Beispiel #1
0
 public static void main(final String args[]) {
   ForesterUtil.printProgramInformation(nhx_too.PRG_NAME, nhx_too.PRG_VERSION, nhx_too.PRG_DATE);
   if ((args.length < 3) || (args.length > 3)) {
     System.out.println();
     System.out.println(nhx_too.PRG_NAME + ": wrong number of arguments");
     System.out.println();
     System.out.println("Usage: \"" + nhx_too.PRG_NAME + " [options] <infile> <outfile>\n");
     System.out.println(
         " Options: -"
             + nhx_too.INT_NODE_NAME_IS_SUPPORT
             + ": internal node names are support values (i.e. MrBayes output)");
     System.out.println();
     System.exit(-1);
   }
   CommandLineArguments cla = null;
   try {
     cla = new CommandLineArguments(args);
   } catch (final Exception e) {
     ForesterUtil.fatalError(PRG_NAME, e.getMessage());
   }
   final List<String> allowed_options = new ArrayList<String>();
   allowed_options.add(nhx_too.INT_NODE_NAME_IS_SUPPORT);
   final String dissallowed_options = cla.validateAllowedOptionsAsString(allowed_options);
   if (dissallowed_options.length() > 0) {
     ForesterUtil.fatalError(nhx_too.PRG_NAME, "Unknown option(s): " + dissallowed_options);
   }
   final File phylogeny_infile = cla.getFile(0);
   final File phylogeny_outfile = cla.getFile(1);
   boolean int_node_name_is_support = false;
   if (cla.isOptionSet(nhx_too.INT_NODE_NAME_IS_SUPPORT)) {
     int_node_name_is_support = true;
   }
   Phylogeny p = null;
   try {
     final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
     final PhylogenyParser pp =
         ForesterUtil.createParserDependingOnFileType(phylogeny_infile, true);
     p = factory.create(phylogeny_infile, pp)[0];
   } catch (final Exception e) {
     ForesterUtil.fatalError(
         nhx_too.PRG_NAME, "Could not read \"" + phylogeny_infile + "\" [" + e.getMessage() + "]");
   }
   if (int_node_name_is_support) {
     try {
       ForesterUtil.transferInternalNodeNamesToConfidence(p);
     } catch (final Exception e) {
       ForesterUtil.unexpectedFatalError(
           nhx_too.PRG_NAME,
           "Failure during moving of internal names to support values [" + e.getMessage() + "]");
     }
   }
   try {
     final PhylogenyWriter w = new PhylogenyWriter();
     w.toNewHampshireX(p, phylogeny_outfile);
   } catch (final IOException e) {
     ForesterUtil.fatalError(nhx_too.PRG_NAME, "Failure to write output [" + e.getMessage() + "]");
   }
   System.out.println();
   System.out.println("Done [wrote \"" + phylogeny_outfile + "\"].");
   System.out.println();
 }
 synchronized void readPhylogeniesFromWebservice() {
   final long start_time = new Date().getTime();
   URL url = null;
   Phylogeny[] trees = null;
   final WebservicesManager webservices_manager = WebservicesManager.getInstance();
   final PhylogeniesWebserviceClient client =
       webservices_manager.getAvailablePhylogeniesWebserviceClient(_webservice_client_index);
   String identifier =
       JOptionPane.showInputDialog(
           _main_frame,
           client.getInstructions() + "\n(Reference: " + client.getReference() + ")",
           client.getDescription(),
           JOptionPane.QUESTION_MESSAGE);
   if ((identifier != null) && (identifier.trim().length() > 0)) {
     identifier = identifier.trim();
     if (client.isQueryInteger()) {
       int id = -1;
       try {
         id = Integer.parseInt(identifier);
       } catch (final NumberFormatException e) {
         id = -1;
       }
       if (id < 1) {
         JOptionPane.showMessageDialog(
             _main_frame,
             "Identifier is expected to be a number",
             "Can not open URL",
             JOptionPane.ERROR_MESSAGE);
         return;
       }
       identifier = id + "";
     }
     try {
       String url_str = client.getUrl();
       url_str = url_str.replaceFirst(PhylogeniesWebserviceClient.QUERY_PLACEHOLDER, identifier);
       url = new URL(url_str);
       PhylogenyParser parser = null;
       switch (client.getReturnFormat()) {
         case TOL_XML_RESPONSE:
           parser = new TolParser();
           break;
         case NEXUS:
           parser = new NexusPhylogeniesParser();
           ((NexusPhylogeniesParser) parser).setReplaceUnderscores(true);
           break;
         case NH:
           parser = new NHXParser();
           ((NHXParser) parser).setTaxonomyExtraction(TAXONOMY_EXTRACTION.NO);
           ((NHXParser) parser).setReplaceUnderscores(true);
           ((NHXParser) parser).setGuessRootedness(true);
           break;
         case NH_EXTRACT_TAXONOMY:
           parser = new NHXParser();
           ((NHXParser) parser).setTaxonomyExtraction(TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY);
           ((NHXParser) parser).setReplaceUnderscores(false);
           ((NHXParser) parser).setGuessRootedness(true);
           break;
         case PFAM:
           parser = new NHXParser();
           ((NHXParser) parser).setTaxonomyExtraction(TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY);
           ((NHXParser) parser).setReplaceUnderscores(false);
           ((NHXParser) parser).setGuessRootedness(true);
           break;
         case NHX:
           parser = new NHXParser();
           ((NHXParser) parser).setTaxonomyExtraction(TAXONOMY_EXTRACTION.NO);
           ((NHXParser) parser).setReplaceUnderscores(false);
           ((NHXParser) parser).setGuessRootedness(true);
           break;
         case PHYLOXML:
           parser = new PhyloXmlParser();
           break;
         default:
           throw new IllegalArgumentException("unknown format: " + client.getReturnFormat());
       }
       if (_main_frame.getMainPanel().getCurrentTreePanel() != null) {
         _main_frame.getMainPanel().getCurrentTreePanel().setWaitCursor();
       } else {
         _main_frame.getMainPanel().setWaitCursor();
       }
       final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
       trees = factory.create(url.openStream(), parser);
     } catch (final MalformedURLException e) {
       JOptionPane.showMessageDialog(
           _main_frame,
           "Malformed URL: " + url + "\n" + e.getLocalizedMessage(),
           "Malformed URL",
           JOptionPane.ERROR_MESSAGE);
     } catch (final IOException e) {
       JOptionPane.showMessageDialog(
           _main_frame,
           "Could not read from " + url + "\n" + e.getLocalizedMessage(),
           "Failed to read tree from " + client.getName() + " for " + identifier,
           JOptionPane.ERROR_MESSAGE);
     } catch (final NumberFormatException e) {
       JOptionPane.showMessageDialog(
           _main_frame,
           "Could not read from " + url + "\n" + e.getLocalizedMessage(),
           "Failed to read tree from " + client.getName() + " for " + identifier,
           JOptionPane.ERROR_MESSAGE);
     } catch (final Exception e) {
       e.printStackTrace();
       JOptionPane.showMessageDialog(
           _main_frame,
           e.getLocalizedMessage(),
           "Unexpected Exception",
           JOptionPane.ERROR_MESSAGE);
     } finally {
       if (_main_frame.getCurrentTreePanel() != null) {
         _main_frame.getCurrentTreePanel().setArrowCursor();
       } else {
         _main_frame.getMainPanel().setArrowCursor();
       }
     }
     if ((trees != null) && (trees.length > 0)) {
       for (final Phylogeny phylogeny : trees) {
         if (client.getName().equals(WebserviceUtil.TREE_FAM_NAME)) {
           phylogeny.setRerootable(false);
         }
         if (client.getName().equals(WebserviceUtil.PFAM_NAME)) {
           phylogeny.setRerootable(false);
           ForesterUtil.transferInternalNodeNamesToConfidence(phylogeny);
         }
         if (client.getProcessingInstructions() != null) {
           WebserviceUtil.processInstructions(client, phylogeny);
         }
         if (client.getNodeField() != null) {
           ForesterUtil.transferNodeNameToField(phylogeny, client.getNodeField());
         }
         phylogeny.setIdentifier(new Identifier(identifier, client.getName()));
         _main_frame.getJMenuBar().remove(_main_frame.getHelpMenu());
         _main_frame.getMenuBarOfMainFrame().add(_main_frame.getHelpMenu());
         _main_frame
             .getMainPanel()
             .addPhylogenyInNewTab(
                 phylogeny,
                 _main_frame.getConfiguration(),
                 new File(url.getFile()).getName(),
                 url.toString());
         String my_name_for_file = "";
         if (!ForesterUtil.isEmpty(phylogeny.getName())) {
           my_name_for_file = new String(phylogeny.getName()).replaceAll(" ", "_");
         } else if (phylogeny.getIdentifier() != null) {
           final StringBuffer sb = new StringBuffer();
           if (!ForesterUtil.isEmpty(phylogeny.getIdentifier().getProvider())) {
             sb.append(phylogeny.getIdentifier().getProvider());
             sb.append("_");
           }
           sb.append(phylogeny.getIdentifier().getValue());
           my_name_for_file = new String(sb.toString().replaceAll(" ", "_"));
         }
         _main_frame.getMainPanel().getCurrentTreePanel().setTreeFile(new File(my_name_for_file));
         Util.lookAtSomeTreePropertiesForAptxControlSettings(
             phylogeny,
             _main_frame.getMainPanel().getControlPanel(),
             _main_frame.getConfiguration());
         _main_frame.getMainPanel().getControlPanel().showWhole();
       }
     }
     _main_frame.getContentPane().repaint();
     if (((trees != null) && (trees.length > 0))
         && ((new Date().getTime() - start_time) > 20000)) {
       try {
         JOptionPane.showMessageDialog(
             null,
             ForesterUtil.wordWrap(
                 "Successfully read in "
                     + trees.length
                     + " evolutionry tree(s) from ["
                     + url
                     + "]",
                 80),
             "Success",
             JOptionPane.INFORMATION_MESSAGE);
       } catch (final Exception e) {
         // Not important if this fails, do nothing.
       }
       _main_frame.getContentPane().repaint();
     }
   }
   _main_frame.activateSaveAllIfNeeded();
   System.gc();
 }
Beispiel #3
0
 private static boolean testExternalNodeBasedCoverage() {
   try {
     final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
     final String ps1 =
         "((((A:0.1,B:0.7):0.2,C:1.0):2.0,D:1.7):1.3,((E:0.3,F:0.4):1.1,(G:0.5,H:0.6):1.2):1.4,X:2.0)";
     final Phylogeny p1 = factory.create(ps1, new NHXParser())[0];
     final List<Phylogeny> phylogenies = new ArrayList<Phylogeny>();
     final List<String> names = new ArrayList<String>();
     phylogenies.add(p1);
     names.add("A");
     names.add("A");
     final CoverageCalculationOptions options =
         new ExternalNodeBasedCoverageMethodOptions(
             "org.forester.pccx.BranchCountingBasedScoringMethod");
     final CoverageCalculator cc =
         CoverageCalculator.getInstance(new ExternalNodeBasedCoverageMethod(), options);
     Coverage cov = cc.calculateCoverage(phylogenies, names, false);
     if (!TestPccx.isEqual(
         cov.getScore(),
         (1.0 + 1.0 / 2 + 1.0 / 3 + 1.0 / 4 + 1.0 / 7 + 1.0 / 7 + 1.0 / 7 + 1.0 / 7 + 1.0 / 5)
             / 9)) {
       return false;
     }
     names.add("B");
     names.add("B");
     cov = cc.calculateCoverage(phylogenies, names, false);
     if (!TestPccx.isEqual(
         cov.getScore(),
         (1.0 + 1.0 + 1.0 / 3 + 1.0 / 4 + 1.0 / 7 + 1.0 / 7 + 1.0 / 7 + 1.0 / 7 + 1.0 / 5) / 9)) {
       return false;
     }
     names.add("G");
     cov = cc.calculateCoverage(phylogenies, names, false);
     if (!TestPccx.isEqual(
         cov.getScore(),
         (1.0 + 1.0 + 1.0 / 3 + 1.0 / 4 + 1.0 / 4 + 1.0 / 4 + 1.0 + 1.0 / 2 + 1.0 / 4) / 9)) {
       return false;
     }
     names.add("E");
     cov = cc.calculateCoverage(phylogenies, names, false);
     if (!TestPccx.isEqual(
         cov.getScore(),
         (1.0 + 1.0 + 1.0 / 3 + 1.0 / 4 + 1.0 + 1.0 / 2 + 1.0 + 1.0 / 2 + 1.0 / 4) / 9)) {
       return false;
     }
     names.add("X");
     cov = cc.calculateCoverage(phylogenies, names, false);
     if (!TestPccx.isEqual(
         cov.getScore(),
         (1.0 + 1.0 + 1.0 / 3 + 1.0 / 3 + 1.0 + 1.0 / 2 + 1.0 + 1.0 / 2 + 1.0) / 9)) {
       return false;
     }
     names.add("C");
     names.add("C");
     names.add("C");
     cov = cc.calculateCoverage(phylogenies, names, false);
     if (!TestPccx.isEqual(
         cov.getScore(), (1.0 + 1.0 + 1.0 + 1.0 / 3 + 1.0 + 1.0 / 2 + 1.0 + 1.0 / 2 + 1.0) / 9)) {
       return false;
     }
     names.add("D");
     cov = cc.calculateCoverage(phylogenies, names, false);
     if (!TestPccx.isEqual(
         cov.getScore(), (1.0 + 1.0 + 1.0 + 1.0 + 1.0 + 1.0 / 2 + 1.0 + 1.0 / 2 + 1.0) / 9)) {
       return false;
     }
     names.add("F");
     cov = cc.calculateCoverage(phylogenies, names, false);
     if (!TestPccx.isEqual(
         cov.getScore(), (1.0 + 1.0 + 1.0 + 1.0 + 1.0 + 1.0 + 1.0 + 1.0 / 2 + 1.0) / 9)) {
       return false;
     }
     names.add("H");
     cov = cc.calculateCoverage(phylogenies, names, false);
     if (!TestPccx.isEqual(
         cov.getScore(), (1.0 + 1.0 + 1.0 + 1.0 + 1.0 + 1.0 + 1.0 + 1.0 + 1.0) / 9)) {
       return false;
     }
     final CoverageExtender ce = new BasicExternalNodeBasedCoverageExtender();
     List<String> l =
         ce.find(
             phylogenies,
             null,
             0,
             new ExternalNodeBasedCoverageMethodOptions(
                 "org.forester.pccx.BranchCountingBasedScoringMethod"),
             null);
     if (!l.get(0).equals("X")) {
       return false;
     }
     if (!l.get(1).equals("A")) {
       return false;
     }
     if (!l.get(2).equals("E")) {
       return false;
     }
     if (!l.get(3).equals("G")) {
       return false;
     }
     if (!l.get(4).equals("C")) {
       return false;
     }
     if (!l.get(5).equals("D")) {
       return false;
     }
     if (!l.get(6).equals("B")) {
       return false;
     }
     if (!l.get(7).equals("F")) {
       return false;
     }
     if (!l.get(8).equals("H")) {
       return false;
     }
     final List<String> already_covered = new ArrayList<String>();
     already_covered.add("A");
     already_covered.add("X");
     already_covered.add("H");
     already_covered.add("C");
     l =
         ce.find(
             phylogenies,
             already_covered,
             0,
             new ExternalNodeBasedCoverageMethodOptions(
                 "org.forester.pccx.BranchCountingBasedScoringMethod"),
             null);
     if (!l.get(0).equals("E")) {
       return false;
     }
     if (!l.get(1).equals("D")) {
       return false;
     }
     if (!l.get(2).equals("B")) {
       return false;
     }
     if (!l.get(3).equals("F")) {
       return false;
     }
     if (!l.get(4).equals("G")) {
       return false;
     }
     final String ps2 =
         "((((A:0.1,B:0.7):0.2,C:1.0):2.0,D:1.7):1.3,((E:0.3,F:0.4):1.1,(G:0.5,H:0.6):1.2):1.4,X:2.0)";
     final String ps3 =
         "((((A:0.1,B:0.1):0.2,C:1.0):2.0,D:1.7):1.3,((E:0.3,F:0.4):1.1,(G:0.5,H:0.6):1.2):1.4,X:2.0)";
     final String ps4 =
         "((((A:0.1,B:0.05):0.2,C:1.0):2.0,D:1.7):1.3,((E:0.3,F:0.4):1.1,(G:0.5,H:0.6):1.2):1.4,X:2.0)";
     final Phylogeny p2 = factory.create(ps2, new NHXParser())[0];
     final Phylogeny p3 = factory.create(ps3, new NHXParser())[0];
     final Phylogeny p4 = factory.create(ps4, new NHXParser())[0];
     final List<Phylogeny> phylogenies2 = new ArrayList<Phylogeny>();
     final List<String> names2 = new ArrayList<String>();
     phylogenies2.add(p2);
     phylogenies2.add(p3);
     phylogenies2.add(p4);
     names2.add("A");
     names2.add("A");
     final CoverageCalculationOptions options2 =
         new ExternalNodeBasedCoverageMethodOptions(
             "org.forester.pccx.BranchLengthBasedScoringMethod");
     final CoverageCalculator cc2 =
         CoverageCalculator.getInstance(new ExternalNodeBasedCoverageMethod(), options2);
     Coverage cov2 = cc2.calculateCoverage(phylogenies2, names2, false);
     final double nf =
         1
             / (1 / 0.1 + 1 / 0.7 + 1 / 1.0 + 1 / 1.7 + 1 / 0.3 + 1 / 0.4 + 1 / 0.5 + 1 / 0.6
                 + 1 / 2.0);
     if (!TestPccx.isEqual(
         cov2.getScore(),
         (1 / 0.1
                 + (1 / 0.8 + 1 / 0.2 + 1 / 0.15) / 3
                 + 1 / 1.3
                 + 1 / 4.0
                 + 1 / 6.4
                 + 1 / 6.5
                 + 1 / 6.7
                 + 1 / 6.8
                 + 1 / 5.6)
             * nf)) {
       return false;
     }
     names2.add("C");
     cov2 = cc2.calculateCoverage(phylogenies2, names2, false);
     if (!TestPccx.isEqual(
         cov2.getScore(),
         (1 / 0.1
                 + (1 / 0.8 + 1 / 0.2 + 1 / 0.15) / 3
                 + 1 / 1.0
                 + 1 / 4.0
                 + 1 / 6.4
                 + 1 / 6.5
                 + 1 / 6.7
                 + 1 / 6.8
                 + 1 / 5.6)
             * nf)) {
       return false;
     }
     names2.add("E");
     cov2 = cc2.calculateCoverage(phylogenies2, names2, false);
     if (!TestPccx.isEqual(
         cov2.getScore(),
         (1 / 0.1
                 + (1 / 0.8 + 1 / 0.2 + 1 / 0.15) / 3
                 + 1 / 1.0
                 + +1 / 4.0
                 + 1 / 0.3
                 + 1 / 0.7
                 + 1 / 3.1
                 + 1 / 3.2
                 + 1 / 4.8)
             * nf)) {
       return false;
     }
     final CoverageCalculationOptions options_log =
         new ExternalNodeBasedCoverageMethodOptions(
             "org.forester.pccx.LogBranchLengthBasedScoringMethod");
     final CoverageCalculator cclog =
         CoverageCalculator.getInstance(new ExternalNodeBasedCoverageMethod(), options_log);
     final Coverage cov_log = cclog.calculateCoverage(phylogenies2, names2, false);
     if (!TestPccx.isEqual(cov_log.getScore(), 0.8534252108361485)) {
       return false;
     }
     final String ps10 =
         "((((A:0.1,B:0.7):0.2,C:1.0):2.0,D:1.7):1.3,((E:0.3,F:0.4):1.1,(G:0.5,H:0.6):1.2):1.4,((((I:0.1,J:0.7):0.2,K:1.0):2.0,L:1.7):1.3,((M:0.3,N:0.4,O:0.1,P:0.2):1.1,(Q:0.5,R:0.6):1.2):1.4,S:2.0):2.0)";
     final Phylogeny p10 = factory.create(ps10, new NHXParser())[0];
     final List<Phylogeny> phylogenies10 = new ArrayList<Phylogeny>();
     final List<String> names10 = new ArrayList<String>();
     phylogenies10.add(p10);
     names10.add("A");
     names10.add("B");
     names10.add("N");
     names10.add("O");
     final CoverageCalculationOptions options10 =
         new ExternalNodeBasedCoverageMethodOptions(
             "org.forester.pccx.BranchCountingBasedScoringMethod");
     final CoverageCalculator cc10 =
         CoverageCalculator.getInstance(new ExternalNodeBasedCoverageMethod(), options10);
     cc10.calculateCoverage(phylogenies10, names10, true);
   } catch (final Exception e) {
     e.printStackTrace(System.out);
     return false;
   }
   return true;
 }
Beispiel #4
0
 public static void main(final String args[]) {
   ForesterUtil.printProgramInformation(PRG_NAME, PRG_VERSION, PRG_DATE);
   CommandLineArguments cla = null;
   try {
     cla = new CommandLineArguments(args);
   } catch (final Exception e) {
     ForesterUtil.fatalError(PRG_NAME, e.getMessage());
   }
   if (cla.isOptionSet(HELP_OPTION_1) || cla.isOptionSet(HELP_OPTION_2)) {
     System.out.println();
     print_help();
     System.exit(0);
   } else if ((args.length < 2) || (cla.getNumberOfNames() < 2) || (cla.getNumberOfNames() > 3)) {
     System.out.println();
     System.out.println("Wrong number of arguments.");
     System.out.println();
     print_help();
     System.exit(-1);
   }
   final List<String> allowed_options = new ArrayList<String>();
   allowed_options.add(STRIP_OPTION);
   allowed_options.add(SDISE_OPTION);
   allowed_options.add(MOST_PARSIMONIOUS_OPTION);
   final String dissallowed_options = cla.validateAllowedOptionsAsString(allowed_options);
   if (dissallowed_options.length() > 0) {
     ForesterUtil.fatalError(PRG_NAME, "unknown option(s): " + dissallowed_options);
   }
   boolean use_sdise = false;
   boolean strip = false;
   boolean most_parsimonous_duplication_model = false;
   if (cla.isOptionSet(STRIP_OPTION)) {
     strip = true;
   }
   if (cla.isOptionSet(SDISE_OPTION)) {
     use_sdise = true;
   }
   if (cla.isOptionSet(MOST_PARSIMONIOUS_OPTION)) {
     if (use_sdise) {
       ForesterUtil.fatalError(
           PRG_NAME, "Can only use most parsimonious duplication mode with GSDI");
     }
     most_parsimonous_duplication_model = true;
   }
   Phylogeny species_tree = null;
   Phylogeny gene_tree = null;
   File gene_tree_file = null;
   File species_tree_file = null;
   File out_file = null;
   try {
     gene_tree_file = cla.getFile(0);
     species_tree_file = cla.getFile(1);
     if (cla.getNumberOfNames() == 3) {
       out_file = cla.getFile(2);
     } else {
       out_file = new File(DEFAULT_OUTFILE);
     }
   } catch (final IllegalArgumentException e) {
     ForesterUtil.fatalError(PRG_NAME, "error in command line: " + e.getMessage());
   }
   if (ForesterUtil.isReadableFile(gene_tree_file) != null) {
     ForesterUtil.fatalError(PRG_NAME, ForesterUtil.isReadableFile(gene_tree_file));
   }
   if (ForesterUtil.isReadableFile(species_tree_file) != null) {
     ForesterUtil.fatalError(PRG_NAME, ForesterUtil.isReadableFile(species_tree_file));
   }
   if (ForesterUtil.isWritableFile(out_file) != null) {
     ForesterUtil.fatalError(PRG_NAME, ForesterUtil.isWritableFile(out_file));
   }
   try {
     final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
     final PhylogenyParser pp =
         ForesterUtil.createParserDependingOnFileType(species_tree_file, true);
     species_tree = factory.create(species_tree_file, pp)[0];
   } catch (final IOException e) {
     ForesterUtil.fatalError(
         PRG_NAME,
         "Failed to read species tree from \"" + gene_tree_file + "\" [" + e.getMessage() + "]");
   }
   try {
     final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
     final PhylogenyParser pp = ForesterUtil.createParserDependingOnFileType(gene_tree_file, true);
     gene_tree = factory.create(gene_tree_file, pp)[0];
   } catch (final IOException e) {
     ForesterUtil.fatalError(
         PRG_NAME,
         "Failed to read gene tree from \"" + gene_tree_file + "\" [" + e.getMessage() + "]");
   }
   gene_tree.setRooted(true);
   species_tree.setRooted(true);
   if (!gene_tree.isCompletelyBinary()) {
     ForesterUtil.fatalError(PRG_NAME, "gene tree is not completely binary.");
   }
   if (use_sdise) {
     if (!species_tree.isCompletelyBinary()) {
       ForesterUtil.fatalError(PRG_NAME, "species tree is not completely binary.");
     }
   }
   // For timing.
   // gene_tree = Helper.createBalancedTree( 10 );
   // species_tree = Helper.createBalancedTree( 13 );
   // species_tree = Helper.createUnbalancedTree( 1024 );
   // gene_tree = Helper.createUnbalancedTree( 8192 );
   // species_tree = gene_tree.copyTree();
   // gene_tree = species_tree.copyTree();
   // Helper.numberSpeciesInOrder( species_tree );
   // Helper.numberSpeciesInOrder( gene_tree );
   // Helper.randomizeSpecies( 1, 8192, gene_tree );
   // Helper.intervalNumberSpecies( gene_tree, 4096 );
   // Helper.numberSpeciesInDescOrder( gene_tree );
   System.out.println();
   System.out.println("Strip species tree: " + strip);
   SDI sdi = null;
   final long start_time = new Date().getTime();
   try {
     if (use_sdise) {
       System.out.println();
       System.out.println("Using SDIse algorithm.");
       sdi = new SDIse(gene_tree, species_tree);
     } else {
       System.out.println();
       System.out.println("Using GSDI algorithm.");
       System.out.println();
       System.out.println(
           "Use most parsimonous duplication model: " + most_parsimonous_duplication_model);
       sdi = new GSDI(gene_tree, species_tree, most_parsimonous_duplication_model);
     }
   } catch (final Exception e) {
     ForesterUtil.unexpectedFatalError(PRG_NAME, e);
   }
   System.out.println();
   System.out.println(
       "Running time (excluding I/O): " + (new Date().getTime() - start_time) + "ms");
   try {
     final PhylogenyWriter writer = new PhylogenyWriter();
     writer.toPhyloXML(out_file, gene_tree, 1);
   } catch (final IOException e) {
     ForesterUtil.fatalError(
         PRG_NAME, "Failed to write to \"" + out_file + "\" [" + e.getMessage() + "]");
   }
   System.out.println();
   System.out.println("Successfully wrote resulting gene tree to: " + out_file);
   System.out.println();
   //        if ( use_sdise ) {
   //            computeMappingCostL();
   //            System.out.println( "Mapping cost                    : " + computeMappingCostL()
   // );
   //        }
   //        System.out.println( "Number of duplications          : " + getDuplicationsSum() );
   if (!use_sdise && !most_parsimonous_duplication_model) {
     System.out.println(
         "Number of potential duplications: "
             + ((GSDI) sdi).getSpeciationOrDuplicationEventsSum());
   }
   if (!use_sdise) {
     System.out.println("Number speciations              : " + ((GSDI) sdi).getSpeciationsSum());
   }
   System.out.println();
 } // main( final String args[] )
Beispiel #5
0
 public static void main(final String args[]) {
   ForesterUtil.printProgramInformation(PRG_NAME, PRG_VERSION, PRG_DATE, E_MAIL, WWW);
   CommandLineArguments cla = null;
   try {
     cla = new CommandLineArguments(args);
   } catch (final Exception e) {
     ForesterUtil.fatalError(PRG_NAME, e.getMessage());
   }
   if (cla.isOptionSet(HELP_OPTION_1) || cla.isOptionSet(HELP_OPTION_2) || (args.length == 0)) {
     printHelp();
     System.exit(0);
   }
   if ((args.length < 3) || (cla.getNumberOfNames() != 2)) {
     System.out.println();
     System.out.println("[" + PRG_NAME + "] incorrect number of arguments");
     System.out.println();
     printHelp();
     System.exit(-1);
   }
   final List<String> allowed_options = new ArrayList<String>();
   allowed_options.add(MIN_MAPPING_COST_OPTION);
   allowed_options.add(MIN_DUPS_OPTION);
   allowed_options.add(MIN_HEIGHT_OPTION);
   final String dissallowed_options = cla.validateAllowedOptionsAsString(allowed_options);
   if (dissallowed_options.length() > 0) {
     ForesterUtil.fatalError(PRG_NAME, "unknown option(s): " + dissallowed_options);
   }
   final File outfile = new File("sdir_outfile.xml");
   if (outfile.exists()) {
     ForesterUtil.fatalError(PRG_NAME, "outfile \"" + outfile + "\" already exists");
   }
   final File gene_tree_file = cla.getFile(0);
   final File species_tree_file = cla.getFile(1);
   boolean minimize_cost = false;
   if (cla.isOptionSet(MIN_MAPPING_COST_OPTION)) {
     minimize_cost = true;
   }
   boolean minimize_sum_of_dup = false;
   if (cla.isOptionSet(MIN_DUPS_OPTION)) {
     minimize_sum_of_dup = true;
   }
   boolean minimize_height = false;
   if (cla.isOptionSet(MIN_HEIGHT_OPTION)) {
     minimize_height = true;
   }
   int r = 0;
   Phylogeny[] gene_trees = null;
   Phylogeny species_tree = null;
   if (minimize_cost && minimize_sum_of_dup) {
     minimize_sum_of_dup = false;
   }
   final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
   try {
     final PhylogenyParser pp = new PhyloXmlParser();
     species_tree = factory.create(species_tree_file, pp)[0];
   } catch (final IOException e) {
     ForesterUtil.fatalError(
         PRG_NAME,
         "failed to read species tree [" + species_tree_file + "]: " + e.getLocalizedMessage());
   }
   if (!species_tree.isRooted()) {
     ForesterUtil.fatalError(PRG_NAME, "species tree [" + species_tree_file + "] is not rooted");
   }
   try {
     final PhylogenyParser pp = new PhyloXmlParser();
     gene_trees = factory.create(gene_tree_file, pp);
   } catch (final IOException e) {
     ForesterUtil.fatalError(
         PRG_NAME,
         "failed to read gene trees [" + gene_tree_file + "]: " + e.getLocalizedMessage());
   }
   // Removes from gene_tree all species not found in species_tree.
   int gene_tree_counter = 0;
   final List<Phylogeny> all_result_trees = new ArrayList<Phylogeny>();
   for (final Phylogeny gene_tree : gene_trees) {
     r = PhylogenyMethods.taxonomyBasedDeletionOfExternalNodes(species_tree, gene_tree);
     ForesterUtil.programMessage(PRG_NAME, "Removed " + r + " external nodes from gene tree");
     final SDIR sdiunrooted = new SDIR();
     final long start_time = new Date().getTime();
     Phylogeny[] result_trees = null;
     try {
       result_trees =
           sdiunrooted.infer(
               gene_tree,
               species_tree,
               minimize_cost,
               minimize_sum_of_dup,
               minimize_height,
               true,
               sdi_r.TREES_TO_RETURN);
     } catch (final Exception e) {
       ForesterUtil.fatalError(PRG_NAME, e.getLocalizedMessage());
     }
     final long time_req = new Date().getTime() - start_time;
     if (minimize_cost) {
       ForesterUtil.programMessage(PRG_NAME, "Rooted by minimizing mapping cost L");
       if (minimize_height) {
         ForesterUtil.programMessage(
             PRG_NAME, "Selected tree(s) with minimal height out of resulting trees");
       }
       ForesterUtil.programMessage(
           PRG_NAME,
           "Number differently rooted trees minimizing criterion  : " + sdiunrooted.getCount());
       ForesterUtil.programMessage(
           PRG_NAME,
           "Minimal cost                                          : "
               + sdiunrooted.getMinimalMappingCost());
       ForesterUtil.programMessage(
           PRG_NAME,
           "Minimal duplications                                  : "
               + sdiunrooted.getMinimalDuplications());
       if (minimize_height) {
         ForesterUtil.programMessage(
             PRG_NAME,
             "Phylogeny height                                      : "
                 + ForesterUtil.FORMATTER_06.format(sdiunrooted.getMinimalTreeHeight()));
         ForesterUtil.programMessage(
             PRG_NAME,
             "Difference in subtree heights                         : "
                 + ForesterUtil.FORMATTER_06.format(sdiunrooted.getMinimalDiffInSubTreeHeights()));
       }
     } else if (minimize_sum_of_dup) {
       ForesterUtil.programMessage(PRG_NAME, "Rooted by minimizing sum of duplications");
       if (minimize_height) {
         ForesterUtil.programMessage(
             PRG_NAME, "Selected tree(s) with minimal height out of resulting trees");
       }
       ForesterUtil.programMessage(
           PRG_NAME,
           "Number differently rooted trees minimizing criterion        : "
               + sdiunrooted.getCount());
       ForesterUtil.programMessage(
           PRG_NAME,
           "Minimal duplications                                        : "
               + sdiunrooted.getMinimalDuplications());
       if (minimize_height) {
         ForesterUtil.programMessage(
             PRG_NAME,
             "Phylogeny height                                            : "
                 + ForesterUtil.FORMATTER_06.format(sdiunrooted.getMinimalTreeHeight()));
         ForesterUtil.programMessage(
             PRG_NAME,
             "Difference in subtree heights                               : "
                 + ForesterUtil.FORMATTER_06.format(sdiunrooted.getMinimalDiffInSubTreeHeights()));
       }
     } else if (minimize_height) {
       ForesterUtil.programMessage(
           PRG_NAME, "Rooted by minimizing tree height (midpoint rooting).");
       ForesterUtil.programMessage(
           PRG_NAME,
           "Minimal tree height                  : "
               + ForesterUtil.FORMATTER_06.format(sdiunrooted.getMinimalTreeHeight()));
       ForesterUtil.programMessage(
           PRG_NAME,
           "Minimal difference in subtree heights: "
               + ForesterUtil.FORMATTER_06.format(sdiunrooted.getMinimalDiffInSubTreeHeights()));
       ForesterUtil.programMessage(
           PRG_NAME,
           "Duplications in midpoint rooted tree : " + sdiunrooted.getMinimalDuplications());
     } else {
       ForesterUtil.programMessage(PRG_NAME, "No (re) rooting was performed.");
       ForesterUtil.programMessage(
           PRG_NAME, "Duplications in tree: " + sdiunrooted.getMinimalDuplications());
     }
     ForesterUtil.programMessage(
         PRG_NAME, "Time requirement (minus I/O)                          : " + time_req + "ms");
     for (int i = 0; i < result_trees.length; ++i) {
       final String name = result_trees[i].getName();
       if (ForesterUtil.isEmpty(name)) {
         result_trees[i].setName("SDIR result [gene tree + " + gene_tree_counter + "]" + " " + i);
       } else {
         result_trees[i].setName(
             name + " SDIR result [gene tree + " + gene_tree_counter + "]" + " " + i);
       }
       all_result_trees.add(result_trees[i]);
     }
     ++gene_tree_counter;
   } // for( final Phylogeny gene_tree : gene_trees )
   try {
     final PhylogenyWriter w = new PhylogenyWriter();
     w.toPhyloXML(outfile, all_result_trees, 0, ForesterUtil.LINE_SEPARATOR);
   } catch (final IOException e) {
     ForesterUtil.fatalError(
         PRG_NAME, "failure to write output to [" + outfile + "]: " + e.getLocalizedMessage());
   }
   ForesterUtil.programMessage(PRG_NAME, "Wrote: " + outfile);
   ForesterUtil.programMessage(PRG_NAME, "OK.");
 }