Projects/laydi
Projects
/
laydi
Archived
7
0
Fork 0
This repository has been archived on 2024-07-04. You can view files and clone it, but cannot push or open issues or pull requests.
laydi/laydi/annotations.py

101 lines
2.8 KiB
Python

_dim_annotation_handlers = {}
def get_dim_annotations(dimname, annotation, ids):
"""Returns a list of annotations corresponding to the given ids in
dimension dimname"""
global _dim_annotation_handlers
if _dim_annotation_handlers.has_key(dimname):
return _dim_annotation_handlers[dimname].get_annotations(annotation, ids)
return None
def set_dim_handler(dimname, handler):
"""Set the handler for the given dimension."""
global _dim_annotation_handlers
_dim_annotation_handlers[dimname] = handler
def get_dim_handler(dimname):
"""Get the handler for the given dimension."""
global _dim_annotation_handlers
return _dim_annotation_handlers.get(dimname, None)
class AnnotationHandler:
def __init__(self):
pass
def get_annotations(self, annotationname, ids, default=None):
return None
def get_annotation_names(self):
return []
class DictAnnotationHandler(AnnotationHandler):
def __init__(self, d=None):
if d == None:
d = {}
self._dict = d
def get_annotations(self, annotationname, ids, default=None):
d = self._dict
retval = []
for id in ids:
if d[annotationname].has_key(id):
retval.append(d[annotationname][id])
else:
retval.append(default)
return retval
def add_annotations(self, annotationname, d):
self._dict[annotationname] = d
def get_annotation_names(self):
return self._dict.keys()
def read_annotations_file(filename):
"""Read annotations from file.
Reads annotations from a tab delimited file of the format::
dimname annotation_name1 annotation_name2 ...
id1 Foo 0.43
id2 Bar 0.59
"""
ann = DictAnnotationHandler()
dimname = None
annotation_dicts = []
annotation_names = []
fd = open(filename)
## Read the first line, which contains the dimension name and
## annotation names.
line = fd.readline()
values = [x.strip() for x in line.split('\t')]
dimname = values[0]
annotation_names = values[1:]
annotation_dicts = [{} for x in annotation_names]
## Read the lines containing the annotations. The first value on
## each line is an id along the dimension.
while line:
values = [x.strip() for x in line.split('\t')]
for i, x in enumerate(values[1:]):
annotation_dicts[i][values[0]] = x
line = fd.readline()
fd.close()
## Add everything to the annotation object and add the object to
## the specified dimension.
for i, a in enumerate(annotation_names):
ann.add_annotations(a, annotation_dicts[i])
_dim_annotation_handlers[dimname] = ann
return ann