info.bioinfweb.treegraph.document.io.newick
Class NewickStringReader

java.lang.Object
  info.bioinfweb.treegraph.document.io.newick.NewickStringChars
      info.bioinfweb.treegraph.document.io.newick.NewickStringReader

public class NewickStringReader
extends NewickStringChars

This class converts a tree in the newick format to a Document. First the string is decomposed into Tokens by a NewickParser and then the developed token list is syntactically analyzed. The following grammar is used:

Tree --> Branch TERMINAL_SYMBOL

Subtree --> Leaf | Internal

Leaf --> Name

Internal --> SUBTREE_START BranchList SUBTREE_END Name

BranchList --> Branch | Branch ELEMENT_SEPERATOR BranchList

Branch --> Subtree Length

Name --> ε | NAME

Length --> ε | LENGTH

Note that this grammar differs from the usual Newick grammar becuase it allows the root node to have a branch length.

Author:

Ben Stöver

Field Summary

static BranchLengthAdapter	BRANCH_LENGTH_ADAPTER
static NodeNameAdapter	LEAF_ADAPTER

Fields inherited from class info.bioinfweb.treegraph.document.io.newick.NewickStringChars

COMMENT_END, COMMENT_START, ELEMENT_SEPERATOR, FREE_NAME_BLANK, LENGTH_SEPERATOR, NAME_DELIMITER, SUBTREE_END, SUBTREE_START, TERMINAL_SYMBOL

Constructor Summary

NewickStringReader()

Method Summary

static Tree	read(String newick)
static Tree	read(String newick, NodeDataAdapter internalAdapter, NodeDataAdapter branchLengthsAdapter)
static Tree	read(String newick, NodeDataAdapter internalAdapter, NodeDataAdapter branchLengthsAdapter, TranslTable translTable, boolean translateInternals)
private static Node	readBranch(Vector<NewickToken> tokens, int start, int end, Node root, NodeDataAdapter internalAdapter, NodeDataAdapter branchLengthAdapter, TranslTable translTable, boolean translateInternals)
private static void	readBranchList(Vector<NewickToken> tokens, int start, int end, Node root, NodeDataAdapter internalAdapter, NodeDataAdapter branchLengthAdapter, TranslTable translTable, boolean translateInternals)
private static Node	readInternal(Vector<NewickToken> tokens, int start, int end, NodeDataAdapter internalAdapter, NodeDataAdapter branchLengthAdapter, TranslTable translTable, boolean translateInternals)
private static Node	readLeaf(Vector<NewickToken> tokens, int start, int end, TranslTable translTable)
private static void	readName(Vector<NewickToken> tokens, int previousEnd, int end, Node root, NodeDataAdapter internalAdapter, TranslTable translTable)
private static Node	readSubtree(Vector<NewickToken> tokens, int start, int end, NodeDataAdapter internalAdapter, NodeDataAdapter branchLengthAdapter, TranslTable translTable, boolean translateInternals)
private static Tree	readTree(Vector<NewickToken> tokens, NodeDataAdapter internalAdapter, NodeDataAdapter branchLengthsAdapter, TranslTable translTable, boolean translateInternals)
private static int	searchSubtreeEnd(Vector<NewickToken> tokens, int start, int end)
private static int	searchToken(Vector<NewickToken> tokens, int start, int end, TokenType type)

Methods inherited from class info.bioinfweb.treegraph.document.io.newick.NewickStringChars

isCharAfterLength, isFreeNameChar, isFreeNameFirstChar

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

LEAF_ADAPTER

public static final NodeNameAdapter LEAF_ADAPTER

BRANCH_LENGTH_ADAPTER

public static final BranchLengthAdapter BRANCH_LENGTH_ADAPTER

Constructor Detail

NewickStringReader

public NewickStringReader()

Method Detail

searchSubtreeEnd

private static int searchSubtreeEnd(Vector<NewickToken> tokens,
                                    int start,
                                    int end)

searchToken

private static int searchToken(Vector<NewickToken> tokens,
                               int start,
                               int end,
                               TokenType type)

readBranch

private static Node readBranch(Vector<NewickToken> tokens,
                               int start,
                               int end,
                               Node root,
                               NodeDataAdapter internalAdapter,
                               NodeDataAdapter branchLengthAdapter,
                               TranslTable translTable,
                               boolean translateInternals)
                        throws NewickException

Throws:

NewickException

readBranchList

private static void readBranchList(Vector<NewickToken> tokens,
                                   int start,
                                   int end,
                                   Node root,
                                   NodeDataAdapter internalAdapter,
                                   NodeDataAdapter branchLengthAdapter,
                                   TranslTable translTable,
                                   boolean translateInternals)
                            throws NewickException

Throws:

NewickException

readName

private static void readName(Vector<NewickToken> tokens,
                             int previousEnd,
                             int end,
                             Node root,
                             NodeDataAdapter internalAdapter,
                             TranslTable translTable)
                      throws NewickException

Throws:

NewickException

readInternal

private static Node readInternal(Vector<NewickToken> tokens,
                                 int start,
                                 int end,
                                 NodeDataAdapter internalAdapter,
                                 NodeDataAdapter branchLengthAdapter,
                                 TranslTable translTable,
                                 boolean translateInternals)
                          throws NewickException

Throws:

NewickException

readLeaf

private static Node readLeaf(Vector<NewickToken> tokens,
                             int start,
                             int end,
                             TranslTable translTable)
                      throws NewickException

Throws:

NewickException

readSubtree

private static Node readSubtree(Vector<NewickToken> tokens,
                                int start,
                                int end,
                                NodeDataAdapter internalAdapter,
                                NodeDataAdapter branchLengthAdapter,
                                TranslTable translTable,
                                boolean translateInternals)
                         throws NewickException

Throws:

NewickException

readTree

private static Tree readTree(Vector<NewickToken> tokens,
                             NodeDataAdapter internalAdapter,
                             NodeDataAdapter branchLengthsAdapter,
                             TranslTable translTable,
                             boolean translateInternals)
                      throws NewickException

Throws:

NewickException

read

public static Tree read(String newick)
                 throws NewickException

Throws:

NewickException

read

public static Tree read(String newick,
                        NodeDataAdapter internalAdapter,
                        NodeDataAdapter branchLengthsAdapter)
                 throws NewickException

Throws:

NewickException

read

public static Tree read(String newick,
                        NodeDataAdapter internalAdapter,
                        NodeDataAdapter branchLengthsAdapter,
                        TranslTable translTable,
                        boolean translateInternals)
                 throws NewickException

Throws:

NewickException