fixed more doxygen documentation errors

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 

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

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,

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
 

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;
 
   //@}

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):

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();

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
 

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:

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);