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();
}
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;
}
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.");
}