Added Suffix Tree implementation using Ukkonen algorithm

pydatastructs/strings/__init__.py

@@ -1,10 +1,17 @@
 __all__ = []
 
 from . import (
+    suffix_tree,
     trie,
     algorithms
 )
 
+from .suffix_tree import (
+    SuffixTree
+)
+
+__all__.extend(suffix_tree.__all__)
+
 from .trie import (
     Trie
 )

pydatastructs/strings/suffix_tree.py

@@ -0,0 +1,200 @@
+from pydatastructs.utils.misc_util import (
+    Backend, raise_if_backend_is_not_python)
+
+__all__ = [
+    'SuffixTree'
+]
+
+
+# Ukkonen's algorithm gives a O(n) + O(k) contruction time for a suffix tree,
+# where n is the length of the string and k is the size of the alphabet of that string.
+# Ukkonen's is an online algorithm,
+# processing the input sequentially and producing a valid suffix tree at each character.
+
+class SuffixTreeNode(object):
+    def __new__ (cls, *args, **kwargs):
+        instance = super().__new__(cls)
+        return instance
+
+    def __init__(self):
+        self.suffix_node = -1
+
+    def __repr__(self):
+        return "Node(suffix link: %d)" % self.suffix_node
+
+
+class SuffixTreeEdge(object):
+    def __new__ (cls, *args, **kwargs):
+        instance = super().__new__(cls)
+        return instance
+
+    def __init__(self, first_char_index, last_char_index, source_node_index, dest_node_index):
+        self.first_char_index = first_char_index
+        self.last_char_index = last_char_index
+        self.source_node_index = source_node_index
+        self.dest_node_index = dest_node_index
+
+    @property
+    def length(self):
+        return self.last_char_index - self.first_char_index
+
+    def __repr__(self):
+        return 'Edge(%d, %d, %d, %d)' % (self.source_node_index, self.dest_node_index, self.first_char_index, self.last_char_index)
+
+
+class Suffix(object):
+
+    def __new__ (cls, *args, **kwargs):
+        instance = super().__new__(cls)
+        return instance
+
+    def __init__(self, source_node_index, first_char_index, last_char_index):
+        self.source_node_index = source_node_index
+        self.first_char_index = first_char_index
+        self.last_char_index = last_char_index
+
+    @property
+    def length(self):
+        return self.last_char_index - self.first_char_index
+
+    def explicit(self):
+        """A suffix is explicit if it ends on a node. first_char_index
+        is set greater than last_char_index to indicate this.
+        """
+        return self.first_char_index > self.last_char_index
+
+    def implicit(self):
+        return self.last_char_index >= self.first_char_index
+
+
+class SuffixTree(object):
+    """A suffix tree for string matching. Uses Ukkonen's algorithm
+    for construction.
+    """
+    @classmethod
+    def methods(cls):
+        return ['__new__', '__init__', '__repr__', '_add_prefix',
+                '_insert_edge', '_remove_edge', '_split_edge', '_canonize_suffix',
+                'find_substring', 'has_substring']
+
+    def __new__ (cls, *args, **kwargs):
+        instance = super().__new__(cls)
+        return instance
+
+    def __init__(self, string, case_insensitive=False):
+
+        self.string = string
+        self.case_insensitive = case_insensitive
+        self.N = len(string) - 1
+        self.nodes = [SuffixTreeNode()]
+        self.edges = {}
+        self.active = Suffix(0, 0, -1)
+        if self.case_insensitive:
+            self.string = self.string.lower()
+        for i in range(len(string)):
+            self._add_prefix(i)
+
+    def __repr__(self):
+
+        curr_index = self.N
+        s = "\tStart \tEnd \tSuf \tFirst \tLast \tString\n"
+        values = list(self.edges.values())
+        values.sort(key=lambda x: x.source_node_index)
+        for edge in values:
+            if edge.source_node_index == -1:
+                continue
+            s += "\t%s \t%s \t%s \t%s \t%s \t" % (edge.source_node_index, edge.dest_node_index,
+                                                  self.nodes[edge.dest_node_index].suffix_node, edge.first_char_index, edge.last_char_index)
+
+            top = min(curr_index, edge.last_char_index)
+            s += self.string[edge.first_char_index:top + 1] + "\n"
+        return s
+
+    def _add_prefix(self, last_char_index):
+
+        last_parent_node = -1
+        while True:
+            parent_node = self.active.source_node_index
+            if self.active.explicit():
+                if (self.active.source_node_index, self.string[last_char_index]) in self.edges:
+                    # prefix is already in tree
+                    break
+            else:
+                e = self.edges[self.active.source_node_index,
+                               self.string[self.active.first_char_index]]
+                if self.string[e.first_char_index + self.active.length + 1] == self.string[last_char_index]:
+                    # prefix is already in tree
+                    break
+                parent_node = self._split_edge(e, self.active)
+
+            self.nodes.append(SuffixTreeNode())
+            e = SuffixTreeEdge(last_char_index, self.N, parent_node, len(self.nodes) - 1)
+            self._insert_edge(e)
+
+            if last_parent_node > 0:
+                self.nodes[last_parent_node].suffix_node = parent_node
+            last_parent_node = parent_node
+
+            if self.active.source_node_index == 0:
+                self.active.first_char_index += 1
+            else:
+                self.active.source_node_index = self.nodes[self.active.source_node_index].suffix_node
+            self._canonize_suffix(self.active)
+        if last_parent_node > 0:
+            self.nodes[last_parent_node].suffix_node = parent_node
+        self.active.last_char_index += 1
+        self._canonize_suffix(self.active)
+
+    def _insert_edge(self, edge):
+        self.edges[(edge.source_node_index,
+                    self.string[edge.first_char_index])] = edge
+
+    def _remove_edge(self, edge):
+        self.edges.pop(
+            (edge.source_node_index, self.string[edge.first_char_index]))
+
+    def _split_edge(self, edge, suffix):
+        self.nodes.append(SuffixTreeNode())
+        e = SuffixTreeEdge(edge.first_char_index, edge.first_char_index + suffix.length, suffix.source_node_index,
+                 len(self.nodes) - 1)
+        self._remove_edge(edge)
+        self._insert_edge(e)
+        # need to add node for each edge
+        self.nodes[e.dest_node_index].suffix_node = suffix.source_node_index
+        edge.first_char_index += suffix.length + 1
+        edge.source_node_index = e.dest_node_index
+        self._insert_edge(edge)
+        return e.dest_node_index
+
+    def _canonize_suffix(self, suffix):
+
+        if not suffix.explicit():
+            e = self.edges[suffix.source_node_index,
+                           self.string[suffix.first_char_index]]
+            if e.length <= suffix.length:
+                suffix.first_char_index += e.length + 1
+                suffix.source_node_index = e.dest_node_index
+                self._canonize_suffix(suffix)
+
+    # Public methods
+    def find_substring(self, substring):
+
+        if not substring:
+            return -1
+        if self.case_insensitive:
+            substring = substring.lower()
+        curr_node = 0
+        i = 0
+        while i < len(substring):
+            edge = self.edges.get((curr_node, substring[i]))
+            if not edge:
+                return -1
+            ln = min(edge.length + 1, len(substring) - i)
+            if substring[i:i + ln] != self.string[edge.first_char_index:edge.first_char_index + ln]:
+                return -1
+            i += edge.length + 1
+            curr_node = edge.dest_node_index
+        return edge.first_char_index - len(substring) + ln
+
+    def has_substring(self, substring):
+        return self.find_substring(substring) != -1

pydatastructs/strings/tests/test_suffix_tree.py

@@ -0,0 +1,30 @@
+from pydatastructs.strings.suffix_tree import SuffixTree
+
+def test_suffix_tree():
+    """Some functional tests.
+    """
+
+    # test_empty_string(self):
+    st = SuffixTree('')
+    assert (st.find_substring('not there') == -1)
+    assert (st.find_substring('') == -1)
+    assert (st.has_substring('not there') is False)
+    assert (st.has_substring('') is False)
+
+    # test_repeated_string(self):
+    st = SuffixTree("aaa")
+    assert (st.find_substring('a') == 0)
+    assert (st.find_substring('aa') == 0)
+    assert (st.find_substring('aaa') == 0)
+    assert (st.find_substring('b') == -1)
+    assert (st.has_substring('a') is True)
+    assert (st.has_substring('aa') is True)
+    assert (st.has_substring('aaa') is True)
+
+    assert (st.has_substring('aaaa') is False)
+    assert (st.has_substring('b') is False)
+    # case sensitive by default
+    assert (st.has_substring('A') is False)
+
+if __name__ == '__main__':
+    test_suffix_tree()