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);
}
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.");
}