// Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
//
// Contact: phylosoft @ gmail . com
-// WWW: www.phylosoft.org/forester
+// WWW: https://sites.google.com/site/cmzmasek/home/software/forester
package org.forester.application;
import java.io.File;
import java.io.FileWriter;
import java.io.IOException;
-import java.util.HashSet;
-import java.util.Set;
import java.util.SortedSet;
+import java.util.TreeSet;
-import org.forester.archaeopteryx.tools.SequenceDataRetriver;
import org.forester.io.parsers.util.ParserUtils;
import org.forester.io.writers.PhylogenyWriter;
import org.forester.phylogeny.Phylogeny;
-import org.forester.phylogeny.PhylogenyMethods;
import org.forester.phylogeny.PhylogenyNode;
import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory;
import org.forester.phylogeny.factories.PhylogenyFactory;
import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
import org.forester.util.CommandLineArguments;
import org.forester.util.ForesterUtil;
+import org.forester.ws.seqdb.SequenceDbWsTools;
public class gene_tree_preprocess {
- final static private String HELP_OPTION_1 = "help";
- final static private String HELP_OPTION_2 = "h";
- final static private String PRG_NAME = "gene_tree_preprocess";
- final static private String PRG_DESC = "gene tree preprocessing for SDI analysis";
- final static private String PRG_VERSION = "1.00";
- final static private String PRG_DATE = "2012.06.07";
- final static private String E_MAIL = "phylosoft@gmail.com";
- final static private String WWW = "www.phylosoft.org/forester/";
+ final static private String HELP_OPTION_1 = "help";
+ final static private String HELP_OPTION_2 = "h";
+ final static private String PRG_NAME = "gene_tree_preprocess";
+ final static private String PRG_DESC = "gene tree preprocessing for SDI analysis";
+ final static private String PRG_VERSION = "1.01";
+ final static private String PRG_DATE = "2012.06.07";
+ final static private String E_MAIL = "phylosoft@gmail.com";
+ final static private String WWW = "www.phylosoft.org/forester";
+ private final static int DEFAULT_LINES_TO_RETURN = 50;
public static void main( final String[] args ) {
try {
ForesterUtil.fatalError( PRG_NAME, "phylogeny has " + phy.getNumberOfExternalNodes()
+ " external node(s), aborting" );
}
- final SortedSet<String> not_found = SequenceDataRetriver.obtainSeqInformation( phy, true );
+ final SortedSet<String> not_found = SequenceDbWsTools.obtainSeqInformation( phy,
+ true,
+ false,
+ DEFAULT_LINES_TO_RETURN );
for( final String remove_me : not_found ) {
- // System.out.println( " not found: " + remove_me );
- PhylogenyMethods.removeNode( phy.getNode( remove_me ), phy );
+ phy.deleteSubtree( phy.getNode( remove_me ), true );
}
+ phy.clearHashIdToNodeMap();
+ phy.externalNodesHaveChanged();
if ( phy.getNumberOfExternalNodes() < 2 ) {
ForesterUtil.fatalError( PRG_NAME,
"after removal of unresolvable external nodes, phylogeny has "
ForesterUtil.fatalError( PRG_NAME, "failed to write to [" + outtree + "]: " + e.getLocalizedMessage() );
}
ForesterUtil.programMessage( PRG_NAME, "wrote output phylogeny to: " + outtree );
- final Set<String> species_found = new HashSet<String>();
+ final SortedSet<String> species_set = new TreeSet<String>();
+ for( final PhylogenyNodeIterator iter = phy.iteratorExternalForward(); iter.hasNext(); ) {
+ final PhylogenyNode node = iter.next();
+ if ( node.getNodeData().isHasTaxonomy() ) {
+ final String sn = node.getNodeData().getTaxonomy().getScientificName();
+ if ( !ForesterUtil.isEmpty( sn ) ) {
+ species_set.add( sn );
+ }
+ }
+ }
try {
final BufferedWriter out = new BufferedWriter( new FileWriter( present_species ) );
- for( final PhylogenyNodeIterator iter = phy.iteratorExternalForward(); iter.hasNext(); ) {
- final PhylogenyNode node = iter.next();
- if ( node.getNodeData().isHasTaxonomy() ) {
- final String sn = node.getNodeData().getTaxonomy().getScientificName();
- if ( !ForesterUtil.isEmpty( sn ) ) {
- if ( !species_found.contains( sn ) ) {
- species_found.add( sn );
- out.write( node.getNodeData().getTaxonomy().getScientificName() );
- out.newLine();
- }
- }
- }
+ for( final String species : species_set ) {
+ out.write( species );
+ out.newLine();
}
out.close();
}
}
}
- public static void checkForOutputFileWriteability( final File outfile ) {
+ private static void checkForOutputFileWriteability( final File outfile ) {
final String error = ForesterUtil.isWritableFile( outfile );
if ( !ForesterUtil.isEmpty( error ) ) {
ForesterUtil.fatalError( PRG_NAME, error );