[med-svn] [amap-align] 02/02: Cleanup repository from remainings of a local build process
Andreas Tille
tille at debian.org
Fri Aug 5 07:17:10 UTC 2016
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository amap-align.
commit f1360c520c3e000df03e358cfd003bef0857a4e2
Author: Andreas Tille <tille at debian.org>
Date: Fri Aug 5 09:15:42 2016 +0200
Cleanup repository from remainings of a local build process
---
debian/amap-align/DEBIAN/control | 19 ----
debian/amap-align/DEBIAN/md5sums | 10 --
debian/amap-align/usr/bin/amap | Bin 242384 -> 0 bytes
.../usr/share/doc/amap-align/NEWS.Debian.gz | Bin 381 -> 0 bytes
.../usr/share/doc/amap-align/PROBCONS.README | 102 ---------------------
debian/amap-align/usr/share/doc/amap-align/README | 39 --------
.../usr/share/doc/amap-align/README.Debian | 16 ----
.../usr/share/doc/amap-align/changelog.Debian.gz | Bin 1639 -> 0 bytes
.../amap-align/usr/share/doc/amap-align/copyright | 55 -----------
.../usr/share/doc/amap-align/examples/BB12020.tfa | 16 ----
.../doc/amap-align/examples/BB12020.tfa.out.gz | Bin 21548 -> 0 bytes
debian/amap-align/usr/share/man/man1/amap.1.gz | Bin 2898 -> 0 bytes
12 files changed, 257 deletions(-)
diff --git a/debian/amap-align/DEBIAN/control b/debian/amap-align/DEBIAN/control
deleted file mode 100644
index 64e18d5..0000000
--- a/debian/amap-align/DEBIAN/control
+++ /dev/null
@@ -1,19 +0,0 @@
-Package: amap-align
-Version: 2.2-5
-Architecture: amd64
-Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
-Installed-Size: 286
-Depends: libc6 (>= 2.14), libgcc1 (>= 1:3.0), libstdc++6 (>= 5.2)
-Section: science
-Priority: optional
-Homepage: http://code.google.com/p/amap-align/
-Description: Protein multiple alignment by sequence annealing
- AMAP is a command line tool to perform multiple alignment of peptidic
- sequences. It utilizes posterior decoding, and a sequence-annealing
- alignment, instead of the traditional progressive alignment method. It is
- the only alignment program that allows one to control the sensitivity /
- specificity tradeoff. It is based on the ProbCons source code, but
- uses alignment metric accuracy and eliminates the consistency
- transformation.
- .
- The java visualisation tool of AMAP 2.2 is not yet packaged in Debian.
diff --git a/debian/amap-align/DEBIAN/md5sums b/debian/amap-align/DEBIAN/md5sums
deleted file mode 100644
index eb643f5..0000000
--- a/debian/amap-align/DEBIAN/md5sums
+++ /dev/null
@@ -1,10 +0,0 @@
-aac4ee8ce681dbf64eddb28dbace3576 usr/bin/amap
-700d016e862d09692f569a2375817ef2 usr/share/doc/amap-align/NEWS.Debian.gz
-c06c1a4c550038626184ff7ea9982333 usr/share/doc/amap-align/PROBCONS.README
-0a6e235bf1e4602b1a11c259dd48c559 usr/share/doc/amap-align/README
-a9355edee70f81e338a7841f3cf9d624 usr/share/doc/amap-align/README.Debian
-189c90495f0aaaf2e0da2bf209c304c5 usr/share/doc/amap-align/changelog.Debian.gz
-aaa2261775f4587839f2f5ba9aa3a3d3 usr/share/doc/amap-align/copyright
-81603e893b72c98ca63f37ede7015cd8 usr/share/doc/amap-align/examples/BB12020.tfa
-52f07075b64ed6bdfdda5badff671c0b usr/share/doc/amap-align/examples/BB12020.tfa.out.gz
-19e6e2207f064b3202447ff367213722 usr/share/man/man1/amap.1.gz
diff --git a/debian/amap-align/usr/bin/amap b/debian/amap-align/usr/bin/amap
deleted file mode 100755
index 3581bfa..0000000
Binary files a/debian/amap-align/usr/bin/amap and /dev/null differ
diff --git a/debian/amap-align/usr/share/doc/amap-align/NEWS.Debian.gz b/debian/amap-align/usr/share/doc/amap-align/NEWS.Debian.gz
deleted file mode 100644
index 3fe8268..0000000
Binary files a/debian/amap-align/usr/share/doc/amap-align/NEWS.Debian.gz and /dev/null differ
diff --git a/debian/amap-align/usr/share/doc/amap-align/PROBCONS.README b/debian/amap-align/usr/share/doc/amap-align/PROBCONS.README
deleted file mode 100644
index 76d566c..0000000
--- a/debian/amap-align/usr/share/doc/amap-align/PROBCONS.README
+++ /dev/null
@@ -1,102 +0,0 @@
-
- PROBCONS
- ~~~~~~~~
-
- Probabilistic consistency-based multiple sequence alignment
-
------------------------------------------------------------------
-
-PROBCONS is a novel tool for generating multiple alignments
-of protein sequences. Using a combination of probabilistic
-modeling and consistency-based alignment techniques, PROBCONS
-has achieved the highest accuracy of all alignment methods to
-date.
-
-PROBCONS was developed by Chuong B. Do in collaboration with
-Michael Brudno in the research group of Serafim Batzoglou,
-Department of Computer Science, Stanford University.
-
-For more information on the algorithms, please see
-
- Do, C.B., Brudno, M., and Batzoglou, S. (2004) PROBCONS:
- Probabilistic Consistency-based Multiple Alignment of
- Amino Acid Sequences. 12th International Conference on
- Intelligent Systems for Molecular Biology. In press.
-
-and
-
- Do, C.B., Brudno, M., and Batzoglou, S. (2004) PROBCONS:
- Probabilistic Consistency-based Multiple Alignment of
- Amino Acid Sequences. The 19th National Conference on
- Artificial Intelligence (AAAI-04). In press.
-
------------------------------------------------------------------
-
-PROBCONS has been made freely available as PUBLIC DOMAIN
-software and hence is not subject to copyright in the United
-States. This system and/or any portion of the source code
-may be used, modified, or redistributed without restrictions.
-PROBCONS is distributed WITHOUT WARRANTY, express or implied.
-The authors accept NO LEGAL LIABILITY OR RESPONSIBILITY for
-loss due to reliance on the program.
-
------------------------------------------------------------------
-
-Version History
-
-1.0, 3/23/2004 (Chuong Do)
- -- initial release
-
-1.01, 3/25/2004 (Chuong Do)
- -- fixed error in training procedure
- -- retrained default parameters for 1 and 2 pairs of insert
- states
-
-1.02, 4/17/2004 (Chuong Do)
- -- replaced LOG_ADD and EXP routines
- -- added support for reading MSF format files
- -- added two extra utilities for scoring PROBCONS alignments
- (for benchmarking purposes)
- -- added the "compare" program for scoring alignments
- according to a reference alignment with respect to
- sum-of-pairs and column scores
- -- added the "fixref" program for adjusting PREFAB
- alignments to contain all letters of the input
- sequences; basically the main program for PROBCONS
- "hacked" to get the job done
-
-1.03, 5/3/2004 (Chuong Do)
- -- added option to do all-pairs pairwise alignments instead
- of constructing a full multiple alignment
- -- added support for reading DIALIGN style files
- -- enabled support for using BAliBASE annotations for scoring
- BAliBASE alignments
- -- several minor bug fixes thanks to Bob Edgar
- -- added "project" program to project multiple alignment to
- pairwise alignments
-
-1.04, 5/9/2004 (Chuong Do)
- -- switched over to default of one-insert state pair
- -- retrained default parameters
- -- added annotation scores
- -- small changes to model topology to make end gaps symmetrical
- -- added makegnuplot utility to plot annotation scores
-
-1.05, 5/26/2004 (Chuong Do)
- -- added cutoff filtering for posterior scores
- -- made small corrections to recurrences for computing alignments
- -- added CLUSTALW output support
-
-1.06, 7/13/2004 (Chuong Do)
- -- ProbCons is now PUBLIC DOMAIN software.
-
-1.07, 8/30/2004 (Chuong Do)
- -- Fixed CLUSTALW output for sequence names (thanks to John Calley
- for pointing this out)
-
-1.08, 8/31/2004 (Chuong Do)
- -- Added option for alignment order output (-a).
-
-1.09, 9/1/2004 (Chuong Do)
- -- PROBCONS now allows input files with existing gaps -- these are
- automatically stripped before alignment.
diff --git a/debian/amap-align/usr/share/doc/amap-align/README b/debian/amap-align/usr/share/doc/amap-align/README
deleted file mode 100644
index f9ec8cb..0000000
--- a/debian/amap-align/usr/share/doc/amap-align/README
+++ /dev/null
@@ -1,39 +0,0 @@
-
-See http://baboon.math.berkeley.edu/amap/ for more information.
-
-INSTALL
-=======
-
-To build the AMAP alignment code change to the 'align' directory and type:
-
- % make
-
-
-This distribution includes the compiled AmapDisplay.jar file.
-In case you want to build the AmapDisplay from the source code,
-you'll need ant (http://ant.apache.org) installed.
-Once ant is installed change to the 'display' directory, and type:
-
- % ant all
-
-USE
-===
-To run AMAP with the default options change to the 'align' directory and type:
- % amap <multi-fasta-file-name>
-
-If no file name is provided the list of options are printed.
-
-In order to use the AMAP Display run AMAP with the -gui option, and save the output to a file,
-then use the file as the input to AmapDisplay. For example, type:
-
- % align/amap -gui examples/BB12020.tfa > examples/BB12020.tfa.out
- % java -jar display/AmapDisplay.jar examples/BB12020.tfa.out
-
-
-LICENSE
-=======
-
-The various bits of AMAP code are distributed under the GPL. Please see the license
-in the license directory for details.
-
-
diff --git a/debian/amap-align/usr/share/doc/amap-align/README.Debian b/debian/amap-align/usr/share/doc/amap-align/README.Debian
deleted file mode 100644
index ee56b8c..0000000
--- a/debian/amap-align/usr/share/doc/amap-align/README.Debian
+++ /dev/null
@@ -1,16 +0,0 @@
-amap for Debian
-===============
-
-Please note that the previous upstream homepage
- http://bio.math.berkeley.edu/amap/
-vanished and there is no information left about further updates
-of this program.
-
-The version hosted at
- http://code.google.com/p/amap-align/
-is older than the Debian packaged version.
-
-If you have any knowledge about new location of the code, please
-drop a note to the address below.
-
- -- Andreas Tille <tille at debian.org> Thu, 13 Jan 2011 13:50:30 +0100
diff --git a/debian/amap-align/usr/share/doc/amap-align/changelog.Debian.gz b/debian/amap-align/usr/share/doc/amap-align/changelog.Debian.gz
deleted file mode 100644
index b8d55a1..0000000
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diff --git a/debian/amap-align/usr/share/doc/amap-align/copyright b/debian/amap-align/usr/share/doc/amap-align/copyright
deleted file mode 100644
index 8f9fccc..0000000
--- a/debian/amap-align/usr/share/doc/amap-align/copyright
+++ /dev/null
@@ -1,55 +0,0 @@
-Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
-Upstream-Author: Ariel Schwartz <sariel at cs.berkeley.edu>
-Source: http://bio.math.berkeley.edu/amap/download
- This download area as well as the homepage vanished
-
-Files: *
-Copyright: 2005—2007 Ariel Schwartz <sariel at cs.berkeley.edu>
-License: PD
-
-Files: display/*
-Copyright: © 2007 Michael E. Smoot
-License: GPL-2+
- 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 2 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, write to the Free Software Foundation, Inc.,
- 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
- .
- On Debian systems, the complete text of the GNU General Public
- License can be found in `/usr/share/common-licenses/GPL'.
-
-License: PD
- The current version of AMAP uses the PROBCONS 1.09 code base for some of the
- input/output procedures, and for the calculation of posterior probabilities
- (see PROBCONS.README).
- .
- AMAP has been made freely available as PUBLIC DOMAIN software and hence is
- not subject to copyright in the United States. This system and/or any portion
- of the source code may be used, modified, or redistributed without
- restrictions. AMAP is distributed WITHOUT WARRANTY, express or implied. The
- authors accept NO LEGAL LIABILITY OR RESPONSIBILITY for loss due to reliance on
- the program.
- .
- PROBCONS is copyright © 2004 Chuong Do <chuongdo at cs.stanford.edu>
- .
- PROBCONS has been made freely available as PUBLIC DOMAIN software and
- hence is not subject to copyright in the United States. This system and/or
- any portion of the source code may be used, modified, or redistributed
- without restrictions. PROBCONS is distributed WITHOUT WARRANTY, express or
- implied. The authors accept NO LEGAL LIABILITY OR RESPONSIBILITY for loss
- due to reliance on the program.
-
-Files: debian/*
-Copyright: © 2007 David Paleino <d.paleino at gmail.com>
- © 2006—2008 Charles Plessy <chalres-debian-nospam at plessy.org>
- © 2011-2013 Andreas Tille <tille at debian.org>
-License: PD
diff --git a/debian/amap-align/usr/share/doc/amap-align/examples/BB12020.tfa b/debian/amap-align/usr/share/doc/amap-align/examples/BB12020.tfa
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--- a/debian/amap-align/usr/share/doc/amap-align/examples/BB12020.tfa
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->1vvc_
-VKCQSPPSISNGRHNGYEDFYTDGSVVTYSCNSGYSLIGNSGVLCSGGEW
-SDPPTCQIVKCPHPTISNGYLSSGFKRSYSYNDNVDFKCKYGYKLSGSSS
-STCSPGNTWKPELPKCVR
->1ghq_B
-AISCGSPPPILNGRISYYSTPIAVGTVIRYSCSGTFRLIGEKSLLCITKD
-KVDGTWDKPAPKCEYFNKYSSCPEPIVPGGYKIRGSTPYRHGDSVTFACK
-TNFSMNGNKSVWCQANNMWGPTRLPTCVS
->1ckl_A
-CEEPPTFEAMELIGKPKPYYEIGERVDYKCKKGYFYIPPLATHTICDRNH
-TWLPVSDDACYRETCPYIRDPLNGQAVPANGTYEFGYQMHFICNEGYYLI
-GEEILYCELKGSVAIWSGKPPICEKV
->1nwv_A
-FRSCEVPTRLNSASLKQPYITQNYFPVGTVVEYECRPGYRREPSLSPKLT
-CLQNLKWSTAVEFCKKKSCPNPGEIRNGQIDVPGGILFGATISFSCNTGY
-KLFGSTSSFCLISGSSVQWSDPLPECREH
diff --git a/debian/amap-align/usr/share/doc/amap-align/examples/BB12020.tfa.out.gz b/debian/amap-align/usr/share/doc/amap-align/examples/BB12020.tfa.out.gz
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