import java.util.SortedSet;
import java.util.TreeSet;
-import org.forester.archaeopteryx.Archaeopteryx;
-import org.forester.evoinference.distance.NeighborJoining;
+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.phylogeny.PhylogenyMethods;
import org.forester.sequence.Sequence;
import org.forester.tools.ConfidenceAssessor;
+import org.forester.util.BasicDescriptiveStatistics;
+import org.forester.util.DescriptiveStatistics;
import org.forester.util.ForesterUtil;
public class MsaCompactor {
private static final boolean VERBOSE = true;
private Msa _msa;
private final SortedSet<String> _removed_seq_ids;
+ private String _path_to_mafft;
static {
NF_4.setRoundingMode( RoundingMode.HALF_UP );
NF_3.setRoundingMode( RoundingMode.HALF_UP );
final private GapContribution[] calcGapContribtionsStats( final boolean norm ) {
final GapContribution stats[] = calcGapContribtions( norm );
Arrays.sort( stats );
- for( final GapContribution stat : stats ) {
- final StringBuilder sb = new StringBuilder();
- sb.append( stat.getId() );
- sb.append( "\t" );
- sb.append( NF_4.format( stat.getValue() ) );
- sb.append( "\t" );
- // sb.append( NF_4.format( stat.median() ) );
- // sb.append( "\t" );
- // sb.append( NF_4.format( stat.getMin() ) );
- // sb.append( "\t" );
- // sb.append( NF_4.format( stat.getMax() ) );
- //sb.append( "\t" );
- System.out.println( sb );
+ // for( final GapContribution stat : stats ) {
+ // final StringBuilder sb = new StringBuilder();
+ // sb.append( stat.getId() );
+ // sb.append( "\t" );
+ // sb.append( NF_4.format( stat.getValue() ) );
+ // sb.append( "\t" );
+ // sb.append( NF_4.format( stat.median() ) );
+ // sb.append( "\t" );
+ // sb.append( NF_4.format( stat.getMin() ) );
+ // sb.append( "\t" );
+ // sb.append( NF_4.format( stat.getMax() ) );
+ //sb.append( "\t" );
+ //System.out.println( sb );
+ // }
+ return stats;
+ }
+
+ private static DescriptiveStatistics calculateIdentityRatio( final int from, final int to, final Msa msa ) {
+ final DescriptiveStatistics stats = new BasicDescriptiveStatistics();
+ for( int c = from; c <= to; ++c ) {
+ stats.addValue( MsaMethods.calculateIdentityRatio( msa, c ) );
}
return stats;
}
return gappiness;
}
+ // Returns null if not path found.
+ final public static String guessPathToMafft() {
+ String path;
+ if ( ForesterUtil.OS_NAME.toLowerCase().indexOf( "win" ) >= 0 ) {
+ path = "C:\\Program Files\\mafft-win\\mafft.bat";
+ if ( MsaInferrer.isInstalled( path ) ) {
+ return path;
+ }
+ }
+ path = "/usr/local/bin/mafft";
+ if ( MsaInferrer.isInstalled( path ) ) {
+ return path;
+ }
+ path = "/usr/bin/mafft";
+ if ( MsaInferrer.isInstalled( path ) ) {
+ return path;
+ }
+ path = "/bin/mafft";
+ if ( MsaInferrer.isInstalled( path ) ) {
+ return path;
+ }
+ path = "mafft";
+ if ( MsaInferrer.isInstalled( path ) ) {
+ return path;
+ }
+ return null;
+ }
+
final private void mafft() throws IOException, InterruptedException {
- final MsaInferrer mafft = Mafft
- .createInstance( "/home/czmasek/SOFTWARE/MSA/MAFFT/mafft-7.130-without-extensions/scripts/mafft" );
+ // final MsaInferrer mafft = Mafft
+ // .createInstance( "/home/czmasek/SOFTWARE/MSA/MAFFT/mafft-7.130-without-extensions/scripts/mafft" );
+ final MsaInferrer mafft = Mafft.createInstance( _path_to_mafft );
final List<String> opts = new ArrayList<String>();
- // opts.add( "--maxiterate" );
- // opts.add( "1000" );
- // opts.add( "--localpair" );
+ opts.add( "--maxiterate" );
+ opts.add( "1000" );
+ opts.add( "--localpair" );
opts.add( "--quiet" );
_msa = mafft.infer( _msa.asSequenceList(), opts );
}
sb.append( _msa.getLength() );
sb.append( "\t" );
sb.append( NF_3.format( MsaMethods.calcGapRatio( _msa ) ) );
+ sb.append( "\t" );
+ sb.append( NF_3.format( calculateIdentityRatio( 0, _msa.getLength() - 1, _msa ).arithmeticMean() ) );
return sb;
}
}
}
- Phylogeny pi() {
- final Phylogeny master_phy = inferNJphylogeny( PWD_DISTANCE_METHOD.KIMURA_DISTANCE, _msa );
+ 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( ( BasicMsa ) _msa );
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 );
+ 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 Phylogeny inferNJphylogeny( PWD_DISTANCE_METHOD pwd_distance_method, final Msa msa ) {
+ private 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:
default:
throw new IllegalArgumentException( "invalid pwd method" );
}
- final NeighborJoining nj = NeighborJoining.createInstance();
+ if ( write_matrix ) {
+ try {
+ m.write( ForesterUtil.createBufferedWriter( matrix_name ) );
+ }
+ catch ( final IOException e ) {
+ // TODO Auto-generated catch block
+ e.printStackTrace();
+ }
+ }
+ final NeighborJoiningF nj = NeighborJoiningF.createInstance( false, 5 );
final Phylogeny phy = nj.execute( m );
return phy;
}
final int step,
final boolean realign,
final boolean norm ) throws IOException, InterruptedException {
- final Phylogeny a = pi();
- Archaeopteryx.createApplication( a );
+ //final Phylogeny a = pi( "a.pwd" );
+ //Archaeopteryx.createApplication( a );
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() );
}
- //TODO if verbose/interactve
+ //TODO if verbose/interactive
for( final String id : to_remove_ids ) {
_msa = MsaMethods.removeSequence( _msa, id );
removeGapColumns();
- System.out.print( id );
+ //System.out.print( id );
+ System.out.print( ForesterUtil.pad( id, 20, ' ', false ) );
System.out.print( "\t" );
final StringBuilder sb = msaStatsAsSB();
System.out.println( sb );
if ( realign ) {
mafft();
}
- final Phylogeny b = pi();
- Archaeopteryx.createApplication( b );
+ //final Phylogeny b = pi( "b.pwd" );
+ //Archaeopteryx.createApplication( b );
}
final private void writeMsa( final String outfile, final MSA_FORMAT format ) throws IOException {
final int step,
final boolean realign,
final File out,
- final int minimal_effective_length ) throws IOException,
+ final int minimal_effective_length,
+ final String path_to_mafft ) throws IOException,
InterruptedException {
final MsaCompactor mc = new MsaCompactor( msa );
+ if ( realign ) {
+ mc.setPathToMafft( path_to_mafft );
+ }
mc.removeViaGapAverage( max_gap_average, step, realign, out, minimal_effective_length );
return mc;
}
public final static MsaCompactor reduceLength( final Msa msa,
final int length,
final int step,
- final boolean realign ) throws IOException, InterruptedException {
+ final boolean realign,
+ final String path_to_mafft ) throws IOException,
+ InterruptedException {
final MsaCompactor mc = new MsaCompactor( msa );
+ if ( realign ) {
+ mc.setPathToMafft( path_to_mafft );
+ }
mc.removeViaLength( length, step, realign );
return mc;
}
public final static MsaCompactor removeWorstOffenders( final Msa msa,
final int worst_offenders_to_remove,
final boolean realign,
- final boolean norm ) throws IOException,
+ final boolean norm,
+ final String path_to_mafft ) throws IOException,
InterruptedException {
final MsaCompactor mc = new MsaCompactor( msa );
+ if ( realign ) {
+ mc.setPathToMafft( path_to_mafft );
+ }
mc.removeWorstOffenders( worst_offenders_to_remove, 1, realign, norm );
return mc;
}
+
+ private void setPathToMafft( final String path_to_mafft ) {
+ _path_to_mafft = path_to_mafft;
+ }
}
git://source.jalview.org / jalview.git / blobdiff