Dimension;
32 import java.awt.Graphics2D;
33 import java.awt.Stroke;
34 import java.awt.geom.Rectangle2D;
35 import java.io.IOException;
36 import java.io.Writer;
37 import java.math.BigDecimal;
39 import java.util.SortedMap;
41 import org.forester.archaeopteryx.Configuration;
42 import org.forester.archaeopteryx.TreePanel;
43 import org.forester.phylogeny.data.DomainArchitecture;
44 import org.forester.phylogeny.data.PhylogenyData;
45 import org.forester.phylogeny.data.PhylogenyDataUtil;
46 import org.forester.phylogeny.data.ProteinDomain;
47 import org.forester.util.ForesterUtil;
49 public final class RenderableDomainArchitecture extends DomainArchitecture implements RenderablePhylogenyData {
51 static private Map<String, Color> Domain_colors;
52 final static private int BRIGHTEN_COLOR_BY = 200;
53 final static private int E_VALUE_THRESHOLD_EXP_DEFAULT = 0;
54 private static int _Next_default_domain_color = 0;
55 private final static String[] DEFAULT_DOMAINS_COLORS = { "0xFF0000", "0x0000FF", "0xAAAA00", "0xFF00FF",
56 "0x00FFFF", "0x800000", "0x000080", "0x808000", "0x800080", "0x008080", "0xE1B694" };
57 private int _e_value_threshold_exp = RenderableDomainArchitecture.E_VALUE_THRESHOLD_EXP_DEFAULT;
58 private double _rendering_factor_width = 1.0;
59 private double _rendering_height = 0;
60 private final DomainArchitecture _domain_structure;
61 private final Rectangle2D _rectangle = new Rectangle2D.Float();
62 private final Configuration _configuration;
63 private static final BasicStroke STROKE_1 = new BasicStroke( 1f );
65 public RenderableDomainArchitecture( final DomainArchitecture domain_structure, final Configuration configuration ) {
66 _domain_structure = domain_structure;
67 _configuration = configuration;
70 private Configuration getConfiguration() {
71 return _configuration;
75 public StringBuffer asSimpleText() {
76 return _domain_structure.asSimpleText();
80 public StringBuffer asText() {
81 return _domain_structure.asText();
85 public PhylogenyData copy() {
86 return _domain_structure.copy();
89 private final void drawDomain( final double x,
95 final boolean to_pdf ) {
96 final double h2 = heigth / 2.0;
97 final Color color_one = getColorOne( name );
98 final Color color_two = getColorTwo( color_one );
103 for( double i = 0; i < heigth; i += step ) {
104 g.setColor( org.forester.util.ForesterUtil
105 .calcColor( i >= h2 ? heigth - i : i, 0, h2, color_one, color_two ) );
106 _rectangle.setFrame( x, i + y, width, step );
107 g.fill( _rectangle );
111 private Color getColorOne( final String name ) {
112 Color c = getConfiguration().getDomainStructureBaseColor();
113 if ( RenderableDomainArchitecture.Domain_colors != null ) {
114 c = RenderableDomainArchitecture.Domain_colors.get( name );
116 if ( RenderableDomainArchitecture._Next_default_domain_color < RenderableDomainArchitecture.DEFAULT_DOMAINS_COLORS.length ) {
118 .decode( RenderableDomainArchitecture.DEFAULT_DOMAINS_COLORS[ RenderableDomainArchitecture._Next_default_domain_color++ ] );
119 RenderableDomainArchitecture.Domain_colors.put( name, c );
122 c = getConfiguration().getDomainStructureBaseColor();
129 private Color getColorTwo( final Color color_one ) {
130 final int red = color_one.getRed() + RenderableDomainArchitecture.BRIGHTEN_COLOR_BY;
131 final int green = color_one.getGreen() + RenderableDomainArchitecture.BRIGHTEN_COLOR_BY;
132 final int blue = color_one.getBlue() + RenderableDomainArchitecture.BRIGHTEN_COLOR_BY;
133 return new Color( red > 255 ? 255 : red, green > 255 ? 255 : green, blue > 255 ? 255 : blue );
137 public ProteinDomain getDomain( final int i ) {
138 return _domain_structure.getDomain( i );
142 public SortedMap<BigDecimal, ProteinDomain> getDomains() {
143 return _domain_structure.getDomains();
147 public int getNumberOfDomains() {
148 return _domain_structure.getNumberOfDomains();
152 public Dimension getOriginalSize() {
153 return new Dimension( _domain_structure.getTotalLength(), ForesterUtil.roundToInt( _rendering_height ) );
157 public Object getParameter() {
158 return new Integer( _e_value_threshold_exp );
161 public double getRenderingFactorWidth() {
162 return _rendering_factor_width;
166 public Dimension getRenderingSize() {
167 return new Dimension( ForesterUtil.roundToInt( _domain_structure.getTotalLength() * getRenderingFactorWidth() ),
168 ForesterUtil.roundToInt( _rendering_height ) );
172 public int getTotalLength() {
173 return _domain_structure.getTotalLength();
177 public boolean isEqual( final PhylogenyData data ) {
178 return _domain_structure.isEqual( data );
182 public void render( final double x1,
185 final TreePanel tree_panel,
186 final boolean to_pdf ) {
187 final double f = getRenderingFactorWidth();
188 final double y = y1 + ( _rendering_height / 2 );
189 final double start = x1 + 20.0;
190 final Stroke s = g.getStroke();
191 g.setStroke( STROKE_1 );
192 g.setColor( getConfiguration().getDomainStructureFontColor() );
193 _rectangle.setFrame( start, y - 0.5, _domain_structure.getTotalLength() * f, 1 );
194 g.fill( _rectangle );
195 for( int i = 0; i < _domain_structure.getDomains().size(); ++i ) {
196 final ProteinDomain d = _domain_structure.getDomain( i );
197 if ( d.getConfidence() <= Math.pow( 10, _e_value_threshold_exp ) ) {
198 final double xa = start + ( d.getFrom() * f );
199 final double xb = xa + ( d.getLength() * f );
200 if ( tree_panel.getMainPanel().getOptions().isShowDomainLabels() ) {
201 g.setFont( tree_panel.getMainPanel().getTreeFontSet().getSmallFont() );
202 g.setColor( getConfiguration().getDomainStructureFontColor() );
203 PhylogenyDataUtil.drawString( d.getName(), xa, y1
204 + tree_panel.getMainPanel().getTreeFontSet()._fm_small.getAscent() + 6, g );
206 drawDomain( xa, y1, xb - xa, _rendering_height, d.getName(), g, to_pdf );
213 public void setParameter( final double e_value_threshold_exp ) {
214 _e_value_threshold_exp = ( int ) e_value_threshold_exp;
217 public void setRenderingFactorWidth( final double rendering_factor_width ) {
218 _rendering_factor_width = rendering_factor_width;
222 public void setRenderingHeight( final double rendering_height ) {
223 _rendering_height = rendering_height;
227 public StringBuffer toNHX() {
228 return _domain_structure.toNHX();
232 public void toPhyloXML( final Writer writer, final int level, final String indentation ) throws IOException {
233 _domain_structure.toPhyloXML( writer, level, indentation );
236 public static void setColorMap( final Map<String, Color> domain_colors ) {
237 RenderableDomainArchitecture.Domain_colors = domain_colors;