Use Bio.File._IndexedSeqFileDict in Bio.SearchIO.index(...)

biopython · Dec 2, 2012 · f9cc32f · f9cc32f
1 parent f7e072f
commit f9cc32f
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Showing 3 changed files with 15 additions and 9 deletions.
diff --git a/Bio/File.py b/Bio/File.py
@@ -253,10 +253,13 @@ class _IndexedSeqFileDict(_dict_base):
     Note that this dictionary is essentially read only. You cannot
     add or change values, pop values, nor clear the dictionary.
     """
-    def __init__(self, random_access_proxy, key_function):
+    def __init__(self, random_access_proxy, key_function,
+                 repr, obj_repr):
         #Use key_function=None for default value
         self._proxy = random_access_proxy
         self._key_function = key_function
+        self._repr = repr
+        self._obj_repr = obj_repr
         if key_function:
             offset_iter = (
                 (key_function(k), o, l) for (k, o, l) in random_access_proxy)
@@ -281,15 +284,12 @@ def __init__(self, random_access_proxy, key_function):
         self._offsets = offsets
 
     def __repr__(self):
-        #TODO - How best to handle the __repr__ for SeqIO and SearchIO? 
-        return "SeqIO.index(%r, %r, alphabet=%r, key_function=%r)" \
-               % (self._proxy._handle.name, self._proxy._format,
-                  self._proxy._alphabet, self._key_function)
+        return self._repr
 
     def __str__(self):
         #TODO - How best to handle the __str__ for SeqIO and SearchIO? 
         if self:
-            return "{%s : SeqRecord(...), ...}" % repr(self.keys()[0])
+            return "{%r : %s(...), ...}" % (self.keys()[0], self._obj_repr)
         else:
             return "{}"
 

diff --git a/Bio/SearchIO/__init__.py b/Bio/SearchIO/__init__.py
@@ -463,8 +463,12 @@ def index(filename, format=None, key_function=None, **kwargs):
     if not isinstance(filename, basestring):
         raise TypeError("Need a filename (not a handle)")
 
-    from Bio.SearchIO._index import _IndexedSearch
-    return _IndexedSearch(filename, format, key_function, **kwargs)
+    from Bio.File import _IndexedSeqFileDict
+    proxy_class = get_processor(format, _INDEXER_MAP)
+    repr = "SearchIO.index(%r, %r, key_function=%r)" \
+        % (filename, format, key_function)
+    return _IndexedSeqFileDict(proxy_class(filename, **kwargs),
+                               key_function, repr, "QueryResult")
 
 
 def index_db(index_filename, filenames=None, format=None,

diff --git a/Bio/SeqIO/__init__.py b/Bio/SeqIO/__init__.py
@@ -802,8 +802,10 @@ def index(filename, format, alphabet=None, key_function=None):
         proxy_class = _FormatToRandomAccess[format]
     except KeyError:
         raise ValueError("Unsupported format %r" % format)
+    repr = "SeqIO.index(%r, %r, alphabet=%r, key_function=%r)" \
+        % (filename, format, alphabet, key_function)
     return _IndexedSeqFileDict(proxy_class(filename, format, alphabet),
-                               key_function)
+                               key_function, repr, "SeqRecord")
 
 
 def index_db(index_filename, filenames=None, format=None, alphabet=None,