Initial implementation of selection file input.
authorTeemu Murtola <teemu.murtola@gmail.com>
Mon, 30 Apr 2012 05:58:12 +0000 (08:58 +0300)
committerTeemu Murtola <teemu.murtola@gmail.com>
Thu, 3 May 2012 04:32:50 +0000 (07:32 +0300)
commit672c3b1b5a324a58b9c2c3f880ee82b61a26bbf4
tree85293f6d0aa55b89b61fca779e7a67bf91d11022
parent2983c2898112ddef710c93e45f38301dd3872f19
Initial implementation of selection file input.

- Add SelectionFileOption and related classes to implement an option
  that can be used to provide selections from a file.
- Add SelectionCollection::parseRequestedFromFile() to do the actual
  work.
- Add special handling for the option in command-line help to print it
  together with other selection options.
- Add tests.
- Removed support for specifying a selection option multiple times on
  the command line, since it is not clear how it should work together
  with the new option.
- Temporary exception safety fix for selection file input.
- Updated valgrind suppression rules for MacOS for some
  exception-handling stuff.

Initial implementation for IssueID #656.

Change-Id: Id4ddf545ec13986fa57dac42a8b1dc4075a42840
19 files changed:
cmake/legacy_and_external.supp
src/gromacs/commandline/cmdlinehelpwriter.cpp
src/gromacs/commandline/tests/cmdlinehelpwriter.cpp
src/gromacs/commandline/tests/refdata/CommandLineHelpWriterTest_HandlesOptionTypes.xml
src/gromacs/commandline/tests/refdata/CommandLineHelpWriterTest_HandlesSelectionOptions.xml
src/gromacs/selection/selectioncollection-impl.h
src/gromacs/selection/selectioncollection.cpp
src/gromacs/selection/selectioncollection.h
src/gromacs/selection/selectionfileoption.h [new file with mode: 0644]
src/gromacs/selection/selectionfileoptioninfo.h [new file with mode: 0644]
src/gromacs/selection/selectionfileoptionstorage.h [new file with mode: 0644]
src/gromacs/selection/selectionoption.cpp
src/gromacs/selection/selectionoption.h
src/gromacs/selection/selectionoptioninfo.h
src/gromacs/selection/tests/selectioncollection.cpp
src/gromacs/selection/tests/selectionoption.cpp
src/gromacs/selection/tests/selfile.dat [new file with mode: 0644]
src/gromacs/trajectoryanalysis/runnercommon.cpp
src/gromacs/trajectoryanalysis/tests/test_selection.cpp