2 // FORESTER -- software libraries and applications
3 // for evolutionary biology research and applications.
5 // Copyright (C) 2014 Christian M. Zmasek
6 // Copyright (C) 2014 Sanford-Burnham Medical Research Institute
9 // This library is free software; you can redistribute it and/or
10 // modify it under the terms of the GNU Lesser General Public
11 // License as published by the Free Software Foundation; either
12 // version 2.1 of the License, or (at your option) any later version.
14 // This library is distributed in the hope that it will be useful,
15 // but WITHOUT ANY WARRANTY; without even the implied warranty of
16 // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
17 // Lesser General Public License for more details.
19 // You should have received a copy of the GNU Lesser General Public
20 // License along with this library; if not, write to the Free Software
21 // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
23 // WWW: https://sites.google.com/site/cmzmasek/home/software/forester
25 package org.forester.msa_compactor;
27 import java.awt.BorderLayout;
28 import java.awt.event.ActionListener;
29 import java.text.DecimalFormat;
30 import java.text.NumberFormat;
31 import java.util.List;
33 import javax.swing.JDialog;
34 import javax.swing.JMenu;
35 import javax.swing.JMenuBar;
36 import javax.swing.JMenuItem;
37 import javax.swing.JPanel;
38 import javax.swing.UIManager;
39 import javax.swing.WindowConstants;
41 import org.forester.util.ForesterUtil;
43 import com.approximatrix.charting.coordsystem.BoxCoordSystem;
44 import com.approximatrix.charting.model.MultiScatterDataModel;
45 import com.approximatrix.charting.render.MultiScatterChartRenderer;
46 import com.approximatrix.charting.swing.ChartPanel;
48 public final class Chart extends JDialog implements ActionListener {
50 final private static NumberFormat NF_1 = new DecimalFormat( "0.##" );
51 private static final long serialVersionUID = -5292420246132943515L;
52 private ChartPanel _chart_panel = null;
53 private final int _initial_number_of_seqs;
54 private final JMenuItem _m_exit = new JMenuItem();
55 private final List<MsaProperties> _msa_props;
56 private final boolean _show_msa_qual;
57 private final String _title;
59 private Chart( final List<MsaProperties> msa_props,
60 final int initial_number_of_seqs,
61 final boolean show_msa_qual,
62 final String title ) {
64 _msa_props = msa_props;
66 _initial_number_of_seqs = initial_number_of_seqs;
67 _show_msa_qual = show_msa_qual;
68 setTitle( "msa compactor" );
71 final JPanel content_pane = new JPanel();
72 content_pane.setLayout( new BorderLayout() );
73 setContentPane( content_pane );
74 final JMenuBar menu_bar = new JMenuBar();
75 final JMenu file_menu = new JMenu();
76 file_menu.setText( "File" );
77 _m_exit.setText( "Exit" );
78 file_menu.add( _m_exit );
79 menu_bar.add( file_menu );
80 setJMenuBar( menu_bar );
81 setDefaultCloseOperation( WindowConstants.DISPOSE_ON_CLOSE );
82 _m_exit.addActionListener( this );
83 content_pane.add( obtainChartPanel(), BorderLayout.CENTER );
87 public void actionPerformed( final java.awt.event.ActionEvent e ) {
88 if ( e.getSource() == _m_exit ) {
93 private ChartPanel obtainChartPanel() {
94 if ( _chart_panel == null ) {
95 final MultiScatterDataModel model = new MultiScatterDataModel();
96 final double[][] seqs_length = new double[ _msa_props.size() ][ 2 ];
98 int min_length = Integer.MAX_VALUE;
99 double max_gap_ratio = -1;
100 double min_gap_ratio = Double.MAX_VALUE;
101 double max_avg_gap_count = -1;
102 double min_avg_gap_count = Double.MAX_VALUE;
103 for( int i = 0; i < _msa_props.size(); ++i ) {
104 seqs_length[ i ][ 0 ] = _initial_number_of_seqs - _msa_props.get( i ).getNumberOfSequences();
106 final int length = _msa_props.get( i ).getLength();
107 seqs_length[ i ][ 1 ] = length;
108 if ( length > max_length ) {
111 if ( length < min_length ) {
115 final double gap_ratio = _msa_props.get( i ).getGapRatio();
116 if ( gap_ratio > max_gap_ratio ) {
117 max_gap_ratio = gap_ratio;
119 if ( gap_ratio < min_gap_ratio ) {
120 min_gap_ratio = gap_ratio;
123 final double avg_gap_count = _msa_props.get( i ).getAvgNumberOfGaps();
124 if ( avg_gap_count > max_avg_gap_count ) {
125 max_avg_gap_count = avg_gap_count;
127 if ( avg_gap_count < min_avg_gap_count ) {
128 min_avg_gap_count = avg_gap_count;
131 model.addData( seqs_length, "Length" + " (" + minMaxToString( min_length, max_length ) + ")" );
132 model.setSeriesLine( "Series " + "Length", true );
133 model.setSeriesMarker( "Series " + "Length", false );
134 final double[][] seqs_gaps = new double[ _msa_props.size() ][ 2 ];
135 double max_ent7 = -1;
136 double max_ent21 = -1;
137 double min_ent7 = Double.MAX_VALUE;
138 double min_ent21 = Double.MAX_VALUE;
139 if ( _show_msa_qual ) {
140 for( int i = 0; i < _msa_props.size(); ++i ) {
141 final double ent7 = _msa_props.get( i ).getEntropy7();
142 if ( ent7 > max_ent7 ) {
145 if ( ent7 < max_ent7 ) {
148 final double ent21 = _msa_props.get( i ).getEntropy21();
149 if ( ent21 > min_ent21 ) {
152 if ( ent21 < min_ent21 ) {
157 final double gap_ratio_factor = ( max_length / 2.0 ) / max_gap_ratio;
158 final double avg_gaps_counts_factor = ( max_length / 2.0 ) / max_avg_gap_count;
159 final double ent7_factor = ( max_length / 2.0 ) / max_ent7;
160 final double ent21_factor = ( max_length / 2.0 ) / max_ent21;
161 for( int i = 0; i < _msa_props.size(); ++i ) {
162 seqs_gaps[ i ][ 0 ] = _initial_number_of_seqs - _msa_props.get( i ).getNumberOfSequences();
163 seqs_gaps[ i ][ 1 ] = ForesterUtil.roundToInt( _msa_props.get( i ).getGapRatio() * gap_ratio_factor );
165 model.addData( seqs_gaps, "Gap Ratio" + " (" + minMaxToString( min_gap_ratio, max_gap_ratio ) + ")" );
166 model.setSeriesLine( "Series " + "Gap Ratio", true );
167 model.setSeriesMarker( "Series " + "Gap Ratio", false );
168 final double[][] gap_counts = new double[ _msa_props.size() ][ 2 ];
169 for( int i = 0; i < _msa_props.size(); ++i ) {
170 gap_counts[ i ][ 0 ] = _initial_number_of_seqs - _msa_props.get( i ).getNumberOfSequences();
171 gap_counts[ i ][ 1 ] = ForesterUtil.roundToInt( _msa_props.get( i ).getAvgNumberOfGaps()
172 * avg_gaps_counts_factor );
174 model.addData( gap_counts, "Mean Gap Count" + " (" + minMaxToString( min_avg_gap_count, max_avg_gap_count )
176 model.setSeriesLine( "Series " + "Mean Gap Count", true );
177 model.setSeriesMarker( "Series " + "Mean Gap Count", false );
178 if ( _show_msa_qual ) {
179 final double[][] entropy7 = new double[ _msa_props.size() ][ 2 ];
180 for( int i = 0; i < _msa_props.size(); ++i ) {
181 entropy7[ i ][ 0 ] = _initial_number_of_seqs - _msa_props.get( i ).getNumberOfSequences();
182 entropy7[ i ][ 1 ] = ForesterUtil.roundToInt( _msa_props.get( i ).getEntropy7() * ent7_factor );
184 model.addData( entropy7, "Entropy norm 7" + " (" + minMaxToString( min_ent7, max_ent7 ) + ")" );
185 model.setSeriesLine( "Series " + "Entropy norm 7", true );
186 model.setSeriesMarker( "Series " + "Entropy norm 7", false );
188 final double[][] entropy21 = new double[ _msa_props.size() ][ 2 ];
189 for( int i = 0; i < _msa_props.size(); ++i ) {
190 entropy21[ i ][ 0 ] = _initial_number_of_seqs - _msa_props.get( i ).getNumberOfSequences();
191 entropy21[ i ][ 1 ] = ForesterUtil.roundToInt( _msa_props.get( i ).getEntropy21() * ent21_factor );
193 model.addData( entropy21, "Entropy norm 21" + " (" + minMaxToString( min_ent21, max_ent21 ) + ")" );
194 model.setSeriesLine( "Series " + "Entropy norm 21", true );
195 model.setSeriesMarker( "Series " + "Entropy norm 21", false );
197 final BoxCoordSystem coord = new BoxCoordSystem( model );
198 coord.setUnitFont( coord.getUnitFont().deriveFont( 16.0f ) );
199 coord.setXAxisUnit( "Number of Removed Sequences" );
200 coord.setPaintGrid( true );
201 coord.setYAxisUnit( "MSA Length" );
202 _chart_panel = new ChartPanel( model, _title );
203 _chart_panel.setCoordSystem( coord );
204 final MultiScatterChartRenderer renderer = new MultiScatterChartRenderer( coord, model );
205 renderer.setAllowBuffer( false );
206 _chart_panel.addChartRenderer( renderer, 0 );
211 private final static String minMaxToString( final double min, final double max ) {
212 return NF_1.format( min ) + "-" + NF_1.format( max );
215 public static void display( final List<MsaProperties> msa_props,
216 final int initial_number_of_seqs,
217 final boolean show_msa_qual,
218 final String title ) {
220 UIManager.setLookAndFeel( UIManager.getSystemLookAndFeelClassName() );
222 catch ( final Exception e ) {
225 final Chart chart = new Chart( msa_props, initial_number_of_seqs, show_msa_qual, title );
226 chart.setVisible( true );
229 public static void main( final String[] args ) {
231 UIManager.setLookAndFeel( UIManager.getSystemLookAndFeelClassName() );
233 catch ( final Exception e ) {
236 final Chart temp = new Chart( null, 0, true, "title" );
237 temp.setVisible( true );