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.ProteinDomain;
47 import org.forester.util.ForesterUtil;
49 public final class RenderableDomainArchitecture extends DomainArchitecture implements RenderablePhylogenyData {
51 final static private int BRIGHTEN_COLOR_BY = 200;
52 final static private int E_VALUE_THRESHOLD_EXP_DEFAULT = 0;
53 final static private BasicStroke STROKE_1 = new BasicStroke( 1f );
54 private static Map<String, Color> _domain_colors;
55 private final DomainArchitecture _domain_structure;
56 private int _e_value_threshold_exp = E_VALUE_THRESHOLD_EXP_DEFAULT;
57 private final Rectangle2D _rectangle = new Rectangle2D.Float();
58 private float _rendering_factor_width = 1;
59 private float _rendering_height = 0;
61 public RenderableDomainArchitecture( final DomainArchitecture domain_structure ) {
62 _domain_structure = domain_structure;
65 public static void setColorMap( final Map<String, Color> domain_colors ) {
66 _domain_colors = domain_colors;
70 public StringBuffer asSimpleText() {
71 return _domain_structure.asSimpleText();
75 public StringBuffer asText() {
76 return _domain_structure.asText();
80 public PhylogenyData copy() {
81 return _domain_structure.copy();
84 private final void drawDomain( final double x,
90 final boolean to_pdf ) {
91 final double h2 = heigth / 2.0;
92 final Color color_one = getColorOne( name );
93 final Color color_two = getColorTwo( color_one );
98 for( double i = 0; i < heigth; i += step ) {
99 g.setColor( org.forester.util.ForesterUtil
100 .calcColor( i >= h2 ? heigth - i : i, 0, h2, color_one, color_two ) );
101 _rectangle.setFrame( x, i + y, width, step );
102 g.fill( _rectangle );
106 private final Color getColorOne( final String name ) {
107 Color c = _domain_colors.get( name );
109 c = AptxUtil.calculateColorFromString( name, false );
111 throw new IllegalStateException();
113 _domain_colors.put( name, c );
118 private Color getColorTwo( final Color color_one ) {
119 final int red = color_one.getRed() + RenderableDomainArchitecture.BRIGHTEN_COLOR_BY;
120 final int green = color_one.getGreen() + RenderableDomainArchitecture.BRIGHTEN_COLOR_BY;
121 final int blue = color_one.getBlue() + RenderableDomainArchitecture.BRIGHTEN_COLOR_BY;
122 return new Color( red > 255 ? 255 : red, green > 255 ? 255 : green, blue > 255 ? 255 : blue );
126 public ProteinDomain getDomain( final int i ) {
127 return _domain_structure.getDomain( i );
131 public SortedMap<BigDecimal, ProteinDomain> getDomains() {
132 return _domain_structure.getDomains();
136 public int getNumberOfDomains() {
137 return _domain_structure.getNumberOfDomains();
141 public Dimension getOriginalSize() {
142 return new Dimension( _domain_structure.getTotalLength(), ForesterUtil.roundToInt( _rendering_height ) );
146 public Object getParameter() {
147 return new Integer( _e_value_threshold_exp );
150 public float getRenderingFactorWidth() {
151 return _rendering_factor_width;
155 public Dimension getRenderingSize() {
156 return new Dimension( ForesterUtil.roundToInt( _domain_structure.getTotalLength() * getRenderingFactorWidth() ),
157 ForesterUtil.roundToInt( _rendering_height ) );
161 public int getTotalLength() {
162 return _domain_structure.getTotalLength();
166 public boolean isEqual( final PhylogenyData data ) {
167 return _domain_structure.isEqual( data );
171 public void render( final float x1,
174 final TreePanel tree_panel,
175 final boolean to_pdf ) {
176 final float f = getRenderingFactorWidth();
177 final float y = y1 + ( _rendering_height / 2 );
178 final float start = x1 + 20;
179 final Stroke s = g.getStroke();
180 g.setStroke( STROKE_1 );
182 g.setColor( tree_panel.getTreeColorSet().getDomainBaseColor() );
185 g.setColor( Constants.DOMAIN_BASE_COLOR_FOR_PDF );
187 _rectangle.setFrame( start, y - 0.5, _domain_structure.getTotalLength() * f, 1 );
188 g.fill( _rectangle );
189 for( int i = 0; i < _domain_structure.getDomains().size(); ++i ) {
190 final ProteinDomain d = _domain_structure.getDomain( i );
191 if ( d.getConfidence() <= Math.pow( 10, _e_value_threshold_exp ) ) {
192 final float xa = start + ( d.getFrom() * f );
193 final float xb = xa + ( d.getLength() * f );
194 if ( tree_panel.getMainPanel().getOptions().isShowDomainLabels()
195 && ( tree_panel.getMainPanel().getTreeFontSet().getFontMetricsSmall().getHeight() > 4 ) ) {
196 g.setFont( tree_panel.getMainPanel().getTreeFontSet().getSmallFont() );
198 g.setColor( tree_panel.getTreeColorSet().getDomainLabelColor() );
201 g.setColor( Constants.DOMAIN_LABEL_COLOR_FOR_PDF );
203 g.drawString( d.getName(), xa, y1
204 + tree_panel.getMainPanel().getTreeFontSet().getFontMetricsSmall().getAscent()
205 + _rendering_height );
207 drawDomain( xa, y1, xb - xa, _rendering_height, d.getName(), g, to_pdf );
214 public void setParameter( final double e_value_threshold_exp ) {
215 _e_value_threshold_exp = ( int ) e_value_threshold_exp;
218 public void setRenderingFactorWidth( final float rendering_factor_width ) {
219 _rendering_factor_width = rendering_factor_width;
223 public void setRenderingHeight( final float rendering_height ) {
224 _rendering_height = rendering_height;
228 public StringBuffer toNHX() {
229 return _domain_structure.toNHX();
233 public void toPhyloXML( final Writer writer, final int level, final String indentation ) throws IOException {
234 _domain_structure.toPhyloXML( writer, level, indentation );