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

Constructor Detail

NewickStringReader

public NewickStringReader()

Method Detail

searchSubtreeEnd

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

searchToken

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

readBranch

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

Throws:

NewickException

readBranchList

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

Throws:

NewickException

readName

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

Throws:

NewickException

readInternal

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

Throws:

NewickException

readLeaf

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

Throws:

NewickException

readSubtree

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

Throws:

NewickException

readTree

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

Throws:

NewickException

read

public static Tree read(java.lang.String newick)
                 throws NewickException

Throws:

NewickException

read

public static Tree read(java.lang.String newick,
                        NodeDataAdapter internalAdapter)
                 throws NewickException

Throws:

NewickException

read

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

Throws:

NewickException