Adding suffix tree

pydatastructs/strings/__init__.py

@@ -6,3 +6,10 @@
 )
 
 __all__.extend(trie.__all__)
+
+from . import suffix_tree
+from .suffix_tree import(
+    SuffixTree
+)
+
+__all__.extend(suffix_tree.__all__)

pydatastructs/strings/suffix_tree.py

@@ -0,0 +1,316 @@
+from pydatastructs.utils.misc_util import SuffixNode
+
+__all__ = [
+    'SuffixTree'
+]
+
+class SuffixTree(object):
+    """
+    Represents Suffix Tree.
+
+    Examples
+    ========
+
+    >>> from pydatastructs.strings import SuffixTree as suffix
+    >>> s = suffix('hello')
+    >>> s.find('he')
+    0
+    >>> s.find_all('l')
+    {2, 3}
+    >>> s.find('f')
+    -1
+    >>> lt=["abeceda", "abecednik", "abeabecedabeabeced", "abecedaaaa", "aaabbbeeecceeeddaaaaabeceda"]
+    >>> s1 = suffix(lt)
+    >>> s1.longest_common_substring()
+    'abeced'
+
+    References
+    ==========
+
+    .. [1] https://en.wikipedia.org/wiki/Suffix_tree
+    .. [2] https://en.wikipedia.org/wiki/Generalized_suffix_tree
+    """
+
+    def __new__(cls, input=''):
+        obj = object.__new__(cls)
+        obj.root = SuffixNode()
+        obj.root.depth = 0
+        obj.root.idx = 0
+        obj.root.parent = obj.root
+        obj.root._add_suffix_link(obj.root)
+        if not input == '':
+            obj.build(input)
+        return obj
+
+    @classmethod
+    def methods(cls):
+        return ['__new__', 'lcs', 'find', 'find_all']
+
+    def _check_input(self, input):
+        """
+        Check if the input is str ot list of str.
+        """
+        if isinstance(input, str):
+            return 'str'
+        elif isinstance(input, list):
+            if all(isinstance(item, str) for item in input):
+                return 'list'
+        raise ValueError("String argument should be of type String or a list of strings")
+
+    def build(self, x):
+        """
+        Builds the Suffix tree on the given input.
+
+        Parameters
+        ==========
+
+        x: str or list of str
+
+        Returns
+        =======
+
+        None
+        """
+        type = self._check_input(x)
+        if type == 'str':
+            x += next(self._terminal_symbols_generator())
+            self._build(x)
+        if type == 'list':
+            self._build_generalized(x)
+
+    def _build(self, x):
+        """
+        Builds suffix tree with string.
+        """
+        self.word = x
+        self._build_McCreight(x)
+
+    def _build_McCreight(self, x):
+        u = self.root
+        d = 0
+        for i in range(len(x)):
+            while u.depth == d and u._has_transition(x[d + i]):
+                u = u._get_transition_link(x[d + i])
+                d = d + 1
+                while d < u.depth and x[u.idx + d] == x[i + d]:
+                    d = d + 1
+            if d < u.depth:
+                u = self._create_node(x, u, d)
+            self._create_leaf(x, i, u, d)
+            if not u._get_suffix_link():
+                self._compute_slink(x, u)
+            u = u._get_suffix_link()
+            d = d - 1
+            if d < 0:
+                d = 0
+
+    def _create_node(self, x, u, d):
+        """
+        Creates node for the suffix tree
+        with transition links.
+        """
+        i = u.idx
+        p = u.parent
+        v = SuffixNode(idx=i, depth=d)
+        v._add_transition_link(u, x[i + d])
+        u.parent = v
+        p._add_transition_link(v, x[i + p.depth])
+        v.parent = p
+        return v
+
+    def _create_leaf(self, x, i, u, d):
+        """
+        Creates the leaf node for the
+        suffix tree.
+        """
+        w = SuffixNode()
+        w.idx = i
+        w.depth = len(x) - i
+        u._add_transition_link(w, x[i + d])
+        w.parent = u
+        return w
+
+    def _compute_slink(self, x, u):
+        d = u.depth
+        v = u.parent._get_suffix_link()
+        while v.depth < d - 1:
+            v = v._get_transition_link(x[u.idx + v.depth + 1])
+        if v.depth > d - 1:
+            v = self._create_node(x, v, d - 1)
+        u._add_suffix_link(v)
+
+    def _build_generalized(self, xs):
+        """
+        Builds the generalized suffix tree with list
+        of string.
+        """
+        terminal_gen = self._terminal_symbols_generator()
+        _xs = ''.join([x + next(terminal_gen) for x in xs])
+        self.word = _xs
+        self._generalized_word_starts(xs)
+        self._build(_xs)
+        self.root._traverse(self._label_generalized)
+
+    def _label_generalized(self, node):
+        """
+        Helper method that labels the nodes of GST with
+        indexes of strings found in their descendants.
+        """
+        if node.is_leaf():
+            x = {self._get_word_start_index(node.idx)}
+        else:
+            x = {n for ns in node.transition_links.values() for n in ns.generalized_idxs}
+        node.generalized_idxs = x
+
+    def _get_word_start_index(self, idx):
+        """
+        Helper method that returns the index of the
+        string based on node's starting index.
+        """
+        i = 0
+        for _idx in self.word_starts[1:]:
+            if idx < _idx:
+                return i
+            else:
+                i += 1
+        return i
+
+    def longest_common_substring(self, stringIdxs = -1):
+        """
+        Finds the Largest Common Substring of Strings provided in stringIdxs.
+        If stringIdxs is not provided, the LCS of all strings is returned.
+
+        Parameters
+        ==========
+
+        stringIdxs: int or list of int
+
+        Returns
+        =======
+
+        Longest Common Substring
+        """
+        if stringIdxs == -1 or not isinstance(stringIdxs, list):
+            stringIdxs = set(range(len(self.word_starts)))
+        else:
+            stringIdxs = set(stringIdxs)
+        deepestNode = self._find_lcs(self.root, stringIdxs)
+        start = deepestNode.idx
+        end = deepestNode.idx + deepestNode.depth
+        return self.word[start:end]
+
+    def _find_lcs(self, node, stringIdxs):
+        """
+        Helper method for longest common substring
+        of the labelled Generalized suffix tree.
+        """
+        nodes = [self._find_lcs(n, stringIdxs)
+                 for n in node.transition_links.values()
+                 if n.generalized_idxs.issuperset(stringIdxs)]
+        if nodes == []:
+            return node
+        deepestNode = max(nodes, key=lambda n: n.depth)
+        return deepestNode
+
+    def _generalized_word_starts(self, xs):
+        """
+        Helper method fidning the starting indexes
+        of strings in Generalized suffix tree.
+        """
+        self.word_starts = []
+        i = 0
+        for n in range(len(xs)):
+            self.word_starts.append(i)
+            i += len(xs[n]) + 1
+
+    def find(self, y):
+        """
+        Finds the starting position of the substring y in the string used for
+        building the Suffix tree.
+
+        Parameters
+        ==========
+
+        y: str
+
+        Returns
+        =======
+
+        Index of the starting position of string y in the string used for building the Suffix tree
+        -1 if y is not a substring.
+        """
+        node = self.root
+        while True:
+            edge = self._edge_label(node, node.parent)
+            if edge.startswith(y):
+                return node.idx
+
+            i = 0
+            while (i < len(edge) and edge[i] == y[0]):
+                y = y[1:]
+                i += 1
+
+            if i != 0:
+                if i == len(edge) and y != '':
+                    pass
+                else:
+                    return -1
+
+            node = node._get_transition_link(y[0])
+            if not node:
+                return -1
+
+    def find_all(self, y):
+        """
+        Finds the starting position of the substring y in the string used for
+        building the Suffix tree.
+
+        Parameters
+        ==========
+
+        y: str
+
+        Returns
+        =======
+
+        Set of Index of the starting positions of string y in the string used for building the Suffix tree
+        {} if y is not a substring.
+        """
+        node = self.root
+        while True:
+            edge = self._edge_label(node, node.parent)
+            if edge.startswith(y):
+                break
+            i = 0
+            while (i < len(edge) and edge[i] == y[0]):
+                y = y[1:]
+                i += 1
+            if i != 0:
+                if i == len(edge) and y != '':
+                    pass
+                else:
+                    return {}
+            node = node._get_transition_link(y[0])
+            if not node:
+                return {}
+
+        leaves = node._get_leaves()
+        return {n.idx for n in leaves}
+
+    def _edge_label(self, node, parent):
+        """
+        Helper method returns the edge label
+        between a node and it's parent.
+        """
+        return self.word[node.idx + parent.depth: node.idx + node.depth]
+
+    def _terminal_symbols_generator(self):
+        """
+        Generator of unique terminal symbols used for building the Generalized Suffix Tree.
+        Unicode Private Use Area is used to ensure that terminal symbols are not part
+        of the input string.
+        """
+        unicode = list(list(range(0xE000, 0xF8FF+1)) + list(range(0xF0000, 0xFFFFD+1)) + list(range(0x100000, 0x10FFFD+1)))
+        for i in unicode:
+            yield (chr(i))
+        raise ValueError("To many input strings.")

pydatastructs/strings/tests/test_suffixtree.py

@@ -0,0 +1,28 @@
+from pydatastructs import SuffixTree
+from pydatastructs.utils.raises_util import raises
+import random, string
+
+def test_suffixtree():
+    """
+    References
+    ==========
+    .. https://www.cise.ufl.edu/~sahni/dsaaj/enrich/c16/suffix.htm
+
+    """
+    s = SuffixTree("HelloworldHe")
+    assert s.find("Hel") == 0
+    assert s.find_all("He") == {0, 10}
+    assert s.find("Win") == -1
+    assert s.find_all("go") == {}
+    assert raises(AttributeError, lambda: s.longest_common_substring())
+
+    f = ['integer', 'inteinteger', 'integralerint', 'iaingerntier', 'regetnerireg', 'reger']
+    s = SuffixTree(f)
+    assert s.longest_common_substring() == 'er'
+    f = ['integer', 'inteinteger', 'integralerint', 'iainegerntier', 'regetnerireg', 'reger']
+    s = SuffixTree(f)
+    assert s.longest_common_substring(7) == 'eg'
+
+    assert raises(ValueError, lambda: SuffixTree(123))
+    res = (100, 1, 0)
+    assert raises(ValueError, lambda: SuffixTree(res))

pydatastructs/utils/__init__.py

@@ -13,6 +13,7 @@
     CartesianTreeNode,
     RedBlackTreeNode,
     TrieNode,
+    SuffixNode,
     SkipNode
 )
 __all__.extend(misc_util.__all__)