package org.forester.msa_compactor;
+import java.awt.Color;
import java.io.File;
import java.io.IOException;
import java.io.Writer;
import java.util.SortedSet;
import java.util.TreeSet;
+import org.forester.archaeopteryx.Archaeopteryx;
+import org.forester.archaeopteryx.Configuration;
import org.forester.evoinference.distance.NeighborJoiningF;
import org.forester.evoinference.distance.PairwiseDistanceCalculator;
import org.forester.evoinference.distance.PairwiseDistanceCalculator.PWD_DISTANCE_METHOD;
import org.forester.evoinference.matrix.distance.BasicSymmetricalDistanceMatrix;
import org.forester.evoinference.tools.BootstrapResampler;
+import org.forester.io.parsers.nhx.NHXParser.TAXONOMY_EXTRACTION;
+import org.forester.io.parsers.phyloxml.PhyloXmlDataFormatException;
+import org.forester.io.parsers.util.ParserUtils;
import org.forester.io.writers.SequenceWriter;
import org.forester.io.writers.SequenceWriter.SEQ_FORMAT;
import org.forester.msa.DeleteableMsa;
import org.forester.msa.ResampleableMsa;
import org.forester.phylogeny.Phylogeny;
import org.forester.phylogeny.PhylogenyMethods;
+import org.forester.phylogeny.PhylogenyMethods.DESCENDANT_SORT_PRIORITY;
+import org.forester.phylogeny.PhylogenyNode;
+import org.forester.phylogeny.data.NodeVisualData;
+import org.forester.phylogeny.data.NodeVisualData.NodeFill;
+import org.forester.phylogeny.data.NodeVisualData.NodeShape;
+import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
import org.forester.sequence.Sequence;
import org.forester.tools.ConfidenceAssessor;
+import org.forester.util.BasicDescriptiveStatistics;
import org.forester.util.ForesterUtil;
public class MsaCompactor {
private String _maffts_opts = "--auto";
private int _min_length = -1;
//
+ private String _infile_name = null;
private DeleteableMsa _msa = null;
private boolean _norm = true;
private File _out_file_base = null;
private boolean _report_aln_mean_identity = false;
private int _step = -1;
private int _step_for_diagnostics = -1;
+ private boolean _phylogentic_inference = false;
static {
NF_4.setRoundingMode( RoundingMode.HALF_UP );
NF_3.setRoundingMode( RoundingMode.HALF_UP );
for( final GapContribution gap_gontribution : stats ) {
to_remove_ids.add( gap_gontribution.getId() );
}
- printTableHeader();
- final int x = ForesterUtil.roundToInt( _msa.getNumberOfSequences() / 20.0 );
- MsaProperties msa_prop = new MsaProperties( _msa, _report_aln_mean_identity );
+ if ( !_realign ) {
+ _step = -1;
+ }
+ int x = ForesterUtil.roundToInt( _msa.getNumberOfSequences() / 20.0 );
+ if ( x < 1 ) {
+ x = 1;
+ }
+ MsaProperties msa_prop = new MsaProperties( _msa, "", _report_aln_mean_identity );
msa_props.add( msa_prop );
+ Phylogeny phy = null;
+ if ( _phylogentic_inference ) {
+ System.out.println( "calculating phylogentic tree..." );
+ System.out.println();
+ phy = calcTree();
+ }
+ printTableHeader();
printMsaProperties( "", msa_prop );
System.out.println();
int i = 0;
if ( realign && isPrintMsaStatsWriteOutfileAndRealign( i ) ) {
removeGapColumns();
realignWithMafft();
- msa_prop = new MsaProperties( _msa, _report_aln_mean_identity );
+ msa_prop = new MsaProperties( _msa, id, _report_aln_mean_identity );
msa_props.add( msa_prop );
printMsaProperties( id, msa_prop );
System.out.print( "(realigned)" );
}
else if ( isPrintMsaStats( i ) ) {
removeGapColumns();
- msa_prop = new MsaProperties( _msa, _report_aln_mean_identity );
+ msa_prop = new MsaProperties( _msa, id, _report_aln_mean_identity );
msa_props.add( msa_prop );
printMsaProperties( id, msa_prop );
System.out.println();
}
++i;
}
+ if ( _phylogentic_inference ) {
+ final Phylogeny p2 = phy.copy();
+ decorateTree( p2, to_remove_ids );
+ decorateTree2( phy, msa_props );
+ displayTree( p2 );
+ displayTree( phy );
+ }
return msa_props;
}
+ final public void deleteGapColumns( final double max_allowed_gap_ratio ) {
+ _msa.deleteGapColumns( max_allowed_gap_ratio );
+ }
+
final public Msa getMsa() {
return _msa;
}
return _removed_seq_ids;
}
+ public final void removeSequencesByMinimalLength( final int min_effective_length ) {
+ printMsaProperties( "", new MsaProperties( _msa, "", _report_aln_mean_identity ) );
+ System.out.println();
+ _msa = DeleteableMsa.createInstance( MsaMethods.removeSequencesByMinimalLength( _msa, min_effective_length ) );
+ removeGapColumns();
+ printMsaProperties( "", new MsaProperties( _msa, "", _report_aln_mean_identity ) );
+ System.out.println();
+ }
+
public final List<MsaProperties> removeViaGapAverage( final double mean_gapiness ) throws IOException,
InterruptedException {
final GapContribution stats[] = calcGapContribtionsStats( _norm );
to_remove_ids.add( gap_gontribution.getId() );
}
printTableHeader();
- MsaProperties msa_prop = new MsaProperties( _msa, _report_aln_mean_identity );
+ MsaProperties msa_prop = new MsaProperties( _msa, "", _report_aln_mean_identity );
msa_props.add( msa_prop );
printMsaProperties( "", msa_prop );
System.out.println();
System.out.println();
}
else if ( isPrintMsaStats( i ) ) {
- msa_prop = new MsaProperties( _msa, _report_aln_mean_identity );
+ msa_prop = new MsaProperties( _msa, id, _report_aln_mean_identity );
msa_props.add( msa_prop );
printMsaProperties( id, msa_prop );
System.out.println();
to_remove_ids.add( gap_gontribution.getId() );
}
printTableHeader();
- MsaProperties msa_prop = new MsaProperties( _msa, _report_aln_mean_identity );
+ MsaProperties msa_prop = new MsaProperties( _msa, "", _report_aln_mean_identity );
msa_props.add( msa_prop );
printMsaProperties( "", msa_prop );
System.out.println();
System.out.println();
}
else if ( isPrintMsaStats( i ) ) {
- msa_prop = new MsaProperties( _msa, _report_aln_mean_identity );
+ msa_prop = new MsaProperties( _msa, id, _report_aln_mean_identity );
printMsaProperties( id, msa_prop );
msa_props.add( msa_prop );
System.out.println();
_removed_seq_ids.add( stats[ j ].getId() );
}
printTableHeader();
- MsaProperties msa_prop = new MsaProperties( _msa, _report_aln_mean_identity );
+ MsaProperties msa_prop = new MsaProperties( _msa, "", _report_aln_mean_identity );
msa_props.add( msa_prop );
printMsaProperties( "", msa_prop );
System.out.println();
System.out.println();
}
else if ( isPrintMsaStats( i ) ) {
- msa_prop = new MsaProperties( _msa, _report_aln_mean_identity );
+ msa_prop = new MsaProperties( _msa, id, _report_aln_mean_identity );
msa_props.add( msa_prop );
printMsaProperties( id, msa_prop );
System.out.println();
}
private final boolean isPrintMsaStats( final int i ) {
- return ( ( ( _step < 2 ) && ( _step_for_diagnostics < 2 ) ) || ( ( _step_for_diagnostics > 0 ) && ( ( ( i + 1 ) % _step_for_diagnostics ) == 0 ) ) );
+ return ( ( ( _step == 1 ) && ( _step_for_diagnostics == 1 ) ) || ( ( _step_for_diagnostics > 0 ) && ( ( ( i + 1 ) % _step_for_diagnostics ) == 0 ) ) );
}
private final boolean isPrintMsaStatsWriteOutfileAndRealign( final int i ) {
- return ( ( ( _step < 2 ) && ( _step_for_diagnostics < 2 ) ) || ( ( _step > 0 ) && ( ( ( i + 1 ) % _step ) == 0 ) ) );
+ return ( ( ( _step == 1 ) && ( _step_for_diagnostics == 1 ) ) || ( ( _step > 0 ) && ( ( ( i + 1 ) % _step ) == 0 ) ) );
}
private final StringBuilder msaPropertiesAsSB( final MsaProperties msa_properties ) {
sb.append( msa_properties.getLength() );
sb.append( "\t" );
sb.append( NF_4.format( msa_properties.getGapRatio() ) );
- if ( _report_aln_mean_identity /*msa_properties.getAverageIdentityRatio() >= 0*/) {
+ if ( _report_aln_mean_identity ) {
sb.append( "\t" );
sb.append( NF_4.format( msa_properties.getAverageIdentityRatio() ) );
}
return "";
}
- private final Phylogeny pi( final String matrix ) {
+ private final Phylogeny pi( final String matrix, final int boostrap ) {
final Phylogeny master_phy = inferNJphylogeny( PWD_DISTANCE_METHOD.KIMURA_DISTANCE, _msa, true, matrix );
final int seed = 15;
final int n = 100;
return master_phy;
}
+ public final Phylogeny calcTree() {
+ final Phylogeny phy = inferNJphylogeny( PWD_DISTANCE_METHOD.KIMURA_DISTANCE, _msa, false, "" );
+ PhylogenyMethods.midpointRoot( phy );
+ PhylogenyMethods.orderAppearance( phy.getRoot(), true, true, DESCENDANT_SORT_PRIORITY.NODE_NAME );
+ final boolean x = PhylogenyMethods.extractFastaInformation( phy );
+ if ( !x ) {
+ final PhylogenyNodeIterator it = phy.iteratorExternalForward();
+ while ( it.hasNext() ) {
+ final PhylogenyNode n = it.next();
+ final String name = n.getName().trim();
+ if ( !ForesterUtil.isEmpty( name ) ) {
+ try {
+ ParserUtils.extractTaxonomyDataFromNodeName( n, TAXONOMY_EXTRACTION.AGGRESSIVE );
+ }
+ catch ( final PhyloXmlDataFormatException e ) {
+ // Ignore.
+ }
+ }
+ }
+ }
+ return phy;
+ }
+
+ public final void decorateTree( final Phylogeny phy, final List<String> to_remove_ids ) {
+ for( int i = 0; i < to_remove_ids.size(); ++i ) {
+ final String id = to_remove_ids.get( i );
+ final PhylogenyNode n = phy.getNode( id );
+ n.setName( n.getName() + " [" + ( i + 1 ) + "]" );
+ final NodeVisualData vis = new NodeVisualData();
+ vis.setFillType( NodeFill.SOLID );
+ vis.setShape( NodeShape.RECTANGLE );
+ vis.setSize( 6 );
+ vis.setNodeColor( new Color( i > 255 ? 0 : 255 - i, 0, 0 ) );
+ n.getNodeData().setNodeVisualData( vis );
+ }
+ }
+
+ public final void decorateTree2( final Phylogeny phy, final List<MsaProperties> msa_props ) {
+ final BasicDescriptiveStatistics length_stats = new BasicDescriptiveStatistics();
+ for( int i = 0; i < msa_props.size(); ++i ) {
+ final MsaProperties msa_prop = msa_props.get( i );
+ final String id = msa_prop.getRemovedSeq();
+ if ( !ForesterUtil.isEmpty( id ) ) {
+ length_stats.addValue( msa_prop.getLength() );
+ }
+ }
+ final double mean = length_stats.arithmeticMean();
+ final double min = length_stats.getMin();
+ final double max = length_stats.getMax();
+ final Color min_color = new Color( 0, 255, 0 );
+ final Color max_color = new Color( 255, 0, 0 );
+ final Color mean_color = new Color( 255, 255, 0 );
+ final PhylogenyNodeIterator it = phy.iteratorExternalForward();
+ while ( it.hasNext() ) {
+ final NodeVisualData vis = new NodeVisualData();
+ vis.setFillType( NodeFill.SOLID );
+ vis.setShape( NodeShape.RECTANGLE );
+ vis.setSize( 6 );
+ vis.setNodeColor( min_color );
+ it.next().getNodeData().setNodeVisualData( vis );
+ }
+ for( int i = 0; i < msa_props.size(); ++i ) {
+ final MsaProperties msa_prop = msa_props.get( i );
+ final String id = msa_prop.getRemovedSeq();
+ if ( !ForesterUtil.isEmpty( id ) ) {
+ final PhylogenyNode n = phy.getNode( id );
+ n.setName( n.getName() + " [" + i + "]" );
+ n.getNodeData()
+ .getNodeVisualData()
+ .setNodeColor( ForesterUtil.calcColor( msa_prop.getLength(),
+ min,
+ max,
+ mean,
+ min_color,
+ max_color,
+ mean_color ) );
+ }
+ }
+ }
+
+ public final void displayTree( final Phylogeny phy ) {
+ final Configuration config = new Configuration();
+ config.setDisplayAsPhylogram( true );
+ config.setUseStyle( true );
+ config.setDisplayTaxonomyCode( false );
+ config.setDisplayTaxonomyCommonNames( false );
+ config.setDisplayTaxonomyScientificNames( false );
+ config.setDisplaySequenceNames( false );
+ config.setDisplaySequenceSymbols( false );
+ config.setDisplayGeneNames( false );
+ config.setShowScale( true );
+ config.setAddTaxonomyImagesCB( false );
+ config.setBaseFontSize( 9 );
+ config.setBaseFontFamilyName( "Arial" );
+ Archaeopteryx.createApplication( phy, config, _infile_name );
+ }
+
private final void printMsaProperties( final String id, final MsaProperties msa_properties ) {
- if ( ( _step < 2 ) || ( _step_for_diagnostics < 2 ) ) {
+ if ( ( _step == 1 ) || ( _step_for_diagnostics == 1 ) ) {
System.out.print( ForesterUtil.pad( id, _longest_id_length, ' ', false ) );
System.out.print( "\t" );
}
if ( realign ) {
realignWithMafft();
}
- final MsaProperties msa_prop = new MsaProperties( _msa, _report_aln_mean_identity );
+ final MsaProperties msa_prop = new MsaProperties( _msa, id, _report_aln_mean_identity );
printMsaProperties( id, msa_prop );
final String s = writeOutfile();
System.out.print( "-> " + s + ( realign ? "\t(realigned)" : "" ) );
}
private final void printTableHeader() {
- if ( ( _step < 2 ) || ( _step_for_diagnostics < 2 ) ) {
+ if ( ( _step == 1 ) || ( _step_for_diagnostics == 1 ) ) {
System.out.print( ForesterUtil.pad( "Id", _longest_id_length, ' ', false ) );
System.out.print( "\t" );
}
msa.write( w, format );
w.close();
}
+
+ public void setPeformPhylogenticInference( final boolean phylogentic_inference ) {
+ _phylogentic_inference = phylogentic_inference;
+ }
+
+ public void setInfileName( final String infile_name ) {
+ _infile_name = infile_name;
+ }
}
git://source.jalview.org / jalview.git / blobdiff