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DATE 2016-11-01

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MESSAGE
DATE 2016-11-03
FROM Ruben Safir
SUBJECT Re: [Learn] Fitch Algorithm - C++
From learn-bounces-at-nylxs.com Thu Nov 3 02:15:59 2016
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References: <20161102182751.GA10998-at-www.mrbrklyn.com>
<87k2cl7184.fsf-at-contrapunctus.net>
<2ab889a4-74bd-7670-b872-04bb8af301ce-at-panix.com>

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On 11/03/2016 01:47 AM, Bayna Robertson wrote:
> The language is very interesting I understand it mostly and what it does
> I just might have questions on some parts of the program.
> =


Maybe so but Haskell is not going on my language stack at this point.
I have R, Python and I need to refresh my C++, in addition to the
statistics. And I'm planning on integrating CLIPS into this along the
way for some AI.

If I write the C++ template correctly, I should be able to flip in and
out different algorithms onto the tree, and connect the data to a RBMS
for storage and retrieval.



> On Wednesday, November 2, 2016, Ruben Safir > > wrote:
> =

> On 11/02/2016 10:20 PM, Christopher League wrote:
> > Tonight I put together a small Haskell script for the Fitch algorit=
hm.
> > You specify a tree with its leaves labeled, and it figures out the
> > labels for the interior nodes. There are no transition weights. It
> > outputs the tree in GraphViz format, so we use |dot| to generate the
> > image=E2=80=A6 see attached.
> >
> =

> I knew you were going to go impatient and do that.
> =

> =

> > |{-# LANGUAGE TypeSynonymInstances, FlexibleInstances,
> TupleSections #-}
> > import Data.List (intersperse) import Data.Set (Set) import
> > Control.Monad.State import Control.Monad.Writer import qualified
> > Data.Set as Set data Tree a b =3D Leaf {leafValue :: b } | Branch
> > {branchValue :: a ,branchLeft :: Tree a b ,branchRight :: Tree a b }
> > deriving Show value :: Tree a a -> a value (Leaf a) =3D a value
> (Branch a
> > _ _) =3D a -- Bottom up phase1 :: Ord b =3D> Tree a b -> (Set b, Tr=
ee (Set
> > b) b) phase1 (Leaf b) =3D (Set.singleton b, Leaf b) phase1 (Branch _
> l r)
> > =3D (s3, Branch s3 l' r') where (s1, l') =3D phase1 l (s2, r') =3D
> phase1 r s3
> > =3D if Set.null i then u else i where u =3D Set.union s1 s2 i =3D
> > Set.intersection s1 s2 -- Top down phase2 :: Ord b =3D> Tree (Set b)
> b ->
> > Maybe b -> Tree b b phase2 (Leaf b) _ =3D Leaf b phase2 (Branch set=
left
> > right) parentOpt =3D Branch b (phase2 left (Just b)) (phase2 right =
(Just
> > b)) where b =3D case parentOpt of Just p | Set.member p set -> p _ =
->
> > Set.elemAt 0 set -- Combine them together fitch :: Ord b =3D> Tree a
> b ->
> > Tree b b fitch t =3D phase2 t' Nothing where (_, t') =3D phase1 t
> > ------------------------------------------------------------------ =
--
> > This part is about visualizing the trees using GraphViz (dot) class
> > ToLabel a where toLabel :: a -> String instance ToLabel Char where
> > toLabel c =3D [c] instance ToLabel String where toLabel =3D id inst=
ance
> > ToLabel a =3D> ToLabel (Set a) where toLabel s =3D "{" ++ concat
> > (intersperse "," (map toLabel (Set.toList s))) ++ "}" next ::
> State Int
> > Int next =3D get <* modify (+1) numberTree :: Tree a b -> State Int
> (Tree
> > (Int,a) (Int,b)) numberTree (Leaf b) =3D Leaf . (,b) <$> next numbe=
rTree
> > (Branch a l r) =3D Branch . (,a) <$> next <*> numberTree l <*>
> numberTree
> > r graphViz' :: (ToLabel a, ToLabel b) =3D> Tree (Int,a) (Int,b) ->
> Writer
> > String String graphViz' (Leaf (i,b)) =3D do let n =3D "n" ++ show i
> tell $ n
> > ++ " [shape=3Dbox, label=3D\"" ++ toLabel b ++ "\"]\n" return n gra=
phViz'
> > (Branch (i,a) l r) =3D do n1 <- graphViz' l n2 <- graphViz' r let np
> =3D "n"
> > ++ show i tell $ np ++ " [shape=3Doval, label=3D\"" ++ toLabel a ++
> "\"]\n"
> > tell $ np ++ " -> " ++ n1 ++ "\n" tell $ np ++ " -> " ++ n2 ++ "\n"
> > return np graphViz :: (ToLabel a, ToLabel b) =3D> Tree a b -> String
> > graphViz t =3D "digraph{\n" ++ execWriter (graphViz' t') ++ "}\n"
> where t'
> > =3D evalState (numberTree t) 0 -- Sample tree from
> >
> http://www.cse.nd.edu/~cse/2013fa/40532/lectures/lecture23/lecture23.=
pdf
> 23.pdf>
> > t1 :: Tree () Char t1 =3D Branch () ( Branch () ( Branch () (Leaf '=
C')
> > (Leaf 'G') ) ( Branch () (Leaf 'T') (Leaf 'G') ) ) (Leaf 'A') main
> :: IO
> > () main =3D putStrLn $ graphViz $ fitch t1|
> >
> >
> >
> > _______________________________________________
> > Learn mailing list
> > Learn-at-nylxs.com
> > http://lists.mrbrklyn.com/mailman/listinfo/learn
>
> >
> =

> =

> --
> So many immigrant groups have swept through our town
> that Brooklyn, like Atlantis, reaches mythological
> proportions in the mind of the world - RI Safir 1998
> http://www.mrbrklyn.com
> =

> DRM is THEFT - We are the STAKEHOLDERS - RI Safir 2002
> http://www.nylxs.com - Leadership Development in Free Software
> http://www2.mrbrklyn.com/resources
> - Unpublished Archive
> http://www.coinhangout.com - coins!
> http://www.brooklyn-living.com
> =

> Being so tracked is for FARM ANIMALS and and extermination camps,
> but incompatible with living as a free human being. -RI Safir 2013
> _______________________________________________
> Learn mailing list
> Learn-at-nylxs.com
> http://lists.mrbrklyn.com/mailman/listinfo/learn
>
> =



-- =

So many immigrant groups have swept through our town
that Brooklyn, like Atlantis, reaches mythological
proportions in the mind of the world - RI Safir 1998
http://www.mrbrklyn.com

DRM is THEFT - We are the STAKEHOLDERS - RI Safir 2002
http://www.nylxs.com - Leadership Development in Free Software
http://www2.mrbrklyn.com/resources - Unpublished Archive
http://www.coinhangout.com - coins!
http://www.brooklyn-living.com

Being so tracked is for FARM ANIMALS and and extermination camps,
but incompatible with living as a free human being. -RI Safir 2013
_______________________________________________
Learn mailing list
Learn-at-nylxs.com
http://lists.mrbrklyn.com/mailman/listinfo/learn

  1. 2016-11-01 Ruben Safir <ruben-at-mrbrklyn.com> Re: [Learn] how is it indexing in cuda
  2. 2016-11-01 Ruben Safir <ruben.safir-at-my.liu.edu> Re: [Learn] not adequately speced of explained
  3. 2016-11-01 Ruben Safir <ruben-at-mrbrklyn.com> Subject: [Learn] how is it indexing in cuda
  4. 2016-11-01 Ruben Safir <ruben-at-mrbrklyn.com> Subject: [Learn] not adequately speced of explained
  5. 2016-11-02 Christopher League <league-at-contrapunctus.net> Re: [Learn] Fitch Algorithm - C++
  6. 2016-11-02 Ruben Safir <mrbrklyn-at-panix.com> Re: [Learn] Fitch Algorithm - C++
  7. 2016-11-02 Ruben Safir <ruben-at-mrbrklyn.com> Re: [Learn] how is it indexing in cuda
  8. 2016-11-02 Ruben Safir <ruben-at-mrbrklyn.com> Subject: [Learn] Fitch Algorithm - C++
  9. 2016-11-02 IEEE Computer Society <csconnection-at-computer.org> Subject: [Learn] Hear Google's John Martinis Take on Quantum Computing at
  10. 2016-11-02 Ruben Safir <ruben-at-mrbrklyn.com> Subject: [Learn] opencl
  11. 2016-11-02 Ruben Safir <ruben-at-mrbrklyn.com> Subject: [Learn] scheduled for tommorw
  12. 2016-11-02 Ruben Safir <ruben-at-mrbrklyn.com> Subject: [Learn] threads tutorial
  13. 2016-11-03 Ruben Safir <mrbrklyn-at-panix.com> Re: [Learn] Fitch Algorithm - C++
  14. 2016-11-03 Ruben Safir <mrbrklyn-at-panix.com> Re: [Learn] Fitch Algorithm - C++
  15. 2016-11-03 Ruben Safir <mrbrklyn-at-panix.com> Re: [Learn] Fitch Algorithm - C++
  16. 2016-11-03 Christopher League <league-at-contrapunctus.net> Re: [Learn] huffman code
  17. 2016-11-03 Ruben Safir <ruben-at-mrbrklyn.com> Re: [Learn] huffman code
  18. 2016-11-03 Ruben Safir <ruben.safir-at-my.liu.edu> Re: [Learn] huffman code
  19. 2016-11-03 Ruben Safir <ruben-at-mrbrklyn.com> Subject: [Learn] Fitch algorithm from the beginning
  20. 2016-11-03 From: <mrbrklyn-at-panix.com> Subject: [Learn] huffman code
  21. 2016-11-03 Ruben Safir <ruben-at-mrbrklyn.com> Subject: [Learn] Phenology meeting
  22. 2016-11-03 Ruben Safir <ruben-at-mrbrklyn.com> Subject: [Learn] relevant hackathon
  23. 2016-11-03 Ruben Safir <ruben-at-mrbrklyn.com> Subject: [Learn] relevant hackathon
  24. 2016-11-04 Ruben Safir <mrbrklyn-at-panix.com> Re: [Learn] huffman code
  25. 2016-11-04 Christopher League <league-at-contrapunctus.net> Subject: [Learn] Fitch/Sankoff
  26. 2016-11-05 Christopher League <league-at-contrapunctus.net> Re: [Learn] Fwd: templates within templates
  27. 2016-11-05 ruben safir <ruben-at-mrbrklyn.com> Subject: [Learn] Fwd: Re: const T vs T const
  28. 2016-11-05 ruben safir <ruben-at-mrbrklyn.com> Subject: [Learn] Fwd: Template Library files and Header linking troubles
  29. 2016-11-05 ruben safir <ruben-at-mrbrklyn.com> Subject: [Learn] Fwd: templates within templates
  30. 2016-11-06 Ruben Safir <mrbrklyn-at-panix.com> Re: [Learn] Fwd: templates within templates
  31. 2016-11-06 Ruben Safir <ruben-at-mrbrklyn.com> Re: [Learn] Fwd: templates within templates
  32. 2016-11-06 Ruben Safir <mrbrklyn-at-panix.com> Re: [Learn] Fwd: templates within templates
  33. 2016-11-06 Christopher League <league-at-contrapunctus.net> Re: [Learn] Fwd: templates within templates
  34. 2016-11-06 Ruben Safir <mrbrklyn-at-panix.com> Re: [Learn] Fwd: templates within templates
  35. 2016-11-06 Ruben Safir <ruben-at-mrbrklyn.com> Re: [Learn] Fwd: templates within templates
  36. 2016-11-06 Ruben Safir <ruben-at-mrbrklyn.com> Re: [Learn] Fwd: templates within templates
  37. 2016-11-06 Ruben Safir <ruben-at-mrbrklyn.com> Re: [Learn] GNU Parallel 20161022 ('Matthew') released [stable]
  38. 2016-11-07 Ruben Safir <ruben-at-mrbrklyn.com> Subject: [Learn] templates and ostream for future reference
  39. 2016-11-08 Christopher League <league-at-contrapunctus.net> Re: [Learn] C++ signature ambiguity
  40. 2016-11-08 Ruben Safir <ruben.safir-at-my.liu.edu> Re: [Learn] C++ signature ambiguity
  41. 2016-11-08 Ruben Safir <ruben-at-mrbrklyn.com> Subject: [Learn] C++ signature ambiguity
  42. 2016-11-08 Ruben Safir <ruben-at-mrbrklyn.com> Subject: [Learn] Fwd: Invitation: Phylogeny meeting -at- Weekly from 10:15 to
  43. 2016-11-08 Ruben Safir <mrbrklyn-at-panix.com> Subject: [Learn] Fwd: [nylug-talk] RSVP open: Wed Nov 16,
  44. 2016-11-09 Christopher League <league-at-contrapunctus.net> Re: [Learn] merge sort parallel hw
  45. 2016-11-09 Ruben Safir <ruben-at-mrbrklyn.com> Re: [Learn] merge sort parallel hw
  46. 2016-11-09 Ruben Safir <ruben-at-mrbrklyn.com> Re: [Learn] merge sort parallel hw
  47. 2016-11-09 Christopher League <league-at-contrapunctus.net> Re: [Learn] merge sort parallel hw
  48. 2016-11-09 Ruben Safir <ruben-at-mrbrklyn.com> Re: [Learn] mergesort tutorial
  49. 2016-11-09 Christopher League <league-at-contrapunctus.net> Re: [Learn] mergesort tutorial
  50. 2016-11-09 Christopher League <league-at-contrapunctus.net> Re: [Learn] namespace and external files confusion
  51. 2016-11-09 Ruben Safir <ruben-at-mrbrklyn.com> Re: [Learn] namespace and external files confusion
  52. 2016-11-09 From: "Carlos R. Mafra" <crmafra-at-gmail.com> Re: [Learn] Question about a small change
  53. 2016-11-09 Ruben Safir <ruben-at-mrbrklyn.com> Subject: [Learn] =?utf-8?q?C++_call_of_overloaded_=E2=80=98track=28int*=26?=
  54. 2016-11-09 ruben safir <ruben-at-mrbrklyn.com> Subject: [Learn] Fwd: lost arguments
  55. 2016-11-09 Ruben Safir <ruben-at-mrbrklyn.com> Subject: [Learn] Fwd: [dinosaur] Dating origins of dinosaurs,
  56. 2016-11-09 Ruben Safir <ruben-at-mrbrklyn.com> Subject: [Learn] merge sort parallel hw
  57. 2016-11-09 Ruben Safir <ruben-at-mrbrklyn.com> Subject: [Learn] mergesort tutorial
  58. 2016-11-09 Ruben Safir <ruben-at-mrbrklyn.com> Subject: [Learn] namespace and external files confusion
  59. 2016-11-10 Christopher League <league-at-contrapunctus.net> Re: [Learn] merge sort parallel hw
  60. 2016-11-10 Ruben Safir <mrbrklyn-at-panix.com> Re: [Learn] merge sort parallel hw
  61. 2016-11-10 Ruben Safir <mrbrklyn-at-panix.com> Re: [Learn] merge sort parallel hw
  62. 2016-11-10 Ruben Safir <ruben.safir-at-my.liu.edu> Re: [Learn] merge sort parallel hw
  63. 2016-11-10 Ruben Safir <ruben-at-mrbrklyn.com> Re: [Learn] [Hangout-NYLXS] mergesort tutorial
  64. 2016-11-10 Ruben Safir <mrbrklyn-at-panix.com> Subject: [Learn] Fwd: [Hangout-NYLXS] ease your mind- everything in the
  65. 2016-11-10 Ruben Safir <ruben.safir-at-my.liu.edu> Subject: [Learn] Fwd: [Hangout-NYLXS] R Programming Workshop
  66. 2016-11-10 Ruben Safir <ruben-at-mrbrklyn.com> Subject: [Learn] Paleocast phenogenetic tree building
  67. 2016-11-11 Christopher League <league-at-contrapunctus.net> Re: [Learn] merge sort parallel hw
  68. 2016-11-12 Ruben Safir <ruben-at-mrbrklyn.com> Subject: [Learn] HW of mergesort in parallel
  69. 2016-11-13 Ruben Safir <ruben-at-mrbrklyn.com> Subject: [Learn] merge sort in parallel assignment
  70. 2016-11-14 Christopher League <league-at-contrapunctus.net> Re: [Learn] merge sort in parallel assignment
  71. 2016-11-14 Ruben Safir <ruben-at-mrbrklyn.com> Re: [Learn] merge sort in parallel assignment
  72. 2016-11-14 Ruben Safir <ruben-at-mrbrklyn.com> Re: [Learn] merge sort parallel hw
  73. 2016-11-14 Ruben Safir <ruben-at-mrbrklyn.com> Subject: [Learn] CUDA and video
  74. 2016-11-14 Ruben Safir <ruben-at-mrbrklyn.com> Subject: [Learn] PNG Graphic formats and CRCs
  75. 2016-11-15 ruben safir <ruben-at-mrbrklyn.com> Subject: [Learn] Fwd: PNG coding
  76. 2016-11-15 ruben safir <ruben.safir-at-my.liu.edu> Subject: [Learn] Fwd: PNG Coding
  77. 2016-11-16 Ruben Safir <ruben-at-mrbrklyn.com> Re: [Learn] Fwd: lost arguments
  78. 2016-11-16 Ruben Safir <ruben-at-mrbrklyn.com> Re: [Learn] relevant hackathon
  79. 2016-11-16 Ruben Safir <ruben-at-mrbrklyn.com> Subject: [Learn] C++ Workshop Announcement
  80. 2016-11-16 Ruben Safir <mrbrklyn-at-panix.com> Subject: [Learn] Fwd: Re: ref use
  81. 2016-11-16 Ruben Safir <ruben-at-mrbrklyn.com> Subject: [Learn] ref use
  82. 2016-11-16 Ruben Safir <ruben-at-mrbrklyn.com> Subject: [Learn] why use a reference wrapper int his example
  83. 2016-11-17 Ruben Safir <mrbrklyn-at-panix.com> Re: [Learn] [Hangout-NYLXS] at K&R now
  84. 2016-11-17 Ruben Safir <ruben-at-mrbrklyn.com> Subject: [Learn] Fwd: [Hangout-NYLXS] Fwd: PNG Coding
  85. 2016-11-18 ruben safir <ruben-at-mrbrklyn.com> Subject: [Learn] C++ workshop and usenet responses
  86. 2016-11-19 ruben safir <ruben-at-mrbrklyn.com> Subject: [Learn] Fwd: ref use
  87. 2016-11-20 Ruben Safir <ruben-at-mrbrklyn.com> Subject: [Learn] when is the constructor called for an object
  88. 2016-11-21 ruben safir <ruben-at-mrbrklyn.com> Subject: [Learn] Fwd: creating a binary tree
  89. 2016-11-21 ruben safir <ruben-at-mrbrklyn.com> Subject: [Learn] Fwd: hidden static
  90. 2016-11-21 Ruben Safir <ruben-at-mrbrklyn.com> Subject: [Learn] Fwd: ISBI 2017 Call for Abstracts and Non-Author
  91. 2016-11-21 ruben safir <ruben-at-mrbrklyn.com> Subject: [Learn] Fwd: PNG coding
  92. 2016-11-21 ruben safir <ruben-at-mrbrklyn.com> Subject: [Learn] Fwd: Re: the new {} syntax
  93. 2016-11-21 ruben safir <ruben-at-mrbrklyn.com> Subject: [Learn] Fwd: when is the constructor called for an object
  94. 2016-11-21 ruben safir <ruben-at-mrbrklyn.com> Subject: [Learn] Fwd: when is the constructor called for an object
  95. 2016-11-21 Ruben Safir <ruben-at-mrbrklyn.com> Subject: [Learn] Fwd: [dinosaur] Eoconfuciusornis feather keratin and
  96. 2016-11-21 Ruben Safir <ruben-at-mrbrklyn.com> Subject: [Learn] look what I found
  97. 2016-11-22 Ruben Safir <ruben-at-mrbrklyn.com> Subject: [Learn] Cuccuency book
  98. 2016-11-22 ruben safir <ruben.safir-at-my.liu.edu> Subject: [Learn] declare a func or call an object
  99. 2016-11-22 Ruben Safir <ruben.safir-at-my.liu.edu> Subject: [Learn] Fwd: Re: Using CLIPS as a library
  100. 2016-11-23 Ruben Safir <ruben.safir-at-my.liu.edu> Subject: [Learn] Fwd: Simple C++11 Wrapper for CLIPS 6.30
  101. 2016-11-23 Ruben Safir <ruben-at-mrbrklyn.com> Subject: [Learn] Parrelel Programming HW2 with maxpath
  102. 2016-11-24 Ruben Safir <ruben-at-mrbrklyn.com> Subject: [Learn] great research news for big data
  103. 2016-11-24 Ruben Safir <ruben-at-mrbrklyn.com> Subject: [Learn] mapping algorithms
  104. 2016-11-24 Ruben Safir <ruben-at-mrbrklyn.com> Subject: [Learn] Todays meeting
  105. 2016-11-25 Ruben Safir <ruben-at-mrbrklyn.com> Subject: [Learn] Fwd: [dinosaur] Flightless theropod phylogenetic variation
  106. 2016-11-26 Ruben Safir <ruben-at-mrbrklyn.com> Re: [Learn] Note to self for Thursday
  107. 2016-11-26 Ruben Safir <ruben-at-mrbrklyn.com> Subject: [Learn] Fitch etc
  108. 2016-11-26 Ruben Safir <ruben-at-mrbrklyn.com> Subject: [Learn] Note to self for Thursday
  109. 2016-11-26 Ruben Safir <ruben-at-mrbrklyn.com> Subject: [Learn] operator<<() overloading details and friend
  110. 2016-11-27 Ruben Safir <ruben-at-mrbrklyn.com> Subject: [Learn] 130 year old feathers analysis
  111. 2016-11-27 ruben safir <ruben-at-mrbrklyn.com> Subject: [Learn] Fwd: ACM/SPEC ICPE 2017 - Call for Tutorial Proposals
  112. 2016-11-27 ruben safir <ruben-at-mrbrklyn.com> Subject: [Learn] Fwd: ACM/SPEC ICPE 2017 - Call for Workshop Proposals
  113. 2016-11-27 ruben safir <ruben-at-mrbrklyn.com> Subject: [Learn] Fwd: CfP 22nd Conf. Reliable Software Technologies,
  114. 2016-11-27 ruben safir <ruben-at-mrbrklyn.com> Subject: [Learn] Fwd: Seeking contributors for psyche-c
  115. 2016-11-29 Christopher League <league-at-contrapunctus.net> Re: [Learn] Look at this exciting output by my test program
  116. 2016-11-29 Ruben Safir <ruben-at-mrbrklyn.com> Re: [Learn] Look at this exciting output by my test program
  117. 2016-11-29 Ruben Safir <ruben-at-mrbrklyn.com> Re: [Learn] Look at this exciting output by my test program
  118. 2016-11-29 Christopher League <league-at-contrapunctus.net> Re: [Learn] Quantum Entanglement
  119. 2016-11-29 Ruben Safir <mrbrklyn-at-panix.com> Re: [Learn] Quantum Entanglement
  120. 2016-11-29 Ruben Safir <ruben-at-mrbrklyn.com> Subject: [Learn] Here is the paper I was talking out
  121. 2016-11-29 Ruben Safir <ruben-at-mrbrklyn.com> Subject: [Learn] Look at this exciting output by my test program
  122. 2016-11-29 nylxs <mrbrklyn-at-optonline.net> Subject: [Learn] Look at this exciting output by my test program
  123. 2016-11-29 Ruben Safir <ruben-at-mrbrklyn.com> Subject: [Learn] Quantum Entanglement
  124. 2016-11-29 Ruben Safir <ruben-at-mrbrklyn.com> Subject: [Learn] The Death of PBS
  125. 2016-11-29 Ruben Safir <ruben-at-mrbrklyn.com> Subject: [Learn] witmer lab ohio and 3d imaging
  126. 2016-11-30 Ruben Safir <ruben-at-mrbrklyn.com> Subject: [Learn] phylogenetic crawler

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