diff --git a/cmake_support/CheckLSBTypes.cmake b/cmake_support/CheckLSBTypes.cmake
index 93857bfa4967fc8ff6088d0b82b130b9dacb65cd..991a08c83de9700d0b6ee03e78c8641d098b5323 100644
--- a/cmake_support/CheckLSBTypes.cmake
+++ b/cmake_support/CheckLSBTypes.cmake
@@ -23,11 +23,11 @@
# CoR-Lab, Research Institute for Cognition and Robotics
# Bielefeld University
-SET(LSB_DISTRIBUTOR_ID "unkown")
-SET(LSB_RELEASE "unkown")
-SET(LSB_CODENAME "unkown")
-SET(LSB_BIT_TYPE "unkown")
-SET(LSB_ARCH_TYPE "unkown")
+SET(LSB_DISTRIBUTOR_ID "unknown")
+SET(LSB_RELEASE "unknown")
+SET(LSB_CODENAME "unknown")
+SET(LSB_BIT_TYPE "unknown")
+SET(LSB_ARCH_TYPE "unknown")
# ---- (mgoettin 10/17/2011) TODO: Update this to match all OS ----
SET(LSB_PROCESSOR_ARCH ${CMAKE_SYSTEM_PROCESSOR})
diff --git a/modules/gfx/src/bitmap_io.cc b/modules/gfx/src/bitmap_io.cc
index 8437de3975fbeb601727deb904bca4659d24ace9..af47577c250f9217973dd3b1eaefa8a3b81b9689 100644
--- a/modules/gfx/src/bitmap_io.cc
+++ b/modules/gfx/src/bitmap_io.cc
@@ -152,7 +152,7 @@ Bitmap import_png(const String& filename)
channels=png_get_channels(png_ptr,info_ptr);
if(channels<1 || channels>4) {
- LOG_ERROR("error importing bitmap: " << filename << " has " << channels << " channels, excpected 1-4");
+ LOG_ERROR("error importing bitmap: " << filename << " has " << channels << " channels, expected 1-4");
return bm;
}
diff --git a/modules/gfx/src/povray.cc b/modules/gfx/src/povray.cc
index e50c4ad6f32b233eb5ebe026e736676a845b025d..3097db3e3414db41393e3b3a7b9650096433eb18 100644
--- a/modules/gfx/src/povray.cc
+++ b/modules/gfx/src/povray.cc
@@ -82,7 +82,7 @@ void PovState::write_postamble()
pov_ << " /*\n";
pov_ << " This transformation, together with\n";
pov_ << " the camera translation above,\n";
- pov_ << " mimicks the original scene view:\n";
+ pov_ << " mimics the original scene view:\n";
pov_ << " 1. translate to center of rotation\n";
pov_ << " 2. apply rotation matrix\n";
pov_ << " 3. apply xy translation (z component is in camera)\n";
diff --git a/modules/gfx/src/scene.cc b/modules/gfx/src/scene.cc
index f53323a54302e8f26325048e07cd00084f93b695..a79bee3a3e2e6ef2a0f67a519ab8216fa1395547 100644
--- a/modules/gfx/src/scene.cc
+++ b/modules/gfx/src/scene.cc
@@ -539,7 +539,7 @@ void Scene::InitGL(bool full)
}
if(full) {
- LOG_DEBUG("Scene: initalizing textures");
+ LOG_DEBUG("Scene: initialising textures");
glGenTextures(1,&scene_left_tex_);
glGenTextures(1,&scene_right_tex_);
glGenTextures(1,&bg_tex_);
diff --git a/modules/img/alg/src/conjugate.hh b/modules/img/alg/src/conjugate.hh
index 79409ecf57946d39c0095e3ec3e2fe8ce8f2279b..2e2b65bad4a488276a6fc2f9dddaa90d7d6921de 100644
--- a/modules/img/alg/src/conjugate.hh
+++ b/modules/img/alg/src/conjugate.hh
@@ -42,7 +42,7 @@ void do_conj_ip<Complex>(image_state::ValueHolder<Complex>& vh)
}
}
-// generic case - emtpy
+// generic case - empty
template <typename V>
void do_conj_ip(image_state::ValueHolder<V>& vh) {}
diff --git a/modules/img/alg/src/highest_peak_search_3d.cc b/modules/img/alg/src/highest_peak_search_3d.cc
index a4a80e78e7e066ef576545a5d9f974bdf587ccc4..99d5d917c3d073f8eb53d802880e7c2a32386c49 100644
--- a/modules/img/alg/src/highest_peak_search_3d.cc
+++ b/modules/img/alg/src/highest_peak_search_3d.cc
@@ -151,7 +151,7 @@ template <typename T, class D>
{
ss << " " << (*it);
}
- LOG_DEBUG("exluded regions:" << ss.str());
+ LOG_DEBUG("excluded regions:" << ss.str());
}
detail::PeakCollector peak_collector(max_num_peaks_,exclusion_radius_);
diff --git a/modules/img/alg/src/histogram.hh b/modules/img/alg/src/histogram.hh
index 619a9f845cfc4b825cb55758c24a32e10eb7ac96..4fe930bf4844d03670fb89f6910e8bfa6e4858c7 100644
--- a/modules/img/alg/src/histogram.hh
+++ b/modules/img/alg/src/histogram.hh
@@ -36,7 +36,7 @@ namespace ost { namespace img { namespace alg {
class DLLEXPORT HistogramError: public Error {
public:
HistogramError(const String& s):
- Error(String("A histogram error occured: ") + s)
+ Error(String("A histogram error occurred: ") + s)
{}
};
diff --git a/modules/img/alg/tests/test_fft.cc b/modules/img/alg/tests/test_fft.cc
index 18f25b236effdd8df370dcc804f998f8e745270e..835dbbbde3ff9f68f9f1deca0d7da315d82e2023 100644
--- a/modules/img/alg/tests/test_fft.cc
+++ b/modules/img/alg/tests/test_fft.cc
@@ -388,7 +388,7 @@ void Test_DFT(DataType TYPE)
std::ostringstream msg;
- msg << "fi1 fi2 Extent missmatch: " << fi1.GetExtent() << "!=" << fi2.GetExtent();
+ msg << "fi1 fi2 Extent mismatch: " << fi1.GetExtent() << "!=" << fi2.GetExtent();
BOOST_REQUIRE_MESSAGE(fi1.GetExtent()==fi2.GetExtent(),msg.str());
for(ExtentIterator it(fi1.GetExtent());!it.AtEnd();++it) {
@@ -401,7 +401,7 @@ void Test_DFT(DataType TYPE)
ImageHandle ri3 = fi1.Apply(alg::DFT());
msg.str("");
- msg << "ri1 ri3 Extent missmatch: " << ri3.GetExtent() << "!=" << ri1.GetExtent();
+ msg << "ri1 ri3 Extent mismatch: " << ri3.GetExtent() << "!=" << ri1.GetExtent();
BOOST_REQUIRE_MESSAGE(ri3.GetExtent()==ri1.GetExtent(),msg.str());
for(ExtentIterator it(ri3.GetExtent());!it.AtEnd();++it) {
diff --git a/modules/img/base/pymod/export_data_algorithm.cc b/modules/img/base/pymod/export_data_algorithm.cc
index 167f5c78964deb231f4c9aee3550d9e815e0abec..c984c6d7dfe089e8a101a7e59a77ef49ba8123c1 100644
--- a/modules/img/base/pymod/export_data_algorithm.cc
+++ b/modules/img/base/pymod/export_data_algorithm.cc
@@ -70,7 +70,7 @@ public:
virtual void Visit(ImageHandle& ih) {VisitImage(ih);}
virtual void VisitImage(ImageHandle&) {
- throw(Error("ModIPAlgorithm Base: VisitImage not overidden"));
+ throw(Error("ModIPAlgorithm Base: VisitImage not overridden"));
}
};
@@ -99,7 +99,7 @@ public:
virtual void Visit(ImageHandle& ih) const {VisitImage(ih);}
virtual void VisitImage(ImageHandle&) const {
- throw(Error("ConstModIPAlgorithm Base: VisitImage not overidden"));
+ throw(Error("ConstModIPAlgorithm Base: VisitImage not overridden"));
}
};
@@ -129,7 +129,7 @@ public:
virtual ImageHandle Visit(const ConstImageHandle& ih) {return VisitImage(ih);}
virtual ImageHandle VisitImage(const ConstImageHandle& ih) {
- throw(Error("ModOPAlgorithm Base: VisitImage not overidden"));
+ throw(Error("ModOPAlgorithm Base: VisitImage not overridden"));
}
};
@@ -158,7 +158,7 @@ public:
virtual ImageHandle Visit(const ConstImageHandle& ih) const {return VisitImage(ih);}
virtual ImageHandle VisitImage(const ConstImageHandle& ih) const {
- throw(Error("ConstModOPAlgorithm Base: VisitImage not overidden"));
+ throw(Error("ConstModOPAlgorithm Base: VisitImage not overridden"));
}
};
diff --git a/modules/img/base/src/data_observer.hh b/modules/img/base/src/data_observer.hh
index c061a97c3158b5e3facd4c37b2eb65ed0440a6cc..c3f06dc842114898f548ef302dea8a4ca4444aea 100644
--- a/modules/img/base/src/data_observer.hh
+++ b/modules/img/base/src/data_observer.hh
@@ -36,7 +36,7 @@ namespace ost { namespace img {
class DLLEXPORT InvalidObserver: public Error {
public:
InvalidObserver(const String& s = String("unknown")):
- Error(String("InvalidObserver exception occured: ") + s)
+ Error(String("InvalidObserver exception occurred: ") + s)
{}
};
diff --git a/modules/img/base/src/extent.hh b/modules/img/base/src/extent.hh
index 16978d96ef627ce10328c20f68448549e90844c1..fdff69b7228173ad0c920aa8c6e1c331c2a88824 100644
--- a/modules/img/base/src/extent.hh
+++ b/modules/img/base/src/extent.hh
@@ -47,7 +47,7 @@ namespace ost { namespace img {
struct DLLEXPORT InvalidExtentException: public Error
{
InvalidExtentException(const String& m= String("") ):
- Error(String("an invalid extent occured ("+m+String(")")))
+ Error(String("an invalid extent occurred ("+m+String(")")))
{}
};
diff --git a/modules/img/base/src/image_handle.hh b/modules/img/base/src/image_handle.hh
index 3d7261f9ceafc45b6cdb8b3b044d6ed52bb53fff..c984bc39dbab1bf89b5188124f5caa27053428df 100644
--- a/modules/img/base/src/image_handle.hh
+++ b/modules/img/base/src/image_handle.hh
@@ -126,7 +126,7 @@ public:
//! Creates an empty, ie invalid handle
/*!
The default ctor is provided for e.g. using ImageHandle in STL containers. Any
- attempt to use the interface of an emtpy ImageHandle will throw an
+ attempt to use the interface of an empty ImageHandle will throw an
InvalidImageHandle exception.
*/
ImageHandle();
diff --git a/modules/io/src/img/map_io_dm3_handler.cc b/modules/io/src/img/map_io_dm3_handler.cc
index c7b3351ec81e7eb84f3e58a373dbe653e417d8e8..bfae05eb8af54ef29f8c8bb8628f1d8e22dc312a 100644
--- a/modules/io/src/img/map_io_dm3_handler.cc
+++ b/modules/io/src/img/map_io_dm3_handler.cc
@@ -320,7 +320,7 @@ void DM3Collector::check_image()
image_handle_list_.push_back(ih);
} else {
- LOG_ERROR("missmatch in byte size of data ("
+ LOG_ERROR("mismatch in byte size of data ("
<< data_size*type_sizeof(image_number_type_) << " != "
<< image_data_byte_size_ << "), ignoring this image entry");
}
diff --git a/modules/io/src/img/map_io_spi_handler.cc b/modules/io/src/img/map_io_spi_handler.cc
index 36a08bb3ae383ec53999f9878ff795ca5d36f3c2..d5b47181e4c8b14a436cef7c0161056260cb686e 100644
--- a/modules/io/src/img/map_io_spi_handler.cc
+++ b/modules/io/src/img/map_io_spi_handler.cc
@@ -482,7 +482,7 @@ void MapIOSpiHandler::Import(img::MapHandle& mh, std::istream& infile,const Imag
detail::header_filler<OST_LITTLE_ENDIAN>(infile, header);
break;
default:
- throw(IOException("unkown byte order"));
+ throw(IOException("unknown byte order"));
break;
}
@@ -506,7 +506,7 @@ void MapIOSpiHandler::Import(img::MapHandle& mh, std::istream& infile,const Imag
detail::real_filler<OST_LITTLE_ENDIAN,float>(infile,header,mh,1.0);
break;
default:
- throw(IOException("unkown byte order"));
+ throw(IOException("unknown byte order"));
break;
}
diff --git a/modules/io/src/img/map_io_tiff_handler.cc b/modules/io/src/img/map_io_tiff_handler.cc
index 5de5b240fb5d0293508ea850044783084bfde6c3..d88fc01d7d55b3b6227da0f8d18054fad3b54d2d 100644
--- a/modules/io/src/img/map_io_tiff_handler.cc
+++ b/modules/io/src/img/map_io_tiff_handler.cc
@@ -629,7 +629,7 @@ void MapIOTiffHandler::load_image_data(TIFF* tfile, img::ImageHandle& image, co
buf = _TIFFmalloc(stripsize);
if(image.GetType()==img::WORD) {
- LOG_INFO("I/O Tiff: " << "reseting target image to WORD " << image_extent);
+ LOG_INFO("I/O Tiff: " << "resetting target image to WORD " << image_extent);
image.Reset(image_extent, img::WORD, img::SPATIAL);
img::image_state::WordSpatialImageState *is =
@@ -676,14 +676,14 @@ void MapIOTiffHandler::load_image_data(TIFF* tfile, img::ImageHandle& image, co
img::image_state::RealSpatialImageState *isr=0;
img::image_state::ComplexSpatialImageState *isc=0;
if(fmt==SAMPLEFORMAT_COMPLEXINT || fmt==SAMPLEFORMAT_COMPLEXIEEEFP){
- LOG_INFO("I/O Tiff: " << "reseting target image to complex spatial " << image_extent);
+ LOG_INFO("I/O Tiff: " << "resetting target image to complex spatial " << image_extent);
image.Reset(image_extent,img::COMPLEX,img::SPATIAL);
isc = dynamic_cast<img::image_state::ComplexSpatialImageState*>(image.ImageStatePtr().get());
if(!isc) {
throw IOException("unexpected failure of dynamic_cast in tiff io");
}
}else{
- LOG_INFO("I/O Tiff: " << "reseting target image to Real img::SPATIAL" << image_extent);
+ LOG_INFO("I/O Tiff: " << "resetting target image to Real img::SPATIAL" << image_extent);
image.Reset(image_extent, img::REAL, img::SPATIAL);
isr= dynamic_cast<img::image_state::RealSpatialImageState*>(image.ImageStatePtr().get());
diff --git a/modules/io/src/mol/dcd_io.cc b/modules/io/src/mol/dcd_io.cc
index ec31b4bbf88694f714854645845557c42485a1e2..d70074433c734815669a84c178d4168b1f7b2e0d 100644
--- a/modules/io/src/mol/dcd_io.cc
+++ b/modules/io/src/mol/dcd_io.cc
@@ -267,7 +267,7 @@ mol::CoordGroupHandle load_dcd(const mol::AtomHandleList& alist, // this atom li
bool swap_flag=false, ucell_flag=false, gap_flag=false;
read_dcd_header(istream, header, swap_flag, ucell_flag, gap_flag, detect_swap, byte_swap);
if(alist.size() != static_cast<size_t>(header.t_atom_count)) {
- LOG_ERROR("LoadCHARMMTraj: atom count missmatch: " << alist.size()
+ LOG_ERROR("LoadCHARMMTraj: atom count mismatch: " << alist.size()
<< " in coordinate file, " << header.t_atom_count
<< " in each traj frame");
throw(IOException("invalid trajectory"));
diff --git a/modules/io/src/mol/load_entity.cc b/modules/io/src/mol/load_entity.cc
index a9d34c3eb26030bd00a7facf485d70423056af8d..c35010927ca7bf14f3eb85e3ba6bcea9f6c8d871 100644
--- a/modules/io/src/mol/load_entity.cc
+++ b/modules/io/src/mol/load_entity.cc
@@ -55,7 +55,7 @@ void Import(mol::EntityHandle& eh, const String& filename, const String& format)
mol::EntityHandle LoadEntity(const String& filename, const String& format)
{
- LOG_DEBUG("creating emtpy entity");
+ LOG_DEBUG("creating empty entity");
mol::EntityHandle eh=mol::CreateEntity();
mol::XCSEditor xcs_lock=eh.EditXCS(mol::BUFFERED_EDIT);
Import(eh, filename, format);
diff --git a/modules/io/src/mol/mmcif_reader.hh b/modules/io/src/mol/mmcif_reader.hh
index 925dfde23b3362612a3fe63d5e0f04e6ff6c2df7..9147a234c4f4966b4ac861f45c48f0a2e7bee829 100644
--- a/modules/io/src/mol/mmcif_reader.hh
+++ b/modules/io/src/mol/mmcif_reader.hh
@@ -232,7 +232,7 @@ protected:
const MMCifInfoStructRefs& GetStructRefs() const { return struct_refs_; }
/// \brief convert the seqres data item to canonical form.
///
- /// The seqres sequence lists non-standard residues in paranthesis. For
+ /// The seqres sequence lists non-standard residues in parenthesis. For
/// proper handling of our sequence classes, these need to be converted to
/// one-letter-codes. Ideally, we would use the canonical SEQRES. This is
/// not possible, however, since the PDB assigns multiple one letter codes
diff --git a/modules/mol/alg/src/local_dist_diff_test.hh b/modules/mol/alg/src/local_dist_diff_test.hh
index 794c671e06039c132f3f20bdeac9cc2e564a44a6..41ebf09ac800acf8242295361a6cb877a85315f7 100644
--- a/modules/mol/alg/src/local_dist_diff_test.hh
+++ b/modules/mol/alg/src/local_dist_diff_test.hh
@@ -214,7 +214,7 @@ GlobalRDMap DLLEXPORT_OST_MOL_ALG CreateDistanceList(const EntityView& ref,Real
///
/// If a distance between two atoms is shorter than the inclusion radius in all structures in which the two atoms are
/// present, it is included in the list. However, if the distance is longer than the inclusion radius in at least one
-/// of the structures, it is not be considered a local interaction and is exluded from the list
+/// of the structures, it is not be considered a local interaction and is excluded from the list
///
/// The function takes care of residues with ambigous symmetric sidechains. To decide which naming convention to use, the functions
/// computes a local distance score of each reference structure with the first reference structure in the list, using only non ambigously-named atoms.
diff --git a/modules/mol/base/pymod/export_editors.cc b/modules/mol/base/pymod/export_editors.cc
index 3c5ab790008016ce376da1f353ea9a5fbd4b71c9..e20ee4d4e11b5b8e7b658926667cb85005c2c5e2 100644
--- a/modules/mol/base/pymod/export_editors.cc
+++ b/modules/mol/base/pymod/export_editors.cc
@@ -123,7 +123,7 @@ void set_pos2_t(XCSEditor& e, const AtomHandleList& alist, object pyobj)
PyArrayObject* na=reinterpret_cast<PyArrayObject*>(pyobj.ptr());
if(PyArray_NDIM(na)!=2 || PyArray_DIM(na,0)!=int(acount) || PyArray_DIM(na,1)!=3) {
- throw Error("excpected a numpy array of shape (NAtoms, 3)");
+ throw Error("expected a numpy array of shape (NAtoms, 3)");
return;
}
diff --git a/modules/mol/base/src/coord_frame.cc b/modules/mol/base/src/coord_frame.cc
index 8fb7a39cfcecaab0c161c76ec2dbd671077c97c3..582e6711012dcbb7f1569a9e1cb4c649ba363a0e 100644
--- a/modules/mol/base/src/coord_frame.cc
+++ b/modules/mol/base/src/coord_frame.cc
@@ -289,7 +289,7 @@ namespace ost { namespace mol {
throw Error("not same numbers of CA, C, O and N atoms in the selection");
}
if (n_atoms<=5){
- throw Error("At least five residues are needed to calulate an alpha helix similarity");
+ throw Error("At least five residues are needed to calculate an alpha helix similarity");
}
c=(*this)[indices_c[0]];
n_next=(*this)[indices_n[1]];
diff --git a/modules/mol/base/src/impl/entity_impl.cc b/modules/mol/base/src/impl/entity_impl.cc
index db0731f27583d9bc499183e56c65464188a4037d..c15489bed172612a51904f1061e9b4ba009ee576 100644
--- a/modules/mol/base/src/impl/entity_impl.cc
+++ b/modules/mol/base/src/impl/entity_impl.cc
@@ -544,7 +544,7 @@ void EntityImpl::TraceDirectionality()
{
fragment_list_.clear();
Profile profile_trace("trace directionality");
- // some reseting on the atom level
+ // some resetting on the atom level
for(AtomImplMap::iterator it=atom_map_.begin();it!=atom_map_.end();++it) {
it->second->ClearDirectionality();
it->second->SetVisited(false);
diff --git a/modules/mol/base/src/impl/query_impl.cc b/modules/mol/base/src/impl/query_impl.cc
index a7c2cfb95c495362e1e04b104499fb109ef90263..f5842a7492cddc841c2685dc1ed9c4413da3d760 100644
--- a/modules/mol/base/src/impl/query_impl.cc
+++ b/modules/mol/base/src/impl/query_impl.cc
@@ -797,7 +797,7 @@ Node* QueryImpl::ParseParenSubExpr(QueryLexer& lexer) {
QueryToken end_paren=lexer.CurrentToken();
if (end_paren.GetType()!=tok::RightParen) {
delete n;
- error_desc_.msg="unmatched paranthesis in query string";
+ error_desc_.msg="unmatched parenthesis in query string";
error_desc_.range=paren_token.GetRange();
return NULL;
} else {
diff --git a/modules/mol/base/src/query_error.hh b/modules/mol/base/src/query_error.hh
index c8a092cc9c073cf5f217db4294b51cc32bf46f45..56cfb21db1b516ae227387f3d70c8fc5722c90e8 100644
--- a/modules/mol/base/src/query_error.hh
+++ b/modules/mol/base/src/query_error.hh
@@ -45,7 +45,7 @@ public:
//! Get error description.
const String& GetMessage()const throw();
- // Get range of where the error occured
+ // Get range of where the error occurred
const Range& GetRange() const;
//! Get nicely formatted error message
diff --git a/scripts/ost_config.in b/scripts/ost_config.in
index c8a170a32867eca70cac323aaf723f38f9d0a49a..b3e253c5c5e24fe424851d9ab7a5e68cc73237d4 100644
--- a/scripts/ost_config.in
+++ b/scripts/ost_config.in
@@ -69,7 +69,7 @@ if [ -n "$DNG_PROFILE" ]; then
echo "Profiling activated using cProfile"
pyexec="$pyexec#-m#cProfile#-s#cumulative#--"
else
- echo "Profiling deactivated due to unkown profiler"
+ echo "Profiling deactivated due to unknown profiler"
fi
fi