From 27b14b0cae8e20e403e926284ce5ff54d3acb982 Mon Sep 17 00:00:00 2001
From: Andreas Schenk <andreas_schenk@hms.harvard.edu>
Date: Tue, 2 Dec 2014 15:06:54 -0500
Subject: [PATCH] fixed more doxygen documentation errors
---
modules/base/src/string_ref.hh | 2 +-
modules/bindings/pymod/naccess.py | 19 ++++++++++---------
modules/conop/src/nonstandard.hh | 11 ++++-------
modules/gfx/src/entity.hh | 6 +++---
modules/gfx/src/scene.hh | 3 +--
modules/gui/pymod/__init__.py | 2 +-
modules/img/alg/src/dft.hh | 2 +-
modules/io/doc/io.dox | 2 +-
modules/io/pymod/__init__.py | 2 +-
modules/io/src/mol/star_parser.hh | 2 +-
10 files changed, 24 insertions(+), 27 deletions(-)
diff --git a/modules/base/src/string_ref.hh b/modules/base/src/string_ref.hh
index 802dd5940..38ab290bf 100644
--- a/modules/base/src/string_ref.hh
+++ b/modules/base/src/string_ref.hh
@@ -76,7 +76,7 @@ public:
/// \brief returns a substring of the string
///
/// \param pos the starting position of the substring
- /// \param length is the length of the string. if std::string::npos, the
+ /// \param n is the length of the string. if std::string::npos, the
/// substring goes from \p pos to the end of the string
/// The function does on purpose not perform any boundary check in release
/// mode. It's the duty of the caller to make sure the string has the required
diff --git a/modules/bindings/pymod/naccess.py b/modules/bindings/pymod/naccess.py
index b02aeab7a..c13dc49f9 100644
--- a/modules/bindings/pymod/naccess.py
+++ b/modules/bindings/pymod/naccess.py
@@ -25,9 +25,9 @@ from ost import geom
## \brief Method to check if naccess executable is present
#
-# \param naccess Explicit path to msms executable
-# \return Path to the executable
-# \exception FileNotFound if executable is not found
+# \param naccess_exe Explicit path to naccess executable
+# \return Path to the executable
+# \exception FileNotFound if executable is not found
def _GetExecutable(naccess_exe):
return settings.Locate('naccess', explicit_file_name=naccess_exe)
@@ -101,11 +101,11 @@ def _ParseAsaFile(entity, file, asa_atom):
## \brief Reads Area file (.rsa) and attach asa (absolute + relative) per residue to an entitiy
#
-# \param entity EntityHandle or EntityView for attaching sasa on atom level
-# \param file Filename of .rsa file
-# \param asa_atom Name of the float property for absolute SASA
-# \param asa_atom Name of the float property for relative SASA
-# \exception RuntimeError if residue names are not the same
+# \param enti EntityHandle or EntityView for attaching sasa on atom level
+# \param file Filename of .rsa file
+# \param asa_abs Name of the float property for absolute SASA
+# \param asa_rel Name of the float property for relative SASA
+# \exception RuntimeError if residue names are not the same
def _ParseRsaFile(enti,file, asa_abs, asa_rel):
area_fh = open(file)
@@ -156,6 +156,7 @@ def __CleanupFiles(dir_name):
# This method starts the external MSMS executable and returns the stdout of MSMS
#
# \param command Command to execute
+# \param temp_dir
# \return stdout of MSMS
# \exception CalledProcessError for non-zero return value
def _RunNACCESS(command, temp_dir):
@@ -185,7 +186,7 @@ def _RunNACCESS(command, temp_dir):
# \param include_hetatm Calculate surface including hetatms
# \param include_water Calculate surface including water
# \param selection Calculate surface for subset of entity
-# \param naccess _exe msms executable (full path to executable)
+# \param naccess_exe msms executable (full path to executable)
# \param keep_files Do not delete temporary files
# \param asa_abs Attaches per residue absolute SASA to specified FloatProp on residue level
# \param asa_rel Attaches per residue relative SASA to specified FloatProp on residue level
diff --git a/modules/conop/src/nonstandard.hh b/modules/conop/src/nonstandard.hh
index 374694303..a57022def 100644
--- a/modules/conop/src/nonstandard.hh
+++ b/modules/conop/src/nonstandard.hh
@@ -31,9 +31,6 @@ namespace ost { namespace conop {
/// \brief copies all atom of src_res to dst_res, gets compound lib from builder
-/// \param has_cbeta will be set to true if the src_res has a cbeta and the
-/// dst_residue is not a glycine, it will be inserted if in the dst should
-/// be one and in src it was not present
bool DLLEXPORT_OST_CONOP CopyResidue(ost::mol::ResidueHandle src_res,
@@ -41,16 +38,16 @@ bool DLLEXPORT_OST_CONOP CopyResidue(ost::mol::ResidueHandle src_res,
ost::mol::XCSEditor& edi);
/// \brief copies all atom of src_res to dst_res, requires a compound lib
-/// \param has_cbeta will be set to true if the src_res has a cbeta and the
-/// dst_residue is not a glycine, it will be inserted if in the dst should
-/// be one and in src it was not present
bool DLLEXPORT_OST_CONOP CopyResidue(ost::mol::ResidueHandle src_res,
ost::mol::ResidueHandle dst_res,
ost::mol::XCSEditor& edi, CompoundLibPtr lib);
/// \brief copies all atom of src_res to dst_res
-/// \param has_cbeta will be set to true if the src_res has a cbeta and the
+/// \param src_res
+/// \param dst_res
+/// \param edi
+/// \param has_cbeta will be set to true if the src_res has a cbeta and the
/// dst_residue is not a glycine
bool DLLEXPORT_OST_CONOP CopyIdentical(ost::mol::ResidueHandle src_res,
ost::mol::ResidueHandle dst_res,
diff --git a/modules/gfx/src/entity.hh b/modules/gfx/src/entity.hh
index cddf17d99..9106e2607 100644
--- a/modules/gfx/src/entity.hh
+++ b/modules/gfx/src/entity.hh
@@ -364,13 +364,13 @@ private:
/// \example load_and_display.py
///
-/// Shows how to display one \ref Entity "entity" with several render modes
+/// Shows how to display one \ref ost::gfx::Entity "entity" with several render modes
/// at once. The sidechains are displayed simple mode, whereas the backbone is
/// displayed with smooth lines.
/// \example rendermodes.py
///
-/// Shows how to switch between different \ref RenderMode "render modes" and
+/// Shows how to switch between different \ref ost::gfx::RenderMode "render modes" and
/// explains some of the rendermode parameters.
/// \sa \ref load_and_display.py "Loading and Displaying an Entity"
@@ -387,7 +387,7 @@ private:
/// \example color_by_property.py
///
-/// Color \ref Entity "graphical entity" by property using a gradient
+/// Color \ref ost::gfx::Entity "graphical entity" by property using a gradient
/// \sa \ref gradient.py "Gradient Example"
}} // ns
diff --git a/modules/gfx/src/scene.hh b/modules/gfx/src/scene.hh
index 89717de74..53a935c10 100644
--- a/modules/gfx/src/scene.hh
+++ b/modules/gfx/src/scene.hh
@@ -298,7 +298,6 @@ class DLLEXPORT_OST_GFX Scene {
void Export(const String& fname, unsigned int w,
unsigned int h, bool transparent=false);
/// \brief export into bitmap, using multisample anti-aliasing
- /// \ref Scene::StartOfffscreenMode(unsigned int, unsigned int, int) for more detail
void Export(const String& fname, unsigned int w,
unsigned int h, int max_samples, bool transparent=false);
@@ -308,7 +307,7 @@ class DLLEXPORT_OST_GFX Scene {
/// \brief export scene into povray files named fname.pov and fname.inc
void ExportPov(const std::string& fname, const std::string& wdir=".");
- /// \rbrief export scene via exporter
+ /// \brief export scene via exporter
void Export(Exporter* ex) const;
//@}
diff --git a/modules/gui/pymod/__init__.py b/modules/gui/pymod/__init__.py
index ce813e7ef..227a0db3b 100644
--- a/modules/gui/pymod/__init__.py
+++ b/modules/gui/pymod/__init__.py
@@ -22,7 +22,7 @@ import sip
## \brief Opens a DataViewer
-# \sa \ref fft_li.py "View Fourier Transform Example" \sa \ref modulate_image.py "Modulate Image Example"
+# \sa \example fft_li.py "View Fourier Transform Example" \sa \ref modulate_image.py "Modulate Image Example"
def _close_event_override_(event):
print "close event"
def _set_data_override_(data):
diff --git a/modules/img/alg/src/dft.hh b/modules/img/alg/src/dft.hh
index 9e8d8c674..8265dcc10 100644
--- a/modules/img/alg/src/dft.hh
+++ b/modules/img/alg/src/dft.hh
@@ -30,7 +30,7 @@ namespace ost { namespace img { namespace alg {
/// \brief Computes Fourier Trasnform honoring the origin of the image
///
/// \sa \ref view_phase_diff.py "View Phase Diference Example"
-/// \sa \ref code_fragments/img/fft_li.py "View Fourier Transform Example"
+/// \sa \example fft_li.py "View Fourier Transform Example"
class DLLEXPORT_IMG_ALG DFT: public ConstModOPAlgorithm {
public:
DFT();
diff --git a/modules/io/doc/io.dox b/modules/io/doc/io.dox
index 3c864b38b..b266c977a 100644
--- a/modules/io/doc/io.dox
+++ b/modules/io/doc/io.dox
@@ -28,7 +28,7 @@ control over the exact loading behaviour.
Some of the file formats for molecules do not explicitly define bonds. The
IO handlers for these file formats make use of the conop module to infer
-connectivity information (see \ref ost::conop::Builder "Builder").
+connectivity information.
\subsection io_handler IO Handlers
diff --git a/modules/io/pymod/__init__.py b/modules/io/pymod/__init__.py
index 58b592b01..05a46acc3 100644
--- a/modules/io/pymod/__init__.py
+++ b/modules/io/pymod/__init__.py
@@ -210,7 +210,7 @@ except ImportError:
pass
## loads several images and puts them in an ImageList
- # \sa \ref code_fragments/img/fft_li.py "View Fourier Transform Example"
+ # \sa \example fft_li.py "View Fourier Transform Example"
def LoadImageList (files):
image_list=img.ImageList()
for file in files:
diff --git a/modules/io/src/mol/star_parser.hh b/modules/io/src/mol/star_parser.hh
index c5febf7fb..53e170e72 100644
--- a/modules/io/src/mol/star_parser.hh
+++ b/modules/io/src/mol/star_parser.hh
@@ -114,7 +114,7 @@ public:
/// \brief create a StarParser
///
/// \param stream input stream
- /// \param item_as_row if true, data-items are first gathered (identifier as
+ /// \param items_as_row if true, data-items are first gathered (identifier as
/// header, values as row) and then parsed like a loop
/// (OnBeginLoop(), OnDataRow(), OnEndLoop())
explicit StarParser(std::istream& stream, bool items_as_row=false);
--
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