gmane.linux.debian.devel.medical.scm

r11006 - trunk/packages/libforester-java/trunk/debian

Olivier Sallou — 2012-05-25T12:29:49

Author: osallou
Date: 2012-05-25 12:29:48 +0000 (Fri, 25 May 2012)
New Revision: 11006

Modified:
   trunk/packages/libforester-java/trunk/debian/control
Log:
fix dependency name

Modified: trunk/packages/libforester-java/trunk/debian/control
===================================================================
--- trunk/packages/libforester-java/trunk/debian/control2012-05-25 12:26:45 UTC (rev 11005)
+++ trunk/packages/libforester-java/trunk/debian/control2012-05-25 12:29:48 UTC (rev 11006)
< at >< at > -23,7 +23,7 < at >< at >
 Package: libforester-java
 Architecture: all
 Depends: ${misc:Depends},
- libcommons-codec, libitext-java
+ libcommons-codec-java, libitext-java
 Description: Libraries for evolutionary biology and comparative genomics research
  Forester is a library of Java software for phylogenomics 
  and evolutionary biology research. It can be used to read or

r11005 - trunk/packages/libforester-java/trunk/debian

Olivier Sallou — 2012-05-25T12:26:46

Author: osallou
Date: 2012-05-25 12:26:45 +0000 (Fri, 25 May 2012)
New Revision: 11005

Modified:
   trunk/packages/libforester-java/trunk/debian/control
Log:
fix dependency name

Modified: trunk/packages/libforester-java/trunk/debian/control
===================================================================
--- trunk/packages/libforester-java/trunk/debian/control2012-05-25 12:12:50 UTC (rev 11004)
+++ trunk/packages/libforester-java/trunk/debian/control2012-05-25 12:26:45 UTC (rev 11005)
< at >< at > -5,7 +5,7 < at >< at >
 DM-Upload-Allowed: yes
 Uploaders: Olivier Sallou <osallou< at >debian.org>
 Build-Depends: debhelper (>= 8.0.0),
- default-jdk, junit4, javahelper (>=0.25), libcommons-codec, libitext-java
+ default-jdk, junit4, javahelper (>=0.25), libcommons-codec-java, libitext-java
 Standards-Version: 3.9.3
 Homepage: http://code.google.com/p/forester
 Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/forester/trunk/

r11004 - trunk/packages/fasttree/trunk/debian

Andreas Tille — 2012-05-25T12:12:50

Author: tille
Date: 2012-05-25 12:12:50 +0000 (Fri, 25 May 2012)
New Revision: 11004

Modified:
   trunk/packages/fasttree/trunk/debian/copyright
Log:
DEP5


Modified: trunk/packages/fasttree/trunk/debian/copyright
===================================================================
--- trunk/packages/fasttree/trunk/debian/copyright2012-05-25 12:07:10 UTC (rev 11003)
+++ trunk/packages/fasttree/trunk/debian/copyright2012-05-25 12:12:50 UTC (rev 11004)
< at >< at > -1,10 +1,8 < at >< at >
-Format: http://dep.debian.net/deps/dep5
-Upstream-Name: fasttree
-Source: <url://example.com>
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: FastTree
+Source: http://www.microbesonline.org/fasttree/#Install
 
 Files: *
-Copyright: <years> <put author's name and email here>
-           <years> <likewise for another author>
 Copyright: (C) 2008-2009 The Regents of the University of California
 License: GPL-2.0+
 
< at >< at > -29,13 +27,3 < at >< at >
  On Debian systems, the complete text of the GNU General
  Public License version 3 can be found in "/usr/share/common-licenses/GPL-3".
 
-# Please choose a license for your packaging work. If the program you package
-# uses a mainstream license, using the same license is the safest choice.
-# Please avoid to pick license terms that are more restrictive than the
-# packaged work, as it may make Debian's contributions unacceptable upstream.
-# If you just want it to be GPL version 3, leave the following line in.
-
-and is licensed under the GPL version 3, see above.
-
-# Please also look if there are files or directories which have a
-# different copyright/license attached and list them here.

r11003 - trunk/packages/ecell/trunk/debian

Andreas Tille — 2012-05-25T12:07:11

Author: tille
Date: 2012-05-25 12:07:10 +0000 (Fri, 25 May 2012)
New Revision: 11003

Modified:
   trunk/packages/ecell/trunk/debian/copyright
Log:
Pseudo-DEP5 to enable machine-readable gatherer fetch license


Modified: trunk/packages/ecell/trunk/debian/copyright
===================================================================
--- trunk/packages/ecell/trunk/debian/copyright2012-05-25 12:02:58 UTC (rev 11002)
+++ trunk/packages/ecell/trunk/debian/copyright2012-05-25 12:07:10 UTC (rev 11003)
< at >< at > -1,10 +1,11 < at >< at >
-This package was debianized by Steffen Moeller <moeller< at >unknown> on
-Wed, 10 Mar 2004 22:08:00 +0100.
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: E-Cell
+Source: https://github.com/ecell/ecell.github.com
 
-It was downloaded from <fill in ftp site>
+Files: *
+Copyright: © -2003 ???
+License: GPL
 
-Upstream Author(s): <put author(s) name and email here>
-
-Copyright:
-
-<Must follow here>
+Files: debian/*
+Copyright: © 2004 Steffen Moeller <moeller< at >debian.org>
+License: GPL


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r11002 - trunk/packages/ecell/trunk/debian

Andreas Tille — 2012-05-25T12:02:58

Author: tille
Date: 2012-05-25 12:02:58 +0000 (Fri, 25 May 2012)
New Revision: 11002

Modified:
   trunk/packages/ecell/trunk/debian/control
Log:
Team maintained package


Modified: trunk/packages/ecell/trunk/debian/control
===================================================================
--- trunk/packages/ecell/trunk/debian/control2012-05-25 11:48:20 UTC (rev 11001)
+++ trunk/packages/ecell/trunk/debian/control2012-05-25 12:02:58 UTC (rev 11002)
< at >< at > -1,7 +1,9 < at >< at >
 Source: ecell
 Section: science
 Priority: optional
-Maintainer: Steffen Moeller <moeller< at >pzr.uni-rostock.de>
+Maintainer: Debian Med Packaging Team <debian-med-packaging< at >lists.alioth.debian.org>
+DM-Upload-Allowed: yes
+Uploaders: Steffen Moeller <moeller< at >pzr.uni-rostock.de>
 Build-Depends: debhelper (>= 4.0.0), python-numpy, python-dev, python-gtk2, python-glade2, g++ (>= 3.3), libgsl0-dev, libboost-python-dev, automake, autoconf, libtool, python-gnome2, expect, doxygen, graphviz, docbook-utils, ghostscript, docbook-to-man
 Standards-Version: 3.6.0
 Homepage: http://www.e-cell.org/

r11001 - in trunk/packages: . logomat-m logomat-m/trunklogomat-m/trunk/debian

Andreas Tille — 2012-05-25T11:48:20

Author: tille
Date: 2012-05-25 11:48:20 +0000 (Fri, 25 May 2012)
New Revision: 11001

Added:
   trunk/packages/logomat-m/
   trunk/packages/logomat-m/trunk/
   trunk/packages/logomat-m/trunk/debian/
   trunk/packages/logomat-m/trunk/debian/changelog
   trunk/packages/logomat-m/trunk/debian/compat
   trunk/packages/logomat-m/trunk/debian/control
   trunk/packages/logomat-m/trunk/debian/copyright
   trunk/packages/logomat-m/trunk/debian/upstream
Log:
Inject data from med-bio task file as machine readable packaging files to enable machine-readable gatherer fetching it


Added: trunk/packages/logomat-m/trunk/debian/changelog
===================================================================
--- trunk/packages/logomat-m/trunk/debian/changelog                        (rev 0)
+++ trunk/packages/logomat-m/trunk/debian/changelog2012-05-25 11:48:20 UTC (rev 11001)
< at >< at > -0,0 +1,5 < at >< at >
+logomat-m (0.0.20091119-1) unstable; urgency=low
+
+  * Initial release
+
+ -- Andreas Tille <tille< at >debian.org>  Thu, 24 May 2012 14:30:13 +0200

Added: trunk/packages/logomat-m/trunk/debian/compat
===================================================================
--- trunk/packages/logomat-m/trunk/debian/compat                        (rev 0)
+++ trunk/packages/logomat-m/trunk/debian/compat2012-05-25 11:48:20 UTC (rev 11001)
< at >< at > -0,0 +1 < at >< at >
+9

Added: trunk/packages/logomat-m/trunk/debian/control
===================================================================
--- trunk/packages/logomat-m/trunk/debian/control                        (rev 0)
+++ trunk/packages/logomat-m/trunk/debian/control2012-05-25 11:48:20 UTC (rev 11001)
< at >< at > -0,0 +1,27 < at >< at >
+Source: logomat-m
+Section: science
+Priority: optional
+Maintainer: Debian Med Packaging Team <debian-med-packaging< at >lists.alioth.debian.org>
+DM-Upload-Allowed: yes
+Uploaders: Andreas Tille <tille< at >debian.org>
+Build-Depends: debhelper (>= 9)
+Standards-Version: 3.9.3
+Homepage: http://www.sanger.ac.uk/resources/software/logomat-m/
+Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/logomat-m/trunk/
+Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/logomat-m/trunk/
+
+Package: logomat-m
+Architecture: any
+Depends: ${shlibs:Depends}, ${misc:Depends}
+Description: visualize central aspects of Profile Hidden Markov Models (pHMMs)
+ Profile Hidden Markov Models (pHMMs) are a widely used tool for
+ protein family research. We present a method to visualize all of
+ their central aspects graphically, thus generalizing the concept of
+ sequence logos introduced by Schneider and Stephens. For each
+ emitting state of the pHMM, we display a stack of letters. As for
+ sequence logos, the stack height is determined by the deviation of
+ the position's letter emission frequencies from the background
+ frequencies of the letters. As a new feature, the stack width now
+ visualizes both the probability of reaching the state (the hitting
+ probability) and the expected number of letters the state emits
+ during a pass through the model (the expected contribution).

Added: trunk/packages/logomat-m/trunk/debian/copyright
===================================================================
--- trunk/packages/logomat-m/trunk/debian/copyright                        (rev 0)
+++ trunk/packages/logomat-m/trunk/debian/copyright2012-05-25 11:48:20 UTC (rev 11001)
< at >< at > -0,0 +1,11 < at >< at >
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: LogoMat-M
+Source: ftp://ftp.sanger.ac.uk/pub4/resources/software/logomat-m/
+
+Files: *
+Copyright: © -2009 ???
+License: Artistic
+
+Files: debian/*
+Copyright: © 2012 Andreas Tille <tille< at >debian.org>
+License: Artistic

Added: trunk/packages/logomat-m/trunk/debian/upstream
===================================================================
--- trunk/packages/logomat-m/trunk/debian/upstream                        (rev 0)
+++ trunk/packages/logomat-m/trunk/debian/upstream2012-05-25 11:48:20 UTC (rev 11001)
< at >< at > -0,0 +1,11 < at >< at >
+Reference:
+  Author: Benjamin Schuster-Böckler and Jörg Schultz and Sven Rahmann
+  Title: HMM Logos for visualization of protein families
+  Journal: BMC Bioinformatics
+  Year: 2004
+  Volume: 5
+  Pages: 7
+  DOI: 10.1186/1471-2105-5-7
+  PMID: 14736340
+  URL: http://www.biomedcentral.com/1471-2105/5/7
+  eprint: http://www.biomedcentral.com/content/pdf/1471-2105-5-7.pdf


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r11000 - in trunk/packages/dcmtk/trunk/debian: . patches

Mathieu Malaterre — 2012-05-25T09:51:26

Author: malat
Date: 2012-05-25 09:51:25 +0000 (Fri, 25 May 2012)
New Revision: 11000

Added:
   trunk/packages/dcmtk/trunk/debian/patches/bug674361.patch
Modified:
   trunk/packages/dcmtk/trunk/debian/changelog
   trunk/packages/dcmtk/trunk/debian/control
   trunk/packages/dcmtk/trunk/debian/patches/series
   trunk/packages/dcmtk/trunk/debian/rules
Log:
Work on dcmtk package/gcc 4.7 issue

Modified: trunk/packages/dcmtk/trunk/debian/changelog
===================================================================
--- trunk/packages/dcmtk/trunk/debian/changelog2012-05-25 08:46:12 UTC (rev 10999)
+++ trunk/packages/dcmtk/trunk/debian/changelog2012-05-25 09:51:25 UTC (rev 11000)
< at >< at > -1,3 +1,11 < at >< at >
+dcmtk (3.6.0-11) UNRELEASED; urgency=low
+
+  * Fix compilation with gcc 4.7. Closes: #674361
+   - debian/patches/bug674361.patch
+  * Make sure to link against libxml2
+
+ -- Mathieu Malaterre <malat< at >debian.org>  Fri, 25 May 2012 11:19:22 +0200
+
 dcmtk (3.6.0-10) unstable; urgency=low
 
   [ Andreas Tille ]

Modified: trunk/packages/dcmtk/trunk/debian/control
===================================================================
--- trunk/packages/dcmtk/trunk/debian/control2012-05-25 08:46:12 UTC (rev 10999)
+++ trunk/packages/dcmtk/trunk/debian/control2012-05-25 09:51:25 UTC (rev 11000)
< at >< at > -5,8 +5,8 < at >< at >
 DM-Upload-Allowed: yes
 Uploaders: Juergen Salk <jsa< at >debian.org>,
  Andreas Tille <tille< at >debian.org>,
- Mathieu Malaterre <mathieu.malaterre< at >gmail.com>
-Build-Depends: debhelper (>= 7), autoconf, autotools-dev, zlib1g-dev, libtiff-dev, quilt,
+ Mathieu Malaterre <malat< at >debian.org>
+Build-Depends: debhelper (>= 9), autoconf, autotools-dev, zlib1g-dev, libtiff-dev, quilt,
  libpng-dev, libxml2-dev, libwrap0-dev, libssl-dev, doxygen (>= 1.7.4), graphviz, libcharls-dev
 Standards-Version: 3.9.3
 Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/dcmtk/trunk/

Added: trunk/packages/dcmtk/trunk/debian/patches/bug674361.patch
===================================================================
--- trunk/packages/dcmtk/trunk/debian/patches/bug674361.patch                        (rev 0)
+++ trunk/packages/dcmtk/trunk/debian/patches/bug674361.patch2012-05-25 09:51:25 UTC (rev 11000)
< at >< at > -0,0 +1,1015 < at >< at >
+From dbadc0d8f3760f65504406c8b2cb8633f868a258 Mon Sep 17 00:00:00 2001
+From: Joerg Riesmeier <dicom< at >offis.de>
+Date: Thu, 17 Nov 2011 16:13:14 +0000
+Subject: [PATCH] Minor fixes to keep XCode 4.2 on Mac OS X Lion (clang compiler) quiet.
+
+---
+ CHANGES.361                                |   24 ++++++++++++++++++++++++
+ dcmimage/include/dcmtk/dcmimage/diargpxt.h |   25 ++++++++++++++-----------
+ dcmimage/include/dcmtk/dcmimage/dicmypxt.h |   11 +++++++----
+ dcmimage/include/dcmtk/dcmimage/dicocpt.h  |   11 +++++++----
+ dcmimage/include/dcmtk/dcmimage/dicoflt.h  |   17 ++++++++++-------
+ dcmimage/include/dcmtk/dcmimage/dicorot.h  |   17 ++++++++++-------
+ dcmimage/include/dcmtk/dcmimage/dicosct.h  |   13 ++++++++-----
+ dcmimage/include/dcmtk/dcmimage/dihsvpxt.h |   11 +++++++----
+ dcmimage/include/dcmtk/dcmimage/dipalpxt.h |   11 +++++++----
+ dcmimage/include/dcmtk/dcmimage/dirgbpxt.h |   15 +++++++++------
+ dcmimage/include/dcmtk/dcmimage/diybrpxt.h |   15 +++++++++------
+ dcmimage/include/dcmtk/dcmimage/diyf2pxt.h |   11 +++++++----
+ dcmimage/include/dcmtk/dcmimage/diyp2pxt.h |   11 +++++++----
+ dcmimgle/include/dcmtk/dcmimgle/diflipt.h  |   11 +++++++----
+ dcmimgle/include/dcmtk/dcmimgle/dimoflt.h  |   15 +++++++++------
+ dcmimgle/include/dcmtk/dcmimgle/dimoipxt.h |   13 ++++++++-----
+ dcmimgle/include/dcmtk/dcmimgle/dimorot.h  |   15 +++++++++------
+ dcmimgle/include/dcmtk/dcmimgle/dimosct.h  |   11 +++++++----
+ dcmimgle/include/dcmtk/dcmimgle/dirotat.h  |   11 +++++++----
+ dcmimgle/include/dcmtk/dcmimgle/discalet.h |   19 +++++++++++--------
+ ofstd/include/dcmtk/ofstd/ofoset.h         |   13 ++++++++-----
+ ofstd/libsrc/ofchrenc.cc                   |   13 +++++++++++--
+ 22 files changed, 203 insertions(+), 110 deletions(-)
+
+Index: dcmtk-3.6.0/dcmimage/include/dcmtk/dcmimage/diargpxt.h
+===================================================================
+--- dcmtk-3.6.0.orig/dcmimage/include/dcmtk/dcmimage/diargpxt.h2010-10-14 13:16:29.000000000 +0000
++++ dcmtk-3.6.0/dcmimage/include/dcmtk/dcmimage/diargpxt.h2012-05-25 09:16:23.791876809 +0000
+< at >< at > -1,6 +1,6 < at >< at >
+ /*
+  *
+- *  Copyright (C) 1996-2010, OFFIS e.V.
++ *  Copyright (C) 1996-2011, OFFIS e.V.
+  *  All rights reserved.  See COPYRIGHT file for details.
+  *
+  *  This software and supporting documentation were developed by
+< at >< at > -18,8 +18,8 < at >< at >
+  *  Purpose: DicomARGBPixelTemplate (Header) - UNTESTED !!!
+  *
+  *  Last Update:      $Author: joergr $
+- *  Update Date:      $Date: 2010-10-14 13:16:29 $
+- *  CVS/RCS Revision: $Revision: 1.21 $
++ *  Update Date:      $Date: 2011-11-17 16:13:14 $
++ *  CVS/RCS Revision: $Revision: 1.22 $
+  *  Status:           $State: Exp $
+  *
+  *  CVS/RCS Log at end of file
+< at >< at > -91,7 +91,7 < at >< at >
+                  const unsigned long planeSize,
+                  const int bits)
+     {                                             // not very much optimized, but no one really uses ARGB !!
+-        if (Init(pixel))
++        if (this->Init(pixel))
+         {
+             register T2 value;
+             const T1 offset = OFstatic_cast(T1, DicomImageClass::maxval(bits - 1));
+< at >< at > -103,9 +103,9 < at >< at >
+ /*
+                 register const T1 *a = pixel;                                   // points to alpha plane
+                 const T1 *rgb[3];
+-                rgb[0] = a + this->InputCount;                                        // points to red plane
+-                rgb[1] = rgb[0] + this->InputCount;                                   // points to green plane
+-                rgb[2] = rgb[1] + this->InputCount;                                   // points to blue plane
++                rgb[0] = a + this->InputCount;                                  // points to red plane
++                rgb[1] = rgb[0] + this->InputCount;                             // points to green plane
++                rgb[2] = rgb[1] + this->InputCount;                             // points to blue plane
+                 for (i = 0; i < count; ++i)
+                 {
+                     value = OFstatic_cast(T2, *(a++));                          // get alpha value
+< at >< at > -141,10 +141,10 < at >< at >
+                     /* convert a single frame */
+                     for (l = planeSize; (l != 0) && (i < count); --l, ++i)
+                     {
+-                        value = OFstatic_cast(T2, *(a++));                          // get alpha value
++                        value = OFstatic_cast(T2, *(a++));                      // get alpha value
+                         if (value > 0)
+                         {
+-                            for (int j = 0; j < 3; ++j)                             // set palette color
++                            for (int j = 0; j < 3; ++j)                         // set palette color
+                             {
+                                 if (value <= palette[j]->getFirstEntry(value))
+                                     this->Data[j][i] = OFstatic_cast(T3, palette[j]->getFirstValue());
+< at >< at > -152,12 +152,12 < at >< at >
+                                     this->Data[j][i] = OFstatic_cast(T3, palette[j]->getLastValue());
+                                 else
+                                     this->Data[j][i] = OFstatic_cast(T3, palette[j]->getValue(value));
+-                                ++rgb[j];                                           // skip RGB values
++                                ++rgb[j];                                       // skip RGB values
+                             }
+                         }
+                         else
+                         {
+-                            for (int j = 0; j < 3; ++j)                             // copy RGB values
++                            for (int j = 0; j < 3; ++j)                         // copy RGB values
+                                 this->Data[j][i] = OFstatic_cast(T3, removeSign(*(rgb[j]++), offset));
+                         }
+                     }
+< at >< at > -204,6 +204,9 < at >< at >
+  *
+  * CVS/RCS Log:
+  * $Log: diargpxt.h,v $
++ * Revision 1.22  2011-11-17 16:13:14  joergr
++ * Minor fixes to keep XCode 4.2 on Mac OS X Lion (clang compiler) quiet.
++ *
+  * Revision 1.21  2010-10-14 13:16:29  joergr
+  * Updated copyright header. Added reference to COPYRIGHT file.
+  *
+Index: dcmtk-3.6.0/dcmimage/include/dcmtk/dcmimage/dicmypxt.h
+===================================================================
+--- dcmtk-3.6.0.orig/dcmimage/include/dcmtk/dcmimage/dicmypxt.h2010-10-14 13:16:29.000000000 +0000
++++ dcmtk-3.6.0/dcmimage/include/dcmtk/dcmimage/dicmypxt.h2012-05-25 09:16:23.791876809 +0000
+< at >< at > -1,6 +1,6 < at >< at >
+ /*
+  *
+- *  Copyright (C) 1996-2010, OFFIS e.V.
++ *  Copyright (C) 1996-2011, OFFIS e.V.
+  *  All rights reserved.  See COPYRIGHT file for details.
+  *
+  *  This software and supporting documentation were developed by
+< at >< at > -18,8 +18,8 < at >< at >
+  *  Purpose: DicomCMYKPixelTemplate (Header)
+  *
+  *  Last Update:      $Author: joergr $
+- *  Update Date:      $Date: 2010-10-14 13:16:29 $
+- *  CVS/RCS Revision: $Revision: 1.20 $
++ *  Update Date:      $Date: 2011-11-17 16:13:14 $
++ *  CVS/RCS Revision: $Revision: 1.21 $
+  *  Status:           $State: Exp $
+  *
+  *  CVS/RCS Log at end of file
+< at >< at > -87,7 +87,7 < at >< at >
+                  const unsigned long planeSize,
+                  const int bits)
+     {
+-        if (Init(pixel))
++        if (this->Init(pixel))
+         {
+             // use the number of input pixels derived from the length of the 'PixelData'
+             // attribute), but not more than the size of the intermediate buffer
+< at >< at > -157,6 +157,9 < at >< at >
+  *
+  * CVS/RCS Log:
+  * $Log: dicmypxt.h,v $
++ * Revision 1.21  2011-11-17 16:13:14  joergr
++ * Minor fixes to keep XCode 4.2 on Mac OS X Lion (clang compiler) quiet.
++ *
+  * Revision 1.20  2010-10-14 13:16:29  joergr
+  * Updated copyright header. Added reference to COPYRIGHT file.
+  *
+Index: dcmtk-3.6.0/dcmimage/include/dcmtk/dcmimage/dicocpt.h
+===================================================================
+--- dcmtk-3.6.0.orig/dcmimage/include/dcmtk/dcmimage/dicocpt.h2010-10-14 13:16:29.000000000 +0000
++++ dcmtk-3.6.0/dcmimage/include/dcmtk/dcmimage/dicocpt.h2012-05-25 09:16:23.791876809 +0000
+< at >< at > -1,6 +1,6 < at >< at >
+ /*
+  *
+- *  Copyright (C) 1998-2010, OFFIS e.V.
++ *  Copyright (C) 1998-2011, OFFIS e.V.
+  *  All rights reserved.  See COPYRIGHT file for details.
+  *
+  *  This software and supporting documentation were developed by
+< at >< at > -18,8 +18,8 < at >< at >
+  *  Purpose: DicomColorCopyTemplate (Header)
+  *
+  *  Last Update:      $Author: joergr $
+- *  Update Date:      $Date: 2010-10-14 13:16:29 $
+- *  CVS/RCS Revision: $Revision: 1.12 $
++ *  Update Date:      $Date: 2011-11-17 16:13:14 $
++ *  CVS/RCS Revision: $Revision: 1.13 $
+  *  Status:           $State: Exp $
+  *
+  *  CVS/RCS Log at end of file
+< at >< at > -86,7 +86,7 < at >< at >
+     inline void copy(const T *pixel[3],
+                      const unsigned long offset)
+     {
+-        if (Init(pixel))
++        if (this->Init(pixel))
+         {
+             for (int j = 0; j < 3; j++)
+                 OFBitmanipTemplate<T>::copyMem(pixel[j] + offset, this->Data[j], this->getCount());
+< at >< at > -102,6 +102,9 < at >< at >
+  *
+  * CVS/RCS Log:
+  * $Log: dicocpt.h,v $
++ * Revision 1.13  2011-11-17 16:13:14  joergr
++ * Minor fixes to keep XCode 4.2 on Mac OS X Lion (clang compiler) quiet.
++ *
+  * Revision 1.12  2010-10-14 13:16:29  joergr
+  * Updated copyright header. Added reference to COPYRIGHT file.
+  *
+Index: dcmtk-3.6.0/dcmimage/include/dcmtk/dcmimage/dicoflt.h
+===================================================================
+--- dcmtk-3.6.0.orig/dcmimage/include/dcmtk/dcmimage/dicoflt.h2010-10-14 13:16:29.000000000 +0000
++++ dcmtk-3.6.0/dcmimage/include/dcmtk/dcmimage/dicoflt.h2012-05-25 09:16:23.795876809 +0000
+< at >< at > -1,6 +1,6 < at >< at >
+ /*
+  *
+- *  Copyright (C) 1998-2010, OFFIS e.V.
++ *  Copyright (C) 1998-2011, OFFIS e.V.
+  *  All rights reserved.  See COPYRIGHT file for details.
+  *
+  *  This software and supporting documentation were developed by
+< at >< at > -18,8 +18,8 < at >< at >
+  *  Purpose: DicomColorFlipTemplate (Header)
+  *
+  *  Last Update:      $Author: joergr $
+- *  Update Date:      $Date: 2010-10-14 13:16:29 $
+- *  CVS/RCS Revision: $Revision: 1.15 $
++ *  Update Date:      $Date: 2011-11-17 16:13:14 $
++ *  CVS/RCS Revision: $Revision: 1.16 $
+  *  Status:           $State: Exp $
+  *
+  *  CVS/RCS Log at end of file
+< at >< at > -98,14 +98,14 < at >< at >
+                      const int horz,
+                      const int vert)
+     {
+-        if (Init(pixel))
++        if (this->Init(pixel))
+         {
+             if (horz && vert)
+-                flipHorzVert(pixel, this->Data);
++                this->flipHorzVert(pixel, this->Data);
+             else if (horz)
+-                flipHorz(pixel, this->Data);
++                this->flipHorz(pixel, this->Data);
+             else if (vert)
+-                flipVert(pixel, this->Data);
++                this->flipVert(pixel, this->Data);
+         }
+     }
+ };
+< at >< at > -118,6 +118,9 < at >< at >
+  *
+  * CVS/RCS Log:
+  * $Log: dicoflt.h,v $
++ * Revision 1.16  2011-11-17 16:13:14  joergr
++ * Minor fixes to keep XCode 4.2 on Mac OS X Lion (clang compiler) quiet.
++ *
+  * Revision 1.15  2010-10-14 13:16:29  joergr
+  * Updated copyright header. Added reference to COPYRIGHT file.
+  *
+Index: dcmtk-3.6.0/dcmimage/include/dcmtk/dcmimage/dicorot.h
+===================================================================
+--- dcmtk-3.6.0.orig/dcmimage/include/dcmtk/dcmimage/dicorot.h2010-10-14 13:16:29.000000000 +0000
++++ dcmtk-3.6.0/dcmimage/include/dcmtk/dcmimage/dicorot.h2012-05-25 09:16:23.795876809 +0000
+< at >< at > -1,6 +1,6 < at >< at >
+ /*
+  *
+- *  Copyright (C) 1998-2010, OFFIS e.V.
++ *  Copyright (C) 1998-2011, OFFIS e.V.
+  *  All rights reserved.  See COPYRIGHT file for details.
+  *
+  *  This software and supporting documentation were developed by
+< at >< at > -18,8 +18,8 < at >< at >
+  *  Purpose: DicomColorRotateTemplate (Header)
+  *
+  *  Last Update:      $Author: joergr $
+- *  Update Date:      $Date: 2010-10-14 13:16:29 $
+- *  CVS/RCS Revision: $Revision: 1.15 $
++ *  Update Date:      $Date: 2011-11-17 16:13:14 $
++ *  CVS/RCS Revision: $Revision: 1.16 $
+  *  Status:           $State: Exp $
+  *
+  *  CVS/RCS Log at end of file
+< at >< at > -98,14 +98,14 < at >< at >
+     inline void rotate(const T *pixel[3],
+                        const int degree)
+     {
+-        if (Init(pixel))
++        if (this->Init(pixel))
+         {
+             if (degree == 90)
+-                rotateRight(pixel, this->Data);
++                this->rotateRight(pixel, this->Data);
+             else if (degree == 180)
+-                rotateTopDown(pixel, this->Data);
++                this->rotateTopDown(pixel, this->Data);
+             else  if (degree == 270)
+-                rotateLeft(pixel, this->Data);
++                this->rotateLeft(pixel, this->Data);
+         }
+     }
+ };
+< at >< at > -118,6 +118,9 < at >< at >
+  *
+  * CVS/RCS Log:
+  * $Log: dicorot.h,v $
++ * Revision 1.16  2011-11-17 16:13:14  joergr
++ * Minor fixes to keep XCode 4.2 on Mac OS X Lion (clang compiler) quiet.
++ *
+  * Revision 1.15  2010-10-14 13:16:29  joergr
+  * Updated copyright header. Added reference to COPYRIGHT file.
+  *
+Index: dcmtk-3.6.0/dcmimage/include/dcmtk/dcmimage/dicosct.h
+===================================================================
+--- dcmtk-3.6.0.orig/dcmimage/include/dcmtk/dcmimage/dicosct.h2010-10-14 13:16:29.000000000 +0000
++++ dcmtk-3.6.0/dcmimage/include/dcmtk/dcmimage/dicosct.h2012-05-25 09:16:23.795876809 +0000
+< at >< at > -1,6 +1,6 < at >< at >
+ /*
+  *
+- *  Copyright (C) 1996-2010, OFFIS e.V.
++ *  Copyright (C) 1996-2011, OFFIS e.V.
+  *  All rights reserved.  See COPYRIGHT file for details.
+  *
+  *  This software and supporting documentation were developed by
+< at >< at > -18,8 +18,8 < at >< at >
+  *  Purpose: DicomColorScaleTemplate (Header)
+  *
+  *  Last Update:      $Author: joergr $
+- *  Update Date:      $Date: 2010-10-14 13:16:29 $
+- *  CVS/RCS Revision: $Revision: 1.21 $
++ *  Update Date:      $Date: 2011-11-17 16:13:14 $
++ *  CVS/RCS Revision: $Revision: 1.22 $
+  *  Status:           $State: Exp $
+  *
+  *  CVS/RCS Log at end of file
+< at >< at > -107,8 +107,8 < at >< at >
+     inline void scale(const T *pixel[3],
+                       const int interpolate)
+     {
+-        if (Init(pixel))
+-            scaleData(pixel, this->Data, interpolate);
++        if (this->Init(pixel))
++            this->scaleData(pixel, this->Data, interpolate);
+     }
+ };
+ 
+< at >< at > -120,6 +120,9 < at >< at >
+  *
+  * CVS/RCS Log:
+  * $Log: dicosct.h,v $
++ * Revision 1.22  2011-11-17 16:13:14  joergr
++ * Minor fixes to keep XCode 4.2 on Mac OS X Lion (clang compiler) quiet.
++ *
+  * Revision 1.21  2010-10-14 13:16:29  joergr
+  * Updated copyright header. Added reference to COPYRIGHT file.
+  *
+Index: dcmtk-3.6.0/dcmimage/include/dcmtk/dcmimage/dihsvpxt.h
+===================================================================
+--- dcmtk-3.6.0.orig/dcmimage/include/dcmtk/dcmimage/dihsvpxt.h2010-10-14 13:16:29.000000000 +0000
++++ dcmtk-3.6.0/dcmimage/include/dcmtk/dcmimage/dihsvpxt.h2012-05-25 09:16:23.795876809 +0000
+< at >< at > -1,6 +1,6 < at >< at >
+ /*
+  *
+- *  Copyright (C) 1996-2010, OFFIS e.V.
++ *  Copyright (C) 1996-2011, OFFIS e.V.
+  *  All rights reserved.  See COPYRIGHT file for details.
+  *
+  *  This software and supporting documentation were developed by
+< at >< at > -18,8 +18,8 < at >< at >
+  *  Purpose: DicomHSVPixelTemplate (Header)
+  *
+  *  Last Update:      $Author: joergr $
+- *  Update Date:      $Date: 2010-10-14 13:16:29 $
+- *  CVS/RCS Revision: $Revision: 1.25 $
++ *  Update Date:      $Date: 2011-11-17 16:13:14 $
++ *  CVS/RCS Revision: $Revision: 1.26 $
+  *  Status:           $State: Exp $
+  *
+  *  CVS/RCS Log at end of file
+< at >< at > -87,7 +87,7 < at >< at >
+                  const unsigned long planeSize,
+                  const int bits)
+     {
+-        if (Init(pixel))
++        if (this->Init(pixel))
+         {
+             register T2 *r = this->Data[0];
+             register T2 *g = this->Data[1];
+< at >< at > -221,6 +221,9 < at >< at >
+  *
+  * CVS/RCS Log:
+  * $Log: dihsvpxt.h,v $
++ * Revision 1.26  2011-11-17 16:13:14  joergr
++ * Minor fixes to keep XCode 4.2 on Mac OS X Lion (clang compiler) quiet.
++ *
+  * Revision 1.25  2010-10-14 13:16:29  joergr
+  * Updated copyright header. Added reference to COPYRIGHT file.
+  *
+Index: dcmtk-3.6.0/dcmimage/include/dcmtk/dcmimage/dipalpxt.h
+===================================================================
+--- dcmtk-3.6.0.orig/dcmimage/include/dcmtk/dcmimage/dipalpxt.h2010-10-14 13:16:29.000000000 +0000
++++ dcmtk-3.6.0/dcmimage/include/dcmtk/dcmimage/dipalpxt.h2012-05-25 09:16:23.795876809 +0000
+< at >< at > -1,6 +1,6 < at >< at >
+ /*
+  *
+- *  Copyright (C) 1996-2010, OFFIS e.V.
++ *  Copyright (C) 1996-2011, OFFIS e.V.
+  *  All rights reserved.  See COPYRIGHT file for details.
+  *
+  *  This software and supporting documentation were developed by
+< at >< at > -18,8 +18,8 < at >< at >
+  *  Purpose: DicomPalettePixelTemplate (Header)
+  *
+  *  Last Update:      $Author: joergr $
+- *  Update Date:      $Date: 2010-10-14 13:16:29 $
+- *  CVS/RCS Revision: $Revision: 1.24 $
++ *  Update Date:      $Date: 2011-11-17 16:13:14 $
++ *  CVS/RCS Revision: $Revision: 1.25 $
+  *  Status:           $State: Exp $
+  *
+  *  CVS/RCS Log at end of file
+< at >< at > -92,7 +92,7 < at >< at >
+     void convert(const T1 *pixel,
+                  DiLookupTable *palette[3])
+     {                                                                // can be optimized if necessary !
+-        if (Init(pixel))
++        if (this->Init(pixel))
+         {
+             register const T1 *p = pixel;
+             register T2 value = 0;
+< at >< at > -126,6 +126,9 < at >< at >
+  *
+  * CVS/RCS Log:
+  * $Log: dipalpxt.h,v $
++ * Revision 1.25  2011-11-17 16:13:14  joergr
++ * Minor fixes to keep XCode 4.2 on Mac OS X Lion (clang compiler) quiet.
++ *
+  * Revision 1.24  2010-10-14 13:16:29  joergr
+  * Updated copyright header. Added reference to COPYRIGHT file.
+  *
+Index: dcmtk-3.6.0/dcmimage/include/dcmtk/dcmimage/dirgbpxt.h
+===================================================================
+--- dcmtk-3.6.0.orig/dcmimage/include/dcmtk/dcmimage/dirgbpxt.h2010-10-14 13:16:30.000000000 +0000
++++ dcmtk-3.6.0/dcmimage/include/dcmtk/dcmimage/dirgbpxt.h2012-05-25 09:16:23.795876809 +0000
+< at >< at > -1,6 +1,6 < at >< at >
+ /*
+  *
+- *  Copyright (C) 1996-2010, OFFIS e.V.
++ *  Copyright (C) 1996-2011, OFFIS e.V.
+  *  All rights reserved.  See COPYRIGHT file for details.
+  *
+  *  This software and supporting documentation were developed by
+< at >< at > -18,8 +18,8 < at >< at >
+  *  Purpose: DicomRGBPixelTemplate (Header)
+  *
+  *  Last Update:      $Author: joergr $
+- *  Update Date:      $Date: 2010-10-14 13:16:30 $
+- *  CVS/RCS Revision: $Revision: 1.18 $
++ *  Update Date:      $Date: 2011-11-17 16:13:14 $
++ *  CVS/RCS Revision: $Revision: 1.19 $
+  *  Status:           $State: Exp $
+  *
+  *  CVS/RCS Log at end of file
+< at >< at > -87,7 +87,7 < at >< at >
+                  const unsigned long planeSize,
+                  const int bits)
+     {
+-        if (Init(pixel))
++        if (this->Init(pixel))
+         {
+             // use the number of input pixels derived from the length of the 'PixelData'
+             // attribute), but not more than the size of the intermediate buffer
+< at >< at > -129,9 +129,9 < at >< at >
+             {
+                 register int j;
+                 register unsigned long i;
+-                for (i = 0; i < count; ++i)                         /* for all pixel ... */
++                for (i = 0; i < count; ++i)                             /* for all pixel ... */
+                     for (j = 0; j < 3; ++j)
+-                        this->Data[j][i] = removeSign(*(p++), offset);    /* ... copy planes */
++                        this->Data[j][i] = removeSign(*(p++), offset);  /* ... copy planes */
+             }
+         }
+     }
+< at >< at > -145,6 +145,9 < at >< at >
+  *
+  * CVS/RCS Log:
+  * $Log: dirgbpxt.h,v $
++ * Revision 1.19  2011-11-17 16:13:14  joergr
++ * Minor fixes to keep XCode 4.2 on Mac OS X Lion (clang compiler) quiet.
++ *
+  * Revision 1.18  2010-10-14 13:16:30  joergr
+  * Updated copyright header. Added reference to COPYRIGHT file.
+  *
+Index: dcmtk-3.6.0/dcmimage/include/dcmtk/dcmimage/diybrpxt.h
+===================================================================
+--- dcmtk-3.6.0.orig/dcmimage/include/dcmtk/dcmimage/diybrpxt.h2010-10-14 13:16:30.000000000 +0000
++++ dcmtk-3.6.0/dcmimage/include/dcmtk/dcmimage/diybrpxt.h2012-05-25 09:16:23.795876809 +0000
+< at >< at > -1,6 +1,6 < at >< at >
+ /*
+  *
+- *  Copyright (C) 1998-2010, OFFIS e.V.
++ *  Copyright (C) 1998-2011, OFFIS e.V.
+  *  All rights reserved.  See COPYRIGHT file for details.
+  *
+  *  This software and supporting documentation were developed by
+< at >< at > -18,8 +18,8 < at >< at >
+  *  Purpose: DicomYBRPixelTemplate (Header)
+  *
+  *  Last Update:      $Author: joergr $
+- *  Update Date:      $Date: 2010-10-14 13:16:30 $
+- *  CVS/RCS Revision: $Revision: 1.19 $
++ *  Update Date:      $Date: 2011-11-17 16:13:14 $
++ *  CVS/RCS Revision: $Revision: 1.20 $
+  *  Status:           $State: Exp $
+  *
+  *  CVS/RCS Log at end of file
+< at >< at > -91,7 +91,7 < at >< at >
+                  const int bits,
+                  const OFBool rgb)
+     {
+-        if (Init(pixel))
++        if (this->Init(pixel))
+         {
+             const T1 offset = OFstatic_cast(T1, DicomImageClass::maxval(bits - 1));
+             // use the number of input pixels derived from the length of the 'PixelData'
+< at >< at > -266,9 +266,9 < at >< at >
+                 {
+                     register int j;
+                     register unsigned long i;
+-                    for (i = 0; i < count; ++i)                         /* for all pixel ... */
++                    for (i = 0; i < count; ++i)                             /* for all pixel ... */
+                         for (j = 0; j < 3; ++j)
+-                            this->Data[j][i] = removeSign(*(p++), offset);    /* ... copy planes */
++                            this->Data[j][i] = removeSign(*(p++), offset);  /* ... copy planes */
+                 }
+             }
+         }
+< at >< at > -295,6 +295,9 < at >< at >
+  *
+  * CVS/RCS Log:
+  * $Log: diybrpxt.h,v $
++ * Revision 1.20  2011-11-17 16:13:14  joergr
++ * Minor fixes to keep XCode 4.2 on Mac OS X Lion (clang compiler) quiet.
++ *
+  * Revision 1.19  2010-10-14 13:16:30  joergr
+  * Updated copyright header. Added reference to COPYRIGHT file.
+  *
+Index: dcmtk-3.6.0/dcmimage/include/dcmtk/dcmimage/diyf2pxt.h
+===================================================================
+--- dcmtk-3.6.0.orig/dcmimage/include/dcmtk/dcmimage/diyf2pxt.h2010-10-14 13:16:30.000000000 +0000
++++ dcmtk-3.6.0/dcmimage/include/dcmtk/dcmimage/diyf2pxt.h2012-05-25 09:16:23.795876809 +0000
+< at >< at > -1,6 +1,6 < at >< at >
+ /*
+  *
+- *  Copyright (C) 1998-2010, OFFIS e.V.
++ *  Copyright (C) 1998-2011, OFFIS e.V.
+  *  All rights reserved.  See COPYRIGHT file for details.
+  *
+  *  This software and supporting documentation were developed by
+< at >< at > -18,8 +18,8 < at >< at >
+  *  Purpose: DicomYBR422PixelTemplate (Header)
+  *
+  *  Last Update:      $Author: joergr $
+- *  Update Date:      $Date: 2010-10-14 13:16:30 $
+- *  CVS/RCS Revision: $Revision: 1.25 $
++ *  Update Date:      $Date: 2011-11-17 16:13:14 $
++ *  CVS/RCS Revision: $Revision: 1.26 $
+  *  Status:           $State: Exp $
+  *
+  *  CVS/RCS Log at end of file
+< at >< at > -95,7 +95,7 < at >< at >
+                  const int bits,
+                  const OFBool rgb)
+     {
+-        if (Init(pixel))
++        if (this->Init(pixel))
+         {
+             const T1 offset = OFstatic_cast(T1, DicomImageClass::maxval(bits - 1));
+             register unsigned long i;
+< at >< at > -167,6 +167,9 < at >< at >
+  *
+  * CVS/RCS Log:
+  * $Log: diyf2pxt.h,v $
++ * Revision 1.26  2011-11-17 16:13:14  joergr
++ * Minor fixes to keep XCode 4.2 on Mac OS X Lion (clang compiler) quiet.
++ *
+  * Revision 1.25  2010-10-14 13:16:30  joergr
+  * Updated copyright header. Added reference to COPYRIGHT file.
+  *
+Index: dcmtk-3.6.0/dcmimage/include/dcmtk/dcmimage/diyp2pxt.h
+===================================================================
+--- dcmtk-3.6.0.orig/dcmimage/include/dcmtk/dcmimage/diyp2pxt.h2010-10-14 13:16:30.000000000 +0000
++++ dcmtk-3.6.0/dcmimage/include/dcmtk/dcmimage/diyp2pxt.h2012-05-25 09:16:23.795876809 +0000
+< at >< at > -1,6 +1,6 < at >< at >
+ /*
+  *
+- *  Copyright (C) 1998-2010, OFFIS e.V.
++ *  Copyright (C) 1998-2011, OFFIS e.V.
+  *  All rights reserved.  See COPYRIGHT file for details.
+  *
+  *  This software and supporting documentation were developed by
+< at >< at > -18,8 +18,8 < at >< at >
+  *  Purpose: DicomYBRPart422PixelTemplate (Header)
+  *
+  *  Last Update:      $Author: joergr $
+- *  Update Date:      $Date: 2010-10-14 13:16:30 $
+- *  CVS/RCS Revision: $Revision: 1.23 $
++ *  Update Date:      $Date: 2011-11-17 16:13:14 $
++ *  CVS/RCS Revision: $Revision: 1.24 $
+  *  Status:           $State: Exp $
+  *
+  *  CVS/RCS Log at end of file
+< at >< at > -91,7 +91,7 < at >< at >
+     void convert(const T1 *pixel,
+                  const int bits)
+     {
+-        if (Init(pixel))
++        if (this->Init(pixel))
+         {
+             register T2 *r = this->Data[0];
+             register T2 *g = this->Data[1];
+< at >< at > -147,6 +147,9 < at >< at >
+  *
+  * CVS/RCS Log:
+  * $Log: diyp2pxt.h,v $
++ * Revision 1.24  2011-11-17 16:13:14  joergr
++ * Minor fixes to keep XCode 4.2 on Mac OS X Lion (clang compiler) quiet.
++ *
+  * Revision 1.23  2010-10-14 13:16:30  joergr
+  * Updated copyright header. Added reference to COPYRIGHT file.
+  *
+Index: dcmtk-3.6.0/dcmimgle/include/dcmtk/dcmimgle/diflipt.h
+===================================================================
+--- dcmtk-3.6.0.orig/dcmimgle/include/dcmtk/dcmimgle/diflipt.h2010-10-14 13:16:26.000000000 +0000
++++ dcmtk-3.6.0/dcmimgle/include/dcmtk/dcmimgle/diflipt.h2012-05-25 09:16:23.795876809 +0000
+< at >< at > -1,6 +1,6 < at >< at >
+ /*
+  *
+- *  Copyright (C) 1996-2010, OFFIS e.V.
++ *  Copyright (C) 1996-2011, OFFIS e.V.
+  *  All rights reserved.  See COPYRIGHT file for details.
+  *
+  *  This software and supporting documentation were developed by
+< at >< at > -18,8 +18,8 < at >< at >
+  *  Purpose: DicomFlipTemplate (Header)
+  *
+  *  Last Update:      $Author: joergr $
+- *  Update Date:      $Date: 2010-10-14 13:16:26 $
+- *  CVS/RCS Revision: $Revision: 1.23 $
++ *  Update Date:      $Date: 2011-11-17 16:13:16 $
++ *  CVS/RCS Revision: $Revision: 1.24 $
+  *  Status:           $State: Exp $
+  *
+  *  CVS/RCS Log at end of file
+< at >< at > -129,7 +129,7 < at >< at >
+             else if (vert)
+                 flipVert(src, dest);
+             else
+-                copyPixel(src, dest);
++                this->copyPixel(src, dest);
+         }
+     }
+ 
+< at >< at > -345,6 +345,9 < at >< at >
+  *
+  * CVS/RCS Log:
+  * $Log: diflipt.h,v $
++ * Revision 1.24  2011-11-17 16:13:16  joergr
++ * Minor fixes to keep XCode 4.2 on Mac OS X Lion (clang compiler) quiet.
++ *
+  * Revision 1.23  2010-10-14 13:16:26  joergr
+  * Updated copyright header. Added reference to COPYRIGHT file.
+  *
+Index: dcmtk-3.6.0/dcmimgle/include/dcmtk/dcmimgle/dimoflt.h
+===================================================================
+--- dcmtk-3.6.0.orig/dcmimgle/include/dcmtk/dcmimgle/dimoflt.h2010-10-14 13:16:26.000000000 +0000
++++ dcmtk-3.6.0/dcmimgle/include/dcmtk/dcmimgle/dimoflt.h2012-05-25 09:16:23.795876809 +0000
+< at >< at > -1,6 +1,6 < at >< at >
+ /*
+  *
+- *  Copyright (C) 1996-2010, OFFIS e.V.
++ *  Copyright (C) 1996-2011, OFFIS e.V.
+  *  All rights reserved.  See COPYRIGHT file for details.
+  *
+  *  This software and supporting documentation were developed by
+< at >< at > -18,8 +18,8 < at >< at >
+  *  Purpose: DicomMonochromeFlipTemplate (Header)
+  *
+  *  Last Update:      $Author: joergr $
+- *  Update Date:      $Date: 2010-10-14 13:16:26 $
+- *  CVS/RCS Revision: $Revision: 1.15 $
++ *  Update Date:      $Date: 2011-11-17 16:13:16 $
++ *  CVS/RCS Revision: $Revision: 1.16 $
+  *  Status:           $State: Exp $
+  *
+  *  CVS/RCS Log at end of file
+< at >< at > -106,11 +106,11 < at >< at >
+             if (this->Data != NULL)
+             {
+                 if (horz && vert)
+-                    flipHorzVert(&pixel, &this->Data);
++                    this->flipHorzVert(&pixel, &this->Data);
+                 else if (horz)
+-                    flipHorz(&pixel, &this->Data);
++                    this->flipHorz(&pixel, &this->Data);
+                 else if (vert)
+-                    flipVert(&pixel, &this->Data);
++                    this->flipVert(&pixel, &this->Data);
+             }
+         }
+     }
+< at >< at > -124,6 +124,9 < at >< at >
+  *
+  * CVS/RCS Log:
+  * $Log: dimoflt.h,v $
++ * Revision 1.16  2011-11-17 16:13:16  joergr
++ * Minor fixes to keep XCode 4.2 on Mac OS X Lion (clang compiler) quiet.
++ *
+  * Revision 1.15  2010-10-14 13:16:26  joergr
+  * Updated copyright header. Added reference to COPYRIGHT file.
+  *
+Index: dcmtk-3.6.0/dcmimgle/include/dcmtk/dcmimgle/dimoipxt.h
+===================================================================
+--- dcmtk-3.6.0.orig/dcmimgle/include/dcmtk/dcmimgle/dimoipxt.h2010-10-14 13:16:26.000000000 +0000
++++ dcmtk-3.6.0/dcmimgle/include/dcmtk/dcmimgle/dimoipxt.h2012-05-25 09:16:23.799876809 +0000
+< at >< at > -1,6 +1,6 < at >< at >
+ /*
+  *
+- *  Copyright (C) 1996-2010, OFFIS e.V.
++ *  Copyright (C) 1996-2011, OFFIS e.V.
+  *  All rights reserved.  See COPYRIGHT file for details.
+  *
+  *  This software and supporting documentation were developed by
+< at >< at > -18,8 +18,8 < at >< at >
+  *  Purpose: DicomMonochromeInputPixelTemplate (Header)
+  *
+  *  Last Update:      $Author: joergr $
+- *  Update Date:      $Date: 2010-10-14 13:16:26 $
+- *  CVS/RCS Revision: $Revision: 1.40 $
++ *  Update Date:      $Date: 2011-11-17 16:13:16 $
++ *  CVS/RCS Revision: $Revision: 1.41 $
+  *  Status:           $State: Exp $
+  *
+  *  CVS/RCS Log at end of file
+< at >< at > -76,10 +76,10 < at >< at >
+             else if ((this->Modality != NULL) && this->Modality->hasRescaling())
+             {
+                 rescale(pixel, this->Modality->getRescaleSlope(), this->Modality->getRescaleIntercept());
+-                determineMinMax(OFstatic_cast(T3, this->Modality->getMinValue()), OFstatic_cast(T3, this->Modality->getMaxValue()));
++                this->determineMinMax(OFstatic_cast(T3, this->Modality->getMinValue()), OFstatic_cast(T3, this->Modality->getMaxValue()));
+             } else {
+                 rescale(pixel);                     // "copy" or reference pixel data
+-                determineMinMax(OFstatic_cast(T3, this->Modality->getMinValue()), OFstatic_cast(T3, this->Modality->getMaxValue()));
++                this->determineMinMax(OFstatic_cast(T3, this->Modality->getMinValue()), OFstatic_cast(T3, this->Modality->getMaxValue()));
+             }
+         }
+     }
+< at >< at > -280,6 +280,9 < at >< at >
+  *
+  * CVS/RCS Log:
+  * $Log: dimoipxt.h,v $
++ * Revision 1.41  2011-11-17 16:13:16  joergr
++ * Minor fixes to keep XCode 4.2 on Mac OS X Lion (clang compiler) quiet.
++ *
+  * Revision 1.40  2010-10-14 13:16:26  joergr
+  * Updated copyright header. Added reference to COPYRIGHT file.
+  *
+Index: dcmtk-3.6.0/dcmimgle/include/dcmtk/dcmimgle/dimorot.h
+===================================================================
+--- dcmtk-3.6.0.orig/dcmimgle/include/dcmtk/dcmimgle/dimorot.h2010-10-14 13:16:26.000000000 +0000
++++ dcmtk-3.6.0/dcmimgle/include/dcmtk/dcmimgle/dimorot.h2012-05-25 09:16:23.799876809 +0000
+< at >< at > -1,6 +1,6 < at >< at >
+ /*
+  *
+- *  Copyright (C) 1996-2010, OFFIS e.V.
++ *  Copyright (C) 1996-2011, OFFIS e.V.
+  *  All rights reserved.  See COPYRIGHT file for details.
+  *
+  *  This software and supporting documentation were developed by
+< at >< at > -18,8 +18,8 < at >< at >
+  *  Purpose: DicomMonochromeRotateTemplate (Header)
+  *
+  *  Last Update:      $Author: joergr $
+- *  Update Date:      $Date: 2010-10-14 13:16:26 $
+- *  CVS/RCS Revision: $Revision: 1.16 $
++ *  Update Date:      $Date: 2011-11-17 16:13:16 $
++ *  CVS/RCS Revision: $Revision: 1.17 $
+  *  Status:           $State: Exp $
+  *
+  *  CVS/RCS Log at end of file
+< at >< at > -105,11 +105,11 < at >< at >
+             if (this->Data != NULL)
+             {
+                 if (degree == 90)
+-                    rotateRight(&pixel, &(this->Data));
++                    this->rotateRight(&pixel, &(this->Data));
+                 else if (degree == 180)
+-                    rotateTopDown(&pixel, &(this->Data));
++                    this->rotateTopDown(&pixel, &(this->Data));
+                 else if (degree == 270)
+-                    rotateLeft(&pixel, &(this->Data));
++                    this->rotateLeft(&pixel, &(this->Data));
+             }
+         }
+     }
+< at >< at > -123,6 +123,9 < at >< at >
+  *
+  * CVS/RCS Log:
+  * $Log: dimorot.h,v $
++ * Revision 1.17  2011-11-17 16:13:16  joergr
++ * Minor fixes to keep XCode 4.2 on Mac OS X Lion (clang compiler) quiet.
++ *
+  * Revision 1.16  2010-10-14 13:16:26  joergr
+  * Updated copyright header. Added reference to COPYRIGHT file.
+  *
+Index: dcmtk-3.6.0/dcmimgle/include/dcmtk/dcmimgle/dimosct.h
+===================================================================
+--- dcmtk-3.6.0.orig/dcmimgle/include/dcmtk/dcmimgle/dimosct.h2010-10-14 13:16:26.000000000 +0000
++++ dcmtk-3.6.0/dcmimgle/include/dcmtk/dcmimgle/dimosct.h2012-05-25 09:16:23.799876809 +0000
+< at >< at > -1,6 +1,6 < at >< at >
+ /*
+  *
+- *  Copyright (C) 1996-2010, OFFIS e.V.
++ *  Copyright (C) 1996-2011, OFFIS e.V.
+  *  All rights reserved.  See COPYRIGHT file for details.
+  *
+  *  This software and supporting documentation were developed by
+< at >< at > -18,8 +18,8 < at >< at >
+  *  Purpose: DicomMonochromeScaleTemplate (Header)
+  *
+  *  Last Update:      $Author: joergr $
+- *  Update Date:      $Date: 2010-10-14 13:16:26 $
+- *  CVS/RCS Revision: $Revision: 1.20 $
++ *  Update Date:      $Date: 2011-11-17 16:13:16 $
++ *  CVS/RCS Revision: $Revision: 1.21 $
+  *  Status:           $State: Exp $
+  *
+  *  CVS/RCS Log at end of file
+< at >< at > -124,7 +124,7 < at >< at >
+             {
+                 const T value = OFstatic_cast(T, OFstatic_cast(double, DicomImageClass::maxval(bits)) *
+                     OFstatic_cast(double, pvalue) / OFstatic_cast(double, DicomImageClass::maxval(WIDTH_OF_PVALUES)));
+-                scaleData(&pixel, &this->Data, interpolate, value);
++                this->scaleData(&pixel, &this->Data, interpolate, value);
+              }
+         }
+     }
+< at >< at > -138,6 +138,9 < at >< at >
+  *
+  * CVS/RCS Log:
+  * $Log: dimosct.h,v $
++ * Revision 1.21  2011-11-17 16:13:16  joergr
++ * Minor fixes to keep XCode 4.2 on Mac OS X Lion (clang compiler) quiet.
++ *
+  * Revision 1.20  2010-10-14 13:16:26  joergr
+  * Updated copyright header. Added reference to COPYRIGHT file.
+  *
+Index: dcmtk-3.6.0/dcmimgle/include/dcmtk/dcmimgle/dirotat.h
+===================================================================
+--- dcmtk-3.6.0.orig/dcmimgle/include/dcmtk/dcmimgle/dirotat.h2010-10-14 13:16:27.000000000 +0000
++++ dcmtk-3.6.0/dcmimgle/include/dcmtk/dcmimgle/dirotat.h2012-05-25 09:16:23.799876809 +0000
+< at >< at > -1,6 +1,6 < at >< at >
+ /*
+  *
+- *  Copyright (C) 1996-2010, OFFIS e.V.
++ *  Copyright (C) 1996-2011, OFFIS e.V.
+  *  All rights reserved.  See COPYRIGHT file for details.
+  *
+  *  This software and supporting documentation were developed by
+< at >< at > -18,8 +18,8 < at >< at >
+  *  Purpose: DicomRotateTemplate (Header)
+  *
+  *  Last Update:      $Author: joergr $
+- *  Update Date:      $Date: 2010-10-14 13:16:27 $
+- *  CVS/RCS Revision: $Revision: 1.21 $
++ *  Update Date:      $Date: 2011-11-17 16:13:16 $
++ *  CVS/RCS Revision: $Revision: 1.22 $
+  *  Status:           $State: Exp $
+  *
+  *  CVS/RCS Log at end of file
+< at >< at > -132,7 +132,7 < at >< at >
+         else if (degree == 270)
+             rotateLeft(src, dest);
+         else
+-            copyPixel(src, dest);
++            this->copyPixel(src, dest);
+     }
+ 
+ 
+< at >< at > -358,6 +358,9 < at >< at >
+  *
+  * CVS/RCS Log:
+  * $Log: dirotat.h,v $
++ * Revision 1.22  2011-11-17 16:13:16  joergr
++ * Minor fixes to keep XCode 4.2 on Mac OS X Lion (clang compiler) quiet.
++ *
+  * Revision 1.21  2010-10-14 13:16:27  joergr
+  * Updated copyright header. Added reference to COPYRIGHT file.
+  *
+Index: dcmtk-3.6.0/dcmimgle/include/dcmtk/dcmimgle/discalet.h
+===================================================================
+--- dcmtk-3.6.0.orig/dcmimgle/include/dcmtk/dcmimgle/discalet.h2010-10-14 13:16:27.000000000 +0000
++++ dcmtk-3.6.0/dcmimgle/include/dcmtk/dcmimgle/discalet.h2012-05-25 09:16:23.799876809 +0000
+< at >< at > -1,6 +1,6 < at >< at >
+ /*
+  *
+- *  Copyright (C) 1996-2010, OFFIS e.V.
++ *  Copyright (C) 1996-2011, OFFIS e.V.
+  *  All rights reserved.  See COPYRIGHT file for details.
+  *
+  *  This software and supporting documentation were developed by
+< at >< at > -18,8 +18,8 < at >< at >
+  *  Purpose: DicomScaleTemplates (Header)
+  *
+  *  Last Update:      $Author: joergr $
+- *  Update Date:      $Date: 2010-10-14 13:16:27 $
+- *  CVS/RCS Revision: $Revision: 1.35 $
++ *  Update Date:      $Date: 2011-11-17 16:13:16 $
++ *  CVS/RCS Revision: $Revision: 1.36 $
+  *  Status:           $State: Exp $
+  *
+  *  CVS/RCS Log at end of file
+< at >< at > -206,12 +206,12 < at >< at >
+                 (Left >= OFstatic_cast(signed long, Columns)) || (Top >= OFstatic_cast(signed long, Rows)))
+             {                                                                         // no image to be displayed
+                 DCMIMGLE_DEBUG("clipping area is fully outside the image boundaries");
+-                fillPixel(dest, value);                                               // ... fill bitmap
++                this->fillPixel(dest, value);                                         // ... fill bitmap
+             }
+             else if ((this->Src_X == this->Dest_X) && (this->Src_Y == this->Dest_Y))  // no scaling
+             {
+                 if ((Left == 0) && (Top == 0) && (Columns == this->Src_X) && (Rows == this->Src_Y))
+-                    copyPixel(src, dest);                                             // copying
++                    this->copyPixel(src, dest);                                       // copying
+                 else if ((Left >= 0) && (OFstatic_cast(Uint16, Left + this->Src_X) <= Columns) &&
+                          (Top >= 0) && (OFstatic_cast(Uint16, Top + this->Src_Y) <= Rows))
+                     clipPixel(src, dest);                                             // clipping
+< at >< at > -567,7 +567,7 < at >< at >
+         if ((xtemp == NULL) || (xvalue == NULL))
+         {
+             DCMIMGLE_ERROR("can't allocate temporary buffers for interpolation scaling");
+-            clearPixel(dest);
++            this->clearPixel(dest);
+         } else {
+             for (int j = 0; j < this->Planes; ++j)
+             {
+< at >< at > -905,7 +905,7 < at >< at >
+         if (pTemp == NULL)
+         {
+             DCMIMGLE_ERROR("can't allocate temporary buffer for interpolation scaling");
+-            clearPixel(dest);
++            this->clearPixel(dest);
+         } else {
+ 
+             /*
+< at >< at > -1029,7 +1029,7 < at >< at >
+         if (pTemp == NULL)
+         {
+             DCMIMGLE_ERROR("can't allocate temporary buffer for interpolation scaling");
+-            clearPixel(dest);
++            this->clearPixel(dest);
+         } else {
+ 
+             /*
+< at >< at > -1190,6 +1190,9 < at >< at >
+  *
+  * CVS/RCS Log:
+  * $Log: discalet.h,v $
++ * Revision 1.36  2011-11-17 16:13:16  joergr
++ * Minor fixes to keep XCode 4.2 on Mac OS X Lion (clang compiler) quiet.
++ *
+  * Revision 1.35  2010-10-14 13:16:27  joergr
+  * Updated copyright header. Added reference to COPYRIGHT file.
+  *
+Index: dcmtk-3.6.0/ofstd/include/dcmtk/ofstd/ofoset.h
+===================================================================
+--- dcmtk-3.6.0.orig/ofstd/include/dcmtk/ofstd/ofoset.h2010-10-14 13:15:50.000000000 +0000
++++ dcmtk-3.6.0/ofstd/include/dcmtk/ofstd/ofoset.h2012-05-25 09:16:23.799876809 +0000
+< at >< at > -1,6 +1,6 < at >< at >
+ /*
+  *
+- *  Copyright (C) 2002-2010, OFFIS e.V.
++ *  Copyright (C) 2002-2011, OFFIS e.V.
+  *  All rights reserved.  See COPYRIGHT file for details.
+  *
+  *  This software and supporting documentation were developed by
+< at >< at > -19,8 +19,8 < at >< at >
+  *           of an arbitrary type.
+  *
+  *  Last Update:      $Author: joergr $
+- *  Update Date:      $Date: 2010-10-14 13:15:50 $
+- *  CVS/RCS Revision: $Revision: 1.11 $
++ *  Update Date:      $Date: 2011-11-17 16:13:18 $
++ *  CVS/RCS Revision: $Revision: 1.12 $
+  *  Status:           $State: Exp $
+  *
+  *  CVS/RCS Log at end of file
+< at >< at > -146,7 +146,7 < at >< at >
+       {
+         // if size equals num, we need more space
+         if( this->size == this->num )
+-          Resize( this->size * 2 );
++          this->Resize( this->size * 2 );
+ 
+         // copy item
+         T *newItem = new T( item );
+< at >< at > -189,7 +189,7 < at >< at >
+         {
+           // if size equals num, we need more space
+           if( this->size == this->num )
+-            Resize( this->size * 2 );
++            this->Resize( this->size * 2 );
+ 
+           // copy item
+           T *newItem = new T( item );
+< at >< at > -508,6 +508,9 < at >< at >
+ /*
+ ** CVS/RCS Log:
+ ** $Log: ofoset.h,v $
++** Revision 1.12  2011-11-17 16:13:18  joergr
++** Minor fixes to keep XCode 4.2 on Mac OS X Lion (clang compiler) quiet.
++**
+ ** Revision 1.11  2010-10-14 13:15:50  joergr
+ ** Updated copyright header. Added reference to COPYRIGHT file.
+ **

Modified: trunk/packages/dcmtk/trunk/debian/patches/series
===================================================================
--- trunk/packages/dcmtk/trunk/debian/patches/series2012-05-25 08:46:12 UTC (rev 10999)
+++ trunk/packages/dcmtk/trunk/debian/patches/series2012-05-25 09:51:25 UTC (rev 11000)
< at >< at > -9,3 +9,4 < at >< at >
 dcmtk_version_number.patch
 regression_stacksequenceisodd.patch
 removecharls.patch
+bug674361.patch

Modified: trunk/packages/dcmtk/trunk/debian/rules
===================================================================
--- trunk/packages/dcmtk/trunk/debian/rules2012-05-25 08:46:12 UTC (rev 10999)
+++ trunk/packages/dcmtk/trunk/debian/rules2012-05-25 09:51:25 UTC (rev 11000)
< at >< at > -1,10 +1,4 < at >< at >
 #!/usr/bin/make -f
-# debian/rules for dcmtk
-# Authors: Juergen Salk <juergen.salk< at >gmx.de>
-#          Mathieu Malaterre <mathieu.malaterre< at >gmail.com>
-
-include /usr/share/quilt/quilt.make
-
 #export DH_VERBOSE=1
 
 # These are used for cross-compiling and for saving the configure script
< at >< at > -26,15 +20,11 < at >< at >
 # Library version
 LIB_VERSION=2.0.0
 
-CFLAGS = -Wall -g
-LDFLAGS = -Wl,--no-as-needed
+export DEB_LDFLAGS_MAINT_APPEND = -Wl,--as-needed
+export DEB_BUILD_MAINT_OPTIONS = hardening=+all
+DPKG_EXPORT_BUILDFLAGS = 1
+include /usr/share/dpkg/buildflags.mk
 
-ifneq (,$(findstring noopt,$(DEB_BUILD_OPTIONS)))
-CFLAGS += -O0
-else
-CFLAGS += -O2
-endif
-
 config/config.status: configure
 dh_testdir
 
< at >< at > -69,7 +59,7 < at >< at >
 --with-openssl
 
 
-build-arch: $(QUILT_STAMPFN) config/config.status build-arch-stamp
+build-arch: config/config.status build-arch-stamp
 build-arch-stamp:
 dh_testdir
 
< at >< at > -89,7 +79,7 < at >< at >
 # utilities dynamically against the shared library versions.
 
 mv config/Makefile.def config/Makefile.def.static && \
-sed -e '/^CFLAGS =/s/-O/-fPIC $(CFLAGS)/' -e '/^CXXFLAGS =/s/-O/-fPIC $(CXXFLAGS)/' \
+sed -e '/^CFLAGS =/s/-O/-fPIC/' -e '/^CXXFLAGS =/s/-O/-fPIC/' \
 -e '/^AR =/s/ar/gcc/' -e '/^ARFLAGS =/s/cruv/-shared -Wl,-soname,\$$\< at >.2 -o/' \
 -e '/^LIBEXT =/s/a/so/' -e '/^RANLIB =/s/ranlib/:/' \
 <config/Makefile.def.static >config/Makefile.def && \
< at >< at > -111,7 +101,7 < at >< at >
 
 build: build-arch
 
-clean: unpatch
+clean:
 dh_testdir
 dh_testroot
 if [ -d config/backup ] ; then cd config; mv backup/* . ; rm -rf backup ; fi

r10999 - trunk/packages/sift/trunk/debian

Andreas Tille — 2012-05-25T08:46:13

Author: tille
Date: 2012-05-25 08:46:12 +0000 (Fri, 25 May 2012)
New Revision: 10999

Added:
   trunk/packages/sift/trunk/debian/upstream
Modified:
   trunk/packages/sift/trunk/debian/changelog
Log:
Citation of the day


Modified: trunk/packages/sift/trunk/debian/changelog
===================================================================
--- trunk/packages/sift/trunk/debian/changelog2012-05-24 21:26:20 UTC (rev 10998)
+++ trunk/packages/sift/trunk/debian/changelog2012-05-25 08:46:12 UTC (rev 10999)
< at >< at > -1,3 +1,9 < at >< at >
+sift (4.0.3b-4) UNRELEASED; urgency=low
+
+  * debian/upstream: Add citations
+
+ -- Andreas Tille <tille< at >debian.org>  Fri, 25 May 2012 10:45:33 +0200
+
 sift (4.0.3b-3) unstable; urgency=low
 
   * Added patches from Michael Bienia <geser< at >ubuntu.com>.

Added: trunk/packages/sift/trunk/debian/upstream
===================================================================
--- trunk/packages/sift/trunk/debian/upstream                        (rev 0)
+++ trunk/packages/sift/trunk/debian/upstream2012-05-25 08:46:12 UTC (rev 10999)
< at >< at > -0,0 +1,55 < at >< at >
+Reference:
+ - Author: Prateek Kumar and Steven Henikoff and Pauline C Ng
+   Title: Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm
+   Journal: Nature Protocols
+   Year: 2009
+   Volume: 4
+   Number: 7
+   Pages: 1073-81
+   DOI: 10.1038/nprot.2009.86
+   PMID: 19561590
+   URL: http://www.nature.com/nprot/journal/v4/n7/full/nprot.2009.86.html
+   eprint: http://www.nature.com/nprot/journal/v4/n7/pdf/nprot.2009.86.pdf
+ - Author: Pauline C Ng and Steven Henikoff
+   Title: Predicting the effects of amino acid substitutions on protein function
+   Journal: Annu Rev Genomics Hum Genet.
+   Year: 2006
+   Volume: 7
+   Pages: 61-80
+   DOI: 10.1146/annurev.genom.7.080505.115630
+   PMID: 16824020
+   URL: http://www.annualreviews.org/doi/abs/10.1146/annurev.genom.7.080505.115630
+   eprint: http://www.annualreviews.org/doi/pdf/10.1146/annurev.genom.7.080505.115630
+ - Author: Pauline C Ng and Steven Henikoff
+   Title: "SIFT: Predicting amino acid changes that affect protein function"
+   Journal: Nucleic Acids Research
+   Year: 2003
+   Volume: 31
+   Number: 13
+   Pages: 3812-4
+   DOI: 10.1093/nar/gkg509
+   PMID: 12824425
+   URL: http://nar.oxfordjournals.org/content/31/13/3812.abstract
+   eprint: http://nar.oxfordjournals.org/content/31/13/3812.full.pdf+html
+ - Author: Pauline C Ng and Steven Henikoff
+   Title: "Accounting for human polymorphisms predicted to affect protein function"
+   Journal: Genome Research
+   Year: 2002
+   Volume: 12
+   Number: 3
+   Pages: 436-46
+   DOI: 10.1101/gr.212802
+   PMID: 11875032
+   URL: http://genome.cshlp.org/content/12/3/436
+   eprint: http://genome.cshlp.org/content/12/3/436.full.pdf+html
+ - Author: Pauline C Ng and Steven Henikoff
+   Title: Predicting deleterious amino acid substitutions
+   Journal: Genome Research
+   Year: 2001
+   Volume: 11
+   Number: 5
+   Pages: 863-74
+   DOI: 10.1101/gr.176601
+   PMID: 11337480
+   URL: http://genome.cshlp.org/content/11/5/863
+   eprint: http://genome.cshlp.org/content/11/5/863.full.pdf+html

r10998 - in trunk/packages: . amos amos/trunkamos/trunk/debian

Andreas Tille — 2012-05-24T21:26:20

Author: tille
Date: 2012-05-24 21:26:20 +0000 (Thu, 24 May 2012)
New Revision: 10998

Added:
   trunk/packages/amos/
   trunk/packages/amos/trunk/
   trunk/packages/amos/trunk/debian/
   trunk/packages/amos/trunk/debian/changelog
   trunk/packages/amos/trunk/debian/compat
   trunk/packages/amos/trunk/debian/control
   trunk/packages/amos/trunk/debian/copyright
   trunk/packages/amos/trunk/debian/upstream
   trunk/packages/amos/trunk/debian/watch
Log:
Add machine-readable data for amos-assembler and hawkeye which both build from the same source


Added: trunk/packages/amos/trunk/debian/changelog
===================================================================
--- trunk/packages/amos/trunk/debian/changelog                        (rev 0)
+++ trunk/packages/amos/trunk/debian/changelog2012-05-24 21:26:20 UTC (rev 10998)
< at >< at > -0,0 +1,5 < at >< at >
+amos (3.1.0-1) unstable; urgency=low
+
+  * Initial release
+
+ -- Andreas Tille <tille< at >debian.org>  Thu, 24 May 2012 14:30:13 +0200

Added: trunk/packages/amos/trunk/debian/compat
===================================================================
--- trunk/packages/amos/trunk/debian/compat                        (rev 0)
+++ trunk/packages/amos/trunk/debian/compat2012-05-24 21:26:20 UTC (rev 10998)
< at >< at > -0,0 +1 < at >< at >
+9

Added: trunk/packages/amos/trunk/debian/control
===================================================================
--- trunk/packages/amos/trunk/debian/control                        (rev 0)
+++ trunk/packages/amos/trunk/debian/control2012-05-24 21:26:20 UTC (rev 10998)
< at >< at > -0,0 +1,55 < at >< at >
+Source: amos
+Section: science
+Priority: optional
+Maintainer: Debian Med Packaging Team <debian-med-packaging< at >lists.alioth.debian.org>
+DM-Upload-Allowed: yes
+Uploaders: Andreas Tille <tille< at >debian.org>
+Build-Depends: debhelper (>= 9)
+Standards-Version: 3.9.3
+Homepage: http://amos.sourceforge.net/
+Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/amos/trunk/
+Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/amos/trunk/
+
+Package: amos-assembler
+Architecture: any
+Depends: ${shlibs:Depends}, ${misc:Depends}
+Description: modular whole genome assembler
+ The AMOS consortium is committed to the development of open-source
+ whole genome assembly software. The project acronym (AMOS) represents
+ our primary goal - to produce A Modular, Open-Source whole genome
+ assembler. Open-source so that everyone is welcome to contribute and
+ help build outstanding assembly tools, and modular in nature so that
+ new contributions can be easily inserted into an existing assembly
+ pipeline. This modular design will foster the development of new
+ assembly algorithms and allow the AMOS project to continually grow
+ and improve in hopes of eventually becoming a widely accepted and
+ deployed assembly infrastructure. In this sense, AMOS is both a
+ design philosophy and a software system.
+
+Package: hawkeye
+Architecture: any
+Depends: ${shlibs:Depends}, ${misc:Depends}
+Description: Interactive Visual Analytics Tool for Genome Assemblies
+ Genome assembly remains an inexact science. Even when accomplished
+ with the best software available, the assembly of a genome often
+ contains numerous errors, both small and large. Hawkeye is a visual
+ analytics tool for genome assembly analysis and validation, designed
+ to aid in identifying and correcting assembly errors. Hawkeye blends
+ the best practices from information and scientific visualization to
+ facilitate inspection of large-scale assembly data while minimizing
+ the time needed to detect mis-assemblies and make accurate judgments
+ of assembly quality.
+ .
+ All levels of the assembly data hierarchy are made accessible to
+ users, along with summary statistics and common assembly metrics. A
+ ranking component guides investigation towards likely mis-assemblies
+ or interesting features to support the task at hand. Wherever
+ possible, high-level overviews, dynamic filtering, and automated
+ clustering are leveraged to focus attention and highlight anomalies
+ in the data. Hawkeyes effectiveness has been proven on several genome
+ projects, where it has been used both to improve quality and to
+ validate the correctness of complex genomes.
+ .
+ Hawkeye is compatible with most widely used assemblers, including
+ Phrap, ARACHNE, Celera Assembler, Newbler, AMOS, and assemblies
+ deposited in the NCBI Assembly Archive.

Added: trunk/packages/amos/trunk/debian/copyright
===================================================================
--- trunk/packages/amos/trunk/debian/copyright                        (rev 0)
+++ trunk/packages/amos/trunk/debian/copyright2012-05-24 21:26:20 UTC (rev 10998)
< at >< at > -0,0 +1,11 < at >< at >
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: AMOS
+Source: http://sourceforge.net/projects/amos/files/amos/
+
+Files: *
+Copyright: © 2002-2011 AMOS consortium
+License: Artistic
+
+Files: debian/*
+Copyright: © 2012 Andreas Tille <tille< at >debian.org>
+License: Artistic

Added: trunk/packages/amos/trunk/debian/upstream
===================================================================
--- trunk/packages/amos/trunk/debian/upstream                        (rev 0)
+++ trunk/packages/amos/trunk/debian/upstream2012-05-24 21:26:20 UTC (rev 10998)
< at >< at > -0,0 +1,32 < at >< at >
+Reference:
+ - Author: Michael C. Schatz and Adam M. Phillippy and Daniel D. Sommer and Arthur L. Delcher and Daniela Puiu and Giuseppe Narzisi and Steven L. Salzberg and Mihai Pop
+   Title: "Hawkeye and AMOS: visualizing and assessing the quality of genome assemblies"
+   Journal: Briefings in Bioinform
+   Year: 2011
+   DOI: 10.1093/bib/bbr074
+   PMID: 22199379
+   URL: http://bib.oxfordjournals.org/content/early/2011/12/23/bib.bbr074
+   eprint: http://bib.oxfordjournals.org/content/early/2011/12/23/bib.bbr074.full.pdf+html
+ - Debian-Package: hawkeye
+   Author: Michael C Schatz and Adam M Phillippy and Ben Shneiderman and Steven L Salzberg
+   Title: "Hawkeye: an interactive visual analytics tool for genome assemblies"
+   Journal: Genome Biology
+   Year: 2007
+   Volume: 8
+   Number: 3
+   Pages: R34
+   DOI: 10.1186/gb-2007-8-3-r34
+   PMID: 17349036
+   URL: http://genomebiology.com/2007/8/3/R34
+   eprint: http://genomebiology.com/content/pdf/gb-2007-8-3-r34.pdf
+ - Debian-Package: amos-assembler
+   Author: Todd J Treangen and Dan D Sommer and Florent E Angly and Sergey Koren and Mihai Pop
+   Title: Next generation sequence assembly with AMOS
+   Journal: Curr Protoc Bioinformatics.
+   Year: 2011
+   Volume: Chapter 11
+   Pages: Unit 11.8
+   DOI: 10.1002/0471250953.bi1108s33
+   PMID: 21400694
+   URL: http://onlinelibrary.wiley.com/doi/10.1002/0471250953.bi1108s33/abstract
+   eprint: http://onlinelibrary.wiley.com/doi/10.1002/0471250953.bi1108s33/pdf

Added: trunk/packages/amos/trunk/debian/watch
===================================================================
--- trunk/packages/amos/trunk/debian/watch                        (rev 0)
+++ trunk/packages/amos/trunk/debian/watch2012-05-24 21:26:20 UTC (rev 10998)
< at >< at > -0,0 +1,2 < at >< at >
+version=3
+http://sf.net/amos/amos-([.\d]+)\.tar\.gz


_______________________________________________
debian-med-commit mailing list
debian-med-commit< at >lists.alioth.debian.org
http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit

r10997 - trunk/packages/pdb2pqr/trunk/debian

Michael Banck — 2012-05-24T15:30:50

Author: mbanck
Date: 2012-05-24 15:30:49 +0000 (Thu, 24 May 2012)
New Revision: 10997

Modified:
   trunk/packages/pdb2pqr/trunk/debian/upstream
Log:
Add name, homepage and registration fields to upstream metadata

Modified: trunk/packages/pdb2pqr/trunk/debian/upstream
===================================================================
--- trunk/packages/pdb2pqr/trunk/debian/upstream2012-05-24 15:23:06 UTC (rev 10996)
+++ trunk/packages/pdb2pqr/trunk/debian/upstream2012-05-24 15:30:49 UTC (rev 10997)
< at >< at > -1,3 +1,6 < at >< at >
+Name: PDB2PQR
+Homepage: http://www.poissonboltzmann.org/pdb2pqr
+Registration: http://spreadsheets.google.com/viewform?hl=en&formkey=dHFpa3Nvcnl0cjR1U3g3UTdSYU1pWWc6MA..
 Reference:
  - Author: Todd J Dolinsky and Paul Czodrowski and Hui Li and Jens E Nielsen and Jan H Jensen and Gerhard Klebe and Nathan A Baker
    Title: "PDB2PQR: Expanding and upgrading automated preparation of biomolecular structures for molecular simulations"

r10996 - in trunk/packages/libforester-java/trunk: .debian debian/binary debian/patches debian/source

Olivier Sallou — 2012-05-24T15:23:06

Author: osallou
Date: 2012-05-24 15:23:06 +0000 (Thu, 24 May 2012)
New Revision: 10996

Added:
   trunk/packages/libforester-java/trunk/debian/
   trunk/packages/libforester-java/trunk/debian/binary/
   trunk/packages/libforester-java/trunk/debian/binary/forester
   trunk/packages/libforester-java/trunk/debian/changelog
   trunk/packages/libforester-java/trunk/debian/compat
   trunk/packages/libforester-java/trunk/debian/control
   trunk/packages/libforester-java/trunk/debian/copyright
   trunk/packages/libforester-java/trunk/debian/docs
   trunk/packages/libforester-java/trunk/debian/forester.install
   trunk/packages/libforester-java/trunk/debian/get-orig-source.sh
   trunk/packages/libforester-java/trunk/debian/libforester-java-doc.doc-base
   trunk/packages/libforester-java/trunk/debian/libforester-java-doc.install
   trunk/packages/libforester-java/trunk/debian/libforester-java.jlibs
   trunk/packages/libforester-java/trunk/debian/patches/
   trunk/packages/libforester-java/trunk/debian/patches/change_itext_packagename.patch
   trunk/packages/libforester-java/trunk/debian/patches/fix_jar_path.patch
   trunk/packages/libforester-java/trunk/debian/patches/series
   trunk/packages/libforester-java/trunk/debian/rules
   trunk/packages/libforester-java/trunk/debian/source/
   trunk/packages/libforester-java/trunk/debian/source/format
Log:
[svn-inject] Applying Debian modifications (0.971-1) to trunk


Property changes on: trunk/packages/libforester-java/trunk/debian
___________________________________________________________________
Added: mergeWithUpstream
   + 1

Added: trunk/packages/libforester-java/trunk/debian/binary/forester
===================================================================
--- trunk/packages/libforester-java/trunk/debian/binary/forester                        (rev 0)
+++ trunk/packages/libforester-java/trunk/debian/binary/forester2012-05-24 15:23:06 UTC (rev 10996)
< at >< at > -0,0 +1,3 < at >< at >
+#!/bin/bash
+
+java -jar /usr/share/java/forester.jar


Property changes on: trunk/packages/libforester-java/trunk/debian/binary/forester
___________________________________________________________________
Added: svn:executable
   + *

Added: trunk/packages/libforester-java/trunk/debian/changelog
===================================================================
--- trunk/packages/libforester-java/trunk/debian/changelog                        (rev 0)
+++ trunk/packages/libforester-java/trunk/debian/changelog2012-05-24 15:23:06 UTC (rev 10996)
< at >< at > -0,0 +1,7 < at >< at >
+libforester-java (0.971-1) UNRELEASED; urgency=low
+
+  * Initial release (Closes: #674269)
+   * Wait to know which revision in SVN we should take
+   * Ask upstream to put jars with version
+
+ -- Olivier Sallou <osallou< at >debian.org>  Thu, 24 May 2012 12:28:55 +0200

Added: trunk/packages/libforester-java/trunk/debian/compat
===================================================================
--- trunk/packages/libforester-java/trunk/debian/compat                        (rev 0)
+++ trunk/packages/libforester-java/trunk/debian/compat2012-05-24 15:23:06 UTC (rev 10996)
< at >< at > -0,0 +1 < at >< at >
+8

Added: trunk/packages/libforester-java/trunk/debian/control
===================================================================
--- trunk/packages/libforester-java/trunk/debian/control                        (rev 0)
+++ trunk/packages/libforester-java/trunk/debian/control2012-05-24 15:23:06 UTC (rev 10996)
< at >< at > -0,0 +1,39 < at >< at >
+Source: libforester-java
+Section: java
+Priority: optional
+Maintainer: Debian Med Packaging Team <debian-med-packaging< at >lists.alioth.debian.org>
+DM-Upload-Allowed: yes
+Uploaders: Olivier Sallou <osallou< at >debian.org>
+Build-Depends: debhelper (>= 8.0.0),
+ default-jdk, junit4, javahelper (>=0.25), libcommons-codec, libitext-java
+Standards-Version: 3.9.3
+Homepage: http://code.google.com/p/forester
+Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/forester/trunk/
+Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/forester/trunk/
+
+Package: forester
+Architecture: all
+Depends: ${misc:Depends}, libforester-java
+Description: Graphical vizualiation tool Archaeopteryx
+ Archaeopteryx is a software tool for the visualization, analysis,
+ and editing of potentially large and highly annotated phylogenetic trees.
+ It can be used both as applet (ArchaeopteryxA and ArchaeopteryxE) and
+ as a standalone application.
+
+Package: libforester-java
+Architecture: all
+Depends: ${misc:Depends},
+ libcommons-codec, libitext-java
+Description: Libraries for evolutionary biology and comparative genomics research
+ Forester is a library of Java software for phylogenomics 
+ and evolutionary biology research. It can be used to read or
+ write phylogenetic trees, export trees to graphics file,...
+
+Package: libforester-java-doc
+Section: doc
+Architecture: all
+Depends: ${misc:Depends}
+Description: [Biology] Documentation for forester
+ Forester is a library of Java software for phylogenomics
+ and evolutionary biology research. This package contains the
+ JavaDoc documentation.

Added: trunk/packages/libforester-java/trunk/debian/copyright
===================================================================
--- trunk/packages/libforester-java/trunk/debian/copyright                        (rev 0)
+++ trunk/packages/libforester-java/trunk/debian/copyright2012-05-24 15:23:06 UTC (rev 10996)
< at >< at > -0,0 +1,44 < at >< at >
+Format: http://dep.debian.net/deps/dep5
+Upstream-Name: forester
+Source: http://code.google.com/p/forester
+
+Files: *
+Copyright: 2010 Christian M. Zmasek
+           2010 Sanford-Burnham Medical Research Institute
+License: LGPL 2.1+
+ This library 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 2.1 of the License, or (at your option) any later version.
+ .
+ This library 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 Lesser General Public
+ License along with this library; 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 Lesser General
+ Public License version 2 can be found in "/usr/share/common-licenses/LGPL-2.1".
+
+Files: debian/*
+Copyright: 2012 Olivier Sallou <osallou< at >debian.org>
+License: GPL-2+
+ This package 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 package 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/>
+ .
+ On Debian systems, the complete text of the GNU General
+ Public License version 2 can be found in "/usr/share/common-licenses/GPL-2".
+

Added: trunk/packages/libforester-java/trunk/debian/docs
===================================================================
Added: trunk/packages/libforester-java/trunk/debian/forester.install
===================================================================
--- trunk/packages/libforester-java/trunk/debian/forester.install                        (rev 0)
+++ trunk/packages/libforester-java/trunk/debian/forester.install2012-05-24 15:23:06 UTC (rev 10996)
< at >< at > -0,0 +1 < at >< at >
+debian/binary/forester usr/bin

Added: trunk/packages/libforester-java/trunk/debian/get-orig-source.sh
===================================================================
--- trunk/packages/libforester-java/trunk/debian/get-orig-source.sh                        (rev 0)
+++ trunk/packages/libforester-java/trunk/debian/get-orig-source.sh2012-05-24 15:23:06 UTC (rev 10996)
< at >< at > -0,0 +1,17 < at >< at >
+#!/bin/bash
+
+
+PKG=`dpkg-parsechangelog | awk '/^Source/ { print $2 }'`
+VERSION=`dpkg-parsechangelog | awk '/^Version/ { print $2 }' | cut -d "-" -f1`
+version=$VERSION.svn.`date +"%Y%m%d"|tr -d '\n'`
+targetdir=libforester-java-$version
+origtargz=libforester-java_$VERSION.orig.tar.gz
+cd ..
+mkdir $targetdir
+svn checkout http://forester.googlecode.com/svn/forester/java $targetdir/java
+svn checkout http://forester.googlecode.com/svn/forester/resources $targetdir/resources
+find $targetdir -name ".svn" | xargs -r rm -r
+find $targetdir -name "*.jar" | xargs -r rm -r
+tar czf $origtargz $targetdir
+rm -rf $targetdir
+


Property changes on: trunk/packages/libforester-java/trunk/debian/get-orig-source.sh
___________________________________________________________________
Added: svn:executable
   + *

Added: trunk/packages/libforester-java/trunk/debian/libforester-java-doc.doc-base
===================================================================
--- trunk/packages/libforester-java/trunk/debian/libforester-java-doc.doc-base                        (rev 0)
+++ trunk/packages/libforester-java/trunk/debian/libforester-java-doc.doc-base2012-05-24 15:23:06 UTC (rev 10996)
< at >< at > -0,0 +1,12 < at >< at >
+Document: forester
+Title: forester API
+Author: Forester developers
+Abstract: Javadoc-generated API for the forester library.
+ Forester is a library of Java software for phylogenomics
+ and evolutionary biology research. It can be used to read or
+ write phylogenetic trees, export trees to graphics file,...
+Section: Science/Biology
+
+Format: HTML
+Index: /usr/share/doc/libforester-java/api/index.html
+Files: /usr/share/doc/libforester-java/api/*.html /usr/share/doc/libforester-java/api/*/*/*/*.html /usr/share/doc/libforester-java/api/*/*/*/*/*.html /usr/share/doc/libforester-java/api/*/*/*/*/*/*.html

Added: trunk/packages/libforester-java/trunk/debian/libforester-java-doc.install
===================================================================
--- trunk/packages/libforester-java/trunk/debian/libforester-java-doc.install                        (rev 0)
+++ trunk/packages/libforester-java/trunk/debian/libforester-java-doc.install2012-05-24 15:23:06 UTC (rev 10996)
< at >< at > -0,0 +1 < at >< at >
+doc/* /usr/share/doc/libforester-java/api/

Added: trunk/packages/libforester-java/trunk/debian/libforester-java.jlibs
===================================================================
--- trunk/packages/libforester-java/trunk/debian/libforester-java.jlibs                        (rev 0)
+++ trunk/packages/libforester-java/trunk/debian/libforester-java.jlibs2012-05-24 15:23:06 UTC (rev 10996)
< at >< at > -0,0 +1 < at >< at >
+java/forester.jar

Added: trunk/packages/libforester-java/trunk/debian/patches/change_itext_packagename.patch
===================================================================
--- trunk/packages/libforester-java/trunk/debian/patches/change_itext_packagename.patch                        (rev 0)
+++ trunk/packages/libforester-java/trunk/debian/patches/change_itext_packagename.patch2012-05-24 15:23:06 UTC (rev 10996)
< at >< at > -0,0 +1,29 < at >< at >
+Author: Olivier Sallou <osallou< at >debian.org>
+Subject: change package name for itext
+Description: Upstream refers to com.itext hwile Debian package
+ itext use package name com.lowagie. Replace in the file the package
+ name references
+Last-Updated: 24/05/12
+--- a/java/src/org/forester/archaeopteryx/PdfExporter.java
++++ b/java/src/org/forester/archaeopteryx/PdfExporter.java
+< at >< at > -35,13 +35,13 < at >< at >
+ 
+ import org.forester.phylogeny.Phylogeny;
+ 
+-import com.itextpdf.text.Document;
+-import com.itextpdf.text.DocumentException;
+-import com.itextpdf.text.FontFactory;
+-import com.itextpdf.text.Rectangle;
+-import com.itextpdf.text.pdf.DefaultFontMapper;
+-import com.itextpdf.text.pdf.PdfContentByte;
+-import com.itextpdf.text.pdf.PdfWriter;
++import com.lowagie.text.Document;
++import com.lowagie.text.DocumentException;
++import com.lowagie.text.FontFactory;
++import com.lowagie.text.Rectangle;
++import com.lowagie.text.pdf.DefaultFontMapper;
++import com.lowagie.text.pdf.PdfContentByte;
++import com.lowagie.text.pdf.PdfWriter;
+ 
+ /*
+  * 

Added: trunk/packages/libforester-java/trunk/debian/patches/fix_jar_path.patch
===================================================================
--- trunk/packages/libforester-java/trunk/debian/patches/fix_jar_path.patch                        (rev 0)
+++ trunk/packages/libforester-java/trunk/debian/patches/fix_jar_path.patch2012-05-24 15:23:06 UTC (rev 10996)
< at >< at > -0,0 +1,68 < at >< at >
+Author: Olivier Sallou <osallou< at >debian.org>
+Subject: Change dependency libraries path
+Description: Use Debian libraries instead of upstream
+ included ones
+Last-Updated: 24/05/12
+--- a/java/build.xml
++++ b/java/build.xml
+< at >< at > -3,9 +3,9 < at >< at >
+ 
+ <property name="src.dir" value="src" />
+ <property name="classes.dir" value="classes" />
+-<property name="jars.dir" value="resources" />
+-<property name="itextjar" value="${jars.dir}/itextpdf-5.1.0.jar" />
+-<property name="commonscodecjar" value="${jars.dir}/commons-codec-1.5.jar" />
++<property name="jars.dir" value="/usr/share/java" />
++<property name="itextjar" value="${jars.dir}/itext.jar" />
++<property name="commonscodecjar" value="${jars.dir}/commons-codec.jar" />
+ <property name="forester_jar" value="forester.jar" />
+ <property name="archaeopteryx_applets_jar" value="archaeopteryx_applets.jar" />
+ 
+< at >< at > -40,34 +40,15 < at >< at >
+ </target>
+ 
+ <target name="jar" description="JARs the classes files" depends="compile,copy_resources">
+-<unjar src="${itextjar}" dest="${classes.dir}">
+-            <patternset>
+-                <include name="**/*.class" />
+-                <include name="**/*.afm" />
+-                <include name="**/*.txt" />
+-                <exclude name="**/*Test*.class" />
+-            </patternset>
+-        </unjar>
+-        <unjar src="${commonscodecjar}" dest="${classes.dir}">
+-            <patternset>
+-                <include name="**/*.class" />
+-                <exclude name="**/*Test*.class" />
+-            </patternset>
+-        </unjar>
+ <jar level="9" destfile="${forester_jar}" basedir="${classes.dir}" excludes="**/Test.class" duplicate="fail" index="true">
+ <manifest>
+ <attribute name="Main-Class" value="org.forester.archaeopteryx.Archaeopteryx" />
++<attribute name="Class-Path" value="${itextjar};${commonscodecjar}"/>
+ </manifest>
+ </jar>
+ </target>
+ 
+ <target name="jar_applets_only" description="JARs the classes files" depends="compile_applets_only,copy_resources">
+-<unjar src="${commonscodecjar}" dest="${classes.dir}">
+-            <patternset>
+-                <include name="**/*.class" />
+-                <exclude name="**/*Test*.class" />
+-            </patternset>
+-        </unjar>
+ <jar level="9" destfile="${archaeopteryx_applets_jar}" basedir="${classes.dir}" excludes="org/forester/application/** 
+           org/forester/development/**
+           org/forester/evoinference/**
+< at >< at > -87,4 +68,11 < at >< at >
+ <target name="applets_only" description="" depends="jar_applets_only">
+ </target>
+ 
++        <target name="javadoc">
++                <mkdir dir="../doc"/>
++                <javadoc destdir="../doc" sourcepath="${src.dir}" >
++                        <link href="http://java.sun.com/j2se/1.6.0/docs/api/"/>
++                </javadoc>
++        </target>
++
+ </project>

Added: trunk/packages/libforester-java/trunk/debian/patches/series
===================================================================
--- trunk/packages/libforester-java/trunk/debian/patches/series                        (rev 0)
+++ trunk/packages/libforester-java/trunk/debian/patches/series2012-05-24 15:23:06 UTC (rev 10996)
< at >< at > -0,0 +1,2 < at >< at >
+fix_jar_path.patch
+change_itext_packagename.patch

Added: trunk/packages/libforester-java/trunk/debian/rules
===================================================================
--- trunk/packages/libforester-java/trunk/debian/rules                        (rev 0)
+++ trunk/packages/libforester-java/trunk/debian/rules2012-05-24 15:23:06 UTC (rev 10996)
< at >< at > -0,0 +1,19 < at >< at >
+#!/usr/bin/make -f
+
+# Uncomment this to turn on verbose mode.
+#export DH_VERBOSE=1
+
+%:
+dh $< at >  --with javahelper
+
+override_dh_auto_build:
+cd java && ant
+cd java && ant javadoc
+
+override_dh_clean:
+cd java && ant clean
+rm -rf doc
+dh_clean
+
+get-orig-source:
+debian/get-orig-source.sh


Property changes on: trunk/packages/libforester-java/trunk/debian/rules
___________________________________________________________________
Added: svn:executable
   + *

Added: trunk/packages/libforester-java/trunk/debian/source/format
===================================================================
--- trunk/packages/libforester-java/trunk/debian/source/format                        (rev 0)
+++ trunk/packages/libforester-java/trunk/debian/source/format2012-05-24 15:23:06 UTC (rev 10996)
< at >< at > -0,0 +1 < at >< at >
+3.0 (quilt)

r10995 - trunk/packages/libforester-java

Olivier Sallou — 2012-05-24T15:23:02

Author: osallou
Date: 2012-05-24 15:23:01 +0000 (Thu, 24 May 2012)
New Revision: 10995

Added:
   trunk/packages/libforester-java/trunk/
Log:
Creating trunk directory

r10994 - in trunk/packages: . libforester-java

Olivier Sallou — 2012-05-24T15:22:57

Author: osallou
Date: 2012-05-24 15:22:57 +0000 (Thu, 24 May 2012)
New Revision: 10994

Added:
   trunk/packages/libforester-java/
   trunk/packages/libforester-java/tags/
Log:
[svn-inject] Creating libforester-java/tags/ directory.

r10993 - trunk

Olivier Sallou — 2012-05-24T15:22:04

Author: osallou
Date: 2012-05-24 15:22:04 +0000 (Thu, 24 May 2012)
New Revision: 10993

Removed:
   trunk/forester/
Log:
Wrong place, remove for reinject

[SCM] ssaha tag, master, created. upstream/3.1c-1-gc3f9f23

Andreas Tille — 2012-05-24T15:00:07

The tag, master has been created
        at  c3f9f23d488bd1e35554190019bc87844c53eb24 (commit)

- Shortlog ------------------------------------------------------------
commit c3f9f23d488bd1e35554190019bc87844c53eb24
Author: Andreas Tille <tille< at >debian.org>
Date:   Thu May 24 16:56:06 2012 +0200

    Addemble data from med-bio task file and WNPP to enable machine-readable gatherer fetch the data properly (no intend to build a package myself, but it seems to make sense to conserve the code here because even the latest version 3.3 seems to be lost)
-----------------------------------------------------------------------

[SCM] ssaha tag, prospective/3.1c,created. upstream/3.1c-1-gc3f9f23

Andreas Tille — 2012-05-24T14:58:28

The tag, prospective/3.1c has been created
        at  c3f9f23d488bd1e35554190019bc87844c53eb24 (commit)

- Shortlog ------------------------------------------------------------
commit c3f9f23d488bd1e35554190019bc87844c53eb24
Author: Andreas Tille <tille< at >debian.org>
Date:   Thu May 24 16:56:06 2012 +0200

    Addemble data from med-bio task file and WNPP to enable machine-readable gatherer fetch the data properly (no intend to build a package myself, but it seems to make sense to conserve the code here because even the latest version 3.3 seems to be lost)
-----------------------------------------------------------------------

[SCM] ssaha annotated tag, upstream/3.1c,created. upstream/3.1c

Andreas Tille — 2012-05-24T14:40:34

The annotated tag, upstream/3.1c has been created
        at  89102a701415e39efb74ae71141879b153f6c6a7 (tag)
   tagging  0818f2111a84138232068f1c1edc2fd441392c84 (commit)
 tagged by  Andreas Tille
        on  Thu May 24 16:39:44 2012 +0200

- Shortlog ------------------------------------------------------------
Upstream version 3.1c

Andreas Tille (1):
      Imported Upstream version 3.1c

-----------------------------------------------------------------------

r10992 - in trunk/forester/libforester-java/trunk: .debian debian/binary debian/patches debian/source

Olivier Sallou — 2012-05-24T13:08:47

Author: osallou
Date: 2012-05-24 13:08:46 +0000 (Thu, 24 May 2012)
New Revision: 10992

Added:
   trunk/forester/libforester-java/trunk/debian/
   trunk/forester/libforester-java/trunk/debian/binary/
   trunk/forester/libforester-java/trunk/debian/binary/forester
   trunk/forester/libforester-java/trunk/debian/changelog
   trunk/forester/libforester-java/trunk/debian/compat
   trunk/forester/libforester-java/trunk/debian/control
   trunk/forester/libforester-java/trunk/debian/copyright
   trunk/forester/libforester-java/trunk/debian/docs
   trunk/forester/libforester-java/trunk/debian/forester.install
   trunk/forester/libforester-java/trunk/debian/get-orig-source.sh
   trunk/forester/libforester-java/trunk/debian/libforester-java-doc.doc-base
   trunk/forester/libforester-java/trunk/debian/libforester-java-doc.install
   trunk/forester/libforester-java/trunk/debian/libforester-java.jlibs
   trunk/forester/libforester-java/trunk/debian/patches/
   trunk/forester/libforester-java/trunk/debian/patches/change_itext_packagename.patch
   trunk/forester/libforester-java/trunk/debian/patches/fix_jar_path.patch
   trunk/forester/libforester-java/trunk/debian/patches/series
   trunk/forester/libforester-java/trunk/debian/rules
   trunk/forester/libforester-java/trunk/debian/source/
   trunk/forester/libforester-java/trunk/debian/source/format
Log:
[svn-inject] Applying Debian modifications (0.971-1) to trunk


Property changes on: trunk/forester/libforester-java/trunk/debian
___________________________________________________________________
Added: mergeWithUpstream
   + 1

Added: trunk/forester/libforester-java/trunk/debian/binary/forester
===================================================================
--- trunk/forester/libforester-java/trunk/debian/binary/forester                        (rev 0)
+++ trunk/forester/libforester-java/trunk/debian/binary/forester2012-05-24 13:08:46 UTC (rev 10992)
< at >< at > -0,0 +1,3 < at >< at >
+#!/bin/bash
+
+java -jar /usr/share/java/forester.jar


Property changes on: trunk/forester/libforester-java/trunk/debian/binary/forester
___________________________________________________________________
Added: svn:executable
   + *

Added: trunk/forester/libforester-java/trunk/debian/changelog
===================================================================
--- trunk/forester/libforester-java/trunk/debian/changelog                        (rev 0)
+++ trunk/forester/libforester-java/trunk/debian/changelog2012-05-24 13:08:46 UTC (rev 10992)
< at >< at > -0,0 +1,7 < at >< at >
+libforester-java (0.971-1) UNRELEASED; urgency=low
+
+  * Initial release (Closes: #674269)
+   * Wait to know which revision in SVN we should take
+   * Ask upstream to put jars with version
+
+ -- Olivier Sallou <osallou< at >debian.org>  Thu, 24 May 2012 12:28:55 +0200

Added: trunk/forester/libforester-java/trunk/debian/compat
===================================================================
--- trunk/forester/libforester-java/trunk/debian/compat                        (rev 0)
+++ trunk/forester/libforester-java/trunk/debian/compat2012-05-24 13:08:46 UTC (rev 10992)
< at >< at > -0,0 +1 < at >< at >
+8

Added: trunk/forester/libforester-java/trunk/debian/control
===================================================================
--- trunk/forester/libforester-java/trunk/debian/control                        (rev 0)
+++ trunk/forester/libforester-java/trunk/debian/control2012-05-24 13:08:46 UTC (rev 10992)
< at >< at > -0,0 +1,39 < at >< at >
+Source: libforester-java
+Section: java
+Priority: optional
+Maintainer: Debian Med Packaging Team <debian-med-packaging< at >lists.alioth.debian.org>
+DM-Upload-Allowed: yes
+Uploaders: Olivier Sallou <osallou< at >debian.org>
+Build-Depends: debhelper (>= 8.0.0),
+ default-jdk, junit4, javahelper (>=0.25), libcommons-codec, libitext-java
+Standards-Version: 3.9.3
+Homepage: http://code.google.com/p/forester
+Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/forester/trunk/
+Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/forester/trunk/
+
+Package: forester
+Architecture: all
+Depends: ${misc:Depends}, libforester-java
+Description: Graphical vizualiation tool Archaeopteryx
+ Archaeopteryx is a software tool for the visualization, analysis,
+ and editing of potentially large and highly annotated phylogenetic trees.
+ It can be used both as applet (ArchaeopteryxA and ArchaeopteryxE) and
+ as a standalone application.
+
+Package: libforester-java
+Architecture: all
+Depends: ${misc:Depends},
+ libcommons-codec, libitext-java
+Description: Libraries for evolutionary biology and comparative genomics research
+ Forester is a library of Java software for phylogenomics 
+ and evolutionary biology research. It can be used to read or
+ write phylogenetic trees, export trees to graphics file,...
+
+Package: libforester-java-doc
+Section: doc
+Architecture: all
+Depends: ${misc:Depends}
+Description: [Biology] Documentation for forester
+ Forester is a library of Java software for phylogenomics
+ and evolutionary biology research. This package contains the
+ JavaDoc documentation.

Added: trunk/forester/libforester-java/trunk/debian/copyright
===================================================================
--- trunk/forester/libforester-java/trunk/debian/copyright                        (rev 0)
+++ trunk/forester/libforester-java/trunk/debian/copyright2012-05-24 13:08:46 UTC (rev 10992)
< at >< at > -0,0 +1,44 < at >< at >
+Format: http://dep.debian.net/deps/dep5
+Upstream-Name: forester
+Source: http://code.google.com/p/forester
+
+Files: *
+Copyright: 2010 Christian M. Zmasek
+           2010 Sanford-Burnham Medical Research Institute
+License: LGPL 2.1+
+ This library 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 2.1 of the License, or (at your option) any later version.
+ .
+ This library 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 Lesser General Public
+ License along with this library; 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 Lesser General
+ Public License version 2 can be found in "/usr/share/common-licenses/LGPL-2.1".
+
+Files: debian/*
+Copyright: 2012 Olivier Sallou <osallou< at >debian.org>
+License: GPL-2+
+ This package 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 package 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/>
+ .
+ On Debian systems, the complete text of the GNU General
+ Public License version 2 can be found in "/usr/share/common-licenses/GPL-2".
+

Added: trunk/forester/libforester-java/trunk/debian/docs
===================================================================
Added: trunk/forester/libforester-java/trunk/debian/forester.install
===================================================================
--- trunk/forester/libforester-java/trunk/debian/forester.install                        (rev 0)
+++ trunk/forester/libforester-java/trunk/debian/forester.install2012-05-24 13:08:46 UTC (rev 10992)
< at >< at > -0,0 +1 < at >< at >
+debian/binary/forester usr/bin

Added: trunk/forester/libforester-java/trunk/debian/get-orig-source.sh
===================================================================
--- trunk/forester/libforester-java/trunk/debian/get-orig-source.sh                        (rev 0)
+++ trunk/forester/libforester-java/trunk/debian/get-orig-source.sh2012-05-24 13:08:46 UTC (rev 10992)
< at >< at > -0,0 +1,17 < at >< at >
+#!/bin/bash
+
+
+PKG=`dpkg-parsechangelog | awk '/^Source/ { print $2 }'`
+VERSION=`dpkg-parsechangelog | awk '/^Version/ { print $2 }' | cut -d "-" -f1`
+version=$VERSION.svn.`date +"%Y%m%d"|tr -d '\n'`
+targetdir=libforester-java-$version
+origtargz=libforester-java_$VERSION.orig.tar.gz
+cd ..
+mkdir $targetdir
+svn checkout http://forester.googlecode.com/svn/forester/java $targetdir/java
+svn checkout http://forester.googlecode.com/svn/forester/resources $targetdir/resources
+find $targetdir -name ".svn" | xargs -r rm -r
+find $targetdir -name "*.jar" | xargs -r rm -r
+tar czf $origtargz $targetdir
+rm -rf $targetdir
+


Property changes on: trunk/forester/libforester-java/trunk/debian/get-orig-source.sh
___________________________________________________________________
Added: svn:executable
   + *

Added: trunk/forester/libforester-java/trunk/debian/libforester-java-doc.doc-base
===================================================================
--- trunk/forester/libforester-java/trunk/debian/libforester-java-doc.doc-base                        (rev 0)
+++ trunk/forester/libforester-java/trunk/debian/libforester-java-doc.doc-base2012-05-24 13:08:46 UTC (rev 10992)
< at >< at > -0,0 +1,12 < at >< at >
+Document: forester
+Title: forester API
+Author: Forester developers
+Abstract: Javadoc-generated API for the forester library.
+ Forester is a library of Java software for phylogenomics
+ and evolutionary biology research. It can be used to read or
+ write phylogenetic trees, export trees to graphics file,...
+Section: Science/Biology
+
+Format: HTML
+Index: /usr/share/doc/libforester-java/api/index.html
+Files: /usr/share/doc/libforester-java/api/*.html /usr/share/doc/libforester-java/api/*/*/*/*.html /usr/share/doc/libforester-java/api/*/*/*/*/*.html /usr/share/doc/libforester-java/api/*/*/*/*/*/*.html

Added: trunk/forester/libforester-java/trunk/debian/libforester-java-doc.install
===================================================================
--- trunk/forester/libforester-java/trunk/debian/libforester-java-doc.install                        (rev 0)
+++ trunk/forester/libforester-java/trunk/debian/libforester-java-doc.install2012-05-24 13:08:46 UTC (rev 10992)
< at >< at > -0,0 +1 < at >< at >
+doc/* /usr/share/doc/libforester-java/api/

Added: trunk/forester/libforester-java/trunk/debian/libforester-java.jlibs
===================================================================
--- trunk/forester/libforester-java/trunk/debian/libforester-java.jlibs                        (rev 0)
+++ trunk/forester/libforester-java/trunk/debian/libforester-java.jlibs2012-05-24 13:08:46 UTC (rev 10992)
< at >< at > -0,0 +1 < at >< at >
+java/forester.jar

Added: trunk/forester/libforester-java/trunk/debian/patches/change_itext_packagename.patch
===================================================================
--- trunk/forester/libforester-java/trunk/debian/patches/change_itext_packagename.patch                        (rev 0)
+++ trunk/forester/libforester-java/trunk/debian/patches/change_itext_packagename.patch2012-05-24 13:08:46 UTC (rev 10992)
< at >< at > -0,0 +1,29 < at >< at >
+Author: Olivier Sallou <osallou< at >debian.org>
+Subject: change package name for itext
+Description: Upstream refers to com.itext hwile Debian package
+ itext use package name com.lowagie. Replace in the file the package
+ name references
+Last-Updated: 24/05/12
+--- a/java/src/org/forester/archaeopteryx/PdfExporter.java
++++ b/java/src/org/forester/archaeopteryx/PdfExporter.java
+< at >< at > -35,13 +35,13 < at >< at >
+ 
+ import org.forester.phylogeny.Phylogeny;
+ 
+-import com.itextpdf.text.Document;
+-import com.itextpdf.text.DocumentException;
+-import com.itextpdf.text.FontFactory;
+-import com.itextpdf.text.Rectangle;
+-import com.itextpdf.text.pdf.DefaultFontMapper;
+-import com.itextpdf.text.pdf.PdfContentByte;
+-import com.itextpdf.text.pdf.PdfWriter;
++import com.lowagie.text.Document;
++import com.lowagie.text.DocumentException;
++import com.lowagie.text.FontFactory;
++import com.lowagie.text.Rectangle;
++import com.lowagie.text.pdf.DefaultFontMapper;
++import com.lowagie.text.pdf.PdfContentByte;
++import com.lowagie.text.pdf.PdfWriter;
+ 
+ /*
+  * 

Added: trunk/forester/libforester-java/trunk/debian/patches/fix_jar_path.patch
===================================================================
--- trunk/forester/libforester-java/trunk/debian/patches/fix_jar_path.patch                        (rev 0)
+++ trunk/forester/libforester-java/trunk/debian/patches/fix_jar_path.patch2012-05-24 13:08:46 UTC (rev 10992)
< at >< at > -0,0 +1,68 < at >< at >
+Author: Olivier Sallou <osallou< at >debian.org>
+Subject: Change dependency libraries path
+Description: Use Debian libraries instead of upstream
+ included ones
+Last-Updated: 24/05/12
+--- a/java/build.xml
++++ b/java/build.xml
+< at >< at > -3,9 +3,9 < at >< at >
+ 
+ <property name="src.dir" value="src" />
+ <property name="classes.dir" value="classes" />
+-<property name="jars.dir" value="resources" />
+-<property name="itextjar" value="${jars.dir}/itextpdf-5.1.0.jar" />
+-<property name="commonscodecjar" value="${jars.dir}/commons-codec-1.5.jar" />
++<property name="jars.dir" value="/usr/share/java" />
++<property name="itextjar" value="${jars.dir}/itext.jar" />
++<property name="commonscodecjar" value="${jars.dir}/commons-codec.jar" />
+ <property name="forester_jar" value="forester.jar" />
+ <property name="archaeopteryx_applets_jar" value="archaeopteryx_applets.jar" />
+ 
+< at >< at > -40,34 +40,15 < at >< at >
+ </target>
+ 
+ <target name="jar" description="JARs the classes files" depends="compile,copy_resources">
+-<unjar src="${itextjar}" dest="${classes.dir}">
+-            <patternset>
+-                <include name="**/*.class" />
+-                <include name="**/*.afm" />
+-                <include name="**/*.txt" />
+-                <exclude name="**/*Test*.class" />
+-            </patternset>
+-        </unjar>
+-        <unjar src="${commonscodecjar}" dest="${classes.dir}">
+-            <patternset>
+-                <include name="**/*.class" />
+-                <exclude name="**/*Test*.class" />
+-            </patternset>
+-        </unjar>
+ <jar level="9" destfile="${forester_jar}" basedir="${classes.dir}" excludes="**/Test.class" duplicate="fail" index="true">
+ <manifest>
+ <attribute name="Main-Class" value="org.forester.archaeopteryx.Archaeopteryx" />
++<attribute name="Class-Path" value="${itextjar};${commonscodecjar}"/>
+ </manifest>
+ </jar>
+ </target>
+ 
+ <target name="jar_applets_only" description="JARs the classes files" depends="compile_applets_only,copy_resources">
+-<unjar src="${commonscodecjar}" dest="${classes.dir}">
+-            <patternset>
+-                <include name="**/*.class" />
+-                <exclude name="**/*Test*.class" />
+-            </patternset>
+-        </unjar>
+ <jar level="9" destfile="${archaeopteryx_applets_jar}" basedir="${classes.dir}" excludes="org/forester/application/** 
+           org/forester/development/**
+           org/forester/evoinference/**
+< at >< at > -87,4 +68,11 < at >< at >
+ <target name="applets_only" description="" depends="jar_applets_only">
+ </target>
+ 
++        <target name="javadoc">
++                <mkdir dir="../doc"/>
++                <javadoc destdir="../doc" sourcepath="${src.dir}" >
++                        <link href="http://java.sun.com/j2se/1.6.0/docs/api/"/>
++                </javadoc>
++        </target>
++
+ </project>

Added: trunk/forester/libforester-java/trunk/debian/patches/series
===================================================================
--- trunk/forester/libforester-java/trunk/debian/patches/series                        (rev 0)
+++ trunk/forester/libforester-java/trunk/debian/patches/series2012-05-24 13:08:46 UTC (rev 10992)
< at >< at > -0,0 +1,2 < at >< at >
+fix_jar_path.patch
+change_itext_packagename.patch

Added: trunk/forester/libforester-java/trunk/debian/rules
===================================================================
--- trunk/forester/libforester-java/trunk/debian/rules                        (rev 0)
+++ trunk/forester/libforester-java/trunk/debian/rules2012-05-24 13:08:46 UTC (rev 10992)
< at >< at > -0,0 +1,19 < at >< at >
+#!/usr/bin/make -f
+
+# Uncomment this to turn on verbose mode.
+#export DH_VERBOSE=1
+
+%:
+dh $< at >  --with javahelper
+
+override_dh_auto_build:
+cd java && ant
+cd java && ant javadoc
+
+override_dh_clean:
+cd java && ant clean
+rm -rf doc
+dh_clean
+
+get-orig-source:
+debian/get-orig-source.sh


Property changes on: trunk/forester/libforester-java/trunk/debian/rules
___________________________________________________________________
Added: svn:executable
   + *

Added: trunk/forester/libforester-java/trunk/debian/source/format
===================================================================
--- trunk/forester/libforester-java/trunk/debian/source/format                        (rev 0)
+++ trunk/forester/libforester-java/trunk/debian/source/format2012-05-24 13:08:46 UTC (rev 10992)
< at >< at > -0,0 +1 < at >< at >
+3.0 (quilt)

r10991 - trunk/forester/libforester-java

Olivier Sallou — 2012-05-24T13:08:39

Author: osallou
Date: 2012-05-24 13:08:39 +0000 (Thu, 24 May 2012)
New Revision: 10991

Added:
   trunk/forester/libforester-java/trunk/
Log:
Creating trunk directory

r10990 - in trunk: . forester forester/libforester-java

Olivier Sallou — 2012-05-24T13:08:35

Author: osallou
Date: 2012-05-24 13:08:34 +0000 (Thu, 24 May 2012)
New Revision: 10990

Added:
   trunk/forester/
   trunk/forester/libforester-java/
   trunk/forester/libforester-java/tags/
Log:
[svn-inject] Creating forester/libforester-java/tags/ directory.

r10989 - in trunk/packages: . proalign proalign/trunkproalign/trunk/debian

Andreas Tille — 2012-05-24T12:42:37

Author: tille
Date: 2012-05-24 12:42:36 +0000 (Thu, 24 May 2012)
New Revision: 10989

Added:
   trunk/packages/proalign/
   trunk/packages/proalign/trunk/
   trunk/packages/proalign/trunk/debian/
   trunk/packages/proalign/trunk/debian/changelog
   trunk/packages/proalign/trunk/debian/compat
   trunk/packages/proalign/trunk/debian/control
   trunk/packages/proalign/trunk/debian/copyright
   trunk/packages/proalign/trunk/debian/upstream
   trunk/packages/proalign/trunk/debian/watch
Log:
Turn information from tasks file and WNPP in something machine readable


Added: trunk/packages/proalign/trunk/debian/changelog
===================================================================
--- trunk/packages/proalign/trunk/debian/changelog                        (rev 0)
+++ trunk/packages/proalign/trunk/debian/changelog2012-05-24 12:42:36 UTC (rev 10989)
< at >< at > -0,0 +1,5 < at >< at >
+proalign (0.603-1) unstable; urgency=low
+
+  * Initial release (Closes: #378290)
+
+ -- Andreas Tille <tille< at >debian.org>  Thu, 24 May 2012 14:30:13 +0200

Added: trunk/packages/proalign/trunk/debian/compat
===================================================================
--- trunk/packages/proalign/trunk/debian/compat                        (rev 0)
+++ trunk/packages/proalign/trunk/debian/compat2012-05-24 12:42:36 UTC (rev 10989)
< at >< at > -0,0 +1 < at >< at >
+9

Added: trunk/packages/proalign/trunk/debian/control
===================================================================
--- trunk/packages/proalign/trunk/debian/control                        (rev 0)
+++ trunk/packages/proalign/trunk/debian/control2012-05-24 12:42:36 UTC (rev 10989)
< at >< at > -0,0 +1,28 < at >< at >
+Source: proalign
+Section: science
+Priority: optional
+Maintainer: Debian Med Packaging Team <debian-med-packaging< at >lists.alioth.debian.org>
+DM-Upload-Allowed: yes
+Uploaders: Andreas Tille <tille< at >debian.org>
+Build-Depends: debhelper (>= 9)
+Standards-Version: 3.9.3
+Homepage: http://ueg.ulb.ac.be/ProAlign/
+Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/proalign/trunk/
+Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/proalign/trunk/
+
+Package: proalign
+Architecture: any
+Depends: ${shlibs:Depends}, ${misc:Depends}
+Description: Probabilistic multiple alignment program
+ ProAlign performs probabilistic sequence alignments using hidden Markov
+ models (HMM). It includes a graphical interface (GUI) allowing to (i)
+ perform alignments of nucleotide or amino-acid sequences, (ii) view the
+ quality of solutions, (iii) filter the unreliable alignment regions and
+ (iv) export alignments to other softwares.
+ .
+ ProAlign uses a progressive method, such that multiple alignment is
+ created stepwise by performing pairwise alignments in the nodes of a
+ guide tree. Sequences are described with vectors of character
+ probabilities, and each pairwise alignment reconstructs the ancestral
+ (parent) sequence by computing the probabilities of different
+ characters according to an evolutionary model.
\ No newline at end of file

Added: trunk/packages/proalign/trunk/debian/copyright
===================================================================
--- trunk/packages/proalign/trunk/debian/copyright                        (rev 0)
+++ trunk/packages/proalign/trunk/debian/copyright2012-05-24 12:42:36 UTC (rev 10989)
< at >< at > -0,0 +1,35 < at >< at >
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: ProAlign
+Upstream-Contact: Ari Löytynoja & Michel C. Milinkovitch
+Source: http://ueg.ulb.ac.be/ProAlign/
+
+Files: *
+Copyright: © 2002-2003 Ari Löytynoja and Michel C. Milinkovitch.
+License: GPL-2+
+
+Files: debian/*
+Copyright: © 2012 Andreas Tille <tille< at >debian.org>
+License: GPL-2+
+
+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 package; if not, write to the Free
+ Software Foundation, Inc., 51 Franklin St, Fifth Floor,
+ Boston, MA  02110-1301 USA
+ .
+ On Debian systems, the full text of the GNU General Public
+ License version 2 can be found in the file
+ `/usr/share/common-licenses/GPL-2'.
+

Added: trunk/packages/proalign/trunk/debian/upstream
===================================================================
--- trunk/packages/proalign/trunk/debian/upstream                        (rev 0)
+++ trunk/packages/proalign/trunk/debian/upstream2012-05-24 12:42:36 UTC (rev 10989)
< at >< at > -0,0 +1,12 < at >< at >
+Reference:
+  Author: Ari Löytynoja and Michel C Milinkovitch
+  Title: A hidden Markov model for progressive multiple alignment
+  Journal: Bioinformatics
+  Year: 2003
+  Volume: 19
+  Number: 12
+  Pages: 1505-13
+  DOI: 10.1093/bioinformatics/btg193
+  PMID: 12912831
+  URL: http://bioinformatics.oxfordjournals.org/content/19/12/1505
+  eprint: http://bioinformatics.oxfordjournals.org/content/19/12/1505.full.pdf+html

Added: trunk/packages/proalign/trunk/debian/watch
===================================================================
--- trunk/packages/proalign/trunk/debian/watch                        (rev 0)
+++ trunk/packages/proalign/trunk/debian/watch2012-05-24 12:42:36 UTC (rev 10989)
< at >< at > -0,0 +1,4 < at >< at >
+version=3
+
+opts=dversionmangle=s/\.// \
+  http://ueg.ulb.ac.be/ProAlign/download/src/proalign_(.+)\.tgz


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