import java.awt.BorderLayout;
import java.awt.event.ActionListener;
-import java.util.ArrayList;
+import java.text.DecimalFormat;
+import java.text.NumberFormat;
import java.util.List;
import javax.swing.JDialog;
public final class Chart extends JDialog implements ActionListener {
- private static final long serialVersionUID = -5292420246132943515L;
- private ChartPanel _chart_panel = null;
- private final JMenuItem _m_exit = new JMenuItem();
- private List<MsaProperties> _msa_props;
- private final int _initial_number_of_seqs;
+ final private static NumberFormat NF_1 = new DecimalFormat( "0.##" );
+ private static final long serialVersionUID = -5292420246132943515L;
+ private ChartPanel _chart_panel = null;
+ private final int _initial_number_of_seqs;
+ private final JMenuItem _m_exit = new JMenuItem();
+ private final List<MsaProperties> _msa_props;
+ private final boolean _show_msa_qual;
+ private final String _title;
- private Chart( final List<MsaProperties> msa_props, final int initial_number_of_seqs ) {
+ private Chart( final List<MsaProperties> msa_props,
+ final int initial_number_of_seqs,
+ final boolean show_msa_qual,
+ final String title ) {
super();
_msa_props = msa_props;
+ _title = title;
_initial_number_of_seqs = initial_number_of_seqs;
+ _show_msa_qual = show_msa_qual;
setTitle( "msa compactor" );
- setSize( 500, 400 );
+ setSize( 600, 500 );
setResizable( true );
final JPanel content_pane = new JPanel();
content_pane.setLayout( new BorderLayout() );
private ChartPanel obtainChartPanel() {
if ( _chart_panel == null ) {
final MultiScatterDataModel model = new MultiScatterDataModel();
- if ( ( _msa_props == null ) || _msa_props.isEmpty() ) {
- _msa_props = new ArrayList<MsaProperties>();
- final MsaProperties p0 = new MsaProperties( 10, 200, 0.5, 0.1 );
- final MsaProperties p1 = new MsaProperties( 9, 190, 0.49, 0.2 );
- final MsaProperties p2 = new MsaProperties( 8, 150, 0.2, 0.3 );
- final MsaProperties p3 = new MsaProperties( 7, 145, 0.2, 0.4 );
- _msa_props.add( p0 );
- _msa_props.add( p1 );
- _msa_props.add( p2 );
- _msa_props.add( p3 );
- }
final double[][] seqs_length = new double[ _msa_props.size() ][ 2 ];
+ int max_length = -1;
+ int min_length = Integer.MAX_VALUE;
+ double max_gap_ratio = -1;
+ double min_gap_ratio = Double.MAX_VALUE;
+ double max_avg_gap_count = -1;
+ double min_avg_gap_count = Double.MAX_VALUE;
for( int i = 0; i < _msa_props.size(); ++i ) {
seqs_length[ i ][ 0 ] = _initial_number_of_seqs - _msa_props.get( i ).getNumberOfSequences();
- seqs_length[ i ][ 1 ] = _msa_props.get( i ).getLength();
+ //
+ final int length = _msa_props.get( i ).getLength();
+ seqs_length[ i ][ 1 ] = length;
+ if ( length > max_length ) {
+ max_length = length;
+ }
+ if ( length < min_length ) {
+ min_length = length;
+ }
+ //
+ final double gap_ratio = _msa_props.get( i ).getGapRatio();
+ if ( gap_ratio > max_gap_ratio ) {
+ max_gap_ratio = gap_ratio;
+ }
+ if ( gap_ratio < min_gap_ratio ) {
+ min_gap_ratio = gap_ratio;
+ }
+ //
+ final double avg_gap_count = _msa_props.get( i ).getAvgNumberOfGaps();
+ if ( avg_gap_count > max_avg_gap_count ) {
+ max_avg_gap_count = avg_gap_count;
+ }
+ if ( avg_gap_count < min_avg_gap_count ) {
+ min_avg_gap_count = avg_gap_count;
+ }
}
- model.addData( seqs_length, "Length" );
+ model.addData( seqs_length, "Length" + " (" + minMaxToString( min_length, max_length ) + ")" );
model.setSeriesLine( "Series " + "Length", true );
model.setSeriesMarker( "Series " + "Length", false );
final double[][] seqs_gaps = new double[ _msa_props.size() ][ 2 ];
+ double max_ent7 = -1;
+ double max_ent21 = -1;
+ double min_ent7 = Double.MAX_VALUE;
+ double min_ent21 = Double.MAX_VALUE;
+ if ( _show_msa_qual ) {
+ for( int i = 0; i < _msa_props.size(); ++i ) {
+ final double ent7 = _msa_props.get( i ).getEntropy7();
+ if ( ent7 > max_ent7 ) {
+ max_ent7 = ent7;
+ }
+ if ( ent7 < max_ent7 ) {
+ min_ent7 = ent7;
+ }
+ final double ent21 = _msa_props.get( i ).getEntropy21();
+ if ( ent21 > min_ent21 ) {
+ max_ent21 = ent21;
+ }
+ if ( ent21 < min_ent21 ) {
+ min_ent21 = ent21;
+ }
+ }
+ }
+ final double gap_ratio_factor = ( max_length / 2.0 ) / max_gap_ratio;
+ final double avg_gaps_counts_factor = ( max_length / 2.0 ) / max_avg_gap_count;
+ final double ent7_factor = ( max_length / 2.0 ) / max_ent7;
+ final double ent21_factor = ( max_length / 2.0 ) / max_ent21;
for( int i = 0; i < _msa_props.size(); ++i ) {
seqs_gaps[ i ][ 0 ] = _initial_number_of_seqs - _msa_props.get( i ).getNumberOfSequences();
- seqs_gaps[ i ][ 1 ] = ForesterUtil.roundToInt( _msa_props.get( i ).getGapRatio() * 100 );
+ seqs_gaps[ i ][ 1 ] = ForesterUtil.roundToInt( _msa_props.get( i ).getGapRatio() * gap_ratio_factor );
}
- model.addData( seqs_gaps, "Gaps" );
- model.setSeriesLine( "Series " + "Gaps", true );
- model.setSeriesMarker( "Series " + "Gaps", false );
- final double[][] seqs_identity = new double[ _msa_props.size() ][ 2 ];
+ model.addData( seqs_gaps, "Gap Ratio" + " (" + minMaxToString( min_gap_ratio, max_gap_ratio ) + ")" );
+ model.setSeriesLine( "Series " + "Gap Ratio", true );
+ model.setSeriesMarker( "Series " + "Gap Ratio", false );
+ final double[][] gap_counts = new double[ _msa_props.size() ][ 2 ];
for( int i = 0; i < _msa_props.size(); ++i ) {
- seqs_identity[ i ][ 0 ] = _initial_number_of_seqs - _msa_props.get( i ).getNumberOfSequences();
- seqs_identity[ i ][ 1 ] = ForesterUtil.roundToInt( _msa_props.get( i ).getAverageIdentityRatio() * 100 );
+ gap_counts[ i ][ 0 ] = _initial_number_of_seqs - _msa_props.get( i ).getNumberOfSequences();
+ gap_counts[ i ][ 1 ] = ForesterUtil.roundToInt( _msa_props.get( i ).getAvgNumberOfGaps()
+ * avg_gaps_counts_factor );
+ }
+ model.addData( gap_counts, "Mean Gap Count" + " (" + minMaxToString( min_avg_gap_count, max_avg_gap_count )
+ + ")" );
+ model.setSeriesLine( "Series " + "Mean Gap Count", true );
+ model.setSeriesMarker( "Series " + "Mean Gap Count", false );
+ if ( _show_msa_qual ) {
+ final double[][] entropy7 = new double[ _msa_props.size() ][ 2 ];
+ for( int i = 0; i < _msa_props.size(); ++i ) {
+ entropy7[ i ][ 0 ] = _initial_number_of_seqs - _msa_props.get( i ).getNumberOfSequences();
+ entropy7[ i ][ 1 ] = ForesterUtil.roundToInt( _msa_props.get( i ).getEntropy7() * ent7_factor );
+ }
+ model.addData( entropy7, "Entropy norm 7" + " (" + minMaxToString( min_ent7, max_ent7 ) + ")" );
+ model.setSeriesLine( "Series " + "Entropy norm 7", true );
+ model.setSeriesMarker( "Series " + "Entropy norm 7", false );
+ //
+ final double[][] entropy21 = new double[ _msa_props.size() ][ 2 ];
+ for( int i = 0; i < _msa_props.size(); ++i ) {
+ entropy21[ i ][ 0 ] = _initial_number_of_seqs - _msa_props.get( i ).getNumberOfSequences();
+ entropy21[ i ][ 1 ] = ForesterUtil.roundToInt( _msa_props.get( i ).getEntropy21() * ent21_factor );
+ }
+ model.addData( entropy21, "Entropy norm 21" + " (" + minMaxToString( min_ent21, max_ent21 ) + ")" );
+ model.setSeriesLine( "Series " + "Entropy norm 21", true );
+ model.setSeriesMarker( "Series " + "Entropy norm 21", false );
}
- model.addData( seqs_identity, "Id" );
- model.setSeriesLine( "Series " + "Id", true );
- model.setSeriesMarker( "Series " + "Id", false );
final BoxCoordSystem coord = new BoxCoordSystem( model );
- coord.setUnitFont( coord.getUnitFont().deriveFont( 20.0f ) );
- coord.setXAxisUnit( "Number of Sequences" );
+ coord.setUnitFont( coord.getUnitFont().deriveFont( 16.0f ) );
+ coord.setXAxisUnit( "Number of Removed Sequences" );
coord.setPaintGrid( true );
coord.setYAxisUnit( "MSA Length" );
- _chart_panel = new ChartPanel( model, "msa compactor" );
+ _chart_panel = new ChartPanel( model, _title );
_chart_panel.setCoordSystem( coord );
final MultiScatterChartRenderer renderer = new MultiScatterChartRenderer( coord, model );
renderer.setAllowBuffer( false );
return _chart_panel;
}
- public static void display( final List<MsaProperties> msa_props, final int initial_number_of_seqs ) {
+ private final static String minMaxToString( final double min, final double max ) {
+ return NF_1.format( min ) + "-" + NF_1.format( max );
+ }
+
+ public static void display( final List<MsaProperties> msa_props,
+ final int initial_number_of_seqs,
+ final boolean show_msa_qual,
+ final String title ) {
try {
UIManager.setLookAndFeel( UIManager.getSystemLookAndFeelClassName() );
}
catch ( final Exception e ) {
e.printStackTrace();
}
- final Chart chart = new Chart( msa_props, initial_number_of_seqs );
+ final Chart chart = new Chart( msa_props, initial_number_of_seqs, show_msa_qual, title );
chart.setVisible( true );
}
catch ( final Exception e ) {
e.printStackTrace();
}
- final Chart temp = new Chart( null, 0 );
+ final Chart temp = new Chart( null, 0, true, "title" );
temp.setVisible( true );
}
}
git://source.jalview.org / jalview.git / blobdiff