import java.io.IOException;
import java.util.ArrayList;
import java.util.List;
-import java.util.regex.Matcher;
import javax.swing.JOptionPane;
import org.forester.archaeopteryx.MainFrameApplication;
-import org.forester.evoinference.distance.NeighborJoining;
+import org.forester.evoinference.distance.NeighborJoiningF;
import org.forester.evoinference.distance.PairwiseDistanceCalculator;
import org.forester.evoinference.matrix.distance.BasicSymmetricalDistanceMatrix;
import org.forester.evoinference.tools.BootstrapResampler;
-import org.forester.io.parsers.FastaParser;
import org.forester.msa.BasicMsa;
import org.forester.msa.Mafft;
import org.forester.msa.Msa;
import org.forester.msa.MsaMethods;
import org.forester.msa.ResampleableMsa;
import org.forester.phylogeny.Phylogeny;
-import org.forester.phylogeny.PhylogenyNode;
-import org.forester.phylogeny.data.Accession;
-import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
+import org.forester.phylogeny.PhylogenyMethods;
import org.forester.sequence.Sequence;
import org.forester.tools.ConfidenceAssessor;
import org.forester.util.ForesterUtil;
e.printStackTrace();
}
}
- final NeighborJoining nj = NeighborJoining.createInstance();
+ final NeighborJoiningF nj = NeighborJoiningF.createInstance( false, 5 );
final Phylogeny phy = nj.execute( m );
- PhylogeneticInferrer.extractFastaInformation( phy );
+ PhylogenyMethods.addMolecularSeqsToTree( phy, msa );
+ PhylogenyMethods.extractFastaInformation( phy );
return phy;
}
}
final MsaMethods msa_tools = MsaMethods.createInstance();
if ( _options.isExecuteMsaProcessing() ) {
- msa = msa_tools.removeGapColumns( _options.getMsaProcessingMaxAllowedGapRatio(),
+ msa = msa_tools.deleteGapColumns( _options.getMsaProcessingMaxAllowedGapRatio(),
_options.getMsaProcessingMinAllowedLength(),
msa );
if ( msa == null ) {
}
}
- public static void extractFastaInformation( final Phylogeny phy ) {
- for( final PhylogenyNodeIterator iter = phy.iteratorExternalForward(); iter.hasNext(); ) {
- final PhylogenyNode node = iter.next();
- if ( !ForesterUtil.isEmpty( node.getName() ) ) {
- final Matcher name_m = FastaParser.FASTA_DESC_LINE.matcher( node.getName() );
- if ( name_m.lookingAt() ) {
- System.out.println();
- // System.out.println( name_m.group( 1 ) );
- // System.out.println( name_m.group( 2 ) );
- // System.out.println( name_m.group( 3 ) );
- // System.out.println( name_m.group( 4 ) );
- final String acc_source = name_m.group( 1 );
- final String acc = name_m.group( 2 );
- final String seq_name = name_m.group( 3 );
- final String tax_sn = name_m.group( 4 );
- if ( !ForesterUtil.isEmpty( acc_source ) && !ForesterUtil.isEmpty( acc ) ) {
- ForesterUtil.ensurePresenceOfSequence( node );
- node.getNodeData().getSequence( 0 ).setAccession( new Accession( acc, acc_source ) );
- }
- if ( !ForesterUtil.isEmpty( seq_name ) ) {
- ForesterUtil.ensurePresenceOfSequence( node );
- node.getNodeData().getSequence( 0 ).setName( seq_name );
- }
- if ( !ForesterUtil.isEmpty( tax_sn ) ) {
- ForesterUtil.ensurePresenceOfTaxonomy( node );
- node.getNodeData().getTaxonomy( 0 ).setScientificName( tax_sn );
- }
- }
- }
- }
- }
-
public enum MSA_PRG {
MAFFT;
}