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.sequence.MolecularSequence;
import org.forester.tools.ConfidenceAssessor;
import org.forester.util.BasicDescriptiveStatistics;
+import org.forester.util.DescriptiveStatistics;
import org.forester.util.ForesterUtil;
public class MsaCompactor {
- final private static NumberFormat NF_3 = new DecimalFormat( "#.###" );
- final private static NumberFormat NF_4 = new DecimalFormat( "#.####" );
- private boolean _calculate_shannon_entropy = false;
+ final private static NumberFormat NF_1 = new DecimalFormat( "0.#" );
+ final private static NumberFormat NF_3 = new DecimalFormat( "0.###" );
+ final private static NumberFormat NF_4 = new DecimalFormat( "0.####" );
+ private boolean _calculate_shannon_entropy = false;
//
- private String _infile_name = null;
- private final short _longest_id_length;
+ private String _infile_name = null;
+ private final short _longest_id_length;
//
- private String _maffts_opts = "--auto";
- private DeleteableMsa _msa = null;
- private boolean _norm = true;
- private File _out_file_base = null;
- private MSA_FORMAT _output_format = MSA_FORMAT.FASTA;
- private String _path_to_mafft = null;
- private boolean _phylogentic_inference = false;
+ private String _maffts_opts = "--auto";
+ private DeleteableMsa _msa = null;
+ private boolean _norm = true;
+ private File _out_file_base = null;
+ private MSA_FORMAT _output_format = MSA_FORMAT.FASTA;
+ private String _path_to_mafft = null;
+ private boolean _phylogentic_inference = false;
//
- private boolean _realign = false;
- private final SortedSet<String> _removed_seq_ids;
- private final ArrayList<Sequence> _removed_seqs;
- private File _removed_seqs_out_base = null;
- private int _step = -1;
- private int _step_for_diagnostics = -1;
+ private boolean _realign = false;
+ private final SortedSet<String> _removed_seq_ids;
+ private final ArrayList<MolecularSequence> _removed_seqs;
+ private File _removed_seqs_out_base = null;
+ private int _step = -1;
+ private int _step_for_diagnostics = -1;
static {
+ NF_1.setRoundingMode( RoundingMode.HALF_UP );
NF_4.setRoundingMode( RoundingMode.HALF_UP );
NF_3.setRoundingMode( RoundingMode.HALF_UP );
}
_msa = msa;
_removed_seq_ids = new TreeSet<String>();
_longest_id_length = _msa.determineMaxIdLength();
- _removed_seqs = new ArrayList<Sequence>();
+ _removed_seqs = new ArrayList<MolecularSequence>();
}
public final Phylogeny calcTree() {
}
else {
n.getNodeData()
- .getNodeVisualData()
- .setNodeColor( ForesterUtil.calcColor( msa_prop.getLength(),
- min,
- max,
- mean,
- min_color,
- max_color,
- mean_color ) );
+ .getNodeVisualData()
+ .setNodeColor( ForesterUtil.calcColor( msa_prop.getLength(),
+ min,
+ max,
+ mean,
+ min_color,
+ max_color,
+ mean_color ) );
}
}
}
return _msa;
}
- public final void removeSequencesByMinimalLength( final int min_effective_length ) {
- printMsaProperties( new MsaProperties( _msa, "", _calculate_shannon_entropy ) );
- System.out.println();
+ public final void removeSequencesByMinimalLength( final int min_effective_length ) throws IOException {
_msa = DeleteableMsa.createInstance( MsaMethods.removeSequencesByMinimalLength( _msa, min_effective_length ) );
removeGapColumns();
- printMsaProperties( new MsaProperties( _msa, "", _calculate_shannon_entropy ) );
+ final String s = writeOutfile();
+ final DescriptiveStatistics msa_stats = MsaMethods.calculateEffectiveLengthStatistics( _msa );
+ System.out.println( "Output MSA : " + s );
+ System.out.println( " MSA length : " + _msa.getLength() );
+ System.out.println( " Number of sequences : " + _msa.getNumberOfSequences() );
+ System.out.println( " Median sequence length : " + NF_1.format( msa_stats.median() ) );
+ System.out.println( " Mean sequence length : " + NF_1.format( msa_stats.arithmeticMean() ) );
+ System.out.println( " Max sequence length : " + ( ( int ) msa_stats.getMax() ) );
+ System.out.println( " Min sequence length : " + ( ( int ) msa_stats.getMin() ) );
+ System.out.println( " Gap ratio : " + NF_4.format( MsaMethods.calcGapRatio( _msa ) ) );
+ System.out.println( " Normalized Shannon Entropy (entn21): "
+ + NF_4.format( MsaMethods.calcNormalizedShannonsEntropy( 21, _msa ) ) );
System.out.println();
}
public final List<MsaProperties> removeViaGapAverage( final double mean_gapiness ) throws IOException,
- InterruptedException {
+ InterruptedException {
final GapContribution stats[] = calcGapContribtionsStats( _norm );
final List<String> to_remove_ids = new ArrayList<String>();
final List<MsaProperties> msa_props = new ArrayList<MsaProperties>();
while ( MsaMethods.calcGapRatio( _msa ) > mean_gapiness ) {
final String id = to_remove_ids.get( i );
_removed_seq_ids.add( id );
- final Sequence deleted = _msa.deleteRow( id, true );
+ final MolecularSequence deleted = _msa.deleteRow( id, true );
_removed_seqs.add( deleted );
removeGapColumns();
if ( isPrintMsaStatsWriteOutfileAndRealign( i ) || ( MsaMethods.calcGapRatio( _msa ) <= mean_gapiness ) ) {
while ( _msa.getLength() > length ) {
final String id = to_remove_ids.get( i );
_removed_seq_ids.add( id );
- final Sequence deleted = _msa.deleteRow( id, true );
+ final MolecularSequence deleted = _msa.deleteRow( id, true );
_removed_seqs.add( deleted );
removeGapColumns();
if ( isPrintMsaStatsWriteOutfileAndRealign( i ) || ( _msa.getLength() <= length ) ) {
}
public final List<MsaProperties> removeWorstOffenders( final int to_remove ) throws IOException,
- InterruptedException {
+ InterruptedException {
final GapContribution stats[] = calcGapContribtionsStats( _norm );
final List<String> to_remove_ids = new ArrayList<String>();
final List<MsaProperties> msa_props = new ArrayList<MsaProperties>();
for( int i = 0; i < to_remove_ids.size(); ++i ) {
final String id = to_remove_ids.get( i );
_removed_seq_ids.add( id );
- final Sequence deleted = _msa.deleteRow( id, true );
+ final MolecularSequence deleted = _msa.deleteRow( id, true );
_removed_seqs.add( deleted );
removeGapColumns();
if ( isPrintMsaStatsWriteOutfileAndRealign( i ) || ( i == ( to_remove_ids.size() - 1 ) ) ) {
return s;
}
- final int calcNonGapResidues( final Sequence seq ) {
+ final int calcNonGapResidues( final MolecularSequence seq ) {
int ng = 0;
for( int i = 0; i < seq.getLength(); ++i ) {
if ( !seq.isGapAt( i ) ) {
return gappiness;
}
+ private final Phylogeny collapse( final Msa msa, final int threshold ) {
+ final BasicSymmetricalDistanceMatrix m = PairwiseDistanceCalculator.calcFractionalDissimilarities( msa );
+ //TODO
+ return null;
+ }
+
private final Phylogeny inferNJphylogeny( final PWD_DISTANCE_METHOD pwd_distance_method,
final Msa msa,
final boolean write_matrix,
git://source.jalview.org / jalview.git / blobdiff