Merge branch 'master' into pygromacs

diff --cc src/gromacs/trajectoryanalysis/cmdlinerunner.cpp
index f3e12f4170fff3fb8118006eb60c4f0c5cf005ab,675082f9b0acd6e57f83705c9902750868bb2d84..3dc042e97cbdc77dd178365afa9555a15eb399ae
--- 1/src/gromacs/trajectoryanalysis/cmdlinerunner.cpp
--- 2/src/gromacs/trajectoryanalysis/cmdlinerunner.cpp
+++ b/src/gromacs/trajectoryanalysis/cmdlinerunner.cpp
@@@ -145,12 -139,11 +145,12 @@@ TrajectoryAnalysisCommandLineRunner::Im
  
      common->initIndexGroups(selections, bUseDefaultGroups_);
  
-     const bool bInteractive = File::standardInput().isInteractive();
+     const bool bInteractive = StandardInputStream::instance().isInteractive();
      seloptManager.parseRequestedFromStdin(bInteractive);
 -    common->doneIndexGroups(selections);
  
 +    common->doneIndexGroups(selections);
      common->initTopology(selections);
 +
      selections->compile();
  }