remove _strain_dict_index from StrainCollection class

[CunliangGeng]

Attribute _strain_dict_index(or lookup_index) in StrainCollection class records the indices of strains. However it's mainly used as fixed indices by get_links method, which causes problems when the strains are updated.

• check how _strain_dict_index is used by other functions
• remove _strain_dict_index from the class and update the code that uses it
• Implement removing the strain also from self._lookup indices. [Bug] #90
• Change strains in StrainCollection to be a set instead of list #113