private final String _maffts_opts = "--auto";
private int _min_length = -1;
//
- private DeleteableMsa _msa;
+ private DeleteableMsa _msa = null;
private boolean _norm = true;
- private File _out_file_base;
+ private File _out_file_base = null;
private MSA_FORMAT _output_format = MSA_FORMAT.FASTA;
- private String _path_to_mafft;
+ private String _path_to_mafft = null;
//
private boolean _realign = false;
private final SortedSet<String> _removed_seq_ids;
private final File _removed_seqs_out_base = null;
- private final boolean _report_aln_mean_identity = false;
- private int _step = 1;
- private int _step_for_diagnostics = 1;
+ private boolean _report_aln_mean_identity = false;
+ private int _step = -1;
+ private int _step_for_diagnostics = -1;
static {
NF_4.setRoundingMode( RoundingMode.HALF_UP );
NF_3.setRoundingMode( RoundingMode.HALF_UP );
_removed_seq_ids = new TreeSet<String>();
}
- public final List<MsaProperties> chart( final int step,
- final boolean realign,
- final boolean norm,
- final boolean verbose ) throws IOException, InterruptedException {
- final GapContribution stats[] = calcGapContribtionsStats( norm );
- final List<String> to_remove_ids = new ArrayList<String>();
- final List<MsaProperties> msa_props = new ArrayList<MsaProperties>();
- for( final GapContribution gap_gontribution : stats ) {
- to_remove_ids.add( gap_gontribution.getId() );
- }
- if ( verbose ) {
- printTableHeader();
- }
- int i = 0;
- final int s = _msa.getNumberOfSequences();
- final int x = ForesterUtil.roundToInt( s / 20.0 );
- while ( _msa.getNumberOfSequences() > x ) {
- final String id = to_remove_ids.get( i );
- //~_msa = MsaMethods.removeSequence( _msa, id );
- _msa.deleteRow( id );
- if ( ( s < 500 ) || ( ( step > 0 ) && ( ( ( i + 1 ) % step ) == 0 ) ) ) {
- removeGapColumns();
- if ( realign && ( ( step > 0 ) && ( ( ( i + 1 ) % step ) == 0 ) ) ) {
- realignWithMafft();
- msa_props.add( new MsaProperties( _msa ) );
- if ( verbose ) {
- printMsaStats( id );
- }
- if ( verbose ) {
- System.out.print( "(realigned)" );
- }
- }
- else {
- msa_props.add( new MsaProperties( _msa ) );
- if ( verbose ) {
- printMsaStats( id );
- }
- }
- if ( verbose ) {
- System.out.println();
- }
- }
- ++i;
- }
- return msa_props;
- }
-
final public Msa getMsa() {
return _msa;
}
removeGapColumns();
if ( ( ( _step > 0 ) && ( ( ( i + 1 ) % _step ) == 0 ) )
|| ( MsaMethods.calcGapRatio( _msa ) <= mean_gapiness ) ) {
- printMsaStatsWriteOutfileAndRealign( _realign, verbose, id );
+ printMsaStatsWriteOutfileAndRealign( _realign, id );
}
else if ( verbose ) {
- printMsaStats( id );
+ final MsaProperties msa_prop = new MsaProperties( _msa, _report_aln_mean_identity );
+ printMsaProperties( id, msa_prop );
}
if ( verbose ) {
System.out.println();
_msa.deleteRow( id );
removeGapColumns();
if ( ( ( _step > 0 ) && ( ( ( i + 1 ) % _step ) == 0 ) ) || ( _msa.getLength() <= length ) ) {
- printMsaStatsWriteOutfileAndRealign( _realign, verbose, id );
+ printMsaStatsWriteOutfileAndRealign( _realign, id );
}
else if ( verbose ) {
- printMsaStats( id );
+ final MsaProperties msa_prop = new MsaProperties( _msa, _report_aln_mean_identity );
+ printMsaProperties( id, msa_prop );
}
if ( verbose ) {
System.out.println();
}
}
- public final void removeWorstOffenders( final int to_remove, final boolean verbose ) throws IOException,
- InterruptedException {
+ public final void removeWorstOffenders( final int to_remove ) throws IOException, InterruptedException {
final GapContribution stats[] = calcGapContribtionsStats( _norm );
final List<String> to_remove_ids = new ArrayList<String>();
for( int j = 0; j < to_remove; ++j ) {
to_remove_ids.add( stats[ j ].getId() );
_removed_seq_ids.add( stats[ j ].getId() );
}
- if ( verbose ) {
- printTableHeader();
- }
+ printTableHeader();
for( int i = 0; i < to_remove_ids.size(); ++i ) {
final String id = to_remove_ids.get( i );
_msa.deleteRow( id );
removeGapColumns();
- if ( ( ( _step > 0 ) && ( ( ( i + 1 ) % _step ) == 0 ) ) || ( i == ( to_remove_ids.size() - 1 ) ) ) {
- printMsaStatsWriteOutfileAndRealign( _realign, verbose, id );
+ if ( isPrintMsaStatsWriteOutfileAndRealign( i ) || ( i == ( to_remove_ids.size() - 1 ) ) ) {
+ printMsaStatsWriteOutfileAndRealign( _realign, id );
+ System.out.println();
}
- else if ( verbose ) {
- printMsaStats( id );
+ else if ( isPrintMsaStats( i ) ) {
+ final MsaProperties msa_prop = new MsaProperties( _msa, _report_aln_mean_identity );
+ printMsaProperties( id, msa_prop );
+ System.out.println();
}
- if ( verbose ) {
+ }
+ }
+
+ public final List<MsaProperties> chart( final int step, final boolean realign, final boolean norm )
+ throws IOException, InterruptedException {
+ final GapContribution stats[] = calcGapContribtionsStats( norm );
+ final List<String> to_remove_ids = new ArrayList<String>();
+ final List<MsaProperties> msa_props = new ArrayList<MsaProperties>();
+ for( final GapContribution gap_gontribution : stats ) {
+ to_remove_ids.add( gap_gontribution.getId() );
+ }
+ printTableHeader();
+ int i = 0;
+ final int x = ForesterUtil.roundToInt( _msa.getNumberOfSequences() / 20.0 );
+ MsaProperties msa_prop = new MsaProperties( _msa, _report_aln_mean_identity );
+ msa_props.add( msa_prop );
+ printMsaProperties( "", msa_prop );
+ System.out.println();
+ while ( _msa.getNumberOfSequences() > x ) {
+ final String id = to_remove_ids.get( i );
+ _msa.deleteRow( id );
+ if ( realign && isPrintMsaStatsWriteOutfileAndRealign( i ) ) {
+ removeGapColumns();
+ realignWithMafft();
+ msa_prop = new MsaProperties( _msa, _report_aln_mean_identity );
+ msa_props.add( msa_prop );
+ printMsaProperties( id, msa_prop );
+ System.out.print( "(realigned)" );
System.out.println();
}
+ else if ( isPrintMsaStats( i ) ) {
+ removeGapColumns();
+ msa_prop = new MsaProperties( _msa, _report_aln_mean_identity );
+ msa_props.add( msa_prop );
+ printMsaProperties( id, msa_prop );
+ System.out.println();
+ }
+ ++i;
}
+ return msa_props;
+ }
+
+ private final boolean isPrintMsaStats( final int i ) {
+ return ( ( _step_for_diagnostics < 2 ) || ( ( ( i + 1 ) % _step_for_diagnostics ) == 0 ) );
+ }
+
+ private final boolean isPrintMsaStatsWriteOutfileAndRealign( final int i ) {
+ return ( ( _step < 2 ) || ( ( ( i + 1 ) % _step ) == 0 ) );
}
public final void setGapRatio( final double gap_ratio ) {
_step_for_diagnostics = step_for_diagnostics;
}
+ public final void setReportAlnMeanIdentity( final boolean report_aln_mean_identity ) {
+ _report_aln_mean_identity = report_aln_mean_identity;
+ }
+
final public String writeMsa( final File outfile, final MSA_FORMAT format, final String suffix ) throws IOException {
final Double gr = MsaMethods.calcGapRatio( _msa );
final String s = outfile + "_" + _msa.getNumberOfSequences() + "_" + _msa.getLength() + "_"
return ng;
}
- Phylogeny pi( final String matrix ) {
- final Phylogeny master_phy = inferNJphylogeny( PWD_DISTANCE_METHOD.KIMURA_DISTANCE, _msa, true, matrix );
- final int seed = 15;
- final int n = 100;
- final ResampleableMsa resampleable_msa = new ResampleableMsa( _msa );
- final int[][] resampled_column_positions = BootstrapResampler.createResampledColumnPositions( _msa.getLength(),
- n,
- seed );
- final Phylogeny[] eval_phys = new Phylogeny[ n ];
- for( int i = 0; i < n; ++i ) {
- resampleable_msa.resample( resampled_column_positions[ i ] );
- eval_phys[ i ] = inferNJphylogeny( PWD_DISTANCE_METHOD.KIMURA_DISTANCE, resampleable_msa, false, null );
- }
- ConfidenceAssessor.evaluate( "bootstrap", eval_phys, master_phy, true, 1 );
- PhylogenyMethods.extractFastaInformation( master_phy );
- return master_phy;
- }
-
private final GapContribution[] calcGapContribtions( final boolean normalize_for_effective_seq_length ) {
final double gappiness[] = calcGappiness();
final GapContribution stats[] = new GapContribution[ _msa.getNumberOfSequences() ];
return gappiness;
}
- private Phylogeny inferNJphylogeny( final PWD_DISTANCE_METHOD pwd_distance_method,
- final Msa msa,
- final boolean write_matrix,
- final String matrix_name ) {
+ private final Phylogeny inferNJphylogeny( final PWD_DISTANCE_METHOD pwd_distance_method,
+ final Msa msa,
+ final boolean write_matrix,
+ final String matrix_name ) {
BasicSymmetricalDistanceMatrix m = null;
switch ( pwd_distance_method ) {
case KIMURA_DISTANCE:
return phy;
}
- private StringBuilder msaStatsAsSB() {
- final StringBuilder sb = new StringBuilder();
- sb.append( _msa.getNumberOfSequences() );
- sb.append( "\t" );
- sb.append( _msa.getLength() );
- sb.append( "\t" );
- sb.append( NF_4.format( MsaMethods.calcGapRatio( _msa ) ) );
- sb.append( "\t" );
- sb.append( NF_4.format( MsaMethods.calculateIdentityRatio( 0, _msa.getLength() - 1, _msa ).arithmeticMean() ) );
- return sb;
+ private final Phylogeny pi( final String matrix ) {
+ final Phylogeny master_phy = inferNJphylogeny( PWD_DISTANCE_METHOD.KIMURA_DISTANCE, _msa, true, matrix );
+ final int seed = 15;
+ final int n = 100;
+ final ResampleableMsa resampleable_msa = new ResampleableMsa( _msa );
+ final int[][] resampled_column_positions = BootstrapResampler.createResampledColumnPositions( _msa.getLength(),
+ n,
+ seed );
+ final Phylogeny[] eval_phys = new Phylogeny[ n ];
+ for( int i = 0; i < n; ++i ) {
+ resampleable_msa.resample( resampled_column_positions[ i ] );
+ eval_phys[ i ] = inferNJphylogeny( PWD_DISTANCE_METHOD.KIMURA_DISTANCE, resampleable_msa, false, null );
+ }
+ ConfidenceAssessor.evaluate( "bootstrap", eval_phys, master_phy, true, 1 );
+ PhylogenyMethods.extractFastaInformation( master_phy );
+ return master_phy;
}
- private final void printMsaStats( final String id ) {
+ private final static void printMsaProperties( final String id, final MsaProperties msa_properties ) {
System.out.print( ForesterUtil.pad( id, 20, ' ', false ) );
System.out.print( "\t" );
- final StringBuilder sb = msaStatsAsSB();
+ final StringBuilder sb = msaPropertiesAsSB( msa_properties );
System.out.print( sb );
System.out.print( "\t" );
}
- final private void printMsaStatsWriteOutfileAndRealign( final boolean realign,
- final boolean verbose,
- final String id ) throws IOException, InterruptedException {
+ private final static StringBuilder msaPropertiesAsSB( final MsaProperties msa_properties ) {
+ final StringBuilder sb = new StringBuilder();
+ sb.append( msa_properties.getNumberOfSequences() );
+ sb.append( "\t" );
+ sb.append( msa_properties.getLength() );
+ sb.append( "\t" );
+ sb.append( NF_4.format( msa_properties.getGapRatio() ) );
+ if ( msa_properties.getAverageIdentityRatio() >= 0 ) {
+ sb.append( "\t" );
+ sb.append( NF_4.format( msa_properties.getAverageIdentityRatio() ) );
+ }
+ return sb;
+ }
+
+ final private void printMsaStatsWriteOutfileAndRealign( final boolean realign, final String id )
+ throws IOException, InterruptedException {
if ( realign ) {
realignWithMafft();
}
- if ( verbose ) {
- printMsaStats( id );
- }
+ final MsaProperties msa_prop = new MsaProperties( _msa, _report_aln_mean_identity );
+ printMsaProperties( id, msa_prop );
final String s = writeOutfile();
- if ( verbose ) {
- System.out.print( "-> " + s + ( realign ? "\t(realigned)" : "" ) );
- }
+ System.out.print( "-> " + s + ( realign ? "\t(realigned)" : "" ) );
}
final private void realignWithMafft() throws IOException, InterruptedException {
w.close();
}
- private String writeOutfile() throws IOException {
+ private final String writeOutfile() throws IOException {
final String s = writeMsa( _out_file_base, MSA_FORMAT.PHYLIP, ".aln" );
//writeMsa( _out_file_base, MSA_FORMAT.FASTA, ".fasta" );
return s;
git://source.jalview.org / jalview.git / commitdiff