本文整理汇总了Java中pal.tree.TreeTool类的典型用法代码示例。如果您正苦于以下问题：Java TreeTool类的具体用法？Java TreeTool怎么用？Java TreeTool使用的例子？那么, 这里精选的类代码示例或许可以为您提供帮助。
TreeTool类属于pal.tree包，在下文中一共展示了TreeTool类的3个代码示例，这些例子默认根据受欢迎程度排序。您可以为喜欢或者感觉有用的代码点赞，您的评价将有助于系统推荐出更棒的Java代码示例。
示例1: reroot
import pal.tree.TreeTool; //导入依赖的package包/类
public void reroot(String filename, String outfile) throws Exception {
// Reroot the tree on "seq_1" - the first sequence in the original FASTA file must be the outgroup
// We need to set this so that ancestral reconstruction is done correctly in PAML
Tree tree = TreeTool.readTree(new FileReader(filename));
Tree rerootedTree = TreeManipulator.getRootedBy(tree, new String[]{Constants.OUTGROUP_SEQUENCE_NAME});
PrintWriter pw = new PrintWriter(new FileWriter(outfile));
TreeUtils.printNH(rerootedTree, pw);
pw.close();
}
示例2: getTrees
import pal.tree.TreeTool; //导入依赖的package包/类
private Tree[] getTrees(String file) throws Exception {
Tree[] trees = new Tree[2];
BufferedReader reader = Files.newReader(new File(file), Charsets.US_ASCII);
while (!reader.readLine().startsWith("Ancestral reconstruction by")) { /* empty */ }
String line;
// skip all lines until we read the first tree
while (!(line = reader.readLine()).startsWith("(")) { /* empty */ }
// this is the true tree - use this to get the true branch lengths
trees[0] = TreeTool.readTree(new StringReader(line));
// skip all lines until we have read two more trees
for (int i = 0; i < 2; i++) while (!(line = reader.readLine()).startsWith("(")) { /* empty */ }
// this third tree is tree with the branches labeled - use this to get node/branch names
trees[1] = TreeTool.readTree(new StringReader(line));
reader.close();
return trees;
}
示例3: getTrees_RAxML
import pal.tree.TreeTool; //导入依赖的package包/类
private Tree[] getTrees_RAxML(String file1, String file2) throws Exception {
Tree[] trees = new Tree[2];
// 1. Read original ROOTED RAxML tree
// This is the true tree - use this to get the true branch lengths
BufferedReader reader = Files.newReader(new File(file1), Charsets.US_ASCII);
String line = reader.readLine();
trees[0] = TreeTool.readTree(new StringReader(line));
reader.close();
// 2. Read node-labelled RAxML tree
// This is the tree with the nodes labeled - use this to get ancestral node names
reader = Files.newReader(new File(file2), Charsets.US_ASCII);
line = reader.readLine();
trees[1] = TreeTool.readTree(new StringReader(line));
reader.close();
return trees;
}