protected void writeTimeTreeFile(PrintStream ps) throws IOException {
FlexibleTree tree = new FlexibleTree(treesPanel.getTreeAsViewed());
Regression r =
treesPanel.getTemporalRooting().getRootToTipRegression(treesPanel.getTreeAsViewed());
for (int i = 0; i < tree.getInternalNodeCount(); i++) {
NodeRef node = tree.getInternalNode(i);
double height = tree.getNodeHeight(node);
tree.setNodeHeight(node, height / r.getGradient());
}
TreeUtils.setHeightsFromDates(tree);
NexusExporter nexusExporter = new NexusExporter(new PrintStream(ps));
nexusExporter.exportTree(tree);
}
protected boolean readFromFile(File file) throws IOException {
Reader reader = new FileReader(file);
BufferedReader bufferedReader = new BufferedReader(reader);
String line = bufferedReader.readLine();
while (line != null && line.length() == 0) {
line = bufferedReader.readLine();
}
boolean isNexus = (line != null && line.toUpperCase().contains("#NEXUS"));
reader = new FileReader(file);
Tree tree = null;
try {
if (isNexus) {
NexusImporter importer = new NexusImporter(reader);
tree = importer.importTree(taxa);
} else {
NewickImporter importer = new NewickImporter(reader);
tree = importer.importTree(taxa);
}
} catch (Importer.ImportException ime) {
JOptionPane.showMessageDialog(
this,
"Error parsing imported file: " + ime,
"Error reading file",
JOptionPane.ERROR_MESSAGE);
ime.printStackTrace();
return false;
} catch (IOException ioex) {
JOptionPane.showMessageDialog(
this, "File I/O Error: " + ioex, "File I/O Error", JOptionPane.ERROR_MESSAGE);
ioex.printStackTrace();
return false;
} catch (Exception ex) {
JOptionPane.showMessageDialog(
this, "Fatal exception: " + ex, "Error reading file", JOptionPane.ERROR_MESSAGE);
ex.printStackTrace();
return false;
}
if (tree == null) {
JOptionPane.showMessageDialog(
this,
"The file is not in a suitable format or contains no trees.",
"Error reading file",
JOptionPane.ERROR_MESSAGE);
return false;
}
FlexibleTree binaryTree = new FlexibleTree(tree, true);
binaryTree.resolveTree();
trees.add(binaryTree);
if (taxa == null) {
taxa = binaryTree;
}
getExportTreeAction().setEnabled(true);
getExportDataAction().setEnabled(true);
return true;
}