ó gbc@sVdZddlmZddlmZdefd„ƒYZdefd„ƒYZdS( so Module dedicated to compute observed divergeances from an alignment. No distance correction is applied at all iÿÿÿÿ(timap(tDistanceMatrixtPairewiseGapRemovalcBseZdZd„ZRS(s Observed divergeance matrix from an alignment. Gap are removed from the alignemt on a pairewise sequence base cCsY|j|}|j|}td„d„td||ƒDƒdƒ\}}t|ƒ|S(s  Compute the observed divergeance from two sequences of an aligment. @attention: For performance purpose this method should be directly used. use instead the __getitem__ method from DistanceMatrix. @see: L{__getitem__} @param x: number of the fisrt sequence in the aligment @type x: int @param y: umber of the second sequence in the aligment @type y: int cSs|d||ddfS(Nii((txty((s:lib/python2.7/site-packages/obitools/distances/observed.pyt'scss/|]%}d|kr|d|dkVqdS(t-iiN((t.0tz((s:lib/python2.7/site-packages/obitools/distances/observed.pys (siN(ii(taligmenttreduceRtNonetfloat(tselfRRtseq1tseq2tdiffttot((s:lib/python2.7/site-packages/obitools/distances/observed.pyt evaluateDists    (t__name__t __module__t__doc__R(((s:lib/python2.7/site-packages/obitools/distances/observed.pyR st PairewisecBseZdZd„ZRS(s[ Observed divergeance matrix from an alignment. Gap are kept from the alignemt cCsY|j|}|j|}td„d„td||ƒDƒdƒ\}}t|ƒ|S(s  Compute the observed divergeance from two sequences of an aligment. @attention: For performance purpose this method should be directly used. use instead the __getitem__ method from DistanceMatrix. @see: L{__getitem__} @param x: number of the fisrt sequence in the aligment @type x: int @param y: umber of the second sequence in the aligment @type y: int cSs|d||ddfS(Nii((RR((s:lib/python2.7/site-packages/obitools/distances/observed.pyRIscss#|]}|d|dkVqdS(iiN((RR((s:lib/python2.7/site-packages/obitools/distances/observed.pys JsiN(ii(R R RR R (R RRRRRR((s:lib/python2.7/site-packages/obitools/distances/observed.pyR3s    (RRRR(((s:lib/python2.7/site-packages/obitools/distances/observed.pyR-sN(Rt itertoolsRtobitools.distancesRRR(((s:lib/python2.7/site-packages/obitools/distances/observed.pyts#