use GPL 2 and assign copyright to correct author

sandain · Mar 4, 2017 · 6d185ac · 6d185ac
1 parent 17f6ecf
commit 6d185ac
Show file tree

Hide file tree

Showing 53 changed files with 364 additions and 849 deletions.
diff --git a/LICENSE b/LICENSE
diff --git a/src/fortran/binningdanny.f90 b/src/fortran/binningdanny.f90
@@ -3,14 +3,12 @@
 !    and drift, yielding a certain number of ecotypes.
 ! 
 !    Copyright (C) 2009  Fred Cohan, Wesleyan University
-!                        Carlo Francisco, Wesleyan University
 !                        Danny Krizanc, Wesleyan University
-!                        Andrew Warner, Wesleyan University
-!                        Jason Wood, Montana State University
+!                        Jason M. Wood, Montana State University
 !
 !    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
+!    the Free Software Foundation, either version 2 of the License, or
 !    (at your option) any later version.
 !
 !    This program is distributed in the hope that it will be useful,

diff --git a/src/fortran/bruteforce.f90 b/src/fortran/bruteforce.f90
@@ -3,14 +3,12 @@
 !    and drift, yielding a certain number of ecotypes.
 ! 
 !    Copyright (C) 2009  Fred Cohan, Wesleyan University
-!                        Carlo Francisco, Wesleyan University
 !                        Danny Krizanc, Wesleyan University
-!                        Andrew Warner, Wesleyan University
-!                        Jason Wood, Montana State University
+!                        Jason M. Wood, Montana State University
 !
 !    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
+!    the Free Software Foundation, either version 2 of the License, or
 !    (at your option) any later version.
 !
 !    This program is distributed in the hope that it will be useful,

diff --git a/src/fortran/correctpcr.f90 b/src/fortran/correctpcr.f90
@@ -9,7 +9,7 @@
 !
 !    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
+!    the Free Software Foundation, either version 2 of the License, or
 !    (at your option) any later version.
 !
 !    This program is distributed in the hope that it will be useful,

diff --git a/src/fortran/darray.f90 b/src/fortran/darray.f90
@@ -7,7 +7,7 @@
 !
 !    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
+!    the Free Software Foundation, either version 2 of the License, or
 !    (at your option) any later version.
 !
 !    This program is distributed in the hope that it will be useful,

diff --git a/src/fortran/demarcation.f90 b/src/fortran/demarcation.f90
@@ -3,14 +3,12 @@
 !    and drift, yielding a certain number of ecotypes.
 ! 
 !    Copyright (C) 2009  Fred Cohan, Wesleyan University
-!                        Carlo Francisco, Wesleyan University
 !                        Danny Krizanc, Wesleyan University
-!                        Andrew Warner, Wesleyan University
-!                        Jason Wood, Montana State University
+!                        Jason M. Wood, Montana State University
 !
 !    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
+!    the Free Software Foundation, either version 2 of the License, or
 !    (at your option) any later version.
 !
 !    This program is distributed in the hope that it will be useful,

diff --git a/src/fortran/divergencematrix.f90 b/src/fortran/divergencematrix.f90
@@ -9,7 +9,7 @@
 !
 !    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
+!    the Free Software Foundation, either version 2 of the License, or
 !    (at your option) any later version.
 !
 !    This program is distributed in the hope that it will be useful,

diff --git a/src/fortran/driftCI.f90 b/src/fortran/driftCI.f90
@@ -3,14 +3,12 @@
 !    and drift, yielding a certain number of ecotypes.
 ! 
 !    Copyright (C) 2009  Fred Cohan, Wesleyan University
-!                        Carlo Francisco, Wesleyan University
 !                        Danny Krizanc, Wesleyan University
-!                        Andrew Warner, Wesleyan University
-!                        Jason Wood, Montana State University
+!                        Jason M. Wood, Montana State University
 !
 !    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
+!    the Free Software Foundation, either version 2 of the License, or
 !    (at your option) any later version.
 !
 !    This program is distributed in the hope that it will be useful,

diff --git a/src/fortran/hillclimb.f90 b/src/fortran/hillclimb.f90
@@ -3,14 +3,12 @@
 !    and drift, yielding a certain number of ecotypes.
 ! 
 !    Copyright (C) 2009  Fred Cohan, Wesleyan University
-!                        Carlo Francisco, Wesleyan University
 !                        Danny Krizanc, Wesleyan University
-!                        Andrew Warner, Wesleyan University
-!                        Jason Wood, Montana State University
+!                        Jason M. Wood, Montana State University
 !
 !    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
+!    the Free Software Foundation, either version 2 of the License, or
 !    (at your option) any later version.
 !
 !    This program is distributed in the hope that it will be useful,

diff --git a/src/fortran/methods.f90 b/src/fortran/methods.f90
@@ -9,7 +9,7 @@
 !
 !    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
+!    the Free Software Foundation, either version 2 of the License, or
 !    (at your option) any later version.
 !
 !    This program is distributed in the hope that it will be useful,

diff --git a/src/fortran/npopCI.f90 b/src/fortran/npopCI.f90
@@ -3,14 +3,12 @@
 !    and drift, yielding a certain number of ecotypes.
 ! 
 !    Copyright (C) 2009  Fred Cohan, Wesleyan University
-!                        Carlo Francisco, Wesleyan University
 !                        Danny Krizanc, Wesleyan University
-!                        Andrew Warner, Wesleyan University
-!                        Jason Wood, Montana State University
+!                        Jason M. Wood, Montana State University
 !
 !    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
+!    the Free Software Foundation, either version 2 of the License, or
 !    (at your option) any later version.
 !
 !    This program is distributed in the hope that it will be useful,

diff --git a/src/fortran/omegaCI.f90 b/src/fortran/omegaCI.f90
@@ -3,14 +3,12 @@
 !    and drift, yielding a certain number of ecotypes.
 ! 
 !    Copyright (C) 2009  Fred Cohan, Wesleyan University
-!                        Carlo Francisco, Wesleyan University
 !                        Danny Krizanc, Wesleyan University
-!                        Andrew Warner, Wesleyan University
-!                        Jason Wood, Montana State University
+!                        Jason M. Wood, Montana State University
 !
 !    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
+!    the Free Software Foundation, either version 2 of the License, or
 !    (at your option) any later version.
 !
 !    This program is distributed in the hope that it will be useful,

diff --git a/src/fortran/readsynec.f90 b/src/fortran/readsynec.f90
@@ -9,7 +9,7 @@
 !
 !    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
+!    the Free Software Foundation, either version 2 of the License, or
 !    (at your option) any later version.
 !
 !    This program is distributed in the hope that it will be useful,

diff --git a/src/fortran/removegaps.f90 b/src/fortran/removegaps.f90
@@ -3,14 +3,12 @@
 !    and drift, yielding a certain number of ecotypes.
 ! 
 !    Copyright (C) 2009  Fred Cohan, Wesleyan University
-!                        Carlo Francisco, Wesleyan University
 !                        Danny Krizanc, Wesleyan University
-!                        Andrew Warner, Wesleyan University
-!                        Jason Wood, Montana State University
+!                        Jason M. Wood, Montana State University
 !
 !    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
+!    the Free Software Foundation, either version 2 of the License, or
 !    (at your option) any later version.
 !
 !    This program is distributed in the hope that it will be useful,

diff --git a/src/fortran/sigmaCI.f90 b/src/fortran/sigmaCI.f90
@@ -3,14 +3,12 @@
 !    and drift, yielding a certain number of ecotypes.
 ! 
 !    Copyright (C) 2009  Fred Cohan, Wesleyan University
-!                        Carlo Francisco, Wesleyan University
 !                        Danny Krizanc, Wesleyan University
-!                        Andrew Warner, Wesleyan University
-!                        Jason Wood, Montana State University
+!                        Jason M. Wood, Montana State University
 !
 !    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
+!    the Free Software Foundation, either version 2 of the License, or
 !    (at your option) any later version.
 !
 !    This program is distributed in the hope that it will be useful,

diff --git a/src/fortran/simplexmethod.f90 b/src/fortran/simplexmethod.f90
@@ -16,7 +16,7 @@
 ! CSIRO Division of Mathematics & Statistics
 ! Private Bag 10, Clayton, VIC. 3168
 !
-! Further amended by Fred Cohan and Jason M Wood
+! Further amended by Fred Cohan and Jason M. Wood
 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
 
 

diff --git a/src/fortran/tmatrix.f90 b/src/fortran/tmatrix.f90
@@ -7,7 +7,7 @@
 !
 !    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
+!    the Free Software Foundation, either version 2 of the License, or
 !    (at your option) any later version.
 !
 !    This program is distributed in the hope that it will be useful,

diff --git a/src/fortran/ziggurat.f90 b/src/fortran/ziggurat.f90
@@ -8,7 +8,7 @@
 !
 !    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
+!    the Free Software Foundation, either version 2 of the License, or
 !    (at your option) any later version.
 !
 !    This program is distributed in the hope that it will be useful,

diff --git a/src/java/BinningAndFred.java b/src/java/BinningAndFred.java
@@ -3,15 +3,11 @@
  *    the evolutionary result of net ecotype formation, periodic selection,
  *    and drift, yielding a certain number of ecotypes.
  * 
- *    Copyright (C) 2009  Fred Cohan, Wesleyan University
- *                        Carlo Francisco, Wesleyan University
- *                        Danny Krizanc, Wesleyan University
- *                        Andrew Warner, Wesleyan University
- *                        Jason Wood, Montana State University
+ *    Copyright (C) 2009  Andrew Warner, Wesleyan University
  *
  *    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
+ *    the Free Software Foundation, either version 2 of the License, or
  *    (at your option) any later version.
  *
  *    This program is distributed in the hope that it will be useful,

diff --git a/src/java/BinningFasta.java b/src/java/BinningFasta.java
@@ -3,15 +3,11 @@
  *    the evolutionary result of net ecotype formation, periodic selection,
  *    and drift, yielding a certain number of ecotypes.
  * 
- *    Copyright (C) 2009  Fred Cohan, Wesleyan University
- *                        Carlo Francisco, Wesleyan University
- *                        Danny Krizanc, Wesleyan University
- *                        Andrew Warner, Wesleyan University
- *                        Jason Wood, Montana State University
+ *    Copyright (C) 2009  Andrew Warner, Wesleyan University
  *
  *    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
+ *    the Free Software Foundation, either version 2 of the License, or
  *    (at your option) any later version.
  *
  *    This program is distributed in the hope that it will be useful,

diff --git a/src/java/CIReader.java b/src/java/CIReader.java
@@ -3,15 +3,11 @@
  *    the evolutionary result of net ecotype formation, periodic selection,
  *    and drift, yielding a certain number of ecotypes.
  * 
- *    Copyright (C) 2009  Fred Cohan, Wesleyan University
- *                        Carlo Francisco, Wesleyan University
- *                        Danny Krizanc, Wesleyan University
- *                        Andrew Warner, Wesleyan University
- *                        Jason Wood, Montana State University
+ *    Copyright (C) 2009  Andrew Warner, Wesleyan University
  *
  *    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
+ *    the Free Software Foundation, either version 2 of the License, or
  *    (at your option) any later version.
  *
  *    This program is distributed in the hope that it will be useful,

diff --git a/src/java/ChooseFredOutVal.java b/src/java/ChooseFredOutVal.java
@@ -3,15 +3,11 @@
  *    the evolutionary result of net ecotype formation, periodic selection,
  *    and drift, yielding a certain number of ecotypes.
  * 
- *    Copyright (C) 2009  Fred Cohan, Wesleyan University
- *                        Carlo Francisco, Wesleyan University
- *                        Danny Krizanc, Wesleyan University
- *                        Andrew Warner, Wesleyan University
- *                        Jason Wood, Montana State University
+ *    Copyright (C) 2009  Andrew Warner, Wesleyan University
  *
  *    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
+ *    the Free Software Foundation, either version 2 of the License, or
  *    (at your option) any later version.
  *
  *    This program is distributed in the hope that it will be useful,

diff --git a/src/java/ConfidenceInterval.java b/src/java/ConfidenceInterval.java
@@ -3,15 +3,11 @@
  *    the evolutionary result of net ecotype formation, periodic selection,
  *    and drift, yielding a certain number of ecotypes.
  * 
- *    Copyright (C) 2009  Fred Cohan, Wesleyan University
- *                        Carlo Francisco, Wesleyan University
- *                        Danny Krizanc, Wesleyan University
- *                        Andrew Warner, Wesleyan University
- *                        Jason Wood, Montana State University
+ *    Copyright (C) 2009  Andrew Warner, Wesleyan University
  *
  *    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
+ *    the Free Software Foundation, either version 2 of the License, or
  *    (at your option) any later version.
  *
  *    This program is distributed in the hope that it will be useful,

diff --git a/src/java/CustomTokenizer.java b/src/java/CustomTokenizer.java
@@ -3,15 +3,11 @@
  *    the evolutionary result of net ecotype formation, periodic selection,
  *    and drift, yielding a certain number of ecotypes.
  * 
- *    Copyright (C) 2009  Fred Cohan, Wesleyan University
- *                        Carlo Francisco, Wesleyan University
- *                        Danny Krizanc, Wesleyan University
- *                        Andrew Warner, Wesleyan University
- *                        Jason Wood, Montana State University
+ *    Copyright (C) 2009  Andrew Warner, Wesleyan University
  *
  *    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
+ *    the Free Software Foundation, either version 2 of the License, or
  *    (at your option) any later version.
  *
  *    This program is distributed in the hope that it will be useful,

diff --git a/src/java/DemarcationConfidence.java b/src/java/DemarcationConfidence.java
@@ -3,15 +3,11 @@
  *    the evolutionary result of net ecotype formation, periodic selection,
  *    and drift, yielding a certain number of ecotypes.
  * 
- *    Copyright (C) 2009  Fred Cohan, Wesleyan University
- *                        Carlo Francisco, Wesleyan University
- *                        Danny Krizanc, Wesleyan University
- *                        Andrew Warner, Wesleyan University
- *                        Jason Wood, Montana State University
+ *    Copyright (C) 2009  Andrew Warner, Wesleyan University
  *
  *    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
+ *    the Free Software Foundation, either version 2 of the License, or
  *    (at your option) any later version.
  *
  *    This program is distributed in the hope that it will be useful,

diff --git a/src/java/Demarcations.java b/src/java/Demarcations.java
@@ -2,16 +2,12 @@
  *    Ecotype Simulation models the sequence diversity within a bacterial clade as
  *    the evolutionary result of net ecotype formation, periodic selection,
  *    and drift, yielding a certain number of ecotypes.
- * 
- *    Copyright (C) 2009  Fred Cohan, Wesleyan University
- *                        Carlo Francisco, Wesleyan University
- *                        Danny Krizanc, Wesleyan University
- *                        Andrew Warner, Wesleyan University
- *                        Jason Wood, Montana State University
+ *
+ *    Copyright (C) 2009  Andrew Warner, Wesleyan University
  *
  *    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
+ *    the Free Software Foundation, either version 2 of the License, or
  *    (at your option) any later version.
  *
  *    This program is distributed in the hope that it will be useful,

diff --git a/src/java/DemarcationsAuto.java b/src/java/DemarcationsAuto.java
@@ -3,15 +3,11 @@
  *    the evolutionary result of net ecotype formation, periodic selection,
  *    and drift, yielding a certain number of ecotypes.
  *
- *    Copyright (C) 2009  Fred Cohan, Wesleyan University
- *                        Carlo Francisco, Wesleyan University
- *                        Danny Krizanc, Wesleyan University
- *                        Andrew Warner, Wesleyan University
- *                        Jason Wood, Montana State University
+ *    Copyright (C) 2009  Carlo Francisco, Wesleyan University
  *
  *    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
+ *    the Free Software Foundation, either version 2 of the License, or
  *    (at your option) any later version.
  *
  *    This program is distributed in the hope that it will be useful,