Package pal.tree
Class ReadTree
- java.lang.Object
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- pal.tree.SimpleTree
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- pal.tree.ReadTree
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- All Implemented Interfaces:
java.io.Serializable
,IdGroup
,Report
,Units
,UnitsProvider
,Tree
public class ReadTree extends SimpleTree
constructs a tree reading in a New Hampshire treefile, taking care for internal labels and branch lengths and binary/nonbinary and rooted/unrooted trees- Version:
- $Id: ReadTree.java,v 1.10 2002/10/14 06:54:25 matt Exp $
- Author:
- Korbinian Strimmer, Alexei Drummond
- See Also:
- Serialized Form
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Nested Class Summary
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Nested classes/interfaces inherited from interface pal.misc.IdGroup
IdGroup.Utils
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Nested classes/interfaces inherited from interface pal.tree.Tree
Tree.TreeBase
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Field Summary
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Fields inherited from interface pal.misc.Units
DAYS, EXPECTED_SUBSTITUTIONS, GENERATIONS, MONTHS, SAMPLE, SHORT_UNIT_NAMES, UNIT_NAMES, UNKNOWN, YEARS
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Method Summary
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Methods inherited from class pal.tree.SimpleTree
createNodeList, findNode, getAttribute, getCopy, getExternalNode, getExternalNodeCount, getIdCount, getIdentifier, getInternalNode, getInternalNodeCount, getRoot, getUnits, report, reroot, reroot, setAttribute, setIdentifier, setRoot, setUnits, toString, whichIdNumber
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Constructor Detail
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ReadTree
public ReadTree(java.io.PushbackReader input) throws TreeParseException
read tree from input stream- Parameters:
input
- input stream- Throws:
TreeParseException
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ReadTree
public ReadTree(java.lang.String file) throws TreeParseException, java.io.IOException
read tree from file- Parameters:
file
- name of file- Throws:
TreeParseException
java.io.IOException
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