[pygr-notify] [pygr commit] r77 - wiki

[codesite-noreply at google.com]

Author: titus at idyll.org
Date: Tue Jul 22 11:20:04 2008
New Revision: 77

Added:
   wiki/SimpleAnnotationDB.wiki

Log:
Created wiki page through web user interface.

Added: wiki/SimpleAnnotationDB.wiki
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+++ wiki/SimpleAnnotationDB.wiki	Tue Jul 22 11:20:04 2008
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+#summary Notes on making the simplest possible (?) annotation DB
+
+= Introduction =
+
+Sometimes it's nice to know exactly what behavior you need to 
implement to get
+something minimal going.  Here are some notes on doing that with an AnnotationDB-a-like
+object that doesn't support pickling or anything fancy; it just acts 
as an AnnotationDB.
+
+
+= Details =
+
+Here's the basic code:
+
+{{{
+class MyAnno(SeqPath):
+    step = 1
+
+    def __init__(self,id,db,parent,start,stop):
+        self.id = id                    # unique name of this feature
+        self.db = db                    # annotation database for lookups
+        # self.start -> 0
+        self.stop = stop-start          # reset to start at 0
+        self._anno_seq = parent         # actual sequence
+        self._anno_start = start        # offset within sequence
+        self.path = self                # simple SeqPath obj
+
+class MyAnnoDB(object):
+    def __init__(self, seqDB):
+        self.d = {}
+        self.seqDB = seqDB
+
+    def add(self, f):
+        self.d[f.id] = f
+
+    def __getitem__(self, k):
+        return self.d[k]
+
+}}}
+
+OK, a few notes:
+
+ - MyAnnoDB.seqDB is necessay for lookups, e.g. annotation.sequence 
will look for annodb.seqDB.
+ - apart from that, MyAnnoDB really only needs to implement the 
__getitem__ protocol for retrieving values by key.
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