Created
November 6, 2012 20:44
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Newick Parser, much simplified, with printer
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package dk.linnk | |
import scala.util.parsing.combinator._ | |
sealed abstract class Tree | |
case class Node(edges: List[Edge], name: Option[String]) extends Tree | |
case class Leaf(name: Option[String]) extends Tree | |
case class Edge(to: Tree, weight: Option[Double]) extends Tree | |
trait Newick { | |
val OPEN_PAREN = "(" | |
val CLOSE_PAREN = ")" | |
val SEMICOLON = ";" | |
val COLON = ":" | |
val COMMA = "," | |
} | |
object newickParser extends RegexParsers with Newick { | |
private[this] def number: Parser[Double] = """\d+(\.\d*)?""".r ^^ { _.toDouble } | |
private[this] def string: Parser[String] = """[a-zA-Z0-9#!?=&%$@_|.- ]+""".r ^^ { _.toString } | |
private[this] def name: Parser[Option[String]] = string.? | |
private[this] def length: Parser[Option[Double]] = (COLON ~> number).? | |
private[this] def edges: Parser[List[Edge]] = repsep(edge, COMMA) | |
private[this] def node: Parser[Node] = (OPEN_PAREN ~> edges <~ CLOSE_PAREN) ~ name ^^ { | |
case edges ~ name => Node(edges, name) | |
} | |
private[this] def leaf: Parser[Leaf] = name ^^ { | |
case name => Leaf(name) | |
} | |
private[this] def edge: Parser[Edge] = subtree ~ length ^^ { | |
case subtree ~ length => Edge(subtree, length) | |
} | |
private[this] def subtree: Parser[Tree] = node | leaf | |
private[this] def tree: Parser[Tree] = (subtree | edge) <~ SEMICOLON | |
def apply(src: String): Tree = parseAll(tree, src) match { | |
case Success(result, _) => result | |
case failure: NoSuccess => throw new Exception(failure.msg) | |
} | |
} | |
object newickPrinter extends Newick { | |
private[this] def printName(name: Option[String]): String = name.getOrElse("") | |
private[this] def printWeight(weight: Option[Double]): String = weight match { | |
case None => "" | |
case Some(w) => COLON + w | |
} | |
private[this] def printTree(e: Tree): String = e match { | |
case Node(edges, name) => | |
OPEN_PAREN + | |
edges.map(printTree).reduceLeft((acc, t) => acc + COMMA + t) + | |
CLOSE_PAREN + | |
printName(name) | |
case Leaf(name) => | |
printName(name) | |
case Edge(to, weight) => | |
printTree(to) //+ printWeight(weight) | |
} | |
def apply(tree: Tree): String = printTree(tree) + SEMICOLON | |
} |
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