Source code for Features

# Features.py
# By MW, Jul 2013
# GPLv3+
#
# Module managing features. A feature is a set of time periods representing
#+something like a phase in the cellular cycle. This feature can have various
#+time representations: a single point, multiple point, a time segment...
# For the moment, there is no constraint between features (e.g.: metaphase
#+ must be followed by anaphase, etc.), but my idea is to add a constraint 
#+function in the definition of a feature. For instance, this constraint can
#+be a Markov model or something like that.

import sys
sys.path.append('./bin/Features/')
sys.path.append('./conf/')
import Feature, features

class Features :
    def __init__(self) :
        self.features_dict = {}
        self.features_typ ={'point' : Feature.Point,
                            'multipoint' : Feature.Multipoint,
                            'segment' : Feature.Segment,
                            'multisegment' : Feature.Multisegment,
                            'cell' : Feature.Cell
                            }
        features.get_features(self) # Load user-defined features.

    def new_feature(self, typ, name, shortname, color, descr, model=None) :
        """This function instanciate a feature (from the Feature class), 
        register it in the features_dict, check ifS the name is not already in
        use (and also the color).

        typ in ['point', 'multipoint', 'segment', 'multisegment']
        color as a RGB color (tuple)
        descr: a str
        """
        cols = []
        for f in self.features_dict.values() :
            cols.append(f.get_color())
        if name in self.features_dict.keys() or color in cols:
            return False
        else :
            f = self.features_typ[typ](name, shortname, color, descr, model)
            self.features_dict[name] = f
            return f
    def get_features_dict(self) :
        return self.features_dict
        
    def get_save_dict(self) :
        dic = {}
        f_d = {}
        for n in self.features_dict.keys() :
            f_d[n] = self.features_dict[n].get_save_dict()
        dic['features_dic'] = {'descr' : 'Dict containting all the features', 'value' : f_d}
        dic['features_typ'] = {'descr' : 'A dict object linking the type of the feature (Point, Segment) with the class to initialize', 'value' : self.features_typ}

        return {'descr' : 'Class describing all the features for a cell', 'value' : dic}

    def load_save_dict(self, dic) :
        #self.features_typ = dic['value']['features_typ']['value']
        for n in dic['value']['features_dic']['value'].keys() :
            d = dic['value']['features_dic']['value'][n]['value']
            if (not self.features_dict.has_key(n)) :
                typ = d['typ']['value']
                col = d['color']['value']
                sn = d['short_name']['value']
                desc = d['descr']['value'] # TYPO TO BE CORRECTED IN V6
                mod = d['model']['value']
                f=self.new_feature(typ, n, sn, col, desc, mod)
            else :
                f = self.features_dict[n]
                f.load_save_dict(d)