From: cmzmasek@gmail.com Date: Wed, 23 Apr 2014 23:20:40 +0000 (+0000) Subject: cleanup X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=1a34ee27d89330a01cac48b79b88c90e9c748542;p=jalview.git cleanup --- diff --git a/forester/java/src/org/forester/msa_compactor/MsaCompactor.java b/forester/java/src/org/forester/msa_compactor/MsaCompactor.java index 56cc729..17e4397 100644 --- a/forester/java/src/org/forester/msa_compactor/MsaCompactor.java +++ b/forester/java/src/org/forester/msa_compactor/MsaCompactor.java @@ -58,23 +58,23 @@ public class MsaCompactor { final private static NumberFormat NF_3 = new DecimalFormat( "#.###" ); final private static NumberFormat NF_4 = new DecimalFormat( "#.####" ); + private double _gap_ratio = -1; // private final String _maffts_opts = "--auto"; - private int _step = 1; - // - private boolean _realign = false; - private boolean _norm = true; - private int _step_for_diagnostics = 1; private int _min_length = -1; - private double _gap_ratio = -1; - private final boolean _report_aln_mean_identity = false; - private MSA_FORMAT _output_format = MSA_FORMAT.FASTA; - private final File _removed_seqs_out_base = null; // private DeleteableMsa _msa; + private boolean _norm = true; private File _out_file_base; + private MSA_FORMAT _output_format = MSA_FORMAT.FASTA; private String _path_to_mafft; + // + private boolean _realign = false; private final SortedSet _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; static { NF_4.setRoundingMode( RoundingMode.HALF_UP ); NF_3.setRoundingMode( RoundingMode.HALF_UP ); @@ -85,6 +85,53 @@ public class MsaCompactor { _removed_seq_ids = new TreeSet(); } + public final List chart( final int step, + final boolean realign, + final boolean norm, + final boolean verbose ) throws IOException, InterruptedException { + final GapContribution stats[] = calcGapContribtionsStats( norm ); + final List to_remove_ids = new ArrayList(); + final List msa_props = new ArrayList(); + 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; } @@ -93,10 +140,125 @@ public class MsaCompactor { return _removed_seq_ids; } + public final void removeViaGapAverage( final double mean_gapiness, final boolean verbose ) throws IOException, + InterruptedException { + final GapContribution stats[] = calcGapContribtionsStats( _norm ); + final List to_remove_ids = new ArrayList(); + for( final GapContribution gap_gontribution : stats ) { + to_remove_ids.add( gap_gontribution.getId() ); + } + if ( verbose ) { + printTableHeader(); + } + int i = 0; + while ( MsaMethods.calcGapRatio( _msa ) > mean_gapiness ) { + final String id = to_remove_ids.get( i ); + _msa.deleteRow( id ); + removeGapColumns(); + if ( ( ( _step > 0 ) && ( ( ( i + 1 ) % _step ) == 0 ) ) + || ( MsaMethods.calcGapRatio( _msa ) <= mean_gapiness ) ) { + printMsaStatsWriteOutfileAndRealign( _realign, verbose, id ); + } + else if ( verbose ) { + printMsaStats( id ); + } + if ( verbose ) { + System.out.println(); + } + ++i; + } + } + + public void removeViaLength( final int length, final boolean verbose ) throws IOException, InterruptedException { + final GapContribution stats[] = calcGapContribtionsStats( _norm ); + final List to_remove_ids = new ArrayList(); + for( final GapContribution gap_gontribution : stats ) { + to_remove_ids.add( gap_gontribution.getId() ); + } + if ( verbose ) { + printTableHeader(); + } + int i = 0; + while ( _msa.getLength() > length ) { + final String id = to_remove_ids.get( i ); + _msa.deleteRow( id ); + removeGapColumns(); + if ( ( ( _step > 0 ) && ( ( ( i + 1 ) % _step ) == 0 ) ) || ( _msa.getLength() <= length ) ) { + printMsaStatsWriteOutfileAndRealign( _realign, verbose, id ); + } + else if ( verbose ) { + printMsaStats( id ); + } + if ( verbose ) { + System.out.println(); + } + ++i; + } + } + + public final void removeWorstOffenders( final int to_remove, final boolean verbose ) throws IOException, + InterruptedException { + final GapContribution stats[] = calcGapContribtionsStats( _norm ); + final List to_remove_ids = new ArrayList(); + 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(); + } + 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 ); + } + else if ( verbose ) { + printMsaStats( id ); + } + if ( verbose ) { + System.out.println(); + } + } + } + + public final void setGapRatio( final double gap_ratio ) { + _gap_ratio = gap_ratio; + } + + public final void setMinLength( final int min_length ) { + _min_length = min_length; + } + + public final void setNorm( final boolean norm ) { + _norm = norm; + } + final public void setOutFileBase( final File out_file_base ) { _out_file_base = out_file_base; } + public final void setOutputFormat( final MSA_FORMAT output_format ) { + _output_format = output_format; + } + + public void setPathToMafft( final String path_to_mafft ) { + _path_to_mafft = path_to_mafft; + } + + public final void setRealign( final boolean realign ) { + _realign = realign; + } + + public final void setStep( final int step ) { + _step = step; + } + + public final void setStepForDiagnostics( final int step_for_diagnostics ) { + _step_for_diagnostics = step_for_diagnostics; + } + 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() + "_" @@ -169,53 +331,6 @@ public class MsaCompactor { return gappiness; } - public final List chart( final int step, - final boolean realign, - final boolean norm, - final boolean verbose ) throws IOException, InterruptedException { - final GapContribution stats[] = calcGapContribtionsStats( norm ); - final List to_remove_ids = new ArrayList(); - final List msa_props = new ArrayList(); - 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; - } - private Phylogeny inferNJphylogeny( final PWD_DISTANCE_METHOD pwd_distance_method, final Msa msa, final boolean write_matrix, @@ -297,93 +412,6 @@ public class MsaCompactor { _msa.deleteGapOnlyColumns(); } - public final void removeViaGapAverage( final double mean_gapiness, final boolean verbose ) throws IOException, - InterruptedException { - final GapContribution stats[] = calcGapContribtionsStats( _norm ); - final List to_remove_ids = new ArrayList(); - for( final GapContribution gap_gontribution : stats ) { - to_remove_ids.add( gap_gontribution.getId() ); - } - if ( verbose ) { - printTableHeader(); - } - int i = 0; - while ( MsaMethods.calcGapRatio( _msa ) > mean_gapiness ) { - final String id = to_remove_ids.get( i ); - _msa.deleteRow( id ); - removeGapColumns(); - if ( ( ( _step > 0 ) && ( ( ( i + 1 ) % _step ) == 0 ) ) - || ( MsaMethods.calcGapRatio( _msa ) <= mean_gapiness ) ) { - printMsaStatsWriteOutfileAndRealign( _realign, verbose, id ); - } - else if ( verbose ) { - printMsaStats( id ); - } - if ( verbose ) { - System.out.println(); - } - ++i; - } - } - - public void removeViaLength( final int length, final boolean verbose ) throws IOException, InterruptedException { - final GapContribution stats[] = calcGapContribtionsStats( _norm ); - final List to_remove_ids = new ArrayList(); - for( final GapContribution gap_gontribution : stats ) { - to_remove_ids.add( gap_gontribution.getId() ); - } - if ( verbose ) { - printTableHeader(); - } - int i = 0; - while ( _msa.getLength() > length ) { - final String id = to_remove_ids.get( i ); - _msa.deleteRow( id ); - removeGapColumns(); - if ( ( ( _step > 0 ) && ( ( ( i + 1 ) % _step ) == 0 ) ) || ( _msa.getLength() <= length ) ) { - printMsaStatsWriteOutfileAndRealign( _realign, verbose, id ); - } - else if ( verbose ) { - printMsaStats( id ); - } - if ( verbose ) { - System.out.println(); - } - ++i; - } - } - - public final void removeWorstOffenders( final int to_remove, final boolean verbose ) throws IOException, - InterruptedException { - final GapContribution stats[] = calcGapContribtionsStats( _norm ); - final List to_remove_ids = new ArrayList(); - 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(); - } - 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 ); - } - else if ( verbose ) { - printMsaStats( id ); - } - if ( verbose ) { - System.out.println(); - } - } - } - - public void setPathToMafft( final String path_to_mafft ) { - _path_to_mafft = path_to_mafft; - } - final private void writeMsa( final String outfile, final MSA_FORMAT format ) throws IOException { final Writer w = ForesterUtil.createBufferedWriter( outfile ); _msa.write( w, format ); @@ -428,34 +456,6 @@ public class MsaCompactor { return null; } - public final void setStep( final int step ) { - _step = step; - } - - public final void setNorm( final boolean norm ) { - _norm = norm; - } - - public final void setStepForDiagnostics( final int step_for_diagnostics ) { - _step_for_diagnostics = step_for_diagnostics; - } - - public final void setMinLength( final int min_length ) { - _min_length = min_length; - } - - public final void setGapRatio( final double gap_ratio ) { - _gap_ratio = gap_ratio; - } - - public final void setOutputFormat( final MSA_FORMAT output_format ) { - _output_format = output_format; - } - - public final void setRealign( final boolean realign ) { - _realign = realign; - } - private final static void printTableHeader() { System.out.print( ForesterUtil.pad( "Id", 20, ' ', false ) ); System.out.print( "\t" );