NewickStringReader

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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
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`
`private NodeBranchDataAdapter`	`branchLengthsAdapter`
`private CommentDataReader`	`commentDataReader`
`private boolean`	`hiddenDataAdded`
`private NodeBranchDataAdapter`	`internalAdapter`
`static NodeNameAdapter`	`LEAF_ADAPTER`
`private String`	`newickDescription`
`private static NewickStringReader`	`sharedInstance`
`private List<NewickToken>`	`tokens`
`private boolean`	`translateInternals`
`private TranslTable`	`translTable`

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
`boolean`	`getHiddenDataAdded()` Returns whether hidden data has been read from commetns in the newick string (e.g. from BEAST) during the last call of `read(String, NodeBranchDataAdapter, NodeBranchDataAdapter, TranslTable, boolean)` or one of its convenience methods.
`static NewickStringReader`	`getSharedInstance()`
`Tree`	`read(String newick)`
`static Tree[]`	`read(String[] newick, NodeBranchDataAdapter internalAdapter, NodeBranchDataAdapter branchLengthsAdapter, TranslTable translTable, boolean translateInternals)`
`Tree`	`read(String newick, NodeBranchDataAdapter internalAdapter, NodeBranchDataAdapter branchLengthsAdapter)`
`Tree`	`read(String newick, NodeBranchDataAdapter internalAdapter, NodeBranchDataAdapter branchLengthsAdapter, TranslTable translTable, boolean translateInternals)`
`private Node`	`readBranch(int start, int end, Node root)`
`private void`	`readBranchList(int start, int end, Node root)`
`private Node`	`readInternal(int start, int end)`
`private Node`	`readLeaf(int start, int end)`
`private void`	`readName(int previousEnd, int end, Node root, NodeBranchDataAdapter adapter, TranslTable translTable)`
`private Node`	`readSubtree(int start, int end)`
`private Tree`	`readTree()`
`private int`	`searchSubtreeEnd(int start, int end)`
`private int`	`searchToken(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

sharedInstance

private static NewickStringReader sharedInstance

newickDescription

private String newickDescription

tokens

private List<NewickToken> tokens

internalAdapter

private NodeBranchDataAdapter internalAdapter

branchLengthsAdapter

private NodeBranchDataAdapter branchLengthsAdapter

translTable

private TranslTable translTable

translateInternals

private boolean translateInternals

hiddenDataAdded

private boolean hiddenDataAdded

commentDataReader

private CommentDataReader commentDataReader

Constructor Detail