public static Phylogeny generateRandomTree(int size, boolean randomNames) {
Random random = new Random();
List<PhylogenyNode> nodes = new ArrayList<>();
for (int i = 0; i < size; i++) {
PhylogenyNode newNode = new PhylogenyNode();
newNode.setName(i + "");
nodes.add(newNode);
}
while (nodes.size() > 1) {
int i = random.nextInt(nodes.size());
PhylogenyNode node1 = nodes.get(i);
nodes.remove(i);
int j = random.nextInt(nodes.size());
PhylogenyNode node2 = nodes.get(j);
nodes.remove(j);
PhylogenyNode newNode = new PhylogenyNode();
newNode.setChild1(node1);
newNode.setChild2(node2);
nodes.add(newNode);
newNode.setName(newNode.getId() + "");
}
Phylogeny tree = new Phylogeny();
tree.setRoot(nodes.get(0));
if (!randomNames) {
renameTreeLeavesLeftToRight(tree);
}
return tree;
}
public static Phylogeny generatePerfectTree(int size, boolean randomNames) {
Phylogeny tree = new Phylogeny();
int currentTreeSize = 0;
Queue<PhylogenyNode> currentLeaves = new LinkedList<>();
PhylogenyNode root = new PhylogenyNode();
tree.setRoot(root);
currentLeaves.add(root);
currentTreeSize++;
while (currentTreeSize < size) {
PhylogenyNode currentNode = currentLeaves.poll();
PhylogenyNode child1 = new PhylogenyNode();
PhylogenyNode child2 = new PhylogenyNode();
currentNode.setChild1(child1);
currentNode.setChild2(child2);
currentLeaves.add(child1);
currentLeaves.add(child2);
currentTreeSize++;
}
if (randomNames) renameTreeLeavesRandomly(tree);
else renameTreeLeavesLeftToRight(tree);
return tree;
}
public static Phylogeny generateBaseCaseTree(int size, boolean randomNames) {
Random random = new Random();
List<PhylogenyNode> nodes = new ArrayList<>();
for (int i = 0; i < size; i++) {
PhylogenyNode newNode = new PhylogenyNode();
newNode.setName(i + "");
nodes.add(newNode);
}
Phylogeny tree = new Phylogeny();
PhylogenyNode root = new PhylogenyNode();
tree.setRoot(root);
PhylogenyNode currentNode = root;
while (nodes.size() > 2) {
int i = random.nextInt(nodes.size());
PhylogenyNode leaf = nodes.get(i);
nodes.remove(i);
currentNode.setChild1(leaf);
PhylogenyNode newInternalNode = new PhylogenyNode();
currentNode.setChild2(newInternalNode);
currentNode = newInternalNode;
}
currentNode.setChild1(nodes.get(0));
currentNode.setChild2(nodes.get(1));
if (!randomNames) {
renameTreeLeavesLeftToRight(tree);
}
return tree;
}
public final Phylogeny execute(final BasicSymmetricalDistanceMatrix distance) {
reset(distance);
final Phylogeny phylogeny = new Phylogeny();
while (_n > 2) {
// Calculates the minimal distance.
// If more than one minimal distances, always the first found is used
updateM();
final int otu1 = _min_i;
final int otu2 = _min_j;
// System.out.println( _min_i + " " + _min_j );
// It is a condition that otu1 < otu2.
final PhylogenyNode node = new PhylogenyNode();
final double d = _d_values[_mappings[otu1]][_mappings[otu2]];
final double d1 = (d / 2) + ((_r[otu1] - _r[otu2]) / (2 * (_n - 2)));
final double d2 = d - d1;
if (_df == null) {
getExternalPhylogenyNode(otu1).setDistanceToParent(d1);
getExternalPhylogenyNode(otu2).setDistanceToParent(d2);
} else {
// yes, yes, slow but only grows with n (and not n^2 or worse)...
getExternalPhylogenyNode(otu1).setDistanceToParent(Double.parseDouble(_df.format(d1)));
getExternalPhylogenyNode(otu2).setDistanceToParent(Double.parseDouble(_df.format(d2)));
}
node.addAsChild(getExternalPhylogenyNode(otu1));
node.addAsChild(getExternalPhylogenyNode(otu2));
if (_verbose) {
printProgress(otu1, otu2);
}
calculateDistancesFromNewNode(otu1, otu2, d);
_external_nodes[_mappings[otu1]] = node;
updateMappings(otu2);
--_n;
}
final double d = _d_values[_mappings[0]][_mappings[1]] / 2;
if (_df == null) {
getExternalPhylogenyNode(0).setDistanceToParent(d);
getExternalPhylogenyNode(1).setDistanceToParent(d);
} else {
final double dd = Double.parseDouble(_df.format(d));
getExternalPhylogenyNode(0).setDistanceToParent(dd);
getExternalPhylogenyNode(1).setDistanceToParent(dd);
}
final PhylogenyNode root = new PhylogenyNode();
root.addAsChild(getExternalPhylogenyNode(0));
root.addAsChild(getExternalPhylogenyNode(1));
if (_verbose) {
printProgress(0, 1);
}
phylogeny.setRoot(root);
phylogeny.setRooted(false);
return phylogeny;
}
public static Pair<Phylogeny, Phylogeny> generateIdenticalRandomTrees(
int size, boolean randomNames) {
Random random = new Random();
List<PhylogenyNode> t1Nodes = new ArrayList<>();
List<PhylogenyNode> t2Nodes = new ArrayList<>();
for (int i = 0; i < size; i++) {
PhylogenyNode t1NewNode = new PhylogenyNode();
PhylogenyNode t2NewNode = new PhylogenyNode();
t1NewNode.setName(i + "");
t2NewNode.setName(i + "");
t1Nodes.add(t1NewNode);
t2Nodes.add(t2NewNode);
}
while (t1Nodes.size() > 1) {
int i = random.nextInt(t1Nodes.size());
PhylogenyNode t1Child1 = t1Nodes.get(i);
PhylogenyNode t2Child1 = t2Nodes.get(i);
t1Nodes.remove(i);
t2Nodes.remove(i);
int j = random.nextInt(t1Nodes.size());
PhylogenyNode t1Child2 = t1Nodes.get(j);
PhylogenyNode t2Child2 = t2Nodes.get(j);
t1Nodes.remove(j);
t2Nodes.remove(j);
PhylogenyNode t1NewNode = new PhylogenyNode();
PhylogenyNode t2NewNode = new PhylogenyNode();
t1NewNode.setChild1(t1Child1);
t1NewNode.setChild2(t1Child2);
t2NewNode.setChild1(t2Child1);
t2NewNode.setChild2(t2Child2);
t1Nodes.add(t1NewNode);
t2Nodes.add(t2NewNode);
t1NewNode.setName(t1NewNode.getId() + "");
t2NewNode.setName(t2NewNode.getId() + "");
}
Phylogeny tree1 = new Phylogeny();
Phylogeny tree2 = new Phylogeny();
tree1.setRoot(t1Nodes.get(0));
tree2.setRoot(t2Nodes.get(0));
if (!randomNames) {
renameTreeLeavesLeftToRight(tree1);
renameTreeLeavesLeftToRight(tree2);
}
return new Pair<>(tree1, tree2);
}
static SortedMap<PhylogenyNode, Double> setUpExternalCoverageHashMap(final Phylogeny phylogeny) {
final SortedMap<PhylogenyNode, Double> external_node_coverage =
new TreeMap<PhylogenyNode, Double>();
for (final PhylogenyNodeIterator iter = phylogeny.iteratorExternalForward(); iter.hasNext(); ) {
external_node_coverage.put(iter.next(), 0.0);
}
return external_node_coverage;
}
public static void renameTreeLeavesRightToLeft(Phylogeny tree) {
List<PhylogenyNode> leaves = tree.getExternalNodes();
int j = 0;
for (int i = leaves.size() - 1; i >= 0; i--) {
PhylogenyNode currentLeaf = leaves.get(i);
currentLeaf.setName(j + "");
j++;
}
}
private static void renameTreeLeavesLeftToRight(Phylogeny tree) {
PhylogenyNodeIterator iterator = tree.iteratorPreorder();
int i = 0;
while (iterator.hasNext()) {
PhylogenyNode currentNode = iterator.next();
if (currentNode.isExternal()) {
currentNode.setName(i + "");
i++;
}
}
}
public static Phylogeny generateTreeExampleH() {
Phylogeny tree = new Phylogeny();
PhylogenyNode root = new PhylogenyNode();
PhylogenyNode[] leaves = new PhylogenyNode[9];
for (int i = 1; i < leaves.length; i++) {
PhylogenyNode leaf = new PhylogenyNode();
leaf.setName(i + "");
leaves[i] = leaf;
}
PhylogenyNode NodeI = new PhylogenyNode();
PhylogenyNode NodeJ = new PhylogenyNode();
PhylogenyNode NodeL = new PhylogenyNode();
PhylogenyNode NodeM = new PhylogenyNode();
PhylogenyNode NodeN = new PhylogenyNode();
PhylogenyNode NodeF = new PhylogenyNode();
NodeJ.setChild1(leaves[1]);
NodeJ.setChild2(leaves[8]);
NodeL.setChild1(leaves[5]);
NodeL.setChild2(leaves[6]);
NodeN.setChild1(leaves[2]);
NodeN.setChild2(leaves[7]);
NodeF.setChild1(leaves[3]);
NodeF.setChild2(leaves[4]);
NodeI.setChild1(NodeJ);
NodeI.setChild2(NodeL);
NodeM.setChild1(NodeN);
NodeM.setChild2(NodeF);
root.setChild1(NodeI);
root.setChild2(NodeM);
tree.setRoot(root);
return tree;
}
public static Phylogeny generateTreeExampleA() {
Phylogeny tree = new Phylogeny();
PhylogenyNode root = new PhylogenyNode();
PhylogenyNode[] leaves = new PhylogenyNode[9];
for (int i = 1; i < leaves.length; i++) {
PhylogenyNode leaf = new PhylogenyNode();
leaf.setName(i + "");
leaves[i] = leaf;
}
PhylogenyNode NodeB = new PhylogenyNode();
PhylogenyNode NodeC = new PhylogenyNode();
PhylogenyNode NodeD = new PhylogenyNode();
PhylogenyNode NodeE = new PhylogenyNode();
PhylogenyNode NodeF = new PhylogenyNode();
PhylogenyNode NodeG = new PhylogenyNode();
NodeC.setChild1(leaves[1]);
NodeC.setChild2(leaves[2]);
NodeD.setChild1(leaves[3]);
NodeD.setChild2(leaves[4]);
NodeF.setChild1(leaves[5]);
NodeF.setChild2(leaves[6]);
NodeG.setChild1(leaves[7]);
NodeG.setChild2(leaves[8]);
NodeB.setChild1(NodeC);
NodeB.setChild2(NodeD);
NodeE.setChild1(NodeF);
NodeE.setChild2(NodeG);
root.setChild1(NodeB);
root.setChild2(NodeE);
tree.setRoot(root);
return tree;
}
public static void renameTreeLeavesRandomly(Phylogeny tree) {
Random random = new Random();
List<PhylogenyNode> leaves = new ArrayList();
PhylogenyNodeIterator iterator = tree.iteratorPostorder();
while (iterator.hasNext()) {
PhylogenyNode node = iterator.next();
if (node.isExternal()) {
leaves.add(node);
}
}
int i = 0;
while (!leaves.isEmpty()) {
int leafIndex = random.nextInt(leaves.size());
PhylogenyNode currentLeaf = leaves.get(leafIndex);
currentLeaf.setName(i + "");
leaves.remove(leafIndex);
i++;
}
}
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();
}
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[] )
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.");
}