Example #1
0
 static int calculateBranchSum(final PhylogenyNode n1, final PhylogenyNode n2) {
   final PhylogenyNode lca = PhylogenyMethods.getInstance().getLCA(n1, n2);
   return ModelingUtils.calculateBranchSumHelper(n1, lca)
       + ModelingUtils.calculateBranchSumHelper(n2, lca);
 }
Example #2
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.");
 }