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.util.ArrayList;
30 import java.util.List;
32 import javax.swing.JDialog;
33 import javax.swing.JMenu;
34 import javax.swing.JMenuBar;
35 import javax.swing.JMenuItem;
36 import javax.swing.JPanel;
37 import javax.swing.UIManager;
38 import javax.swing.WindowConstants;
40 import org.forester.util.ForesterUtil;
42 import com.approximatrix.charting.coordsystem.BoxCoordSystem;
43 import com.approximatrix.charting.model.MultiScatterDataModel;
44 import com.approximatrix.charting.render.MultiScatterChartRenderer;
45 import com.approximatrix.charting.swing.ChartPanel;
47 public final class Chart extends JDialog implements ActionListener {
49 private static final long serialVersionUID = -5292420246132943515L;
50 private ChartPanel _chart_panel = null;
51 private final JMenuItem _m_exit = new JMenuItem();
52 private List<MsaProperties> _msa_props;
53 private final boolean _show_msa_qual;
54 private final int _initial_number_of_seqs;
55 private final String _title;
57 private Chart( final List<MsaProperties> msa_props,
58 final int initial_number_of_seqs,
59 final boolean show_msa_qual,
60 final String title ) {
62 _msa_props = msa_props;
64 _initial_number_of_seqs = initial_number_of_seqs;
65 _show_msa_qual = show_msa_qual;
66 setTitle( "msa compactor" );
69 final JPanel content_pane = new JPanel();
70 content_pane.setLayout( new BorderLayout() );
71 setContentPane( content_pane );
72 final JMenuBar menu_bar = new JMenuBar();
73 final JMenu file_menu = new JMenu();
74 file_menu.setText( "File" );
75 _m_exit.setText( "Exit" );
76 file_menu.add( _m_exit );
77 menu_bar.add( file_menu );
78 setJMenuBar( menu_bar );
79 setDefaultCloseOperation( WindowConstants.DISPOSE_ON_CLOSE );
80 _m_exit.addActionListener( this );
81 content_pane.add( obtainChartPanel(), BorderLayout.CENTER );
85 public void actionPerformed( final java.awt.event.ActionEvent e ) {
86 if ( e.getSource() == _m_exit ) {
91 private ChartPanel obtainChartPanel() {
92 if ( _chart_panel == null ) {
93 final MultiScatterDataModel model = new MultiScatterDataModel();
94 if ( ( _msa_props == null ) || _msa_props.isEmpty() ) {
95 _msa_props = new ArrayList<MsaProperties>();
96 final MsaProperties p0 = new MsaProperties( 10, 200, 0.5, 0.1, "" );
97 final MsaProperties p1 = new MsaProperties( 9, 190, 0.49, 0.2, "" );
98 final MsaProperties p2 = new MsaProperties( 8, 150, 0.2, 0.3, "" );
99 final MsaProperties p3 = new MsaProperties( 7, 145, 0.2, 0.4, "" );
100 _msa_props.add( p0 );
101 _msa_props.add( p1 );
102 _msa_props.add( p2 );
103 _msa_props.add( p3 );
105 final double[][] seqs_length = new double[ _msa_props.size() ][ 2 ];
106 for( int i = 0; i < _msa_props.size(); ++i ) {
107 seqs_length[ i ][ 0 ] = _initial_number_of_seqs - _msa_props.get( i ).getNumberOfSequences();
108 seqs_length[ i ][ 1 ] = _msa_props.get( i ).getLength();
110 model.addData( seqs_length, "Length" );
111 model.setSeriesLine( "Series " + "Length", true );
112 model.setSeriesMarker( "Series " + "Length", false );
113 final double[][] seqs_gaps = new double[ _msa_props.size() ][ 2 ];
114 for( int i = 0; i < _msa_props.size(); ++i ) {
115 seqs_gaps[ i ][ 0 ] = _initial_number_of_seqs - _msa_props.get( i ).getNumberOfSequences();
116 seqs_gaps[ i ][ 1 ] = ForesterUtil.roundToInt( _msa_props.get( i ).getGapRatio() * 200 );
118 model.addData( seqs_gaps, "Gap ratio" );
119 model.setSeriesLine( "Series " + "Gap ratio", true );
120 model.setSeriesMarker( "Series " + "Gap ratio", false );
121 if ( _show_msa_qual ) {
122 final double[][] seqs_identity = new double[ _msa_props.size() ][ 2 ];
123 for( int i = 0; i < _msa_props.size(); ++i ) {
124 seqs_identity[ i ][ 0 ] = _initial_number_of_seqs - _msa_props.get( i ).getNumberOfSequences();
125 seqs_identity[ i ][ 1 ] = ForesterUtil
126 .roundToInt( _msa_props.get( i ).getAverageIdentityRatio() * 200 );
128 model.addData( seqs_identity, "mean MSA column identity" );
129 model.setSeriesLine( "Series " + "mean MSA column identity", true );
130 model.setSeriesMarker( "Series " + "mean MSA column identity", false );
132 final BoxCoordSystem coord = new BoxCoordSystem( model );
133 coord.setUnitFont( coord.getUnitFont().deriveFont( 16.0f ) );
134 coord.setXAxisUnit( "Number of Removed Sequences" );
135 coord.setPaintGrid( true );
136 coord.setYAxisUnit( "MSA Length" );
137 _chart_panel = new ChartPanel( model, _title );
138 _chart_panel.setCoordSystem( coord );
139 final MultiScatterChartRenderer renderer = new MultiScatterChartRenderer( coord, model );
140 renderer.setAllowBuffer( false );
141 _chart_panel.addChartRenderer( renderer, 0 );
146 public static void display( final List<MsaProperties> msa_props,
147 final int initial_number_of_seqs,
148 final boolean show_msa_qual,
149 final String title ) {
151 UIManager.setLookAndFeel( UIManager.getSystemLookAndFeelClassName() );
153 catch ( final Exception e ) {
156 final Chart chart = new Chart( msa_props, initial_number_of_seqs, show_msa_qual, title );
157 chart.setVisible( true );
160 public static void main( final String[] args ) {
162 UIManager.setLookAndFeel( UIManager.getSystemLookAndFeelClassName() );
164 catch ( final Exception e ) {
167 final Chart temp = new Chart( null, 0, true, "title" );
168 temp.setVisible( true );