use of dr.app.beauti.options.PartitionData in project beast-mcmc by beast-dev.
the class OldTreesPanel method createTree.
private void createTree() {
if (generateTreeDialog == null) {
generateTreeDialog = new GenerateTreeDialog(frame);
}
int result = generateTreeDialog.showDialog(options);
if (result != JOptionPane.CANCEL_OPTION) {
GenerateTreeDialog.MethodTypes methodType = generateTreeDialog.getMethodType();
PartitionData partition = generateTreeDialog.getDataPartition();
Patterns patterns = new Patterns(partition.getAlignment());
DistanceMatrix distances = new F84DistanceMatrix(patterns);
Tree tree;
TemporalRooting temporalRooting;
switch(methodType) {
case NJ:
tree = new NeighborJoiningTree(distances);
temporalRooting = new TemporalRooting(tree);
tree = temporalRooting.findRoot(tree, TemporalRooting.RootingFunction.CORRELATION);
break;
case UPGMA:
tree = new UPGMATree(distances);
temporalRooting = new TemporalRooting(tree);
break;
default:
throw new IllegalArgumentException("unknown method type");
}
tree.setId(generateTreeDialog.getName());
options.userTrees.add(tree);
treesTableModel.fireTableDataChanged();
int row = options.userTrees.size() - 1;
treesTable.getSelectionModel().setSelectionInterval(row, row);
}
fireTreePriorsChanged();
}
use of dr.app.beauti.options.PartitionData in project beast-mcmc by beast-dev.
the class BeautiTesterConfig method importFromFile.
public void importFromFile(String fileName, BeautiOptions options, boolean translate) {
TaxonList taxa = null;
Alignment alignment = null;
Tree tree = null;
PartitionSubstitutionModel model = null;
java.util.List<CharSet> charSets = new ArrayList<CharSet>();
try {
FileReader reader = new FileReader(fileName);
NexusApplicationImporter importer = new NexusApplicationImporter(reader);
boolean done = false;
while (!done) {
try {
NexusImporter.NexusBlock block = importer.findNextBlock();
if (block == NexusImporter.TAXA_BLOCK) {
if (taxa != null) {
throw new NexusImporter.MissingBlockException("TAXA block already defined");
}
taxa = importer.parseTaxaBlock();
} else if (block == NexusImporter.CALIBRATION_BLOCK) {
if (taxa == null) {
throw new NexusImporter.MissingBlockException("TAXA or DATA block must be defined before a CALIBRATION block");
}
importer.parseCalibrationBlock(taxa);
} else if (block == NexusImporter.CHARACTERS_BLOCK) {
if (taxa == null) {
throw new NexusImporter.MissingBlockException("TAXA block must be defined before a CHARACTERS block");
}
if (alignment != null) {
throw new NexusImporter.MissingBlockException("CHARACTERS or DATA block already defined");
}
alignment = importer.parseCharactersBlock(options.taxonList);
} else if (block == NexusImporter.DATA_BLOCK) {
if (alignment != null) {
throw new NexusImporter.MissingBlockException("CHARACTERS or DATA block already defined");
}
// A data block doesn't need a taxon block before it
// but if one exists then it will use it.
alignment = importer.parseDataBlock(options.taxonList);
if (taxa == null) {
taxa = alignment;
}
} else if (block == NexusImporter.TREES_BLOCK) {
if (taxa == null) {
throw new NexusImporter.MissingBlockException("TAXA or DATA block must be defined before a TREES block");
}
if (tree != null) {
throw new NexusImporter.MissingBlockException("TREES block already defined");
}
Tree[] trees = importer.parseTreesBlock(taxa);
if (trees.length > 0) {
tree = trees[0];
}
} else if (block == NexusApplicationImporter.PAUP_BLOCK) {
model = importer.parsePAUPBlock(options, charSets);
} else if (block == NexusApplicationImporter.MRBAYES_BLOCK) {
model = importer.parseMrBayesBlock(options, charSets);
} else if (block == NexusApplicationImporter.ASSUMPTIONS_BLOCK) {
importer.parseAssumptionsBlock(charSets, null);
} else {
// Ignore the block..
}
} catch (EOFException ex) {
done = true;
}
}
// Allow the user to load taxa only (perhaps from a tree file) so that they can sample from a prior...
if (alignment == null && taxa == null) {
throw new NexusImporter.MissingBlockException("TAXON, DATA or CHARACTERS block is missing");
}
} catch (FileNotFoundException fnfe) {
System.err.println("File not found: " + fnfe);
System.exit(1);
} catch (Importer.ImportException ime) {
System.err.println("Error parsing imported file: " + ime);
System.exit(1);
} catch (IOException ioex) {
System.err.println("File I/O Error: " + ioex);
System.exit(1);
} catch (Exception ex) {
System.err.println("Fatal exception: " + ex);
System.exit(1);
}
if (options.taxonList == null) {
// This is the first partition to be loaded...
options.taxonList = new Taxa(taxa);
// check the taxon names for invalid characters
boolean foundAmp = false;
for (int i = 0; i < taxa.getTaxonCount(); i++) {
String name = taxa.getTaxon(i).getId();
if (name.indexOf('&') >= 0) {
foundAmp = true;
}
}
if (foundAmp) {
System.err.println("One or more taxon names include an illegal character ('&').");
return;
}
// make sure they all have dates...
for (int i = 0; i < taxa.getTaxonCount(); i++) {
if (taxa.getTaxonAttribute(i, "date") == null) {
java.util.Date origin = new java.util.Date(0);
dr.evolution.util.Date date = dr.evolution.util.Date.createTimeSinceOrigin(0.0, Units.Type.YEARS, origin);
taxa.getTaxon(i).setAttribute("date", date);
}
}
} else {
// This is an additional partition so check it uses the same taxa
java.util.List<String> oldTaxa = new ArrayList<String>();
for (int i = 0; i < options.taxonList.getTaxonCount(); i++) {
oldTaxa.add(options.taxonList.getTaxon(i).getId());
}
java.util.List<String> newTaxa = new ArrayList<String>();
for (int i = 0; i < taxa.getTaxonCount(); i++) {
newTaxa.add(taxa.getTaxon(i).getId());
}
if (!(oldTaxa.containsAll(newTaxa) && oldTaxa.size() == newTaxa.size())) {
System.err.println("This file contains different taxa from the previously loaded");
return;
}
}
String fileNameStem = dr.app.util.Utils.trimExtensions(fileName, new String[] { "NEX", "NEXUS", "TRE", "TREE" });
if (alignment != null) {
if (translate) {
alignment = new ConvertAlignment(AminoAcids.INSTANCE, GeneticCode.UNIVERSAL, alignment);
}
java.util.List<PartitionData> partitions = new ArrayList<PartitionData>();
if (charSets != null && charSets.size() > 0) {
for (CharSet charSet : charSets) {
partitions.add(new PartitionData(options, charSet.getName(), fileName, new CharSetAlignment(charSet, alignment)));
}
} else {
partitions.add(new PartitionData(options, fileNameStem, fileName, alignment));
}
for (PartitionData partition : partitions) {
if (model != null) {
partition.setPartitionSubstitutionModel(model);
// options.addPartitionSubstitutionModel(model);
} else {
for (PartitionSubstitutionModel pm : options.getPartitionSubstitutionModels()) {
if (pm.getDataType() == alignment.getDataType()) {
partition.setPartitionSubstitutionModel(pm);
}
}
if (partition.getPartitionSubstitutionModel() == null) {
PartitionSubstitutionModel pm = new PartitionSubstitutionModel(options, "default", partition);
partition.setPartitionSubstitutionModel(pm);
// options.addPartitionSubstitutionModel(pm);
}
}
options.dataPartitions.add(partition);
}
}
calculateHeights(options);
}
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