import java.util.TreeMap;
import java.util.TreeSet;
-import org.forester.io.parsers.PhylogenyParser;
-import org.forester.io.parsers.nhx.NHXParser;
+import org.forester.io.parsers.nhx.NHXParser.TAXONOMY_EXTRACTION;
import org.forester.io.parsers.phyloxml.PhyloXmlDataFormatException;
import org.forester.io.parsers.phyloxml.PhyloXmlParser;
-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.sdi.SDIException;
import org.forester.sdi.SDIutil;
import org.forester.sdi.SDIutil.ALGORITHM;
-import org.forester.sdi.SDIutil.TaxonomyComparisonBase;
import org.forester.util.CommandLineArguments;
import org.forester.util.EasyWriter;
import org.forester.util.ForesterConstants;
gene_tree = factory.create( gene_tree_file, new PhyloXmlParser() )[ 0 ];
}
catch ( final IOException e ) {
- fatalError( "ERROR",
- "Failed to read gene tree from [" + gene_tree_file + "]: " + e.getMessage(),
+ fatalError( "error",
+ "failed to read gene tree from [" + gene_tree_file + "]: " + e.getMessage(),
log_writer );
}
try {
- final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
- final PhylogenyParser p = ParserUtils.createParserDependingOnFileType( species_tree_file, true );
- if ( p instanceof PhyloXmlParser ) {
- species_tree = factory.create( species_tree_file, p )[ 0 ];
- }
- else {
- if ( REPLACE_UNDERSCORES_IN_NH_SPECIES_TREE && ( p instanceof NHXParser ) ) {
- ( ( NHXParser ) p ).setReplaceUnderscores( true );
- }
- species_tree = factory.create( species_tree_file, p )[ 0 ];
- final TaxonomyComparisonBase comp_base = SDIutil.determineTaxonomyComparisonBase( gene_tree );
- switch ( comp_base ) {
- case SCIENTIFIC_NAME:
- try {
- PhylogenyMethods
- .transferNodeNameToField( species_tree,
- PhylogenyMethods.PhylogenyNodeField.TAXONOMY_SCIENTIFIC_NAME,
- true );
- }
- catch ( final PhyloXmlDataFormatException e ) {
- fatalError( "USER ERROR", "Failed to transfer general node name to scientific name, in ["
- + species_tree_file + "]: " + e.getMessage(), log_writer );
- }
- break;
- case CODE:
- try {
- PhylogenyMethods
- .transferNodeNameToField( species_tree,
- PhylogenyMethods.PhylogenyNodeField.TAXONOMY_CODE,
- true );
- }
- catch ( final PhyloXmlDataFormatException e ) {
- fatalError( "USER ERROR", "Failed to transfer general node name to taxonomy code, in ["
- + species_tree_file + "]: " + e.getMessage(), log_writer );
- }
- break;
- case ID:
- try {
- PhylogenyMethods.transferNodeNameToField( species_tree,
- PhylogenyMethods.PhylogenyNodeField.TAXONOMY_ID,
- true );
- }
- catch ( final PhyloXmlDataFormatException e ) {
- fatalError( "USER ERROR", "Failed to transfer general node name to taxonomy id, in ["
- + species_tree_file + "]: " + e.getMessage(), log_writer );
- }
- break;
- default:
- fatalError( "UNEXPECTED ERROR", "unable to determine comparison base", log_writer );
- }
- }
+ species_tree = SDIutil.parseSpeciesTree( gene_tree,
+ species_tree_file,
+ REPLACE_UNDERSCORES_IN_NH_SPECIES_TREE,
+ true,
+ TAXONOMY_EXTRACTION.NO );
+ }
+ catch ( final PhyloXmlDataFormatException e ) {
+ fatalError( "user error",
+ "failed to transfer general node name, in [" + species_tree_file + "]: " + e.getMessage(),
+ log_writer );
}
catch ( final SDIException e ) {
fatalError( "user error", e.getMessage(), log_writer );
}
catch ( final IOException e ) {
- fatalError( "ERROR",
+ fatalError( "error",
"Failed to read species tree from [" + species_tree_file + "]: " + e.getMessage(),
log_writer );
}
catch ( final IOException e ) {
fatalError( "error", e.toString(), log_writer );
}
+ catch ( final OutOfMemoryError e ) {
+ ForesterUtil.outOfMemoryError( e );
+ }
catch ( final Exception e ) {
e.printStackTrace();
fatalError( "unexpected error", e.toString(), log_writer );
log_writer.close();
}
- private static void writeToRemappedFile( final File out_file,
- final SortedSet<String> remapped,
- final EasyWriter log_writer ) throws IOException {
- final File file = new File( ForesterUtil.removeSuffix( out_file.toString() ) + REMAPPED_SUFFIX );
- final EasyWriter remapped_writer = ForesterUtil.createEasyWriter( file );
- for( final String s : remapped ) {
- remapped_writer.println( s );
- }
- remapped_writer.close();
- System.out.println( "Wrote remapped gene tree species to : " + file.getCanonicalPath() );
- log_writer.println( "Wrote remapped gene tree species to : " + file.getCanonicalPath() );
- }
-
- private static void printMappedNodesToLog( final EasyWriter log_writer, final GSDII gsdi ) throws IOException {
- final SortedSet<String> ss = new TreeSet<String>();
- for( final PhylogenyNode n : gsdi.getMappedExternalSpeciesTreeNodes() ) {
- ss.add( n.toString() );
- }
- log_writer.println( "The following " + ss.size() + " species were used: " );
- for( final String s : ss ) {
- log_writer.println( " " + s );
- }
- }
-
private static void fatalError( final String type, final String msg, final EasyWriter log_writer ) {
try {
log_writer.flush();
ForesterUtil.fatalError( gsdi.PRG_NAME, msg );
}
- private static void printStrippedGeneTreeNodesToLog( final EasyWriter log_writer, final GSDII gsdi )
- throws IOException {
- final SortedMap<String, Integer> sm = new TreeMap<String, Integer>();
- for( final PhylogenyNode n : gsdi.getStrippedExternalGeneTreeNodes() ) {
- final String s = n.toString();
- if ( sm.containsKey( s ) ) {
- sm.put( s, sm.get( s ) + 1 );
- }
- else {
- sm.put( s, 1 );
- }
- }
- log_writer.println( "The following " + sm.size() + " nodes were stripped from the gene tree: " );
- for( final String s : sm.keySet() ) {
- final int count = sm.get( s );
- if ( count == 1 ) {
- log_writer.println( " " + s );
- }
- else {
- log_writer.println( " " + s + " [" + count + "]" );
- }
- }
- }
-
private static void print_help() {
System.out.println( "Usage: " + gsdi.PRG_NAME
+ " [-options] <gene tree in phyloXML format> <species tree> <outfile>" );
+ " gene_tree.xml tree_of_life.xml out.xml" );
System.out.println();
}
+
+ private static void printMappedNodesToLog( final EasyWriter log_writer, final GSDII gsdi ) throws IOException {
+ final SortedSet<String> ss = new TreeSet<String>();
+ for( final PhylogenyNode n : gsdi.getMappedExternalSpeciesTreeNodes() ) {
+ ss.add( n.toString() );
+ }
+ log_writer.println( "The following " + ss.size() + " species were used: " );
+ for( final String s : ss ) {
+ log_writer.println( " " + s );
+ }
+ }
+
+ private static void printStrippedGeneTreeNodesToLog( final EasyWriter log_writer, final GSDII gsdi )
+ throws IOException {
+ final SortedMap<String, Integer> sm = new TreeMap<String, Integer>();
+ for( final PhylogenyNode n : gsdi.getStrippedExternalGeneTreeNodes() ) {
+ final String s = n.toString();
+ if ( sm.containsKey( s ) ) {
+ sm.put( s, sm.get( s ) + 1 );
+ }
+ else {
+ sm.put( s, 1 );
+ }
+ }
+ log_writer.println( "The following " + sm.size() + " nodes were stripped from the gene tree: " );
+ for( final String s : sm.keySet() ) {
+ final int count = sm.get( s );
+ if ( count == 1 ) {
+ log_writer.println( " " + s );
+ }
+ else {
+ log_writer.println( " " + s + " [" + count + "]" );
+ }
+ }
+ }
+
+ private static void writeToRemappedFile( final File out_file,
+ final SortedSet<String> remapped,
+ final EasyWriter log_writer ) throws IOException {
+ final File file = new File( ForesterUtil.removeSuffix( out_file.toString() ) + REMAPPED_SUFFIX );
+ final EasyWriter remapped_writer = ForesterUtil.createEasyWriter( file );
+ for( final String s : remapped ) {
+ remapped_writer.println( s );
+ }
+ remapped_writer.close();
+ System.out.println( "Wrote remapped gene tree species to : " + file.getCanonicalPath() );
+ log_writer.println( "Wrote remapped gene tree species to : " + file.getCanonicalPath() );
+ }
}
git://source.jalview.org / jalview.git / blobdiff