Update headers, fix style for some py files

[alexxy/gromacs.git] / src / python / sip / trajectoryanalysis / TrajectoryAnalysis.sip

diff --git a/src/python/sip/trajectoryanalysis/TrajectoryAnalysis.sip b/src/python/sip/trajectoryanalysis/TrajectoryAnalysis.sip
index e05cb01465d096fd01bef94c8db81eb8d1f43e5b..cbcd919b4e8d70b989eff1993c642c2292dac582 100644 (file)
--- a/src/python/sip/trajectoryanalysis/TrajectoryAnalysis.sip
+++ b/src/python/sip/trajectoryanalysis/TrajectoryAnalysis.sip
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2011,2012,2013,2014, by the GROMACS development team, led by
+ * Copyright (c) 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.
@@ -35,9 +35,78 @@
 
 %Module gromacs.TrajectoryAnalysis
 
+%DefaultEncoding "UTF-8"
+
 %Import options/Options.sip
+%Import topology/Topology.sip
 
 %Include definitions.sip
 
 %Include analysissettings.sip
+%Include analysisdata.sip
 %Include analysismodule.sip
+
+%Include modules.sip
+
+%ModuleCode
+#include "gromacs/trajectoryanalysis/analysismodule.h"
+#include "gromacs/trajectoryanalysis/cmdlinerunner.h"
+#include "gromacs/utility/exceptions.h"
+
+class PyFactory : public gmx::TrajectoryAnalysisCommandLineRunner::ModuleFactoryFunctor {
+public:
+    PyFactory(PyObject *mod) : mod(mod) {} ;
+    gmx::TrajectoryAnalysisModulePointer operator () () {
+        int iserr = 0;
+        int can = sipCanConvertToType(mod, sipType_TrajectoryAnalysisModule, 0);
+        // TODO: throw if can't
+        gmx::TrajectoryAnalysisModule *module = (gmx::TrajectoryAnalysisModule*) sipConvertToType(
+            mod, sipType_TrajectoryAnalysisModule, NULL, 0, NULL, &iserr);
+        return TrajectoryAnalysisModulePointer(module);
+    }
+private:
+    PyObject *mod;
+};
+
+void runAsMain(PyObject *mod, PyObject *py_argv) {
+    int argc = PyList_GET_SIZE(py_argv);
+
+    char **argv = new char *[argc + 1];
+    bool to_free[argc];
+    std::fill(to_free, to_free+argc, false);
+
+    // Convert the list.
+    // TODO: Use something better than AsLatin1String to avoid unicode errors
+    for (int a = 0; a < argc; ++a)
+    {
+        PyObject *arg_obj = PyList_GET_ITEM(py_argv, a);
+        const char *arg = sipString_AsLatin1String(&arg_obj);
+
+        if (arg)
+        {
+            arg = strdup(arg);
+            Py_DECREF(arg_obj);
+            to_free[a] = true;
+        }
+        else
+        {
+            arg = "unknown";
+        }
+
+        argv[a] = const_cast<char *>(arg);
+    }
+
+    argv[argc] = NULL;
+
+    PyFactory factory(mod);
+    TrajectoryAnalysisCommandLineRunner::runAsMain(argc, argv, &factory);
+
+    for (int i = 0; i < argc; i++)
+        if (to_free[i])
+            free(argv[i]);
+    delete[] argv;
+}
+
+%End
+
+void runAsMain(SIP_PYOBJECT mod, SIP_PYLIST argv);