info.bioinfweb.treegraph.document.io.nexus
Class NexusDocument
java.lang.Object
info.bioinfweb.treegraph.document.io.nexus.NexusDocument
public class NexusDocument
- extends Object
Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
translTable
private TranslTable translTable
names
private List<String> names
trees
private List<String> trees
NexusDocument
public NexusDocument()
getTranslTable
public TranslTable getTranslTable()
add
public boolean add(String name,
String tree)
getName
public String getName(int pos)
getTree
public String getTree(int pos)
namesToArray
public String[] namesToArray()
treesToArray
public String[] treesToArray()
size
public int size()
createTrees
public Tree[] createTrees(NodeBranchDataAdapter internalAdapter,
NodeBranchDataAdapter branchLengthsAdapter,
boolean translateInternals)
- Creates a
Tree
object from each stored Newick string.
- Parameters:
internalAdapter
- branchLengthsAdapter
- translateInternals
-
- Returns:
- an array containing all
Tree
-objects