Merge branch 'master' into pygromacs

[alexxy/gromacs.git] / src / gromacs / trajectoryanalysis / cmdlinerunner.cpp

diff --git a/src/gromacs/trajectoryanalysis/cmdlinerunner.cpp b/src/gromacs/trajectoryanalysis/cmdlinerunner.cpp
index f3e12f4170fff3fb8118006eb60c4f0c5cf005ab..912db6c9633ce7b530abc8cfa47fd645b1659da2 100644 (file)
--- a/src/gromacs/trajectoryanalysis/cmdlinerunner.cpp
+++ b/src/gromacs/trajectoryanalysis/cmdlinerunner.cpp
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2010,2011,2012,2013,2014, by the GROMACS development team, led by
+ * Copyright (c) 2010,2011,2012,2013,2014,2015, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.
@@ -58,7 +58,7 @@
 #include "gromacs/trajectoryanalysis/analysismodule.h"
 #include "gromacs/trajectoryanalysis/analysissettings.h"
 #include "gromacs/utility/exceptions.h"
-#include "gromacs/utility/file.h"
+#include "gromacs/utility/filestream.h"
 #include "gromacs/utility/gmxassert.h"
 
 #include "runnercommon.h"
@@ -145,7 +145,7 @@ TrajectoryAnalysisCommandLineRunner::Impl::parseOptions(
 
     common->initIndexGroups(selections, bUseDefaultGroups_);
 
-    const bool bInteractive = File::standardInput().isInteractive();
+    const bool bInteractive = StandardInputStream::instance().isInteractive();
     seloptManager.parseRequestedFromStdin(bInteractive);
 
     common->doneIndexGroups(selections);
@@ -327,7 +327,7 @@ TrajectoryAnalysisCommandLineRunner::writeHelp(const CommandLineHelpContext &con
     selections.initOptions(&selectionOptions);
 
     CommandLineHelpWriter(options)
-        .setShowDescriptions(true)
+        .setHelpText(settings.helpText())
         .setTimeUnitString(settings.timeUnitManager().timeUnitAsString())
         .writeHelp(context);
 }
@@ -339,7 +339,7 @@ TrajectoryAnalysisCommandLineRunner::writeHelp(const CommandLineHelpContext &con
  * \ingroup module_trajectoryanalysis
  */
 class TrajectoryAnalysisCommandLineRunner::Impl::RunnerCommandLineModule
-    : public CommandLineModuleInterface
+    : public ICommandLineModule
 {
     public:
         /*! \brief