X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Fmsa_compactor%2FChart.java;h=3ea86f472b3d53d95857ee45cdc9499fb711986c;hb=e572f0142daf64409db0461f15215288137603f8;hp=38da2b418e2c67eb94012b1295398747e8aeab1c;hpb=cea9261d689486e31e8abd13a25ffbff3c826e2e;p=jalview.git diff --git a/forester/java/src/org/forester/msa_compactor/Chart.java b/forester/java/src/org/forester/msa_compactor/Chart.java index 38da2b4..3ea86f4 100644 --- a/forester/java/src/org/forester/msa_compactor/Chart.java +++ b/forester/java/src/org/forester/msa_compactor/Chart.java @@ -26,6 +26,8 @@ package org.forester.msa_compactor; import java.awt.BorderLayout; import java.awt.event.ActionListener; +import java.text.DecimalFormat; +import java.text.NumberFormat; import java.util.List; import javax.swing.JDialog; @@ -45,6 +47,7 @@ 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; @@ -92,50 +95,93 @@ public final class Chart extends JDialog implements ActionListener { 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(); - seqs_length[ i ][ 1 ] = _msa_props.get( i ).getLength(); - if ( _msa_props.get( i ).getLength() > max_length ) { - max_length = _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_gap_ratio = -1; double max_ent7 = -1; double max_ent21 = -1; - for( int i = 0; i < _msa_props.size(); ++i ) { - if ( _msa_props.get( i ).getGapRatio() > max_gap_ratio ) { - max_gap_ratio = _msa_props.get( i ).getGapRatio(); - } - if ( _show_msa_qual ) { - if ( _msa_props.get( i ).getEntropy7() > max_ent7 ) { - max_ent7 = _msa_props.get( i ).getEntropy7(); + 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; } - if ( _msa_props.get( i ).getEntropy21() > max_ent21 ) { - max_ent21 = _msa_props.get( i ).getEntropy21(); + 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" ); - model.setSeriesLine( "Series " + "Gap ratio", true ); - model.setSeriesMarker( "Series " + "Gap ratio", false ); + 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" ); + 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 ); // @@ -144,7 +190,7 @@ public final class Chart extends JDialog implements ActionListener { 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" ); + 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 ); } @@ -162,6 +208,10 @@ public final class Chart extends JDialog implements ActionListener { 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,