[med-svn] [phipack] 01/05: Imported Upstream version 0.0.20160623
Andreas Tille
tille at debian.org
Thu Jun 23 14:06:03 UTC 2016
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository phipack.
commit d9d52ffb4290ebfe8ee6def33f672e86090dbf9d
Author: Andreas Tille <tille at debian.org>
Date: Thu Jun 23 16:01:45 2016 +0200
Imported Upstream version 0.0.20160623
---
ATP6.phy | 0
README | 18 +++++
ppma_2_bmp | Bin 0 -> 58172 bytes
src/COPYING.LESSER | 165 ++++++++++++++++++++++++++++++++++++++++++++
src/Makefile | 0
src/fasta.c | 20 +++++-
src/fasta.h | 17 +++++
src/global.c | 16 +++++
src/global.h | 15 ++++
src/graphCode.c | 19 ++++-
src/graphCode.h | 16 +++++
src/main.c | 19 ++++-
src/maxChi.c | 18 ++++-
src/maxChi.h | 16 +++++
src/mem.c | 16 +++++
src/mem.h | 16 ++++-
src/misc.c | 16 +++++
src/misc.h | 16 +++++
src/options.h | 16 +++++
src/pairScore.c | 19 ++++-
src/pairScore.h | 15 ++++
src/phylip.c | 17 ++++-
src/phylip.h | 16 +++++
src/ppma_2_bmp/Makefile | 0
src/ppma_2_bmp/ppma_2_bmp | Bin 0 -> 58172 bytes
src/ppma_2_bmp/ppma_2_bmp.C | 1 +
src/ppma_2_bmp/ppma_io.C | 1 +
src/profile.c | 17 ++++-
src/profile_options.h | 16 +++++
src/queue.c | 19 ++++-
src/queue.h | 15 ++++
src/seqManip.c | 19 ++++-
src/seqManip.h | 15 ++++
src/stats.c | 19 ++++-
src/stats.h | 15 ++++
35 files changed, 603 insertions(+), 20 deletions(-)
diff --git a/ATP6.phy b/ATP6.phy
old mode 100755
new mode 100644
diff --git a/README b/README
index b5d7c46..3c4ae8b 100644
--- a/README
+++ b/README
@@ -18,3 +18,21 @@ See the file manual.pdf for further details.
Email comments or questions to trevor at mcb.mcgill.ca
See also: www.mcb.mcgill.ca/~trevor
+
+
+/* This file is part of PhiPack.
+ Copyright (c)2005, Trevor Bruen
+ Foobar is free software: you can redistribute it and/or modify
+ it under the terms of the GNU Lesser General Public License as published by
+ the Free Software Foundation, either version 3 of the License, or
+ (at your option) any later version.
+
+ Foobar 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 Lesser General Public License for more details.
+
+ You should have received a copy of the GNU General Public License
+ along with PhiPack. If not, see <http://www.gnu.org/licenses/>.
+ */
+
diff --git a/ppma_2_bmp b/ppma_2_bmp
new file mode 100644
index 0000000..c8c1df4
Binary files /dev/null and b/ppma_2_bmp differ
diff --git a/src/COPYING.LESSER b/src/COPYING.LESSER
new file mode 100644
index 0000000..65c5ca8
--- /dev/null
+++ b/src/COPYING.LESSER
@@ -0,0 +1,165 @@
+ GNU LESSER GENERAL PUBLIC LICENSE
+ Version 3, 29 June 2007
+
+ Copyright (C) 2007 Free Software Foundation, Inc. <http://fsf.org/>
+ Everyone is permitted to copy and distribute verbatim copies
+ of this license document, but changing it is not allowed.
+
+
+ This version of the GNU Lesser General Public License incorporates
+the terms and conditions of version 3 of the GNU General Public
+License, supplemented by the additional permissions listed below.
+
+ 0. Additional Definitions.
+
+ As used herein, "this License" refers to version 3 of the GNU Lesser
+General Public License, and the "GNU GPL" refers to version 3 of the GNU
+General Public License.
+
+ "The Library" refers to a covered work governed by this License,
+other than an Application or a Combined Work as defined below.
+
+ An "Application" is any work that makes use of an interface provided
+by the Library, but which is not otherwise based on the Library.
+Defining a subclass of a class defined by the Library is deemed a mode
+of using an interface provided by the Library.
+
+ A "Combined Work" is a work produced by combining or linking an
+Application with the Library. The particular version of the Library
+with which the Combined Work was made is also called the "Linked
+Version".
+
+ The "Minimal Corresponding Source" for a Combined Work means the
+Corresponding Source for the Combined Work, excluding any source code
+for portions of the Combined Work that, considered in isolation, are
+based on the Application, and not on the Linked Version.
+
+ The "Corresponding Application Code" for a Combined Work means the
+object code and/or source code for the Application, including any data
+and utility programs needed for reproducing the Combined Work from the
+Application, but excluding the System Libraries of the Combined Work.
+
+ 1. Exception to Section 3 of the GNU GPL.
+
+ You may convey a covered work under sections 3 and 4 of this License
+without being bound by section 3 of the GNU GPL.
+
+ 2. Conveying Modified Versions.
+
+ If you modify a copy of the Library, and, in your modifications, a
+facility refers to a function or data to be supplied by an Application
+that uses the facility (other than as an argument passed when the
+facility is invoked), then you may convey a copy of the modified
+version:
+
+ a) under this License, provided that you make a good faith effort to
+ ensure that, in the event an Application does not supply the
+ function or data, the facility still operates, and performs
+ whatever part of its purpose remains meaningful, or
+
+ b) under the GNU GPL, with none of the additional permissions of
+ this License applicable to that copy.
+
+ 3. Object Code Incorporating Material from Library Header Files.
+
+ The object code form of an Application may incorporate material from
+a header file that is part of the Library. You may convey such object
+code under terms of your choice, provided that, if the incorporated
+material is not limited to numerical parameters, data structure
+layouts and accessors, or small macros, inline functions and templates
+(ten or fewer lines in length), you do both of the following:
+
+ a) Give prominent notice with each copy of the object code that the
+ Library is used in it and that the Library and its use are
+ covered by this License.
+
+ b) Accompany the object code with a copy of the GNU GPL and this license
+ document.
+
+ 4. Combined Works.
+
+ You may convey a Combined Work under terms of your choice that,
+taken together, effectively do not restrict modification of the
+portions of the Library contained in the Combined Work and reverse
+engineering for debugging such modifications, if you also do each of
+the following:
+
+ a) Give prominent notice with each copy of the Combined Work that
+ the Library is used in it and that the Library and its use are
+ covered by this License.
+
+ b) Accompany the Combined Work with a copy of the GNU GPL and this license
+ document.
+
+ c) For a Combined Work that displays copyright notices during
+ execution, include the copyright notice for the Library among
+ these notices, as well as a reference directing the user to the
+ copies of the GNU GPL and this license document.
+
+ d) Do one of the following:
+
+ 0) Convey the Minimal Corresponding Source under the terms of this
+ License, and the Corresponding Application Code in a form
+ suitable for, and under terms that permit, the user to
+ recombine or relink the Application with a modified version of
+ the Linked Version to produce a modified Combined Work, in the
+ manner specified by section 6 of the GNU GPL for conveying
+ Corresponding Source.
+
+ 1) Use a suitable shared library mechanism for linking with the
+ Library. A suitable mechanism is one that (a) uses at run time
+ a copy of the Library already present on the user's computer
+ system, and (b) will operate properly with a modified version
+ of the Library that is interface-compatible with the Linked
+ Version.
+
+ e) Provide Installation Information, but only if you would otherwise
+ be required to provide such information under section 6 of the
+ GNU GPL, and only to the extent that such information is
+ necessary to install and execute a modified version of the
+ Combined Work produced by recombining or relinking the
+ Application with a modified version of the Linked Version. (If
+ you use option 4d0, the Installation Information must accompany
+ the Minimal Corresponding Source and Corresponding Application
+ Code. If you use option 4d1, you must provide the Installation
+ Information in the manner specified by section 6 of the GNU GPL
+ for conveying Corresponding Source.)
+
+ 5. Combined Libraries.
+
+ You may place library facilities that are a work based on the
+Library side by side in a single library together with other library
+facilities that are not Applications and are not covered by this
+License, and convey such a combined library under terms of your
+choice, if you do both of the following:
+
+ a) Accompany the combined library with a copy of the same work based
+ on the Library, uncombined with any other library facilities,
+ conveyed under the terms of this License.
+
+ b) Give prominent notice with the combined library that part of it
+ is a work based on the Library, and explaining where to find the
+ accompanying uncombined form of the same work.
+
+ 6. Revised Versions of the GNU Lesser General Public License.
+
+ The Free Software Foundation may publish revised and/or new versions
+of the GNU Lesser General Public License from time to time. Such new
+versions will be similar in spirit to the present version, but may
+differ in detail to address new problems or concerns.
+
+ Each version is given a distinguishing version number. If the
+Library as you received it specifies that a certain numbered version
+of the GNU Lesser General Public License "or any later version"
+applies to it, you have the option of following the terms and
+conditions either of that published version or of any later version
+published by the Free Software Foundation. If the Library as you
+received it does not specify a version number of the GNU Lesser
+General Public License, you may choose any version of the GNU Lesser
+General Public License ever published by the Free Software Foundation.
+
+ If the Library as you received it specifies that a proxy can decide
+whether future versions of the GNU Lesser General Public License shall
+apply, that proxy's public statement of acceptance of any version is
+permanent authorization for you to choose that version for the
+Library.
diff --git a/src/Makefile b/src/Makefile
old mode 100755
new mode 100644
diff --git a/src/fasta.c b/src/fasta.c
index 1bf58bc..a296a9c 100644
--- a/src/fasta.c
+++ b/src/fasta.c
@@ -1,11 +1,27 @@
/*
Copyright (c)2005, Trevor Bruen
- All rights reserved.
Any feedback is very welcome.
- email: trevor at mcb.mcgill.ca
+ email: david.bryant at otago.ac.nz
*/
+/* This file is part of PhiPack.
+
+Foobar is free software: you can redistribute it and/or modify
+it under the terms of the GNU Lesser General Public License as published by
+the Free Software Foundation, either version 3 of the License, or
+(at your option) any later version.
+
+Foobar 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 Lesser General Public License for more details.
+
+You should have received a copy of the GNU General Public License
+along with PhiPack. If not, see <http://www.gnu.org/licenses/>.
+ */
+
+
#include "global.h"
#include "mem.h"
diff --git a/src/fasta.h b/src/fasta.h
index 2b4abbb..6066f74 100644
--- a/src/fasta.h
+++ b/src/fasta.h
@@ -1,6 +1,23 @@
#ifndef FASTA
#define FASTA
+/* This file is part of PhiPack.
+ Copyright (c)2005, Trevor Bruen
+ Foobar is free software: you can redistribute it and/or modify
+ it under the terms of the GNU Lesser General Public License as published by
+ the Free Software Foundation, either version 3 of the License, or
+ (at your option) any later version.
+
+ Foobar 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 Lesser General Public License for more details.
+
+ You should have received a copy of the GNU General Public License
+ along with PhiPack. If not, see <http://www.gnu.org/licenses/>.
+ */
+
+
void write_fasta(FILE* cur_stream, char **taxa_names,align_type **alignment, int num_taxa,int num_sites);
void read_fasta(const char* file_name, char ***taxa_names, align_type ***alignment, int *num_taxa, int *num_sites);
diff --git a/src/global.c b/src/global.c
index d4f091b..3da8a45 100644
--- a/src/global.c
+++ b/src/global.c
@@ -1,3 +1,19 @@
+/* This file is part of PhiPack.
+ Copyright (c)2005, Trevor Bruen
+ Foobar is free software: you can redistribute it and/or modify
+ it under the terms of the GNU Lesser General Public License as published by
+ the Free Software Foundation, either version 3 of the License, or
+ (at your option) any later version.
+
+ Foobar 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 Lesser General Public License for more details.
+
+ You should have received a copy of the GNU General Public License
+ along with PhiPack. If not, see <http://www.gnu.org/licenses/>.
+ */
+
#include "global.h"
const char DNA_ALPHA[] = {'A','C','G','T'};
const int DNA_ALPHA_SIZE=4;
diff --git a/src/global.h b/src/global.h
index 7c7babe..05c6a82 100644
--- a/src/global.h
+++ b/src/global.h
@@ -1,3 +1,18 @@
+/* This file is part of PhiPack.
+ Copyright (c)2005, Trevor Bruen
+ Foobar is free software: you can redistribute it and/or modify
+ it under the terms of the GNU Lesser General Public License as published by
+ the Free Software Foundation, either version 3 of the License, or
+ (at your option) any later version.
+
+ Foobar 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 Lesser General Public License for more details.
+
+ You should have received a copy of the GNU General Public License
+ along with PhiPack. If not, see <http://www.gnu.org/licenses/>.
+ */
#ifndef GLOBAL
#define GLOBAL
diff --git a/src/graphCode.c b/src/graphCode.c
index c9744f7..1eb17ce 100644
--- a/src/graphCode.c
+++ b/src/graphCode.c
@@ -1,9 +1,22 @@
/*
- Copyright (c)2005, Trevor Bruen
- All rights reserved.
+ /* This file is part of PhiPack.
+ Copyright (c)2005, Trevor Bruen
+ Foobar is free software: you can redistribute it and/or modify
+ it under the terms of the GNU Lesser General Public License as published by
+ the Free Software Foundation, either version 3 of the License, or
+ (at your option) any later version.
+
+ Foobar 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 Lesser General Public License for more details.
+
+ You should have received a copy of the GNU General Public License
+ along with PhiPack. If not, see <http://www.gnu.org/licenses/>.
+
Any feedback is very welcome.
- email: trevor at mcb.mcgill.ca
+ email: david.bryant at otago.ac.nz
*/
#include <stdlib.h>
diff --git a/src/graphCode.h b/src/graphCode.h
index 46bbb1f..0b619e8 100644
--- a/src/graphCode.h
+++ b/src/graphCode.h
@@ -1,3 +1,19 @@
+/* This file is part of PhiPack.
+ Copyright (c)2005, Trevor Bruen
+ Foobar is free software: you can redistribute it and/or modify
+ it under the terms of the GNU Lesser General Public License as published by
+ the Free Software Foundation, either version 3 of the License, or
+ (at your option) any later version.
+
+ Foobar 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 Lesser General Public License for more details.
+
+ You should have received a copy of the GNU General Public License
+ along with PhiPack. If not, see <http://www.gnu.org/licenses/>.
+ */
+
#ifndef GRAPH
#define GRAPH
diff --git a/src/main.c b/src/main.c
index 8d2a183..9cb6983 100644
--- a/src/main.c
+++ b/src/main.c
@@ -1,10 +1,25 @@
-/*
+/*
Copyright (c)2005, Trevor Bruen
All rights reserved.
Any feedback is very welcome.
- email: trevor at mcb.mcgill.ca
+ email: david.bryant at otago.ac.nz
*/
+/* This file is part of PhiPack.
+ Copyright (c)2005, Trevor Bruen
+ Foobar is free software: you can redistribute it and/or modify
+ it under the terms of the GNU Lesser General Public License as published by
+ the Free Software Foundation, either version 3 of the License, or
+ (at your option) any later version.
+
+ Foobar 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 Lesser General Public License for more details.
+
+ You should have received a copy of the GNU General Public License
+ along with PhiPack. If not, see <http://www.gnu.org/licenses/>.
+ */
#include <time.h>
diff --git a/src/maxChi.c b/src/maxChi.c
index 5eafa87..63b6e22 100644
--- a/src/maxChi.c
+++ b/src/maxChi.c
@@ -3,9 +3,23 @@
All rights reserved.
Any feedback is very welcome.
- email: trevor at mcb.mcgill.ca
+ email: david.bryant at otago.ac.nz
*/
-
+/* This file is part of PhiPack.
+ Copyright (c)2005, Trevor Bruen
+ Foobar is free software: you can redistribute it and/or modify
+ it under the terms of the GNU Lesser General Public License as published by
+ the Free Software Foundation, either version 3 of the License, or
+ (at your option) any later version.
+
+ Foobar 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 Lesser General Public License for more details.
+
+ You should have received a copy of the GNU General Public License
+ along with PhiPack. If not, see <http://www.gnu.org/licenses/>.
+ */
#include "global.h"
#include "mem.h"
diff --git a/src/maxChi.h b/src/maxChi.h
index f96ca53..40a6628 100644
--- a/src/maxChi.h
+++ b/src/maxChi.h
@@ -1,3 +1,19 @@
+/* This file is part of PhiPack.
+ Copyright (c)2005, Trevor Bruen
+ Foobar is free software: you can redistribute it and/or modify
+ it under the terms of the GNU Lesser General Public License as published by
+ the Free Software Foundation, either version 3 of the License, or
+ (at your option) any later version.
+
+ Foobar 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 Lesser General Public License for more details.
+
+ You should have received a copy of the GNU General Public License
+ along with PhiPack. If not, see <http://www.gnu.org/licenses/>.
+ */
+
#include "global.h"
#ifndef MAXCHI
#define MAXCHI
diff --git a/src/mem.c b/src/mem.c
index cd1f640..c92877e 100644
--- a/src/mem.c
+++ b/src/mem.c
@@ -1,3 +1,19 @@
+/* This file is part of PhiPack.
+ Copyright (c)2005, Trevor Bruen
+ Foobar is free software: you can redistribute it and/or modify
+ it under the terms of the GNU Lesser General Public License as published by
+ the Free Software Foundation, either version 3 of the License, or
+ (at your option) any later version.
+
+ Foobar 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 Lesser General Public License for more details.
+
+ You should have received a copy of the GNU General Public License
+ along with PhiPack. If not, see <http://www.gnu.org/licenses/>.
+ */
+
#include "global.h"
#include "mem.h"
diff --git a/src/mem.h b/src/mem.h
index 8fccfe1..1e08864 100644
--- a/src/mem.h
+++ b/src/mem.h
@@ -1,4 +1,18 @@
-
+/* This file is part of PhiPack.
+ Copyright (c)2005, Trevor Bruen
+ Foobar is free software: you can redistribute it and/or modify
+ it under the terms of the GNU Lesser General Public License as published by
+ the Free Software Foundation, either version 3 of the License, or
+ (at your option) any later version.
+
+ Foobar 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 Lesser General Public License for more details.
+
+ You should have received a copy of the GNU General Public License
+ along with PhiPack. If not, see <http://www.gnu.org/licenses/>.
+ */
#ifndef MEM
#define MEM
diff --git a/src/misc.c b/src/misc.c
index acb563c..cec98c4 100644
--- a/src/misc.c
+++ b/src/misc.c
@@ -1,3 +1,19 @@
+/* This file is part of PhiPack.
+ Copyright (c)2005, Trevor Bruen
+ Foobar is free software: you can redistribute it and/or modify
+ it under the terms of the GNU Lesser General Public License as published by
+ the Free Software Foundation, either version 3 of the License, or
+ (at your option) any later version.
+
+ Foobar 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 Lesser General Public License for more details.
+
+ You should have received a copy of the GNU General Public License
+ along with PhiPack. If not, see <http://www.gnu.org/licenses/>.
+ */
+
#include "misc.h"
#include <ctype.h>
diff --git a/src/misc.h b/src/misc.h
index e313fbb..bc89c6a 100644
--- a/src/misc.h
+++ b/src/misc.h
@@ -1,3 +1,19 @@
+/* This file is part of PhiPack.
+ Copyright (c)2005, Trevor Bruen
+ Foobar is free software: you can redistribute it and/or modify
+ it under the terms of the GNU Lesser General Public License as published by
+ the Free Software Foundation, either version 3 of the License, or
+ (at your option) any later version.
+
+ Foobar 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 Lesser General Public License for more details.
+
+ You should have received a copy of the GNU General Public License
+ along with PhiPack. If not, see <http://www.gnu.org/licenses/>.
+ */
+
#include<stdlib.h>
#include<stdio.h>
#ifndef MISC
diff --git a/src/options.h b/src/options.h
index 87dc7c6..dc24205 100644
--- a/src/options.h
+++ b/src/options.h
@@ -1,3 +1,19 @@
+/* This file is part of PhiPack.
+ Copyright (c)2005, Trevor Bruen
+ Foobar is free software: you can redistribute it and/or modify
+ it under the terms of the GNU Lesser General Public License as published by
+ the Free Software Foundation, either version 3 of the License, or
+ (at your option) any later version.
+
+ Foobar 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 Lesser General Public License for more details.
+
+ You should have received a copy of the GNU General Public License
+ along with PhiPack. If not, see <http://www.gnu.org/licenses/>.
+ */
+
#ifndef OPTIONS
#define OPTIONS
diff --git a/src/pairScore.c b/src/pairScore.c
index de7afca..d7bfd7f 100644
--- a/src/pairScore.c
+++ b/src/pairScore.c
@@ -1,9 +1,24 @@
-/*
+/* This file is part of PhiPack.
+ Copyright (c)2005, Trevor Bruen
+ Foobar is free software: you can redistribute it and/or modify
+ it under the terms of the GNU Lesser General Public License as published by
+ the Free Software Foundation, either version 3 of the License, or
+ (at your option) any later version.
+
+ Foobar 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 Lesser General Public License for more details.
+
+ You should have received a copy of the GNU General Public License
+ along with PhiPack. If not, see <http://www.gnu.org/licenses/>.
+ */
+/*
Copyright (c)2005, Trevor Bruen
All rights reserved.
Any feedback is very welcome.
- email: trevor at mcb.mcgill.ca
+ email: david.bryant at otago.ac.nz
*/
#include "global.h"
diff --git a/src/pairScore.h b/src/pairScore.h
index 6ae938e..7f8a901 100644
--- a/src/pairScore.h
+++ b/src/pairScore.h
@@ -1,3 +1,18 @@
+/* This file is part of PhiPack.
+ Copyright (c)2005, Trevor Bruen
+ Foobar is free software: you can redistribute it and/or modify
+ it under the terms of the GNU Lesser General Public License as published by
+ the Free Software Foundation, either version 3 of the License, or
+ (at your option) any later version.
+
+ Foobar 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 Lesser General Public License for more details.
+
+ You should have received a copy of the GNU General Public License
+ along with PhiPack. If not, see <http://www.gnu.org/licenses/>.
+ */
#ifndef PAIRSCORE
#define PAIRSCORE
diff --git a/src/phylip.c b/src/phylip.c
index 3ed7024..0f8a26e 100644
--- a/src/phylip.c
+++ b/src/phylip.c
@@ -3,8 +3,23 @@
All rights reserved.
Any feedback is very welcome.
- email: trevor at mcb.mcgill.ca
+ email: david.bryant at otago.ac.nz
*/
+/* This file is part of PhiPack.
+ Copyright (c)2005, Trevor Bruen
+ Foobar is free software: you can redistribute it and/or modify
+ it under the terms of the GNU Lesser General Public License as published by
+ the Free Software Foundation, either version 3 of the License, or
+ (at your option) any later version.
+
+ Foobar 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 Lesser General Public License for more details.
+
+ You should have received a copy of the GNU General Public License
+ along with PhiPack. If not, see <http://www.gnu.org/licenses/>.
+ */
#include "global.h"
#include "mem.h"
diff --git a/src/phylip.h b/src/phylip.h
index 2a59aac..ef88ab4 100644
--- a/src/phylip.h
+++ b/src/phylip.h
@@ -1,3 +1,19 @@
+/* This file is part of PhiPack.
+ Copyright (c)2005, Trevor Bruen
+ Foobar is free software: you can redistribute it and/or modify
+ it under the terms of the GNU Lesser General Public License as published by
+ the Free Software Foundation, either version 3 of the License, or
+ (at your option) any later version.
+
+ Foobar 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 Lesser General Public License for more details.
+
+ You should have received a copy of the GNU General Public License
+ along with PhiPack. If not, see <http://www.gnu.org/licenses/>.
+ */
+
#ifndef PHYLIP
#define PHYLIP
diff --git a/src/ppma_2_bmp/Makefile b/src/ppma_2_bmp/Makefile
old mode 100755
new mode 100644
diff --git a/src/ppma_2_bmp/ppma_2_bmp b/src/ppma_2_bmp/ppma_2_bmp
new file mode 100644
index 0000000..c8c1df4
Binary files /dev/null and b/src/ppma_2_bmp/ppma_2_bmp differ
diff --git a/src/ppma_2_bmp/ppma_2_bmp.C b/src/ppma_2_bmp/ppma_2_bmp.C
index 885037a..e051ad6 100644
--- a/src/ppma_2_bmp/ppma_2_bmp.C
+++ b/src/ppma_2_bmp/ppma_2_bmp.C
@@ -3,6 +3,7 @@
# include <iomanip>
# include <fstream>
# include <ctime>
+# include <cstring>
using namespace std;
diff --git a/src/ppma_2_bmp/ppma_io.C b/src/ppma_2_bmp/ppma_io.C
index 6ea648c..823bb84 100644
--- a/src/ppma_2_bmp/ppma_io.C
+++ b/src/ppma_2_bmp/ppma_io.C
@@ -4,6 +4,7 @@
# include <fstream>
# include <cmath>
# include <ctime>
+# include <cstring>
using namespace std;
diff --git a/src/profile.c b/src/profile.c
index e018282..74d299c 100644
--- a/src/profile.c
+++ b/src/profile.c
@@ -3,8 +3,23 @@
All rights reserved.
Any feedback is very welcome.
- email: trevor at mcb.mcgill.ca
+ email: david.bryant at otago.ac.nz
*/
+/* This file is part of PhiPack.
+ Copyright (c)2005, Trevor Bruen
+ Foobar is free software: you can redistribute it and/or modify
+ it under the terms of the GNU Lesser General Public License as published by
+ the Free Software Foundation, either version 3 of the License, or
+ (at your option) any later version.
+
+ Foobar 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 Lesser General Public License for more details.
+
+ You should have received a copy of the GNU General Public License
+ along with PhiPack. If not, see <http://www.gnu.org/licenses/>.
+ */
#include <time.h>
diff --git a/src/profile_options.h b/src/profile_options.h
index 08fecbb..ba5d956 100644
--- a/src/profile_options.h
+++ b/src/profile_options.h
@@ -1,3 +1,19 @@
+/* This file is part of PhiPack.
+ Copyright (c)2005, Trevor Bruen
+ Foobar is free software: you can redistribute it and/or modify
+ it under the terms of the GNU Lesser General Public License as published by
+ the Free Software Foundation, either version 3 of the License, or
+ (at your option) any later version.
+
+ Foobar 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 Lesser General Public License for more details.
+
+ You should have received a copy of the GNU General Public License
+ along with PhiPack. If not, see <http://www.gnu.org/licenses/>.
+ */
+
#ifndef PROFILE_OPTIONS
#define PROFILE_OPTIONS
diff --git a/src/queue.c b/src/queue.c
index 2bd90f6..bc48775 100644
--- a/src/queue.c
+++ b/src/queue.c
@@ -1,9 +1,24 @@
-/*
+/* This file is part of PhiPack.
+ Copyright (c)2005, Trevor Bruen
+ Foobar is free software: you can redistribute it and/or modify
+ it under the terms of the GNU Lesser General Public License as published by
+ the Free Software Foundation, either version 3 of the License, or
+ (at your option) any later version.
+
+ Foobar 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 Lesser General Public License for more details.
+
+ You should have received a copy of the GNU General Public License
+ along with PhiPack. If not, see <http://www.gnu.org/licenses/>.
+ */
+/*
Copyright (c)2005, Trevor Bruen
All rights reserved.
Any feedback is very welcome.
- email: trevor at mcb.mcgill.ca
+ email: david.bryant at otago.ac.nz
*/
#include <stdlib.h>
diff --git a/src/queue.h b/src/queue.h
index d139ef5..b80c4d9 100644
--- a/src/queue.h
+++ b/src/queue.h
@@ -1,3 +1,18 @@
+/* This file is part of PhiPack.
+ Copyright (c)2005, Trevor Bruen
+ Foobar is free software: you can redistribute it and/or modify
+ it under the terms of the GNU Lesser General Public License as published by
+ the Free Software Foundation, either version 3 of the License, or
+ (at your option) any later version.
+
+ Foobar 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 Lesser General Public License for more details.
+
+ You should have received a copy of the GNU General Public License
+ along with PhiPack. If not, see <http://www.gnu.org/licenses/>.
+ */
#ifndef QUEUE
#define QUEUE 1
diff --git a/src/seqManip.c b/src/seqManip.c
index 599da88..6dfcd0b 100644
--- a/src/seqManip.c
+++ b/src/seqManip.c
@@ -1,9 +1,24 @@
-/*
+/* This file is part of PhiPack.
+ Copyright (c)2005, Trevor Bruen
+ Foobar is free software: you can redistribute it and/or modify
+ it under the terms of the GNU Lesser General Public License as published by
+ the Free Software Foundation, either version 3 of the License, or
+ (at your option) any later version.
+
+ Foobar 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 Lesser General Public License for more details.
+
+ You should have received a copy of the GNU General Public License
+ along with PhiPack. If not, see <http://www.gnu.org/licenses/>.
+ */
+/*
Copyright (c)2005, Trevor Bruen
All rights reserved.
Any feedback is very welcome.
- email: trevor at mcb.mcgill.ca
+ email: david.bryant at otago.ac.nz
*/
#include "global.h"
diff --git a/src/seqManip.h b/src/seqManip.h
index bb3cb3c..2f09dca 100644
--- a/src/seqManip.h
+++ b/src/seqManip.h
@@ -1,3 +1,18 @@
+/* This file is part of PhiPack.
+ Copyright (c)2005, Trevor Bruen
+ Foobar is free software: you can redistribute it and/or modify
+ it under the terms of the GNU Lesser General Public License as published by
+ the Free Software Foundation, either version 3 of the License, or
+ (at your option) any later version.
+
+ Foobar 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 Lesser General Public License for more details.
+
+ You should have received a copy of the GNU General Public License
+ along with PhiPack. If not, see <http://www.gnu.org/licenses/>.
+ */
#include "global.h"
#ifndef SEQMANIP
#define SEQMANIP
diff --git a/src/stats.c b/src/stats.c
index 725edbe..1f155e7 100644
--- a/src/stats.c
+++ b/src/stats.c
@@ -1,9 +1,24 @@
-/*
+/* This file is part of PhiPack.
+ Copyright (c)2005, Trevor Bruen
+ Foobar is free software: you can redistribute it and/or modify
+ it under the terms of the GNU Lesser General Public License as published by
+ the Free Software Foundation, either version 3 of the License, or
+ (at your option) any later version.
+
+ Foobar 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 Lesser General Public License for more details.
+
+ You should have received a copy of the GNU General Public License
+ along with PhiPack. If not, see <http://www.gnu.org/licenses/>.
+ */
+/*
Copyright (c)2005, Trevor Bruen
All rights reserved.
Any feedback is very welcome.
- email: trevor at mcb.mcgill.ca
+ email: david.bryant at otago.ac.nz
*/
#include "global.h"
diff --git a/src/stats.h b/src/stats.h
index 8ae279c..62e183b 100644
--- a/src/stats.h
+++ b/src/stats.h
@@ -1,3 +1,18 @@
+/* This file is part of PhiPack.
+ Copyright (c)2005, Trevor Bruen
+ Foobar is free software: you can redistribute it and/or modify
+ it under the terms of the GNU Lesser General Public License as published by
+ the Free Software Foundation, either version 3 of the License, or
+ (at your option) any later version.
+
+ Foobar 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 Lesser General Public License for more details.
+
+ You should have received a copy of the GNU General Public License
+ along with PhiPack. If not, see <http://www.gnu.org/licenses/>.
+ */
#ifndef STATS
#define STATS
--
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