// 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.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.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 = "1.01";
- 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";
+ 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, false );
+ final SortedSet<String> not_found = SequenceDbWsTools.obtainSeqInformation( phy,
+ true,
+ false,
+ DEFAULT_LINES_TO_RETURN );
for( final String remove_me : not_found ) {
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 "
}
}
- 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 );