X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=binaries%2Fsrc%2Fglobplot%2Fbiopython-1.50%2FBio%2Ftriefind.py;fp=binaries%2Fsrc%2Fglobplot%2Fbiopython-1.50%2FBio%2Ftriefind.py;h=da862e527d0be4aedd52a9ee8e4e9a8c8d645e04;hb=119df1cedad3d4760e6fd458713da2488eff79cc;hp=0000000000000000000000000000000000000000;hpb=d3806a66f002b93f6dc03447b6628f943a3ba90c;p=jabaws.git

diff --git a/binaries/src/globplot/biopython-1.50/Bio/triefind.py b/binaries/src/globplot/biopython-1.50/Bio/triefind.py
new file mode 100644
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+++ b/binaries/src/globplot/biopython-1.50/Bio/triefind.py
@@ -0,0 +1,92 @@
+"""
+Given a trie, find all occurrences of a word in the trie in a string.
+
+Like searching a string for a substring, except that the substring is
+any word in a trie.
+
+Functions:
+match         Find longest key in a trie matching the beginning of the string.
+match_all     Find all keys in a trie matching the beginning of the string.
+find          Find keys in a trie matching anywhere in a string.
+find_words    Find keys in a trie matching whole words in a string.
+
+"""
+import string
+import re
+
+def match(string, trie):
+    """match(string, trie) -> longest key or None
+
+    Find the longest key in the trie that matches the beginning of the
+    string.
+
+    """
+    longest = None
+    for i in range(len(string)):
+        substr = string[:i+1]
+        if not trie.has_prefix(substr):
+            break
+        if trie.has_key(substr):
+            longest = substr
+    return longest
+
+def match_all(string, trie):
+    """match_all(string, trie) -> list of keys
+
+    Find all the keys in the trie that matches the beginning of the
+    string.
+
+    """
+    matches = []
+    for i in range(len(string)):
+        substr = string[:i+1]
+        if not trie.has_prefix(substr):
+            break
+        if trie.has_key(substr):
+            matches.append(substr)
+    return matches
+
+def find(string, trie):
+    """find(string, trie) -> list of tuples (key, start, end)
+
+    Find all the keys in the trie that match anywhere in the string.
+
+    """
+    results = []
+    start = 0     # index to start the search
+    while start < len(string):
+        # Look for a match.
+        keys = match_all(string[start:], trie)
+        for key in keys:
+            results.append((key, start, start+len(key)))
+        start += 1
+    return results
+
+DEFAULT_BOUNDARY_CHARS = string.punctuation + string.whitespace
+
+def find_words(string, trie):
+    """find_words(string, trie) -> list of tuples (key, start, end)
+
+    Find all the keys in the trie that match full words in the string.
+    Word boundaries are defined as any punctuation or whitespace.
+
+    """
+    _boundary_re = re.compile(r"[%s]+" % re.escape(DEFAULT_BOUNDARY_CHARS))
+        
+    results = []
+    start = 0     # index of word boundary
+    while start < len(string):
+        # Look for a match.
+        keys = match_all(string[start:], trie)
+        for key in keys:
+            l = len(key)
+            # Make sure it ends at a boundary.
+            if start+l == len(string) or \
+               _boundary_re.match(string[start+l]):
+                results.append((key, start, start+l))
+        # Move forward to the next boundary.
+        m = _boundary_re.search(string, start)
+        if m is None:
+            break
+        start = m.end()
+    return results