Subject: forester needs openchart library Description: biojava makes use of a limited set of forester As openchart is not available in Debian, remove openchart related calls to make forester compilation OK in biojava context Author: Olivier Sallou Last-Updated: 2016-12-09 Forwarded: not-needed --- a/forester/org/forester/msa_compactor/Chart.java +++ b/forester/org/forester/msa_compactor/Chart.java @@ -40,47 +40,22 @@ import org.forester.util.ForesterUtil; -import com.approximatrix.charting.coordsystem.BoxCoordSystem; -import com.approximatrix.charting.model.MultiScatterDataModel; -import com.approximatrix.charting.render.MultiScatterChartRenderer; -import com.approximatrix.charting.swing.ChartPanel; public final class Chart extends JDialog implements ActionListener { 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 int _initial_number_of_seqs=0; private final JMenuItem _m_exit = new JMenuItem(); - private final List _msa_props; - private final boolean _show_msa_qual; - private final String _title; + private final List _msa_props=null; + private final boolean _show_msa_qual=false; + private final String _title=null; private Chart( final List 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( 600, 500 ); - setResizable( true ); - final JPanel content_pane = new JPanel(); - content_pane.setLayout( new BorderLayout() ); - setContentPane( content_pane ); - final JMenuBar menu_bar = new JMenuBar(); - final JMenu file_menu = new JMenu(); - file_menu.setText( "File" ); - _m_exit.setText( "Exit" ); - file_menu.add( _m_exit ); - menu_bar.add( file_menu ); - setJMenuBar( menu_bar ); - setDefaultCloseOperation( WindowConstants.DISPOSE_ON_CLOSE ); - _m_exit.addActionListener( this ); - content_pane.add( obtainChartPanel(), BorderLayout.CENTER ); } @Override @@ -90,150 +65,4 @@ } } - private ChartPanel obtainChartPanel() { - if ( _chart_panel == null ) { - final MultiScatterDataModel model = new MultiScatterDataModel(); - 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(); - // - 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" + " (" + 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() * gap_ratio_factor ); - } - 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 ) { - 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 ); - } - final BoxCoordSystem coord = new BoxCoordSystem( model ); - 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, _title ); - _chart_panel.setCoordSystem( coord ); - final MultiScatterChartRenderer renderer = new MultiScatterChartRenderer( coord, model ); - renderer.setAllowBuffer( false ); - _chart_panel.addChartRenderer( renderer, 0 ); - } - return _chart_panel; - } - - 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 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, show_msa_qual, title ); - chart.setVisible( true ); - } - - public static void main( final String[] args ) { - try { - UIManager.setLookAndFeel( UIManager.getSystemLookAndFeelClassName() ); - } - catch ( final Exception e ) { - e.printStackTrace(); - } - final Chart temp = new Chart( null, 0, true, "title" ); - temp.setVisible( true ); - } } --- a/forester/org/forester/application/msa_compactor.java +++ b/forester/org/forester/application/msa_compactor.java @@ -39,7 +39,6 @@ import org.forester.msa.Msa.MSA_FORMAT; import org.forester.msa.MsaInferrer; import org.forester.msa.MsaMethods; -import org.forester.msa_compactor.Chart; import org.forester.msa_compactor.MsaCompactor; import org.forester.msa_compactor.MsaProperties; import org.forester.util.CommandLineArguments; @@ -396,7 +395,7 @@ else { msa_props = mc.chart( step, realign, normalize_for_effective_seq_length ); } - Chart.display( msa_props, initial_number_of_seqs, report_entropy, in.getName() ); + //Chart.display( msa_props, initial_number_of_seqs, report_entropy, in.getName() ); System.out.println(); System.out.println( "Final MSA properties" ); printMsaInfo( msa, MsaMethods.calculateEffectiveLengthStatistics( msa ));