python-biopython 1.58-1 / usr / share / pyshared / Bio / Parsers / spark.py

#  Copyright (c) 1998-2000 John Aycock
#  
#  Permission is hereby granted, free of charge, to any person obtaining
#  a copy of this software and associated documentation files (the
#  "Software"), to deal in the Software without restriction, including
#  without limitation the rights to use, copy, modify, merge, publish,
#  distribute, sublicense, and/or sell copies of the Software, and to
#  permit persons to whom the Software is furnished to do so, subject to
#  the following conditions:
#  
#  The above copyright notice and this permission notice shall be
#  included in all copies or substantial portions of the Software.
#  
#  THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
#  EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
#  MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.
#  IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY
#  CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT,
#  TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE
#  SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

"""Copy of John Aycock's SPARK parser included with Biopython (DEPRECATED).

To clarify, when we say deprecated we just mean to warn you that Biopython will
in a future release no longer include this module. This does not affect the
status of John Aycock's SPARK parser which can be installed separately from:
http://pages.cpsc.ucalgary.ca/~aycock/spark/

Biopython included this copy of SPARK purely for parsing GenBank/EMBL feature
location strings using Bio.GenBank.LocationParser, and that code has now been
replaced with something simpler and faster using regular expressions.
"""
# Don't issue a deprecation warning here, but via Bio.Parsers instead
# This avoids the user seeing multiple deprecation warnings.

__version__ = 'SPARK-0.6.1'

import re
import sys

def _namelist(instance):
    namelist, namedict, classlist = [], {}, [instance.__class__]
    for c in classlist:
        for b in c.__bases__:
            classlist.append(b)
        for name in dir(c):
            if name not in namedict:
                namelist.append(name)
                namedict[name] = 1
    return namelist

class GenericScanner(object):
    def __init__(self):
        pattern = self.reflect()
        self.re = re.compile(pattern, re.VERBOSE)

        self.index2func = {}
        for name, number in self.re.groupindex.items():
            self.index2func[number-1] = getattr(self, 't_' + name)

    def makeRE(self, name):
        doc = getattr(self, name).__doc__
        rv = '(?P<%s>%s)' % (name[2:], doc)
        return rv

    def reflect(self):
        rv = []
        for name in _namelist(self):
            if name[:2] == 't_' and name != 't_default':
                rv.append(self.makeRE(name))

        rv.append(self.makeRE('t_default'))
        return '|'.join(rv)

    def error(self, s, pos):
        print >>sys.stderr, "Lexical error at position %s" % pos
        raise SystemExit

    def tokenize(self, s):
        pos = 0
        n = len(s)
        while pos < n:
            m = self.re.match(s, pos)
            if m is None:
                self.error(s, pos)

            groups = m.groups()
            for i in range(len(groups)):
                if groups[i] and i in self.index2func:
                    self.index2func[i](groups[i])
            pos = m.end()

    def t_default(self, s):
        r'( . | \n )+'
        pass

class GenericParser(object):
    def __init__(self, start):
        self.rules = {}
        self.rule2func = {}
        self.rule2name = {}
        self.collectRules()
        self.startRule = self.augment(start)
        self.ruleschanged = 1

    _START = 'START'
    _EOF = 'EOF'

    #
    #  A hook for GenericASTBuilder and GenericASTMatcher.
    #
    def preprocess(self, rule, func):   return rule, func

    def addRule(self, doc, func):
        rules = doc.split()

        index = []
        for i in range(len(rules)):
            if rules[i] == '::=':
                index.append(i-1)
        index.append(len(rules))

        for i in range(len(index)-1):
            lhs = rules[index[i]]
            rhs = rules[index[i]+2:index[i+1]]
            rule = (lhs, tuple(rhs))

            rule, fn = self.preprocess(rule, func)

            if lhs in self.rules:
                self.rules[lhs].append(rule)
            else:
                self.rules[lhs] = [ rule ]
            self.rule2func[rule] = fn
            self.rule2name[rule] = func.__name__[2:]
        self.ruleschanged = 1

    def collectRules(self):
        for name in _namelist(self):
            if name[:2] == 'p_':
                func = getattr(self, name)
                doc = func.__doc__
                self.addRule(doc, func)

    def augment(self, start):
        #
        #  Tempting though it is, this isn't made into a call
        #  to self.addRule() because the start rule shouldn't
        #  be subject to preprocessing.
        #
        startRule = (self._START, ( start, self._EOF ))
        self.rule2func[startRule] = lambda args: args[0]
        self.rules[self._START] = [ startRule ]
        self.rule2name[startRule] = ''
        return startRule

    def makeFIRST(self):
        union = {}
        self.first = {}
        
        for rulelist in self.rules.values():
            for lhs, rhs in rulelist:
                if lhs not in self.first:
                    self.first[lhs] = {}

                if len(rhs) == 0:
                    self.first[lhs][None] = 1
                    continue

                sym = rhs[0]
                if sym not in self.rules:
                    self.first[lhs][sym] = 1
                else:
                    union[(sym, lhs)] = 1
        changes = 1
        while changes:
            changes = 0
            for src, dest in union.keys():
                destlen = len(self.first[dest])
                self.first[dest].update(self.first[src])
                if len(self.first[dest]) != destlen:
                    changes = 1

    #
    #  An Earley parser, as per J. Earley, "An Efficient Context-Free
    #  Parsing Algorithm", CACM 13(2), pp. 94-102.  Also J. C. Earley,
    #  "An Efficient Context-Free Parsing Algorithm", Ph.D. thesis,
    #  Carnegie-Mellon University, August 1968, p. 27.
    #
    
    def typestring(self, token):
        return None

    def error(self, token):
        print >>sys.stderr, "Syntax error at or near `%s' token" % token
        raise SystemExit

    def parse(self, tokens):
        tree = {}
        tokens.append(self._EOF)
        states = { 0: [ (self.startRule, 0, 0) ] }
        
        if self.ruleschanged:
            self.makeFIRST()

        for i in xrange(len(tokens)):
            states[i+1] = []

            if states[i] == []:
                break               
            self.buildState(tokens[i], states, i, tree)

        #_dump(tokens, states)

        if i < len(tokens)-1 or states[i+1] != [(self.startRule, 2, 0)]:
            del tokens[-1]
            self.error(tokens[i-1])
        rv = self.buildTree(tokens, tree, ((self.startRule, 2, 0), i+1))
        del tokens[-1]
        return rv

    def buildState(self, token, states, i, tree):
        needsCompletion = {}
        state = states[i]
        predicted = {}
        
        for item in state:
            rule, pos, parent = item
            lhs, rhs = rule

            #
            #  A -> a . (completer)
            #
            if pos == len(rhs):
                if len(rhs) == 0:
                    needsCompletion[lhs] = (item, i)

                for pitem in states[parent]:
                    if pitem is item:
                        break

                    prule, ppos, pparent = pitem
                    plhs, prhs = prule

                    if prhs[ppos:ppos+1] == (lhs,):
                        new = (prule,
                               ppos+1,
                               pparent)
                        if new not in state:
                            state.append(new)
                            tree[(new, i)] = [(item, i)]
                        else:
                            tree[(new, i)].append((item, i))
                continue

            nextSym = rhs[pos]

            #
            #  A -> a . B (predictor)
            #
            if nextSym in self.rules:
                #
                #  Work on completer step some more; for rules
                #  with empty RHS, the "parent state" is the
                #  current state we're adding Earley items to,
                #  so the Earley items the completer step needs
                #  may not all be present when it runs.
                #
                if nextSym in needsCompletion:
                    new = (rule, pos+1, parent)
                    olditem_i = needsCompletion[nextSym]
                    if new not in state:
                        state.append(new)
                        tree[(new, i)] = [olditem_i]
                    else:
                        tree[(new, i)].append(olditem_i)

                #
                #  Has this been predicted already?
                #
                if nextSym in predicted:
                    continue
                predicted[nextSym] = 1

                ttype = token is not self._EOF and \
                    self.typestring(token) or \
                    None
                if ttype is not None:
                    #
                    #  Even smarter predictor, when the
                    #  token's type is known.  The code is
                    #  grungy, but runs pretty fast.  Three
                    #  cases are looked for: rules with
                    #  empty RHS; first symbol on RHS is a
                    #  terminal; first symbol on RHS is a
                    #  nonterminal (and isn't nullable).
                    #
                    for prule in self.rules[nextSym]:
                        new = (prule, 0, i)
                        prhs = prule[1]
                        if len(prhs) == 0:
                            state.append(new)
                            continue
                        prhs0 = prhs[0]
                        if prhs0 not in self.rules:
                            if prhs0 != ttype:
                                continue
                            else:
                                state.append(new)
                                continue
                        first = self.first[prhs0]
                        if None not in first and \
                           ttype not in first:
                            continue
                        state.append(new)
                    continue

                for prule in self.rules[nextSym]:
                    #
                    #  Smarter predictor, as per Grune &
                    #  Jacobs' _Parsing Techniques_.  Not
                    #  as good as FIRST sets though.
                    #
                    prhs = prule[1]
                    if len(prhs) > 0 and \
                       prhs[0] not in self.rules and \
                       token != prhs[0]:
                        continue
                    state.append((prule, 0, i))

            #
            #  A -> a . c (scanner)
            #
            elif token == nextSym:
                #assert new not in states[i+1]
                states[i+1].append((rule, pos+1, parent))

    def buildTree(self, tokens, tree, root):
        stack = []
        self.buildTree_r(stack, tokens, -1, tree, root)
        return stack[0]

    def buildTree_r(self, stack, tokens, tokpos, tree, root):
        (rule, pos, parent), state = root
        
        while pos > 0:
            want = ((rule, pos, parent), state)
            if want not in tree:
                #
                #  Since pos > 0, it didn't come from closure,
                #  and if it isn't in tree[], then there must
                #  be a terminal symbol to the left of the dot.
                #  (It must be from a "scanner" step.)
                #
                pos = pos - 1
                state = state - 1
                stack.insert(0, tokens[tokpos])
                tokpos = tokpos - 1
            else:
                #
                #  There's a NT to the left of the dot.
                #  Follow the tree pointer recursively (>1
                #  tree pointers from it indicates ambiguity).
                #  Since the item must have come about from a
                #  "completer" step, the state where the item
                #  came from must be the parent state of the
                #  item the tree pointer points to.
                #
                children = tree[want]
                if len(children) > 1:
                    child = self.ambiguity(children)
                else:
                    child = children[0]
                
                tokpos = self.buildTree_r(stack,
                              tokens, tokpos,
                              tree, child)
                pos = pos - 1
                (crule, cpos, cparent), cstate = child
                state = cparent
                
        lhs, rhs = rule
        result = self.rule2func[rule](stack[:len(rhs)])
        stack[:len(rhs)] = [result]
        return tokpos

    def ambiguity(self, children):
        #
        #  XXX - problem here and in collectRules() if the same
        #    rule appears in >1 method.  But in that case the
        #    user probably gets what they deserve :-)  Also
        #    undefined results if rules causing the ambiguity
        #    appear in the same method.
        #
        sortlist = []
        name2index = {}
        for i in range(len(children)):
            ((rule, pos, parent), index) = children[i]
            lhs, rhs = rule
            name = self.rule2name[rule]
            sortlist.append((len(rhs), name))
            name2index[name] = i
        sortlist.sort()
        list = map(lambda (a,b): b, sortlist)
        return children[name2index[self.resolve(list)]]

    def resolve(self, list):
        #
        #  Resolve ambiguity in favor of the shortest RHS.
        #  Since we walk the tree from the top down, this
        #  should effectively resolve in favor of a "shift".
        #
        return list[0]

#
#  GenericASTBuilder automagically constructs a concrete/abstract syntax tree
#  for a given input.  The extra argument is a class (not an instance!)
#  which supports the "__setslice__" and "__len__" methods.
#
#  XXX - silently overrides any user code in methods.
#

class GenericASTBuilder(GenericParser):
    def __init__(self, AST, start):
        GenericParser.__init__(self, start)
        self.AST = AST

    def preprocess(self, rule, func):
        rebind = lambda lhs, self=self: \
                lambda args, lhs=lhs, self=self: \
                    self.buildASTNode(args, lhs)
        lhs, rhs = rule
        return rule, rebind(lhs)

    def buildASTNode(self, args, lhs):
        children = []
        for arg in args:
            if isinstance(arg, self.AST):
                children.append(arg)
            else:
                children.append(self.terminal(arg))
        return self.nonterminal(lhs, children)

    def terminal(self, token):  return token

    def nonterminal(self, type, args):
        rv = self.AST(type)
        rv[:len(args)] = args
        return rv

#
#  GenericASTTraversal is a Visitor pattern according to Design Patterns.  For
#  each node it attempts to invoke the method n_<node type>, falling
#  back onto the default() method if the n_* can't be found.  The preorder
#  traversal also looks for an exit hook named n_<node type>_exit (no default
#  routine is called if it's not found).  To prematurely halt traversal
#  of a subtree, call the prune() method -- this only makes sense for a
#  preorder traversal.  Node type is determined via the typestring() method.
#

class GenericASTTraversalPruningException(object):
    pass

class GenericASTTraversal(object):
    def __init__(self, ast):
        self.ast = ast

    def typestring(self, node):
        return node.type

    def prune(self):
        raise GenericASTTraversalPruningException

    def preorder(self, node=None):
        if node is None:
            node = self.ast

        try:
            name = 'n_' + self.typestring(node)
            if hasattr(self, name):
                func = getattr(self, name)
                func(node)
            else:
                self.default(node)
        except GenericASTTraversalPruningException:
            return

        for kid in node:
            self.preorder(kid)

        name = name + '_exit'
        if hasattr(self, name):
            func = getattr(self, name)
            func(node)

    def postorder(self, node=None):
        if node is None:
            node = self.ast

        for kid in node:
            self.postorder(kid)

        name = 'n_' + self.typestring(node)
        if hasattr(self, name):
            func = getattr(self, name)
            func(node)
        else:
            self.default(node)


    def default(self, node):
        pass

#
#  GenericASTMatcher.  AST nodes must have "__getitem__" and "__cmp__"
#  implemented.
#
#  XXX - makes assumptions about how GenericParser walks the parse tree.
#

class GenericASTMatcher(GenericParser):
    def __init__(self, start, ast):
        GenericParser.__init__(self, start)
        self.ast = ast

    def preprocess(self, rule, func):
        rebind = lambda func, self=self: \
                lambda args, func=func, self=self: \
                    self.foundMatch(args, func)
        lhs, rhs = rule
        rhslist = list(rhs)
        rhslist.reverse()

        return (lhs, tuple(rhslist)), rebind(func)

    def foundMatch(self, args, func):
        func(args[-1])
        return args[-1]

    def match_r(self, node):
        self.input.insert(0, node)
        children = 0

        for child in node:
            if children == 0:
                self.input.insert(0, '(')
            children = children + 1
            self.match_r(child)

        if children > 0:
            self.input.insert(0, ')')

    def match(self, ast=None):
        if ast is None:
            ast = self.ast
        self.input = []

        self.match_r(ast)
        self.parse(self.input)

    def resolve(self, list):
        #
        #  Resolve ambiguity in favor of the longest RHS.
        #
        return list[-1]

def _dump(tokens, states):
    for i in range(len(states)):
        print 'state', i
        for (lhs, rhs), pos, parent in states[i]:
            print '\t', lhs, '::=',
            print ' '.join(rhs[:pos]),
            print '.',
            print ' '.join(rhs[pos:]),
            print ',', parent
        if i < len(tokens):
            print
            print 'token', str(tokens[i])
            print