[ubuntu/karmic] massxpert 2.0.0-1 (Accepted)

Mon May 11 15:32:11 BST 2009

massxpert (2.0.0-1) unstable; urgency=low

  * Standards version is 3.8.1.

  * Bumped debian/compat to 7.

  * Entirely reworked debian/rules, which now has build-arch and
    build-indep fully separated targets totally fitting the Build-Depends
    and Build-Depends-Indep fields of debian/control.

  * New upstream release:

    - Fixed bug in XpertDef due to not verifying upon removal of a
    modification if it is used by a cross-linker. Crashes. Report by Ron
    Bakus (UCSD domain edu).

    - Fixed bug with storing polymer sequences and polymer chemistry
    definitions with crippled XML;

    - Added configurability to the number of decimal places used to
    display values for pH/pKa, atoms/isotopes, oligomers, polymers;

    - Fixed regression with un-cross-linking;

    - Fixed bug with calculation of right-end fragment boundaries;

    - Big work within the XpertMiner module;

    - Huge internal work with the ionization paradigm in particular within
    the fragmentation framework.

  * Fixes with the debian/* so that the source package now build three
    packages: massxpert-bin, massxpert-data, massxpert-doc.

  * A bunch of improvements in the Debian packaging thanks to Lionel
    Mamane mentoring (parallel support in rules and others).

  * Sponsored upload done by Lionel Elie Mamane <lmamane at debian.org>

massxpert (1.7.8-1) unstable; urgency=low

  * New upstream release:

    - Implemented multi-cleavages;

    - Updated the User Manual

massxpert (1.7.7-1) unstable; urgency=low

  * New upstream release:

    - Implemented multi-region selections;

    - Updated the User Manual.

massxpert (1.7.6-1) unstable; urgency=low

  * New upstream release:

    - Moved the project to GNU GPL version 3;

    - Fixes for GUI bugs;

    - Fixes with the localization of double values in the GUI;

    - First implementation of the mzLab (still experimental feature);

    - Classes rework with better handling of ionization throughout the whole project;

    - Code cleanup, better handling of constness in the whole project;

    - Updated the User Manual.

massxpert (1.7.5-1) unstable; urgency=low

  * New upstream release:

    - Code cleanup throughout the code redesign of some classes and addition
    of Ion class;

    - Implemented namespace massXpert throughout the project;

    - Update of the french translation;

    - Bug fixes;

massxpert (1.7.4-1) unstable; urgency=low

  * New upstream release:

    - Implemented new means to define fragmentation specifications that
    involve the decomposition of the fragmented monomer's side chain;

    - Fixed memory leak and bugs;

    - Updated the french translation and the user manual.

massxpert (1.7.3-1) unstable; urgency=low

  * Upstream release with main new feature: the filtering implemented for
    the previous version was extended also for the fragmentation and mass
    searching oligomer data;

  * Improved the use of the filtering feature thanks to modifications in
    the graphical user interface;

  * Implemented check that a cross-link name cannot be used already as a
    modification name (and vice versa);

  * Fixes to regressions that crept in during last version developments
    and code cleanup;

  * Update of the documentation;

massxpert (1.7.2-1) unstable; urgency=low

  * Upstream release with main new figure: the oligomer data from a
    polymer sequence cleavage might be filtered live and in-place using a
    sortingProxy treeview (powerful feature of the Qt library);

  * User manual update;

  * Minor bugfixes.

massxpert (1.7.1-1) unstable; urgency=low

  * Upstream release with main new feature: intra-molecular cross-links.

  * Bug fixes and small improvements here and there.

  * Modified dh_shlibs line to exclude the plugins from the scan, as these
    are private libraries with no SONAME.

massxpert (1.7.0-1) unstable; urgency=low

  * Upstream bug-fix release. 

  * Fixed crash caused by elemental compositions calculations using
    manually-defined polymer sequence modifications (thanks to as
    calculations session with Fatima Boutimah in my lab);

  * Modified the polymer sequence file format so as to be able to save
    polymer sequence modifications with a fully qualified <mdf> (see
    polChemDef format) element. This allows storing the modifications with
    full qualification (and not only name) even when the modification is
    manually-defined.

  * Added man massxpert-doc.7 page documenting the User manual.

massxpert (1.6.9-1) unstable; urgency=low

  * Upstream release with more flexible monomer modification procedure
    (big inner code changes not visible by the user).

  * Update the documentation.

  * Extended copyright to 2008.

massxpert (1.6.8-1) unstable; urgency=low

  * Upstream release with some small modifications in the debian packaging
    (massxpert.1 man page an massxpert.desktop are installed differently
    so that these files might also be used when generating rpm packages);

  * The user manual now installs properly in /usr/share/doc/massxpert-doc
    and not /usr/share/doc/massxpert, as was the case before. Also, the
    user manual was updated so as to reflect the new polymer chemistry
    definition GUI design.

  * Removed the lintian override file, as I finally found why two of the
    three plugins would make lintian complain about
    shlib-with-non-pic-code.

  * Fully rewritten the polymer chemistry definition graphical interface.

  * Some bug fixes here and there.

massxpert (1.6.7-1) unstable; urgency=low

  * Upstream release with the following modifications:

  * CMake'ization of the source tree.

  * Fixed bug with calculation net charges with any given pH.

  * Standards-Version: 3.7.2

massxpert (1.6.6-1) unstable; urgency=low

  * Upstream release with the following modifications: 

  * Update the french translation and the user manual to reflect the 
    new features of the cleavage- and fragmentation-base oligomer
    generation.

  * The oligomers from cleavage and fragmentation might now be calculated
    as multi-charged oligomers

  * Implemented the fragmentation stuff in new class MxpFragmenter and
    removed the corresponding code from the fragmentation dialog
    class. Also, made the same use of QList<MxpOligomerList *> * instead
    of two nested QList objects as previously performed with the cleavage
    code in the fragmentation code.

  * Implemented ionization level ranges for oligomers, starting with the
    cleavage application bits
  * Reimplemented the gui polymer sequence cleaving stuff to use the
    modified MxpCleaver object
  * Reimplemented the cleaver object to use the new oligomer list object

  * Implemented and added to library 'list of oligomers' new class:
    MxpOligomerList derived from QList<MxpOligomer *>

massxpert (1.6.5-1) unstable; urgency=low

  * Upstream release with the following modifications: 

  * Added possibiliy to restrict monomer modifications to given
    monomers. If the user tries to modify a monomer with a modification
    that is not supported for it, the modification does not occur and the
    user gets a message. Implemented a mechanism by which these monomer
    modification limitations can be overridden.

  * Fixed bug with parsing atom symbols with more than 2 characters.

  * Added fake atoms so as to to allow defining formulas with precise
    masses.

  * Fixed bug with creation of default monomer modification vignette and
    setting it to the hash with a bad key. That would lead to bad
    reference counting and crashes upon unmodification of more than one
    modified monomer.

  * Better feedback messages to the sequence editor window's statusBar
    while doing initial sequence drawing.

  * Updated french translation.

  * Reverted to version 2 of the GPL as the Qt libraries are not using the
    'version 2 or any later version' wording.

massxpert (1.6.4-1) unstable; urgency=low

  * Upstream release with the following modifications:

  * Translated the application into french. Took advantage of the
  translation work to uniformize the messages and the labels on the UI
  widgets.

  * Bug fixes with modifications declared in some polymer chemisty
  definitions but not available as graphics files or not registered in
  the modification_dictionary.

  * Added default modification vignette, so that when a modification
  is defined without assigning a corresponding vignette the program
  does not crash.

  * Switch to 4.3.0 for MS-Windows also.

  * Minor bugfixes

massxpert (1.6.3-1) unstable; urgency=low

  * New upstream release.

  * Fixed glitches in some fields of the debian/control file.	

  * Fixed problems with the modification vignettes and declarations of
    modifications in the modification_dictionary of some polymer
    chemistry definition.

  * Many improvements in the user manual. 

  * Improved handling of polymer sequence modifications. 

  * Improvements the GUI and in the calculator recorder output. 

  * Added possibility to modify a polymer sequence arbitrarily by
  entering a chemical formula and not by choosing a modification in
  the polymer chemistry definition. 

  * Switch to 4.3.0 as the Qt dependency, which showed some glitches
  in the handling of the sequence editor graphics view that were
  fixed.

massxpert (1.6.1-1) unstable; urgency=low

  * Added new feature to the XpertEdit module: a mass list
  laboratory. Updated the documentation.

massxpert (1.6.0-rc2-1) unstable; urgency=low

  * Initial release.

Date: Mon,  11 May 2009 14:55:34 +0100
Changed-By: James Westby <jw+debian at jameswestby.net>
Maintainer: Filippo Rusconi <rusconi-debian at laposte.net>
Origin: Debian/unstable
https://launchpad.net/ubuntu/karmic/+source/massxpert/2.0.0-1
-------------- next part --------------
Origin: Debian/unstable
Format: 1.7
Date: Mon,  11 May 2009 14:55:34 +0100
Source: massxpert
Binary: massxpert-bin, massxpert-data, massxpert-doc
Architecture: source
Version: 2.0.0-1
Distribution: karmic
Urgency: low
Maintainer: Filippo Rusconi <rusconi-debian at laposte.net>
Changed-By: James Westby <jw+debian at jameswestby.net>
Changes: 
 massxpert (2.0.0-1) unstable; urgency=low

   * Standards version is 3.8.1.
 .
   * Bumped debian/compat to 7.

   * Entirely reworked debian/rules, which now has build-arch and
     build-indep fully separated targets totally fitting the Build-Depends
     and Build-Depends-Indep fields of debian/control.

   * New upstream release:

     - Fixed bug in XpertDef due to not verifying upon removal of a
     modification if it is used by a cross-linker. Crashes. Report by Ron
     Bakus (UCSD domain edu).
 .
     - Fixed bug with storing polymer sequences and polymer chemistry
     definitions with crippled XML;

     - Added configurability to the number of decimal places used to
     display values for pH/pKa, atoms/isotopes, oligomers, polymers;

     - Fixed regression with un-cross-linking;

     - Fixed bug with calculation of right-end fragment boundaries;

     - Big work within the XpertMiner module;

     - Huge internal work with the ionization paradigm in particular within
     the fragmentation framework.
 .
   * Fixes with the debian/* so that the source package now build three
     packages: massxpert-bin, massxpert-data, massxpert-doc.

   * A bunch of improvements in the Debian packaging thanks to Lionel
     Mamane mentoring (parallel support in rules and others).
 .
   * Sponsored upload done by Lionel Elie Mamane <lmamane at debian.org>
 .
 massxpert (1.7.8-1) unstable; urgency=low
 .
   * New upstream release:

     - Implemented multi-cleavages;

     - Updated the User Manual
 .
 massxpert (1.7.7-1) unstable; urgency=low
 .
   * New upstream release:

     - Implemented multi-region selections;
 .
     - Updated the User Manual.
 .
 massxpert (1.7.6-1) unstable; urgency=low
 .
   * New upstream release:

     - Moved the project to GNU GPL version 3;

     - Fixes for GUI bugs;

     - Fixes with the localization of double values in the GUI;

     - First implementation of the mzLab (still experimental feature);

     - Classes rework with better handling of ionization throughout the whole project;

     - Code cleanup, better handling of constness in the whole project;

     - Updated the User Manual.
 .
 massxpert (1.7.5-1) unstable; urgency=low
 .
   * New upstream release:

     - Code cleanup throughout the code redesign of some classes and addition
     of Ion class;

     - Implemented namespace massXpert throughout the project;

     - Update of the french translation;

     - Bug fixes;
 .
 massxpert (1.7.4-1) unstable; urgency=low
 .
   * New upstream release:

     - Implemented new means to define fragmentation specifications that
     involve the decomposition of the fragmented monomer's side chain;

     - Fixed memory leak and bugs;

     - Updated the french translation and the user manual.
 .
 massxpert (1.7.3-1) unstable; urgency=low
 .
   * Upstream release with main new feature: the filtering implemented for
     the previous version was extended also for the fragmentation and mass
     searching oligomer data;

   * Improved the use of the filtering feature thanks to modifications in
     the graphical user interface;

   * Implemented check that a cross-link name cannot be used already as a
     modification name (and vice versa);

   * Fixes to regressions that crept in during last version developments
     and code cleanup;

   * Update of the documentation;
 .
 massxpert (1.7.2-1) unstable; urgency=low
 .
   * Upstream release with main new figure: the oligomer data from a
     polymer sequence cleavage might be filtered live and in-place using a
     sortingProxy treeview (powerful feature of the Qt library);

   * User manual update;

   * Minor bugfixes.
 .
 massxpert (1.7.1-1) unstable; urgency=low
 .
   * Upstream release with main new feature: intra-molecular cross-links.

   * Bug fixes and small improvements here and there.
 .
   * Modified dh_shlibs line to exclude the plugins from the scan, as these
     are private libraries with no SONAME.
 .
 massxpert (1.7.0-1) unstable; urgency=low
 .
   * Upstream bug-fix release. 

   * Fixed crash caused by elemental compositions calculations using
     manually-defined polymer sequence modifications (thanks to as
     calculations session with Fatima Boutimah in my lab);

   * Modified the polymer sequence file format so as to be able to save
     polymer sequence modifications with a fully qualified <mdf> (see
     polChemDef format) element. This allows storing the modifications with
     full qualification (and not only name) even when the modification is
     manually-defined.

   * Added man massxpert-doc.7 page documenting the User manual.
 .
 massxpert (1.6.9-1) unstable; urgency=low
 .
   * Upstream release with more flexible monomer modification procedure
     (big inner code changes not visible by the user).

   * Update the documentation.

   * Extended copyright to 2008.
 .
 massxpert (1.6.8-1) unstable; urgency=low
 .
   * Upstream release with some small modifications in the debian packaging
     (massxpert.1 man page an massxpert.desktop are installed differently
     so that these files might also be used when generating rpm packages);
 .
   * The user manual now installs properly in /usr/share/doc/massxpert-doc
     and not /usr/share/doc/massxpert, as was the case before. Also, the
     user manual was updated so as to reflect the new polymer chemistry
     definition GUI design.
 .
   * Removed the lintian override file, as I finally found why two of the
     three plugins would make lintian complain about
     shlib-with-non-pic-code.
 .
   * Fully rewritten the polymer chemistry definition graphical interface.
 .
   * Some bug fixes here and there.
 .
 massxpert (1.6.7-1) unstable; urgency=low
 .
   * Upstream release with the following modifications:

   * CMake'ization of the source tree.

   * Fixed bug with calculation net charges with any given pH.

   * Standards-Version: 3.7.2
 .
 massxpert (1.6.6-1) unstable; urgency=low
 .
   * Upstream release with the following modifications: 

   * Update the french translation and the user manual to reflect the 
     new features of the cleavage- and fragmentation-base oligomer
     generation.

   * The oligomers from cleavage and fragmentation might now be calculated
     as multi-charged oligomers

   * Implemented the fragmentation stuff in new class MxpFragmenter and
     removed the corresponding code from the fragmentation dialog
     class. Also, made the same use of QList<MxpOligomerList *> * instead
     of two nested QList objects as previously performed with the cleavage
     code in the fragmentation code.

   * Implemented ionization level ranges for oligomers, starting with the
     cleavage application bits
   * Reimplemented the gui polymer sequence cleaving stuff to use the
     modified MxpCleaver object
   * Reimplemented the cleaver object to use the new oligomer list object

   * Implemented and added to library 'list of oligomers' new class:
     MxpOligomerList derived from QList<MxpOligomer *>
 .
 massxpert (1.6.5-1) unstable; urgency=low
 .
   * Upstream release with the following modifications: 

   * Added possibiliy to restrict monomer modifications to given
     monomers. If the user tries to modify a monomer with a modification
     that is not supported for it, the modification does not occur and the
     user gets a message. Implemented a mechanism by which these monomer
     modification limitations can be overridden.

   * Fixed bug with parsing atom symbols with more than 2 characters.

   * Added fake atoms so as to to allow defining formulas with precise
     masses.

   * Fixed bug with creation of default monomer modification vignette and
     setting it to the hash with a bad key. That would lead to bad
     reference counting and crashes upon unmodification of more than one
     modified monomer.

   * Better feedback messages to the sequence editor window's statusBar
     while doing initial sequence drawing.

   * Updated french translation.

   * Reverted to version 2 of the GPL as the Qt libraries are not using the
     'version 2 or any later version' wording.
 .
 massxpert (1.6.4-1) unstable; urgency=low
 .
   * Upstream release with the following modifications:

   * Translated the application into french. Took advantage of the
   translation work to uniformize the messages and the labels on the UI
   widgets.
 .
   * Bug fixes with modifications declared in some polymer chemisty
   definitions but not available as graphics files or not registered in
   the modification_dictionary.
 .
   * Added default modification vignette, so that when a modification
   is defined without assigning a corresponding vignette the program
   does not crash.
 .
   * Switch to 4.3.0 for MS-Windows also.
 .
   * Minor bugfixes
 .
 massxpert (1.6.3-1) unstable; urgency=low
 .
   * New upstream release.

   * Fixed glitches in some fields of the debian/control file.	
 .
   * Fixed problems with the modification vignettes and declarations of
     modifications in the modification_dictionary of some polymer
     chemistry definition.
 .
   * Many improvements in the user manual. 

   * Improved handling of polymer sequence modifications. 

   * Improvements the GUI and in the calculator recorder output. 
 .
   * Added possibility to modify a polymer sequence arbitrarily by
   entering a chemical formula and not by choosing a modification in
   the polymer chemistry definition. 
 .
   * Switch to 4.3.0 as the Qt dependency, which showed some glitches
   in the handling of the sequence editor graphics view that were
   fixed.
 .
 massxpert (1.6.1-1) unstable; urgency=low
 .
   * Added new feature to the XpertEdit module: a mass list
   laboratory. Updated the documentation.
 .
 massxpert (1.6.0-rc2-1) unstable; urgency=low
 .
   * Initial release.
Files: 
 38b8bfd17495d2cfb46ab072ecb975bd 13626333 science optional massxpert_2.0.0.orig.tar.gz
 e0360fddb66a78526249d86d190656d2 20 science optional massxpert_2.0.0-1.diff.gz
 26d8e5ea90a917e7330bde3656618fe2 1202 science optional massxpert_2.0.0-1.dsc