diff --git a/modules/base/src/generic_property.hh b/modules/base/src/generic_property.hh
index a7ea0782510763ec3849a4f28fb880a60afb2d99..5220d7741d2df6aff1356dec25603ac41ff036eb 100644
--- a/modules/base/src/generic_property.hh
+++ b/modules/base/src/generic_property.hh
@@ -28,7 +28,6 @@
setter and getter methods for String, Real, int and bool mapping
*/
-#include <exception>
#include <sstream>
#include <map>
#include <vector>
@@ -36,19 +35,15 @@
#include <ost/module_config.hh>
#include <ost/invalid_handle.hh>
+#include <ost/message.hh>
namespace ost {
-struct TEMPLATE_EXPORT GenericPropError: public std::exception
+struct DLLEXPORT GenericPropError: public Error
{
GenericPropError(const String& m):
- m_(m)
+ Error(m)
{}
- virtual ~GenericPropError() throw() {}
- virtual const char* what() const throw() {
- return m_.c_str();
- }
- String m_;
};
typedef boost::variant<String, Real, int, bool> GenericPropValue;
diff --git a/modules/base/src/message.cc b/modules/base/src/message.cc
index 6fc3e6e31dce299cf20b937a8b02cf19f1031c9d..572480206588eaf96cbe29e7f748d8c68c8952d2 100644
--- a/modules/base/src/message.cc
+++ b/modules/base/src/message.cc
@@ -20,7 +20,7 @@
/*
messages and logs
- Authors: Ansgar Philippsen, Andteas Schenk
+ Authors: Ansgar Philippsen, Andreas Schenk
*/
#include "message.hh"
@@ -28,17 +28,7 @@
namespace ost {
Error::Error(const String& m):
- mesg_(m)
+ std::runtime_error(m)
{}
-Error::~Error() throw()
-{
}
-
-const char* Error::what() const throw()
-{
- return mesg_.c_str();
-}
-
-}
-
diff --git a/modules/base/src/message.hh b/modules/base/src/message.hh
index 6a98dbc2bdc3a7983d3654b2c3759d2d6b3eecbc..5dd148264d3f6a867be593fcd0a5725dde377b31 100644
--- a/modules/base/src/message.hh
+++ b/modules/base/src/message.hh
@@ -20,25 +20,21 @@
/*
messages and logs
- Authors: Ansgar Philippsen, Andteas Schenk
+ Authors: Ansgar Philippsen, Andreas Schenk
*/
#ifndef OST_MESSAGE_HH
#define OST_MESSAGE_HH
-#include <exception>
+#include <stdexcept>
#include <ost/module_config.hh>
namespace ost {
-class DLLEXPORT Error: virtual public std::exception {
+class DLLEXPORT Error: public std::runtime_error {
public:
Error(const String& m);
- ~Error() throw();
- virtual const char* what() const throw();
-protected:
- String mesg_;
};
} // namespace
diff --git a/modules/base/src/ptr_observer.hh b/modules/base/src/ptr_observer.hh
index a5f9cfbb10799cbb2ff8df11cd80a678db36f174..4b98e1fd52b972deea02b6207dcb0f1bfedb48bc 100644
--- a/modules/base/src/ptr_observer.hh
+++ b/modules/base/src/ptr_observer.hh
@@ -29,7 +29,7 @@
Author: Ansgar Philippsen
*/
-class DLLEXPORT_OST_BASE InvalidatedPointer: public ost::Error {
+class DLLEXPORT InvalidatedPointer: public ost::Error {
public:
InvalidatedPointer():
ost::Error("access attempt on invalidated Pointer")
diff --git a/modules/conop/pymod/export_compound.cc b/modules/conop/pymod/export_compound.cc
index 05f27a82e01dcb1f969a1c43a44ce875490cc148..6b8196e6768a608745c9c83608a7ddffc6ef50d3 100644
--- a/modules/conop/pymod/export_compound.cc
+++ b/modules/conop/pymod/export_compound.cc
@@ -21,6 +21,7 @@
#include <boost/python/suite/indexing/vector_indexing_suite.hpp>
using namespace boost::python;
+#include <ost/message.hh>
#include <ost/conop/compound.hh>
#include <ost/conop/compound_lib.hh>
using namespace ost::mol;
@@ -44,7 +45,7 @@ Compound::Dialect tr_dialect(const String& dialect)
}
std::stringstream ss;
ss << "unknown compound dialect '" << dialect << "'";
- throw std::runtime_error(ss.str());
+ throw ost::Error(ss.str());
}
void set_dialect(CompoundPtr compound, const String& dialect)
diff --git a/modules/conop/src/conop.cc b/modules/conop/src/conop.cc
index f72956f1a2f732a5734ddd1a8d20bec46e5cc91f..e48b3444e16c4ac7bf1ba5ef70ea28ff8341f93a 100644
--- a/modules/conop/src/conop.cc
+++ b/modules/conop/src/conop.cc
@@ -16,6 +16,7 @@
// along with this library; if not, write to the Free Software Foundation, Inc.,
// 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
//------------------------------------------------------------------------------
+#include <ost/message.hh>
#include <ost/mol/mol.hh>
#include <ost/log.hh>
@@ -161,7 +162,7 @@ void Conopology::SetDefaultBuilder(const String& default_name) {
if (builder)
builder_map_["DEFAULT"]=builder;
else
- throw std::runtime_error("trying to set unknown builder '"+
+ throw ost::Error("trying to set unknown builder '"+
default_name+"' as the default");
}
diff --git a/modules/geom/src/exc.hh b/modules/geom/src/exc.hh
index 67eda2278e8ec380aa154dc16552e04b70a782cc..0c4390030e9d6d3c520a9876722e8ce564be4134 100644
--- a/modules/geom/src/exc.hh
+++ b/modules/geom/src/exc.hh
@@ -33,19 +33,19 @@ namespace geom {
code may choose to catch exceptions from
the geom library undifferentiatedly
*/
-class DLLEXPORT_OST_GEOM GeomException: public std::runtime_error {
+class DLLEXPORT GeomException: public std::runtime_error {
public:
GeomException(const String& m):
std::runtime_error(m) {}
};
-class DLLEXPORT_OST_GEOM DivideByZeroException: public GeomException {
+class DLLEXPORT DivideByZeroException: public GeomException {
public:
DivideByZeroException(const String& m="Divide By Zero"):
GeomException(m) {}
};
-class DLLEXPORT_OST_GEOM OutOfRangeException: public GeomException {
+class DLLEXPORT OutOfRangeException: public GeomException {
public:
OutOfRangeException(const String& m="Out Of Range"):
GeomException(m) {}
diff --git a/modules/geom/src/exception.hh b/modules/geom/src/exception.hh
deleted file mode 100644
index dded875655957f126b6dee28e0ff66f04c4168e4..0000000000000000000000000000000000000000
--- a/modules/geom/src/exception.hh
+++ /dev/null
@@ -1,37 +0,0 @@
-//------------------------------------------------------------------------------
-// This file is part of the OpenStructure project <www.openstructure.org>
-//
-// Copyright (C) 2008-2011 by the OpenStructure authors
-//
-// This library is free software; you can redistribute it and/or modify it under
-// the terms of the GNU Lesser General Public License as published by the Free
-// Software Foundation; either version 3.0 of the License, or (at your option)
-// any later version.
-// This library is distributed in the hope that it will be useful, but WITHOUT
-// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
-// FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
-// details.
-//
-// You should have received a copy of the GNU Lesser General Public License
-// along with this library; if not, write to the Free Software Foundation, Inc.,
-// 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
-//------------------------------------------------------------------------------
-#ifndef GEOM_EXCEPTION_HH
-#define GEOM_EXCEPTION_HH
-
-#include <string>
-#include <ost/message.hh>
-#include "module_config.hh"
-
-namespace geom {
-
-class DLLEXPORT_OST_GEOM GeomException: public Error
-{
-public:
- GeomException(const String& m):
- Error(m) {}
-
-};
-
-}
-
diff --git a/modules/geom/src/vecmat3_op.cc b/modules/geom/src/vecmat3_op.cc
index 50b5b612e939d66e6d8119ddced416ff87e52f99..8a1debee816113fc87d196379b6e0230a241238d 100644
--- a/modules/geom/src/vecmat3_op.cc
+++ b/modules/geom/src/vecmat3_op.cc
@@ -196,7 +196,7 @@ Real DihedralAngle(const Vec3& p1, const Vec3& p2, const Vec3& p3,
Real MinDistance(const Vec3List& l1, const Vec3List& l2)
{
// returns the minimal distance between two sets of points (Vec3List)
- if (l1.size()==0 || l2.size()==0){throw std::runtime_error("cannot calculate minimal distance: empty Vec3List");}
+ if (l1.size()==0 || l2.size()==0){throw GeomException("cannot calculate minimal distance: empty Vec3List");}
Real min=Length2(*l1.begin()-*l2.begin());
Real d;
for (Vec3List::const_iterator p1=l1.begin(),e1=l1.end(); p1!=e1; p1++) {
@@ -212,7 +212,7 @@ Real MinDistanceWithPBC(const Vec3List& l1, const Vec3List& l2, Vec3& basis_vec)
{
// returns the minimal distance between two sets of points (Vec3List)
// given the periodic boundary condition along x,y,z given in the basis_vec
- if (l1.size()==0 || l2.size()==0){throw std::runtime_error("cannot calculate minimal distance: empty Vec3List");}
+ if (l1.size()==0 || l2.size()==0){throw GeomException("cannot calculate minimal distance: empty Vec3List");}
Real min=Length2(*l1.begin()-*l2.begin());
Real d;
Vec3 v;
diff --git a/modules/geom/tests/test_op3.cc b/modules/geom/tests/test_op3.cc
index de7e74843e536b2b635d111752e1142c6cd7dcb2..1d4660b4e8cf92d2f6506bd900bad16aaf480dec 100644
--- a/modules/geom/tests/test_op3.cc
+++ b/modules/geom/tests/test_op3.cc
@@ -52,11 +52,11 @@ BOOST_AUTO_TEST_CASE(vecmat_mult3)
BOOST_AUTO_TEST_CASE(vec3list_op)
{
Vec3List l1,l2;
- BOOST_CHECK_THROW(MinDistance(l1,l2),std::runtime_error);
+ BOOST_CHECK_THROW(MinDistance(l1,l2),GeomException);
l1.push_back(Vec3(0.0,0.0,0.0));
l1.push_back(Vec3(1.0,0.0,0.0));
- BOOST_CHECK_THROW(MinDistance(l1,l2),std::runtime_error);
- BOOST_CHECK_THROW(MinDistance(l2,l1),std::runtime_error);
+ BOOST_CHECK_THROW(MinDistance(l1,l2),GeomException);
+ BOOST_CHECK_THROW(MinDistance(l2,l1),GeomException);
l2.push_back(Vec3(4.0,4.0,0.0));
l2.push_back(Vec3(2.0,4.0,5.0));
l2.push_back(Vec3(0.0,3.0,6.0));
diff --git a/modules/gfx/pymod/export_gradient.cc b/modules/gfx/pymod/export_gradient.cc
index 4832495381ef699dbf871bfc9eaa3449ebe622f9..03eeb5401314968c1dba50967224846c11aa7ad7 100644
--- a/modules/gfx/pymod/export_gradient.cc
+++ b/modules/gfx/pymod/export_gradient.cc
@@ -38,7 +38,7 @@ namespace {
for(int i=0;i<len(keys);++i) {
extract<float> fex(keys[i]);
if(!fex.check()) {
- throw std::runtime_error("expected floats as keys");
+ throw Error("expected floats as keys");
}
float mark = fex();
Color col;
@@ -50,12 +50,12 @@ namespace {
} else {
// try simple sequence
if(len(val)!=3) {
- throw std::runtime_error("expected values of gfx.Color or float triplets");
+ throw Error("expected values of gfx.Color or float triplets");
}
try {
col=gfx::Color(extract<float>(val[0]),extract<float>(val[1]),extract<float>(val[2]));
} catch (...) {
- throw std::runtime_error("expected values of gfx.Color or float triplets");
+ throw Error("expected values of gfx.Color or float triplets");
}
}
grad->SetColorAt(mark,col);
@@ -78,12 +78,12 @@ namespace {
} else {
// try simple sequence
if(len(val)!=3) {
- throw std::runtime_error("expected values of gfx.Color or float triplets");
+ throw Error("expected values of gfx.Color or float triplets");
}
try {
col=gfx::RGB(extract<float>(val[0]),extract<float>(val[1]),extract<float>(val[2]));
} catch (...) {
- throw std::runtime_error("expected values of gfx.Color float triplets");
+ throw Error("expected values of gfx.Color float triplets");
}
}
grad->SetColorAt(mark,col);
diff --git a/modules/gfx/pymod/export_primlist.cc b/modules/gfx/pymod/export_primlist.cc
index 0d6d2bb1623466d3aa81a6c6758fcf9b931f0072..8cdaf32303ae80ff65d787642d2e9a01b8d5bc0d 100644
--- a/modules/gfx/pymod/export_primlist.cc
+++ b/modules/gfx/pymod/export_primlist.cc
@@ -21,6 +21,7 @@ using namespace boost::python;
#include <boost/shared_ptr.hpp>
+#include <ost/message.hh>
#include <ost/gfx/prim_list.hh>
using namespace ost;
using namespace ost::gfx;
@@ -34,18 +35,18 @@ namespace {
{
#if OST_NUMPY_SUPPORT_ENABLED
if(!PyArray_Check(ova.ptr())) {
- throw std::runtime_error("ova is not a numpy array");
+ throw Error("ova is not a numpy array");
}
PyArrayObject* va=reinterpret_cast<PyArrayObject*>(ova.ptr());
if(!PyArray_ISCONTIGUOUS(va)) {
- throw std::runtime_error("expected vertex array to be contiguous");
+ throw Error("expected vertex array to be contiguous");
}
if(!PyArray_TYPE(va)==NPY_FLOAT) {
- throw std::runtime_error("expected vertex array to be of dtype=float32");
+ throw Error("expected vertex array to be of dtype=float32");
}
size_t v_size=PyArray_SIZE(va);
if(v_size%3!=0) {
- throw std::runtime_error("expected vertex array size to be divisible by 3");
+ throw Error("expected vertex array size to be divisible by 3");
}
size_t v_count=v_size/3;
float* vp=reinterpret_cast<float*>(PyArray_DATA(va));
@@ -53,52 +54,52 @@ namespace {
float* cp=0;
if(ona!=object()) {
if(!PyArray_Check(ona.ptr())) {
- throw std::runtime_error("ona is not a numpy array");
+ throw Error("ona is not a numpy array");
}
PyArrayObject* na=reinterpret_cast<PyArrayObject*>(ona.ptr());
if(!PyArray_ISCONTIGUOUS(na)) {
- throw std::runtime_error("expected normal array to be contiguous");
+ throw Error("expected normal array to be contiguous");
}
if(!PyArray_TYPE(na)==NPY_FLOAT) {
- throw std::runtime_error("expected normal array to be of dtype=float32");
+ throw Error("expected normal array to be of dtype=float32");
}
if((size_t)PyArray_SIZE(na)!=v_size) {
- throw std::runtime_error("expected normal array size to match vertex array size");
+ throw Error("expected normal array size to match vertex array size");
}
np=reinterpret_cast<float*>(PyArray_DATA(na));
}
if(oca!=object()) {
if(!PyArray_Check(oca.ptr())) {
- throw std::runtime_error("oca is not a numpy array");
+ throw Error("oca is not a numpy array");
}
PyArrayObject* ca=reinterpret_cast<PyArrayObject*>(oca.ptr());
if(!PyArray_ISCONTIGUOUS(ca)) {
- throw std::runtime_error("expected color array to be contiguous");
+ throw Error("expected color array to be contiguous");
}
if(!PyArray_TYPE(ca)==NPY_FLOAT) {
- throw std::runtime_error("expected color array to be of dtype=float32");
+ throw Error("expected color array to be of dtype=float32");
}
if((size_t)PyArray_SIZE(ca)!=v_count*4) {
- throw std::runtime_error("expected color array size to equal vertex-count x 4");
+ throw Error("expected color array size to equal vertex-count x 4");
}
cp=reinterpret_cast<float*>(PyArray_DATA(ca));
}
if(!PyArray_Check(oia.ptr())) {
- throw std::runtime_error("oia is not a numpy array");
+ throw Error("oia is not a numpy array");
}
PyArrayObject* ia=reinterpret_cast<PyArrayObject*>(oia.ptr());
if(!PyArray_ISCONTIGUOUS(ia)) {
- throw std::runtime_error("expected vertex array to be contiguous");
+ throw Error("expected vertex array to be contiguous");
}
if(!PyArray_TYPE(ia)==NPY_UINT) {
- throw std::runtime_error("expected vertex array to be of dtype=uint32");
+ throw Error("expected vertex array to be of dtype=uint32");
}
size_t i_size=PyArray_SIZE(ia);
unsigned int* ip=reinterpret_cast<unsigned int*>(PyArray_DATA(ia));
p.AddMesh(vp,np,cp,v_count,ip,i_size/3);
#else
- throw std::runtime_error("AddMesh requires compiled-in numpy support");
+ throw Error("AddMesh requires compiled-in numpy support");
#endif
}
}
diff --git a/modules/img/alg/src/histogram.hh b/modules/img/alg/src/histogram.hh
index e6a22592acb24e4dea120b8ca6a20fa286ea4184..820744d31b01ace41437c9d0293a24f086291dfa 100644
--- a/modules/img/alg/src/histogram.hh
+++ b/modules/img/alg/src/histogram.hh
@@ -35,8 +35,7 @@ namespace ost { namespace img { namespace alg {
class DLLEXPORT HistogramError: public Error {
public:
- virtual ~HistogramError() throw() {} // required for typeinfo visibility
- HistogramError(const String& s):
+ HistogramError(const String& s):
Error(String("A histogram error occured: ") + s)
{}
};
diff --git a/modules/img/alg/tests/test_histogram.cc b/modules/img/alg/tests/test_histogram.cc
index 98f323a21c927ec4da09da9dd935699f20bb2042..c5382ce88745c390ebd3a988feeeb4b8b076f202 100644
--- a/modules/img/alg/tests/test_histogram.cc
+++ b/modules/img/alg/tests/test_histogram.cc
@@ -61,6 +61,13 @@ void test()
msg << " expected bins[" << k << "] == 1 but got " << bins[k];
BOOST_CHECK_MESSAGE(bins[k]==1,msg.str());
}
+ try {
+ BOOST_CHECK_THROW(Histogram(1,0.0,1.0),HistogramError);
+ }catch(...){
+ BOOST_ERROR( "Failed to catch HisotgramException." );
+ }
+
+
}
} // namespace
diff --git a/modules/img/base/pymod/export_image_handle.cc b/modules/img/base/pymod/export_image_handle.cc
index ff8197f311a635ea748e9ab034b9c1c43f141fd5..24aace26cb7b1a4d4945296e592c6ee3cd27d8f5 100644
--- a/modules/img/base/pymod/export_image_handle.cc
+++ b/modules/img/base/pymod/export_image_handle.cc
@@ -25,6 +25,7 @@
#include <boost/python.hpp>
using namespace boost::python;
+#include <ost/message.hh>
#include <ost/img/algorithm.hh>
#include <ost/img/image.hh>
#include <ost/img/function.hh>
@@ -94,7 +95,7 @@ img::Point tuple_to_point(size_t dim, tuple t)
{
size_t tuple_len=len(t);
if (tuple_len!=dim) {
- throw std::runtime_error("length of tuple and image dimension must match");
+ throw ost::Error("length of tuple and image dimension must match");
}
img::Point p;
for (size_t i=0; i<tuple_len; ++i) {
@@ -120,7 +121,7 @@ object ih_get_item_a(ConstImageHandle ih, tuple t)
object ih_get_item_c(ConstImageHandle ih, int x)
{
if (ih.GetSize().GetDim()!=1) {
- throw std::runtime_error("Can't address point of multi-dimensional image with scalar");
+ throw ost::Error("Can't address point of multi-dimensional image with scalar");
}
return ih_get_item(ih, img::Point(x, 0, 0));
}
@@ -152,7 +153,7 @@ void ih_set_item_b(ImageHandle ih, img::Point p, object value)
void ih_set_item_c(ImageHandle ih, int x, object value)
{
if (ih.GetSize().GetDim()!=1) {
- throw std::runtime_error("Can't address point of multi-dimensional image with scalar");
+ throw ost::Error("Can't address point of multi-dimensional image with scalar");
}
ih_set_item(ih, img::Point(x, 0, 0), value);
}
diff --git a/modules/img/base/src/point.cc b/modules/img/base/src/point.cc
index 80ac131f97ee3fb198027455c367dd16109dc4d5..3cadd17b077843974d54af42a7bce5610ccbaf52 100644
--- a/modules/img/base/src/point.cc
+++ b/modules/img/base/src/point.cc
@@ -87,7 +87,7 @@ Point::Point(const Vec4& v):
data_()
{
if(std::abs(v[3])<1e-100) {
- throw std::range_error("4th element of Vec4 is too close to zero for normalization");
+ throw geom::OutOfRangeException("4th element of Vec4 is too close to zero for normalization");
} else {
Real sf = 1.0/v[3];
data_[0]=static_cast<int>(round(v[0]*sf));
@@ -245,7 +245,7 @@ int& Point::operator[](unsigned int index)
int Point::operator[](unsigned int index) const
{
- if(index>2) throw std::range_error("Point index out of range");
+ if(index>2) throw geom::OutOfRangeException("Point index out of range");
return data_[index];
}
diff --git a/modules/img/base/src/size.cc b/modules/img/base/src/size.cc
index e8c0ed1b86f9c8f6a00e85d9fe5e2f24995c9cc1..97e1fa46001e1365d21fb3b9e2ed67d9c49f6252 100644
--- a/modules/img/base/src/size.cc
+++ b/modules/img/base/src/size.cc
@@ -108,7 +108,7 @@ unsigned int& Size::operator[](unsigned int index)
if(index==0) return w_;
else if(index==1) return h_;
else if(index==2) return d_;
- else throw std::range_error("Size index out of range");
+ else throw geom::OutOfRangeException("Size index out of range");
}
unsigned int Size::operator[](unsigned int index) const
@@ -116,7 +116,7 @@ unsigned int Size::operator[](unsigned int index) const
if(index==0) return w_;
else if(index==1) return h_;
else if(index==2) return d_;
- else throw std::range_error("Size index out of range");
+ else throw geom::OutOfRangeException("Size index out of range");
}
bool Size::operator==(const Size& s) const
diff --git a/modules/io/tests/test_mmcif_reader.cc b/modules/io/tests/test_mmcif_reader.cc
index b17b22ea8042231aab785d6bf960f3d8146e018b..eb9c852b521990d2195cabc379a82b5d4673dd31 100644
--- a/modules/io/tests/test_mmcif_reader.cc
+++ b/modules/io/tests/test_mmcif_reader.cc
@@ -338,7 +338,7 @@ BOOST_AUTO_TEST_CASE(mmcif_unknown_entity_type)
BOOST_MESSAGE(" unknown type...");
columns.pop_back();
columns.push_back(StringRef("foo", 3));
- BOOST_CHECK_THROW(tmmcif_p.ParseEntity(columns), std::runtime_error);
+ BOOST_CHECK_THROW(tmmcif_p.ParseEntity(columns), Error);
BOOST_MESSAGE(" done.");
BOOST_MESSAGE(" done.");
diff --git a/modules/mol/alg/src/construct_cbeta.cc b/modules/mol/alg/src/construct_cbeta.cc
index 19cdec41dafd5ea4e3a1369d6bd21520e464c1cf..5eaf96046ca42eb475992972b2d7b88c31742a25 100644
--- a/modules/mol/alg/src/construct_cbeta.cc
+++ b/modules/mol/alg/src/construct_cbeta.cc
@@ -1,5 +1,6 @@
#include <cmath>
+#include <ost/message.hh>
#include <ost/mol/mol.hh>
#include <ost/log.hh>
#include "construct_cbeta.hh"
@@ -83,7 +84,7 @@ geom::Vec3 CBetaPosition(const ResidueHandle& residue, Real bond_length)
std::stringstream ss;
ss << "residue " << residue.GetQualifiedName()
<< "doesn't have enough backbone atoms to reconstruct CBeta position";
- throw std::runtime_error(ss.str());
+ throw ost::Error(ss.str());
}
return CBetaPosition(n.GetPos(), ca.GetPos(), c.GetPos(), bond_length);
}
diff --git a/modules/mol/alg/src/entity_to_density.cc b/modules/mol/alg/src/entity_to_density.cc
index 6a15ac44fc68fd179f19b5f1d9405b259ecc3923..a01bd49c173f2f9c6ad2a76ac7c0465df49edfe2 100644
--- a/modules/mol/alg/src/entity_to_density.cc
+++ b/modules/mol/alg/src/entity_to_density.cc
@@ -378,9 +378,9 @@ void EntityToDensityScattering(const mol::EntityView& entity_view,
bool clear_map_flag,
Real source_wavelength)
{
- if(falloff_start<=0.0) throw std::runtime_error("Invalid falloff start");
+ if(falloff_start<=0.0) throw ost::Error("Invalid falloff start");
if(falloff_end<=0.0 || falloff_end>falloff_start)
- throw std::runtime_error("Invalid falloff end");
+ throw ost::Error("Invalid falloff end");
geom ::Vec3 rs_sampl = map.GetSpatialSampling();
geom ::Vec3 abs_orig = map.GetAbsoluteOrigin();
@@ -420,7 +420,7 @@ void EntityToDensityRosetta(const mol::EntityView& entity_view,
Real source_wavelength)
{
- if(resolution <=0.0) throw std::runtime_error("Invalid resolution");
+ if(resolution <=0.0) throw ost::Error("Invalid resolution");
if (clear_map_flag==true) {
img::MapHandle mm=img::CreateImage(img::Extent(img::Point(0,0),
map.GetSize()));
diff --git a/modules/mol/alg/src/superpose_frames.cc b/modules/mol/alg/src/superpose_frames.cc
index 85514d6d73a51ea060af6214dd9a748ca336f684..f5cbba61073416b7c47dd05393c9104f4ee0b0b2 100644
--- a/modules/mol/alg/src/superpose_frames.cc
+++ b/modules/mol/alg/src/superpose_frames.cc
@@ -21,6 +21,7 @@
#include <Eigen/Array>
#include <Eigen/SVD>
#include <Eigen/LU>
+#include <ost/message.hh>
#include <ost/mol/mol.hh>
#include <ost/mol/alg/superpose_frames.hh>
@@ -196,7 +197,7 @@ CoordGroupHandle SuperposeFrames(CoordGroupHandle& cg, EntityView& sel,
//This function superposes the frames of a CoordGroup (cg) with indices between begin and end,
//using a selection of atoms (sel), onto an EntityView (ref_view).
if (!ref_view.IsValid()){
- throw std::runtime_error("Invalid reference view");
+ throw ost::Error("Invalid reference view");
}
int real_end=end==-1 ? cg.GetFrameCount() : end;
CoordFramePtr ref_frame;
@@ -215,7 +216,7 @@ CoordGroupHandle SuperposeFrames(CoordGroupHandle& cg, EntityView& sel,
}
}
if (int(indices.size())!=ref_view.GetAtomCount()){
- throw std::runtime_error("atom counts of the two views are not equal");
+ throw ost::Error("atom counts of the two views are not equal");
}
mol::AtomHandleList alist(cg.GetEntity().GetAtomList());
std::sort(alist.begin(), alist.end(),less_index);
diff --git a/modules/mol/alg/src/svd_superpose.cc b/modules/mol/alg/src/svd_superpose.cc
index 22fa34c1d8c48a9aa370d006a3ab68a5276af091..f6b0a353d23c8ca6db39175082a745960cd570a6 100644
--- a/modules/mol/alg/src/svd_superpose.cc
+++ b/modules/mol/alg/src/svd_superpose.cc
@@ -55,7 +55,7 @@ Real CalculateRMSD(const mol::EntityView& ev1,
int counta=ev1.GetAtomCount();
int countb=ev2.GetAtomCount();
if (counta!=countb){
- throw std::runtime_error("atom counts of the two views are not equal");
+ throw Error("atom counts of the two views are not equal");
}
eht=ev1.GetHandle();
int natoms=ev1.GetAtomCount();
@@ -308,10 +308,10 @@ SuperpositionResult SuperposeAtoms(const mol::AtomViewList& atoms1,
int counta=static_cast<int>(atoms1.size());
int countb=static_cast<int>(atoms2.size());
if (counta!=countb){
- throw std::runtime_error("atom counts do not match");
+ throw Error("atom counts do not match");
}
if ((counta<3)){
- throw std::runtime_error("at least 3 atoms are required");
+ throw Error("at least 3 atoms are required");
}
SuperposerSVD sp(counta, true);
@@ -333,10 +333,10 @@ SuperpositionResult SuperposeSVD(const mol::EntityView& ev1,
int counta=ev1.GetAtomCount();
int countb=ev2.GetAtomCount();
if (counta!=countb){
- throw std::runtime_error("atom counts of the two views are not equal");
+ throw Error("atom counts of the two views are not equal");
}
if ((counta<3)){
- throw std::runtime_error("atom counts of any view must be larger or "
+ throw Error("atom counts of any view must be larger or "
"equal 3");
}
int nrows=counta;
@@ -358,10 +358,10 @@ SuperpositionResult SuperposeSVD(const std::vector<geom::Vec3>& pl1,
const std::vector<geom::Vec3>& pl2)
{
if (pl1.size()!=pl2.size()){
- throw std::runtime_error("pointlist lengths not equal");
+ throw Error("pointlist lengths not equal");
}
if ((pl1.size()<3)){
- throw std::runtime_error("three or more points required");
+ throw Error("three or more points required");
}
SuperposerSVD sp(pl1.size(), true);
SuperpositionResult res=sp.Run(pl1, pl2);
diff --git a/modules/mol/alg/src/trajectory_analysis.cc b/modules/mol/alg/src/trajectory_analysis.cc
index 5adf3c6eb1bc584522abcfec8725ebe2651fe213..a4ce2026b2248fd2ea8144c170e13b2cca46198f 100644
--- a/modules/mol/alg/src/trajectory_analysis.cc
+++ b/modules/mol/alg/src/trajectory_analysis.cc
@@ -138,7 +138,7 @@ std::vector<Real> AnalyzeRMSD(const CoordGroupHandle& traj, const EntityView& re
int count_ref=reference_view.GetAtomCount();
int count_sele=sele_view.GetAtomCount();
if (count_ref!=count_sele){
- throw std::runtime_error("atom counts of the two views are not equal");
+ throw Error("atom counts of the two views are not equal");
}
std::vector<Real> rmsd;
rmsd.reserve(ceil(traj.GetFrameCount()/float(stride)));
@@ -160,10 +160,10 @@ std::vector<Real> AnalyzeMinDistance(const CoordGroupHandle& traj, const Entity
{
CheckHandleValidity(traj);
if (view1.GetAtomCount()==0){
- throw std::runtime_error("first EntityView is empty");
+ throw Error("first EntityView is empty");
}
if (view2.GetAtomCount()==0){
- throw std::runtime_error("second EntityView is empty");
+ throw Error("second EntityView is empty");
}
std::vector<Real> dist;
dist.reserve(ceil(traj.GetFrameCount()/float(stride)));
@@ -184,10 +184,10 @@ std::vector<Real> AnalyzeMinDistanceBetwCenterOfMassAndView(const CoordGroupHand
{
CheckHandleValidity(traj);
if (view_cm.GetAtomCount()==0){
- throw std::runtime_error("first EntityView is empty");
+ throw Error("first EntityView is empty");
}
if (view_atoms.GetAtomCount()==0){
- throw std::runtime_error("second EntityView is empty");
+ throw Error("second EntityView is empty");
}
std::vector<Real> dist, masses_cm;
dist.reserve(ceil(traj.GetFrameCount()/float(stride)));
@@ -211,10 +211,10 @@ std::vector<Real> AnalyzeAromaticRingInteraction(const CoordGroupHandle& traj, c
{
CheckHandleValidity(traj);
if (view_ring1.GetAtomCount()==0){
- throw std::runtime_error("first EntityView is empty");
+ throw Error("first EntityView is empty");
}
if (view_ring2.GetAtomCount()==0){
- throw std::runtime_error("second EntityView is empty");
+ throw Error("second EntityView is empty");
}
std::vector<Real> dist, masses_ring1,masses_ring2;
dist.reserve(ceil(traj.GetFrameCount()/float(stride)));
@@ -239,7 +239,7 @@ std::vector<Real> AnalyzeAromaticRingInteraction(const CoordGroupHandle& traj, c
{
CheckHandleValidity(traj);
if (prot_seg.GetAtomCount()==0){
- throw std::runtime_error("EntityView is empty");
+ throw Error("EntityView is empty");
}
std::vector<unsigned long> indices_ca;
geom::Line3 axis;
@@ -266,7 +266,7 @@ std::vector<Real> AnalyzeAromaticRingInteraction(const CoordGroupHandle& traj, c
{
CheckHandleValidity(traj);
if (prot_seg.GetAtomCount()==0){
- throw std::runtime_error("EntityView is empty");
+ throw Error("EntityView is empty");
}
std::vector<unsigned long> indices_ca;
geom::Line3 axis;
@@ -287,7 +287,7 @@ std::vector<Real> AnalyzeAromaticRingInteraction(const CoordGroupHandle& traj, c
{
CheckHandleValidity(traj);
if (prot_seg.GetAtomCount()==0){
- throw std::runtime_error("EntityView is empty");
+ throw Error("EntityView is empty");
}
std::vector<unsigned long> indices_ca;
geom::Plane best_plane;
@@ -308,7 +308,7 @@ std::vector<Real> AnalyzeAromaticRingInteraction(const CoordGroupHandle& traj, c
{
CheckHandleValidity(traj);
if (prot_seg.GetAtomCount()==0){
- throw std::runtime_error("EntityView is empty");
+ throw Error("EntityView is empty");
}
std::vector<unsigned long> indices_c,indices_o, indices_n, indices_ca;
std::vector<Real> helicity;
@@ -329,14 +329,14 @@ std::vector<Real> AnalyzeAromaticRingInteraction(const CoordGroupHandle& traj, c
if (to==-1)to=traj.GetFrameCount();
unsigned int n_atoms=selection.GetAtomCount();
if (to<from) {
- throw std::runtime_error("to smaller than from");
+ throw Error("to smaller than from");
}
unsigned int n_frames=ceil((to-from)/stride);
if (n_atoms==0){
- throw std::runtime_error("EntityView is empty");
+ throw Error("EntityView is empty");
}
if (n_frames<=1) {
- throw std::runtime_error("number of frames is too small");
+ throw Error("number of frames is too small");
}
std::vector<unsigned long> indices;
std::vector<geom::Vec3> mean_positions;
@@ -368,14 +368,14 @@ std::vector<Real> AnalyzeAromaticRingInteraction(const CoordGroupHandle& traj, c
if (to==-1)to=traj.GetFrameCount();
unsigned int n_atoms=selection.GetAtomCount();
if (to<from) {
- throw std::runtime_error("to smaller than from");
+ throw Error("to smaller than from");
}
unsigned int n_frames=ceil((to-from)/stride);
if (n_atoms==0){
- throw std::runtime_error("EntityView is empty");
+ throw Error("EntityView is empty");
}
if (n_frames<=1) {
- throw std::runtime_error("number of frames is too small");
+ throw Error("number of frames is too small");
}
Real rmsf=0.0;
geom::Vec3 v;
diff --git a/modules/mol/base/pymod/export_editors.cc b/modules/mol/base/pymod/export_editors.cc
index 6cee09765c2ce84e7a07bbddf4d05abebdd84cf6..e53a02d35ffc39d35e826c9f34938dfd2821c4a1 100644
--- a/modules/mol/base/pymod/export_editors.cc
+++ b/modules/mol/base/pymod/export_editors.cc
@@ -82,13 +82,13 @@ void set_pos2_t(XCSEditor& e, const AtomHandleList& alist, object pyobj)
size_t acount = alist.size();
if(!PyArray_Check(pyobj.ptr())) {
- throw std::runtime_error("expected a numpy array");
+ throw Error("expected a numpy array");
return;
}
PyArrayObject* na=reinterpret_cast<PyArrayObject*>(pyobj.ptr());
if(PyArray_NDIM(na)!=2 || PyArray_DIM(na,0)!=int(acount) || PyArray_DIM(na,1)!=3) {
- throw std::runtime_error("excpected a numpy array of shape (NAtoms, 3)");
+ throw Error("excpected a numpy array of shape (NAtoms, 3)");
return;
}
@@ -106,20 +106,20 @@ void set_pos2_t(XCSEditor& e, const AtomHandleList& alist, object pyobj)
e.SetAtomTransformedPos(alist,reinterpret_cast<double*>(PyArray_DATA(na)));
}
} else {
- throw std::runtime_error("expected a numpy array of type float or double");
+ throw Error("expected a numpy array of type float or double");
return;
}
} else {
// non-contiguous
#if 0
- throw std::runtime_error("expected contiguous numpy array");
+ throw Error("expected contiguous numpy array");
#else
if(PyArray_TYPE(na)==NPY_FLOAT) {
set_pos2_nc_t<float,O>(e,alist,na);
} else if(PyArray_TYPE(na)==NPY_DOUBLE) {
set_pos2_nc_t<double,O>(e,alist,na);
} else {
- throw std::runtime_error("expected a numpy array of type float or double");
+ throw Error("expected a numpy array of type float or double");
return;
}
#endif
@@ -172,7 +172,7 @@ void set_pos(XCSEditor& e, object o1, object o2, bool trans)
}
#else
- throw std::runtime_error("SetAtom*Pos(...,ndarray) not available, because numpy support not compiled in");
+ throw Error("SetAtom*Pos(...,ndarray) not available, because numpy support not compiled in");
#endif
}
diff --git a/modules/mol/base/pymod/export_entity_property_mapper.cc b/modules/mol/base/pymod/export_entity_property_mapper.cc
index fa271bed83a04df8773f8110e773b94e5a7676e1..df008566a416b74fe97d151f76660b2ab29157e8 100644
--- a/modules/mol/base/pymod/export_entity_property_mapper.cc
+++ b/modules/mol/base/pymod/export_entity_property_mapper.cc
@@ -40,7 +40,7 @@ EntityPropertyMapper create_epm(const String& prop_name, char level)
case 'u':
return EntityPropertyMapper(prop_name, Prop::UNSPECIFIED);
default:
- throw std::runtime_error(String("unknown property level '")+level+"'");
+ throw Error(String("unknown property level '")+level+"'");
}
}
diff --git a/modules/mol/base/src/chain_type.cc b/modules/mol/base/src/chain_type.cc
index 6b3841d8909e4378db492db306efe86ece0bba44..2c6c091b9b9cb37608c8a067175ae64eb7961e4b 100644
--- a/modules/mol/base/src/chain_type.cc
+++ b/modules/mol/base/src/chain_type.cc
@@ -17,7 +17,7 @@
// 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
//------------------------------------------------------------------------------
-#include <stdexcept>
+#include <ost/message.hh>
#include "chain_type.hh"
namespace ost { namespace mol {
@@ -52,7 +52,7 @@ ChainType ChainTypeFromString(StringRef identifier)
return CHAINTYPE_UNKNOWN;
}
- throw std::runtime_error("Unrecognised chain type descriptor found: '" +
+ throw Error("Unrecognised chain type descriptor found: '" +
identifier.str() +"'!");
}
@@ -92,7 +92,7 @@ String StringFromChainType(ChainType type)
std::stringstream ss("Unknonw ChainType item found: '");
ss << type << "'!";
- throw std::runtime_error(ss.str());
+ throw Error(ss.str());
}
}} //ns
diff --git a/modules/mol/base/src/chain_type.hh b/modules/mol/base/src/chain_type.hh
index 4167280fc6a7a7b0b09376d6da0665532f2a1831..513cb1d51b3c295376d4b7094844b58967091336 100644
--- a/modules/mol/base/src/chain_type.hh
+++ b/modules/mol/base/src/chain_type.hh
@@ -47,7 +47,7 @@ typedef enum {
/// \param identifier StringRef to be translated
///
/// \return The ChainType corresponding to the input, throws a
-/// std::runtime_error on unknown type
+/// ost:Error on unknown type
ChainType DLLEXPORT_OST_MOL ChainTypeFromString(const StringRef identifier);
/// \brief Create a ChainType item for a given string
@@ -55,14 +55,14 @@ ChainType DLLEXPORT_OST_MOL ChainTypeFromString(const StringRef identifier);
/// \param identifier String to be translated
///
/// \return The ChainType corresponding to the input, throws a
-/// std::runtime_error on unknown type
+/// ost::Error on unknown type
ChainType DLLEXPORT_OST_MOL ChainTypeFromString(const String& identifier);
/// \brief Return the String identifier for a given type
///
/// \param type ChainType to be translated
///
-/// \return String corresponding to the input, throws a std::runtime_error on
+/// \return String corresponding to the input, throws a ost::Error on
/// unknown type
String DLLEXPORT_OST_MOL StringFromChainType(ChainType type);
diff --git a/modules/mol/base/src/coord_frame.cc b/modules/mol/base/src/coord_frame.cc
index 97803e242b4f057c9e02a166fd303334c0f6af72..52907d7f771aea5aa1e980cc11e6ba1546d7ae1c 100644
--- a/modules/mol/base/src/coord_frame.cc
+++ b/modules/mol/base/src/coord_frame.cc
@@ -145,7 +145,7 @@ namespace ost { namespace mol {
int count_ref=reference_view.GetAtomCount();
int count_sele=sele_view.GetAtomCount();
if (count_ref!=count_sele){
- throw std::runtime_error("atom counts of the two views are not equal");
+ throw Error("atom counts of the two views are not equal");
}
std::vector<unsigned long> indices_sele;
std::vector<geom::Vec3> ref_pos;
@@ -285,10 +285,10 @@ namespace ost { namespace mol {
dist.reserve(n_atoms-2);
dist2.reserve(n_atoms-2);
if (n_atoms!=indices_n.size()||n_atoms!=indices_c.size()||n_atoms!=indices_o.size()){
- throw std::runtime_error("not same numbers of CA, C, O and N atoms in the selection");
+ throw Error("not same numbers of CA, C, O and N atoms in the selection");
}
if (n_atoms<=5){
- throw std::runtime_error("At least five residues are needed to calulate an alpha helix similarity");
+ throw Error("At least five residues are needed to calulate an alpha helix similarity");
}
c=(*this)[indices_c[0]];
n_next=(*this)[indices_n[1]];
@@ -358,7 +358,7 @@ namespace ost { namespace mol {
indices_ca.reserve(residues.size());
//for (ResidueViewList::const_iterator res=residues.begin()+1,
// e=residues.end(); res!=e-1; ++res){
- // if (!InSequence((*res).GetHandle(),(*(res+1)).GetHandle())) throw std::runtime_error("Residues are not in a continuous sequence");
+ // if (!InSequence((*res).GetHandle(),(*(res+1)).GetHandle())) throw Error("Residues are not in a continuous sequence");
//}
for (ResidueViewList::const_iterator res=residues.begin(),
e=residues.end(); res!=e; ++res) {
@@ -378,7 +378,7 @@ namespace ost { namespace mol {
indices_o.reserve(residues.size());
for (ResidueViewList::const_iterator res=residues.begin()+1,
e=residues.end(); res!=e-1; ++res){
- if (!InSequence((*res).GetHandle(),(*(res+1)).GetHandle())) throw std::runtime_error("Residues are not in a continuous sequence");
+ if (!InSequence((*res).GetHandle(),(*(res+1)).GetHandle())) throw Error("Residues are not in a continuous sequence");
}
for (ResidueViewList::const_iterator res=residues.begin(),
e=residues.end(); res!=e; ++res) {
diff --git a/modules/mol/base/src/not_connected_error.hh b/modules/mol/base/src/not_connected_error.hh
index cce9f1b4f8b6bf6d227716b048cf0ecd0217f9a9..ac736c74e4eff141c20a3345fd05ac9e0c31e948 100644
--- a/modules/mol/base/src/not_connected_error.hh
+++ b/modules/mol/base/src/not_connected_error.hh
@@ -26,7 +26,7 @@ namespace ost { namespace mol {
/// \brief Error to indicate that two atoms that are supposed to be connected
/// are not.
-class DLLEXPORT_OST_MOL NotConnectedError : public Error {
+class DLLEXPORT NotConnectedError : public Error {
public:
NotConnectedError(AtomHandle one, AtomHandle two);
virtual ~NotConnectedError() throw() {}
diff --git a/modules/mol/base/src/property_id.hh b/modules/mol/base/src/property_id.hh
index 3632f996ac468a9891139a69a107d87aa2f8d711..981b747cfe500b8b7f41c8b294036527a29522d3 100644
--- a/modules/mol/base/src/property_id.hh
+++ b/modules/mol/base/src/property_id.hh
@@ -87,15 +87,13 @@ Prop::ID DLLEXPORT_OST_MOL PropertyIDFromString(const String& prop);
Prop DLLEXPORT_OST_MOL PropertyFromString(const String& prop);
-struct DLLEXPORT PropertyError: public std::exception
+struct DLLEXPORT PropertyError: public ost::Error
{
PropertyError(ost::mol::Prop::ID prop):
+ ost::Error("invalid property"),
prop_(prop)
{}
virtual ~PropertyError() throw() {}
- virtual const char* what() const throw() {
- return "invalid property";
- }
ost::mol::Prop::ID Prop() const
{
diff --git a/modules/mol/base/src/query_error.cc b/modules/mol/base/src/query_error.cc
index 1cdce0fe205b6ed04a0aa4d4fa3a5d42cca8f638..34bb3b83c919e7b3fcea9fd54019b908de88b27e 100644
--- a/modules/mol/base/src/query_error.cc
+++ b/modules/mol/base/src/query_error.cc
@@ -39,7 +39,7 @@ String QueryError::GetFormattedMessage() const throw() {
QueryError::QueryError(const String& query,
const QueryErrorDesc& desc) throw()
- : query_(query),desc_(desc) {
+ : ost::Error(""),query_(query),desc_(desc) {
}
QueryError::~QueryError() throw() {
diff --git a/modules/mol/base/src/query_error.hh b/modules/mol/base/src/query_error.hh
index 4d2fe8639fb8a63ba2431a8db406d98e44f03d9e..84d0164997afe8a3e4d9365ef8c75b8cef064d8b 100644
--- a/modules/mol/base/src/query_error.hh
+++ b/modules/mol/base/src/query_error.hh
@@ -19,6 +19,7 @@
#ifndef OST_QUERY_ERROR_HH
#define OST_QUERY_ERROR_HH
+#include <ost/message.hh>
#include <ost/range.hh>
#include <ost/mol/module_config.hh>
@@ -35,7 +36,7 @@ struct DLLEXPORT_OST_MOL QueryErrorDesc {
Range range;
};
-class DLLEXPORT_OST_MOL QueryError : public std::exception {
+class DLLEXPORT_OST_MOL QueryError : public ost::Error {
public:
QueryError(const String& query, const QueryErrorDesc& desc) throw();
diff --git a/modules/mol/base/tests/test_chain.cc b/modules/mol/base/tests/test_chain.cc
index e6587c2992be6486d31bb173625db9e9dbc670ac..ee4d933d0c095766079bb4278774d41d97a74ae3 100644
--- a/modules/mol/base/tests/test_chain.cc
+++ b/modules/mol/base/tests/test_chain.cc
@@ -301,7 +301,7 @@ BOOST_AUTO_TEST_CASE(chain_type)
CHAINTYPE_POLY_DN_RN);
BOOST_CHECK(ChainTypeFromString("other") == CHAINTYPE_UNKNOWN);
BOOST_CHECK_THROW(ChainTypeFromString("supposed to fail"),
- std::runtime_error);
+ Error);
// chain type -> string
BOOST_CHECK(StringFromChainType(CHAINTYPE_POLY) == "polymer");
@@ -322,7 +322,7 @@ BOOST_AUTO_TEST_CASE(chain_type)
"polydeoxyribonucleotide/polyribonucleotide hybrid");
BOOST_CHECK(StringFromChainType(CHAINTYPE_UNKNOWN) == "other");
BOOST_CHECK_THROW(StringFromChainType(CHAINTYPE_N_CHAINTYPES),
- std::runtime_error);
+ Error);
}
BOOST_AUTO_TEST_CASE(chain_description)
diff --git a/modules/mol/base/tests/test_query.cc b/modules/mol/base/tests/test_query.cc
index 52fece59d284408ef8e5e7cdc2adda6d1f48f836..9f85dbcf1a8585f584354d525ff76f261af68d79 100644
--- a/modules/mol/base/tests/test_query.cc
+++ b/modules/mol/base/tests/test_query.cc
@@ -270,15 +270,15 @@ BOOST_AUTO_TEST_CASE(test_query_throw)
EntityHandle e=make_query_test_entity();
BOOST_CHECK_NO_THROW(e.Select("gatestpropa:0=1"));
BOOST_CHECK_NO_THROW(e.Select("gatestpropa:1=1"));
- BOOST_CHECK_THROW(e.Select("gatestpropa=1"), std::exception);
+ BOOST_CHECK_THROW(e.Select("gatestpropa=1"), ost::Error);
BOOST_CHECK_NO_THROW(e.Select("grtestpropr:0=1"));
BOOST_CHECK_NO_THROW(e.Select("grtestpropr:1=1"));
- BOOST_CHECK_THROW(e.Select("grtestpropr=1"), std::exception);
+ BOOST_CHECK_THROW(e.Select("grtestpropr=1"), ost::Error);
BOOST_CHECK_NO_THROW(e.Select("gctestprop_c:0=1"));
BOOST_CHECK_NO_THROW(e.Select("gctestprop_c:1=1"));
- BOOST_CHECK_THROW(e.Select("ganotsetprop=1"), std::exception);
- BOOST_CHECK_THROW(e.Select("grnotsetprop=1"), std::exception);
- BOOST_CHECK_THROW(e.Select("gcnotsetprop=1"), std::exception);
+ BOOST_CHECK_THROW(e.Select("ganotsetprop=1"), ost::Error);
+ BOOST_CHECK_THROW(e.Select("grnotsetprop=1"), ost::Error);
+ BOOST_CHECK_THROW(e.Select("gcnotsetprop=1"), ost::Error);
BOOST_CHECK_NO_THROW(e.Select("ganotsetprop:0=1"));
BOOST_CHECK_NO_THROW(e.Select("grnotsetprop:0=1"));
BOOST_CHECK_NO_THROW(e.Select("gcnotsetprop:0=1"));
diff --git a/modules/seq/base/src/alignment_handle.cc b/modules/seq/base/src/alignment_handle.cc
index c91fa3bbc93168a82b2870d31ed4f9c3f115d537..8b8f2fc282bd50c14f1c2cce31130e59fac29e68 100644
--- a/modules/seq/base/src/alignment_handle.cc
+++ b/modules/seq/base/src/alignment_handle.cc
@@ -71,7 +71,7 @@ void AlignmentHandle::AddSequence(const ConstSequenceHandle& sequence)
}
if (impl_->GetCount()>0 &&
impl_->GetSequence(0)->GetLength()!=sequence.GetLength()) {
- throw std::runtime_error("sequence doesn't have the same length as the "
+ throw Error("sequence doesn't have the same length as the "
"alignment");
}
return impl_->AddSequence(sequence.Impl());
@@ -141,7 +141,7 @@ AlignmentHandle AlignmentFromSequenceList(const SequenceList& seq_list)
if (seq_list.IsValid() && seq_list.SequencesHaveEqualLength()) {
return AlignmentHandle(seq_list.Impl());
}
- throw std::runtime_error("sequences have different lengths");
+ throw Error("sequences have different lengths");
}
ConstSequenceList AlignmentHandle::GetSequences() const
@@ -289,7 +289,7 @@ mol::EntityViewPair AlignmentHandle::GetMatchingBackboneViews(int idx0, int idx1
const impl::SequenceImpl& s1=*impl_->GetSequence(idx0).get();
const impl::SequenceImpl& s2=*impl_->GetSequence(idx1).get();
if (!s1.HasAttachedView() || !s2.HasAttachedView()) {
- throw std::runtime_error("both sequences must have a view attached");
+ throw Error("both sequences must have a view attached");
}
mol::EntityView v1=s1.GetAttachedView().CreateEmptyView();
mol::EntityView v2=s2.GetAttachedView().CreateEmptyView();
diff --git a/modules/seq/base/tests/test_alignment.cc b/modules/seq/base/tests/test_alignment.cc
index 6b438e304e06367e76e2667643af4ece2aad6e06..a70c19b226cb46140aa1fb70b5a8518b581156bd 100644
--- a/modules/seq/base/tests/test_alignment.cc
+++ b/modules/seq/base/tests/test_alignment.cc
@@ -65,11 +65,11 @@ BOOST_AUTO_TEST_CASE(alignment_triv)
BOOST_CHECK_NO_THROW(a.AddSequence(CreateSequence("S1","-asdf-")));
BOOST_CHECK_THROW(a.AddSequence(SequenceHandle()),InvalidSequence);
BOOST_CHECK_THROW(a.AddSequence(CreateSequence("S2","-asdf-f")),
- std::runtime_error);
+ Error);
SequenceList list = CreateSequenceList();
list.AddSequence(CreateSequence("S1", "-asdf-"));
list.AddSequence(CreateSequence("S2", "fasdfas"));
- BOOST_CHECK_THROW(AlignmentFromSequenceList(list), std::runtime_error);
+ BOOST_CHECK_THROW(AlignmentFromSequenceList(list), Error);
list = CreateSequenceList();
list.AddSequence(CreateSequence("S1", "-asdf-"));
list.AddSequence(CreateSequence("S2", "fasdfa"));