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.AptxUtil;
42 import org.forester.archaeopteryx.Constants;
43 import org.forester.archaeopteryx.TreePanel;
44 import org.forester.phylogeny.data.DomainArchitecture;
45 import org.forester.phylogeny.data.PhylogenyData;
46 import org.forester.phylogeny.data.PhylogenyDataUtil;
47 import org.forester.phylogeny.data.ProteinDomain;
48 import org.forester.util.ForesterUtil;
50 public final class RenderableDomainArchitecture extends DomainArchitecture implements RenderablePhylogenyData {
52 final static private int BRIGHTEN_COLOR_BY = 200;
53 final static private int E_VALUE_THRESHOLD_EXP_DEFAULT = 0;
54 final static private BasicStroke STROKE_1 = new BasicStroke( 1f );
55 private static Map<String, Color> _domain_colors;
56 private final DomainArchitecture _domain_structure;
57 private int _e_value_threshold_exp = E_VALUE_THRESHOLD_EXP_DEFAULT;
58 private final Rectangle2D _rectangle = new Rectangle2D.Float();
59 private float _rendering_factor_width = 1;
60 private float _rendering_height = 0;
62 public RenderableDomainArchitecture( final DomainArchitecture domain_structure ) {
63 _domain_structure = domain_structure;
66 public static void setColorMap( final Map<String, Color> domain_colors ) {
67 _domain_colors = domain_colors;
71 public StringBuffer asSimpleText() {
72 return _domain_structure.asSimpleText();
76 public StringBuffer asText() {
77 return _domain_structure.asText();
81 public PhylogenyData copy() {
82 return _domain_structure.copy();
85 private final void drawDomain( final double x,
91 final boolean to_pdf ) {
92 final double h2 = heigth / 2.0;
93 final Color color_one = getColorOne( name );
94 final Color color_two = getColorTwo( color_one );
99 for( double i = 0; i < heigth; i += step ) {
100 g.setColor( org.forester.util.ForesterUtil
101 .calcColor( i >= h2 ? heigth - i : i, 0, h2, color_one, color_two ) );
102 _rectangle.setFrame( x, i + y, width, step );
103 g.fill( _rectangle );
107 private final Color getColorOne( final String name ) {
108 Color c = _domain_colors.get( name );
110 c = AptxUtil.calculateColorFromString( name, false );
112 throw new IllegalStateException();
114 _domain_colors.put( name, c );
119 private Color getColorTwo( final Color color_one ) {
120 final int red = color_one.getRed() + RenderableDomainArchitecture.BRIGHTEN_COLOR_BY;
121 final int green = color_one.getGreen() + RenderableDomainArchitecture.BRIGHTEN_COLOR_BY;
122 final int blue = color_one.getBlue() + RenderableDomainArchitecture.BRIGHTEN_COLOR_BY;
123 return new Color( red > 255 ? 255 : red, green > 255 ? 255 : green, blue > 255 ? 255 : blue );
127 public ProteinDomain getDomain( final int i ) {
128 return _domain_structure.getDomain( i );
132 public SortedMap<BigDecimal, ProteinDomain> getDomains() {
133 return _domain_structure.getDomains();
137 public int getNumberOfDomains() {
138 return _domain_structure.getNumberOfDomains();
142 public Dimension getOriginalSize() {
143 return new Dimension( _domain_structure.getTotalLength(), ForesterUtil.roundToInt( _rendering_height ) );
147 public Object getParameter() {
148 return new Integer( _e_value_threshold_exp );
151 public float getRenderingFactorWidth() {
152 return _rendering_factor_width;
156 public Dimension getRenderingSize() {
157 return new Dimension( ForesterUtil.roundToInt( _domain_structure.getTotalLength() * getRenderingFactorWidth() ),
158 ForesterUtil.roundToInt( _rendering_height ) );
162 public int getTotalLength() {
163 return _domain_structure.getTotalLength();
167 public boolean isEqual( final PhylogenyData data ) {
168 return _domain_structure.isEqual( data );
172 public void render( final float x1,
175 final TreePanel tree_panel,
176 final boolean to_pdf ) {
177 final float f = getRenderingFactorWidth();
178 final float y = y1 + ( _rendering_height / 2 );
179 final float start = x1 + 20;
180 final Stroke s = g.getStroke();
181 g.setStroke( STROKE_1 );
183 g.setColor( tree_panel.getTreeColorSet().getDomainBaseColor() );
186 g.setColor( Constants.DOMAIN_BASE_COLOR_FOR_PDF );
188 _rectangle.setFrame( start, y - 0.5, _domain_structure.getTotalLength() * f, 1 );
189 g.fill( _rectangle );
190 for( int i = 0; i < _domain_structure.getDomains().size(); ++i ) {
191 final ProteinDomain d = _domain_structure.getDomain( i );
192 if ( d.getConfidence() <= Math.pow( 10, _e_value_threshold_exp ) ) {
193 final float xa = start + ( d.getFrom() * f );
194 final float xb = xa + ( d.getLength() * f );
195 if ( tree_panel.getMainPanel().getOptions().isShowDomainLabels()
196 && ( tree_panel.getMainPanel().getTreeFontSet().getFontMetricsSmall().getHeight() > 4 ) ) {
197 g.setFont( tree_panel.getMainPanel().getTreeFontSet().getSmallFont() );
199 g.setColor( tree_panel.getTreeColorSet().getDomainLabelColor() );
202 g.setColor( Constants.DOMAIN_LABEL_COLOR_FOR_PDF );
204 g.drawString( d.getName(),
207 + tree_panel.getMainPanel().getTreeFontSet().getFontMetricsSmall().getAscent()
208 + _rendering_height );
212 drawDomain( xa, y1, xb - xa, _rendering_height, d.getName(), g, to_pdf );
219 public void setParameter( final double e_value_threshold_exp ) {
220 _e_value_threshold_exp = ( int ) e_value_threshold_exp;
223 public void setRenderingFactorWidth( final float rendering_factor_width ) {
224 _rendering_factor_width = rendering_factor_width;
228 public void setRenderingHeight( final float rendering_height ) {
229 _rendering_height = rendering_height;
233 public StringBuffer toNHX() {
234 return _domain_structure.toNHX();
238 public void toPhyloXML( final Writer writer, final int level, final String indentation ) throws IOException {
239 _domain_structure.toPhyloXML( writer, level, indentation );