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code header cleanup; AUTHORS file; closes gh-4.

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Erick Matsen
Erick Matsen committed Feb 21, 2011
1 parent e505cfd commit 5963f43659c1d379e628b82aa5155e0aef1adedb
Showing with 70 additions and 498 deletions.
  1. +12 −0 AUTHORS
  2. +1 −1 common_src/algMap.ml
  3. +0 −4 common_src/alignment.ml
  4. +1 −4 common_src/base.ml
  5. +0 −4 common_src/common_base.ml
  6. +1 −3 common_src/fam_batteries.ml
  7. +1 −4 common_src/fam_gsl_matvec.ml
  8. +0 −4 common_src/file_parsing.ml
  9. +0 −4 common_src/mapsSets.ml
  10. +0 −69 common_src/multiset.ml
  11. +0 −4 common_src/ppr.ml
  12. +1 −4 common_src/subcommand.ml
  13. +0 −4 common_src/uptri.ml
  14. +0 −4 myocamlbuild.ml
  15. +1 −4 pplacer_src/alignment_funs.ml
  16. +1 −4 pplacer_src/bark_map.ml
  17. +0 −5 pplacer_src/bootstrap.ml
  18. +1 −3 pplacer_src/bootsubfunc.ml
  19. +0 −6 pplacer_src/bootviz.ml
  20. +1 −4 pplacer_src/check.ml
  21. +1 −4 pplacer_src/cluster_common.ml
  22. +1 −3 pplacer_src/clusterfunc.ml
  23. +1 −4 pplacer_src/core.ml
  24. +1 −4 pplacer_src/decor.ml
  25. +1 −4 pplacer_src/decor_bark.ml
  26. +1 −4 pplacer_src/decor_gtree.ml
  27. +1 −4 pplacer_src/diagd.ml
  28. +1 −4 pplacer_src/dist_stree.ml
  29. +1 −4 pplacer_src/distance_mat.ml
  30. +1 −4 pplacer_src/edge_rdist.ml
  31. +1 −4 pplacer_src/edpl.ml
  32. +1 −4 pplacer_src/errplace.ml
  33. +1 −4 pplacer_src/fantasy.ml
  34. +1 −4 pplacer_src/fasta_channel.ml
  35. +1 −3 pplacer_src/friendly.ml
  36. +1 −4 pplacer_src/gamma.ml
  37. +1 −4 pplacer_src/glv.ml
  38. +1 −4 pplacer_src/glv_arr.ml
  39. +1 −4 pplacer_src/glv_edge.ml
  40. +1 −4 pplacer_src/gtree.ml
  41. +0 −4 pplacer_src/heat_tree.ml
  42. +1 −4 pplacer_src/induced.ml
  43. +1 −3 pplacer_src/integration.ml
  44. +1 −4 pplacer_src/kr_distance.ml
  45. +1 −4 pplacer_src/like_stree.ml
  46. +1 −4 pplacer_src/linear.ml
  47. +1 −3 pplacer_src/linear_c.c
  48. +0 −75 pplacer_src/list_classify.ml
  49. +1 −4 pplacer_src/mass_map.ml
  50. +0 −5 pplacer_src/minimization.ml
  51. +1 −4 pplacer_src/model.ml
  52. +0 −4 pplacer_src/mokaphy_base.ml
  53. +0 −5 pplacer_src/mutpick.ml
  54. +1 −4 pplacer_src/newick.ml
  55. +1 −4 pplacer_src/newick_bark.ml
  56. +1 −4 pplacer_src/newick_lexer.mll
  57. +0 −4 pplacer_src/newick_parser.mly
  58. +1 −4 pplacer_src/nuc_models.ml
  59. +1 −4 pplacer_src/parse_stats.ml
  60. +0 −1 pplacer_src/pca.ml
  61. +0 −5 pplacer_src/pd.ml
  62. +1 −4 pplacer_src/placement.ml
  63. +1 −3 pplacer_src/placerun.ml
  64. +0 −4 pplacer_src/placerun_io.ml
  65. +0 −4 pplacer_src/placeutil.ml
  66. +1 −4 pplacer_src/placeutil_core.ml
  67. +0 −4 pplacer_src/placeutil_demulti.ml
  68. +0 −4 pplacer_src/placeutil_round.ml
  69. +0 −4 pplacer_src/placeutil_to_json.ml
  70. +1 −4 pplacer_src/placeviz_core.ml
  71. +0 −3 pplacer_src/pplacer.ml
  72. +1 −5 pplacer_src/pquery.ml
  73. +1 −4 pplacer_src/pquery_distances.ml
  74. +1 −4 pplacer_src/pquery_io.ml
  75. +1 −4 pplacer_src/prefs.ml
  76. +0 −4 pplacer_src/prot_models.ml
  77. +0 −4 pplacer_src/refpkg.ml
  78. +0 −4 pplacer_src/refpkg_parse.ml
  79. +1 −4 pplacer_src/stree.ml
  80. +1 −4 pplacer_src/string_matrix.ml
  81. +1 −4 pplacer_src/tax_bark.ml
  82. +0 −4 pplacer_src/tax_classify.ml
  83. +0 −5 pplacer_src/tax_gtree.ml
  84. +1 −4 pplacer_src/tax_id.ml
  85. +1 −4 pplacer_src/tax_map.ml
  86. +0 −4 pplacer_src/tax_mass.ml
  87. +1 −4 pplacer_src/tax_seqinfo.ml
  88. +1 −4 pplacer_src/tax_taxonomy.ml
  89. +0 −4 pplacer_src/taxpick.ml
  90. +0 −4 pplacer_src/tensor.ml
  91. +1 −4 pplacer_src/three_tax.ml
  92. +0 −4 pplacer_src/version.ml
  93. +0 −4 pplacer_src/version_pre.ml
View
12 AUTHORS
@@ -0,0 +1,12 @@
+# Authors
+
+Erick Matsen
+ - original code base for pplacer and mokaphy
+ - alignment script design
+
+Aaron Gallagher
+ - visionary subcommand options objects
+ - much file format magic
+
+Brian Hodges
+ - alignment python scripts
View
@@ -1,4 +1,4 @@
-(*
+(* A map equipped with algebraic operations.
*
* not super-high performance because of map and boxing.
*
View
@@ -1,7 +1,3 @@
-(* Copyright (C) 2009-10 Frederick A Matsen.
- * This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with this program. If not, see <http://www.gnu.org/licenses/>.
- *)
-
exception Unknown_format of string
open Fam_batteries
View
@@ -1,7 +1,4 @@
-(* pplacer v1.0. Copyright (C) 2009-2010 Frederick A Matsen.
- * This file is part of pplacer. pplacer is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. pplacer is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with pplacer. If not, see <http://www.gnu.org/licenses/>.
- *
- * some basic functions.
+(* some basic functions.
*
* This definitely needs some cleaning out, as much functionality isn't used or
* duplicated somewhere else.
@@ -1,7 +1,3 @@
-(* Copyright (C) 2009 Frederick A Matsen.
- * This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with this program. If not, see <http://www.gnu.org/licenses/>.
- *)
-
let time_str_of_seconds secs =
let iSecs = int_of_float secs in
@@ -1,6 +1,4 @@
-(* Copyright (C) 2009 Frederick A Matsen.
- * This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with this program. If not, see <http://www.gnu.org/licenses/>.
-
+(*
LE MENU
-------
ArrayFuns
@@ -1,7 +1,4 @@
-(* Copyright (C) 2009 Frederick A Matsen.
- * This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with this program. If not, see <http://www.gnu.org/licenses/>.
- *
- * some nicer ways to make and use Gsl_vectors and Gsl_matrices.
+(* some nicer ways to make and use Gsl_vectors and Gsl_matrices.
*
* look at
http://www.gnu.org/software/gsl/manual/html_node/GSL-BLAS-Interface.html
@@ -1,7 +1,3 @@
-(* Copyright (C) 2009 Frederick A Matsen.
- * This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with this program. If not, see <http://www.gnu.org/licenses/>.
- *)
-
let empty_line_rex = Str.regexp "^[ \t]*$"
let comment_rex = Str.regexp "^[ \t]*#.*"
View
@@ -1,7 +1,3 @@
-(* Copyright (C) 2009 Frederick A Matsen.
- * This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with this program. If not, see <http://www.gnu.org/licenses/>.
- *)
-
open Ppr
module OrderedFloat = struct
View
@@ -1,69 +0,0 @@
-(* Copyright (C) 2010 Frederick A Matsen.
- * This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with this program. If not, see <http://www.gnu.org/licenses/>.
- *
- * a multiset module. mem tests for membership, while n_mem returns the number
- * of times something is bound.
- *)
-
-open MapsSets
-
-module Multiset (OT: Map.OrderedType) =
- struct
- module M = Map.Make(OT)
-
- type t = int M.t
- let empty = M.empty
- let mem = M.mem
- let find = M.find
-
- let n_mem x s =
- if mem x s then find x s
- else 0
-
- let add x s =
- if mem x s then M.add x ((M.find x s)+1) s
- else M.add x 1 s
-
- let remove x s =
- if mem x s then begin
- let new_val = (M.find x s) - 1 in
- assert(new_val >= 0);
- if new_val = 0 then
- M.remove x s
- else
- M.add x new_val s
- end
- else raise Not_found
-
- let of_list = List.fold_left (fun s x -> add x s) empty
-
- (* sends the multiset to a list _with multiplicity_ *)
- let to_list s =
- let rec multiadd x n l =
- if n <= 0 then l
- else multiadd x (n-1) (x::l)
- in
- List.rev (M.fold multiadd s [])
-
-
- end
-
-
-module FloatMultiset = Multiset(OrderedFloat)
-module IntMultiset = Multiset(OrderedInt)
-module CharMultiset = Multiset(OrderedChar)
-module StringMultiset = Multiset(OrderedString)
-
-
-module MultisetFuns (OT: Map.OrderedType) (SBLE: STRINGABLE with type t = OT.t) =
- struct
- module MF = MapFuns(OT)(SBLE)
-
- let ppr = MF.ppr_int
- end
-
-
-module FloatMultisetFuns = MultisetFuns(OrderedFloat)(StringableFloat)
-module IntMultisetFuns = MultisetFuns(OrderedInt)(StringableInt)
-module CharMultisetFuns = MultisetFuns(OrderedChar)(StringableChar)
-module StringMultisetFuns = MultisetFuns(OrderedString)(StringableString)
View
@@ -1,7 +1,3 @@
-(* Copyright (C) 2009 Frederick A Matsen.
- * This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with this program. If not, see <http://www.gnu.org/licenses/>.
- *)
-
(* ppr generalized nonsense *)
(* ppr_list_inners : assume that we have opened a box *)
View
@@ -1,7 +1,4 @@
-(* Copyright (C) 2009-2010 Frederick A Matsen.
- * This file is part of pplacer. pplacer is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. pplacer is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with pplacer. If not, see <http://www.gnu.org/licenses/>.
- *
- * A specl is a specification list, which gets passed to Arg.parse_argv or
+(* A specl is a specification list, which gets passed to Arg.parse_argv or
* wrap_parse_argv. It specifies the options and the actions which are assocated
* with those options.
*)
View
@@ -1,7 +1,3 @@
-(* Copyright (C) 2009 Frederick A Matsen.
- * This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with this program. If not, see <http://www.gnu.org/licenses/>.
- *)
-
open Fam_batteries
(* a module for STRICTLY uppper tri matrices *)
View
@@ -1,7 +1,3 @@
-(* pplacer v1.0. Copyright (C) 2009-2010 Frederick A Matsen.
- * This file is part of pplacer. pplacer is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. pplacer is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with pplacer. If not, see <http://www.gnu.org/licenses/>.
- *)
-
open Ocamlbuild_plugin;;
open Command;;
@@ -1,7 +1,4 @@
-(* pplacer v1.0. Copyright (C) 2009-2010 Frederick A Matsen.
- * This file is part of pplacer. pplacer is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. pplacer is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with pplacer. If not, see <http://www.gnu.org/licenses/>.
- *
- * functions for dealing with alignments, especially for likelihoods
+(* functions for dealing with alignments, especially for likelihoods
*)
open MapsSets
View
@@ -1,7 +1,4 @@
-(* pplacer v1.0. Copyright (C) 2009-2010 Frederick A Matsen.
- * This file is part of pplacer. pplacer is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. pplacer is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with pplacer. If not, see <http://www.gnu.org/licenses/>.
- *
- * assumes that the bark is at least a newick bark
+(* assumes that the bark is at least a newick bark
*)
open MapsSets
View
@@ -1,8 +1,3 @@
-(* pplacer v1.0. Copyright (C) 2009-2010 Frederick A Matsen.
- * This file is part of pplacer. pplacer is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. pplacer is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with pplacer. If not, see <http://www.gnu.org/licenses/>.
- *
-*)
-
open Fam_batteries
(* bootstrap a list, with an option to modify the elements of the list through f
@@ -1,6 +1,4 @@
-(* mokaphy v1.0. Copyright (C) 2010 Frederick A Matsen.
- * This file is part of mokaphy. mokaphy is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. pplacer is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with pplacer. If not, see <http://www.gnu.org/licenses/>.
- *
+(*
* Say we bootstrap a clustering method.
* If there are samples that don't fit into a tree-like structure, then they
* will wander about and make all of the bootstrap values low.
View
@@ -1,9 +1,3 @@
-(* mokaphy v1.0. Copyright (C) 2010 Frederick A Matsen.
- * This file is part of mokaphy. mokaphy is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. pplacer is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with pplacer. If not, see <http://www.gnu.org/licenses/>.
- *
- * Here we read in t
- *)
-
open MapsSets
module SSS = Cluster_common.StringSetSet
View
@@ -1,7 +1,4 @@
-(* pplacer v1.0. Copyright (C) 2009-2010 Frederick A Matsen.
- * This file is part of pplacer. pplacer is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. pplacer is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with pplacer. If not, see <http://www.gnu.org/licenses/>.
- *
- * routines for doing sanity checks
+(* routines for doing sanity checks
*)
open MapsSets
@@ -1,7 +1,4 @@
-(* mokaphy v1.0. Copyright (C) 2010 Frederick A Matsen.
- * This file is part of mokaphy. mokaphy is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. pplacer is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with pplacer. If not, see <http://www.gnu.org/licenses/>.
- *
- * Note that for much of this clustering work we assume that trees have
+(* Note that for much of this clustering work we assume that trees have
* numberings in their internal nodes, where the bootstrap values go.
*)
@@ -1,6 +1,4 @@
-(* mokaphy v1.0. Copyright (C) 2010 Frederick A Matsen.
- * This file is part of mokaphy. mokaphy is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. pplacer is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with pplacer. If not, see <http://www.gnu.org/licenses/>.
-
+(*
* inner loop
* find minimally distant pair of samples i and j by folding over map
* merge them to make k, and normalize
View
@@ -1,7 +1,4 @@
-(* pplacer v1.0. Copyright (C) 2009-2010 Frederick A Matsen.
- * This file is part of pplacer. pplacer is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. pplacer is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with pplacer. If not, see <http://www.gnu.org/licenses/>.
- *
- * here we actually do the work.
+(* Here we actually do the work.
*)
open Fam_batteries
View
@@ -1,7 +1,4 @@
-(* pplacer v1.0. Copyright (C) 2009-2010 Frederick A Matsen.
- * This file is part of pplacer. pplacer is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. pplacer is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with pplacer. If not, see <http://www.gnu.org/licenses/>.
- *
- * decor gives types and routines for attaching information to trees
+(* decor gives types and routines for attaching information to trees
*)
open MapsSets
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