From 5090a4959ce42ced1f88d400a7a4f70b8bd5af95 Mon Sep 17 00:00:00 2001
From: Gabriel Studer <gabriel.studer@unibas.ch>
Date: Mon, 22 Aug 2022 09:57:33 +0200
Subject: [PATCH] silence deprecation warning - boost bind
Many of them remain, as they're triggered by Boost code too. Specifically
when importing boost python. Relevant Github discussion:
https://github.com/boostorg/python/issues/359
---
modules/gfx/src/gfx_node.cc | 8 ++++----
modules/gfx/src/scene.cc | 18 +++++++++---------
modules/io/src/img/map_io_jpk_handler.cc | 1 -
modules/io/src/img/map_io_tiff_handler.cc | 1 -
modules/io/src/mol/sdf_writer.cc | 5 +++--
modules/mol/alg/src/svd_superpose.cc | 2 --
modules/mol/base/src/chain_view.cc | 9 ++++-----
modules/mol/base/src/entity_view.cc | 7 +++----
modules/mol/base/src/impl/atom_impl.cc | 5 ++---
modules/mol/base/src/impl/chain_impl.cc | 7 +++----
modules/mol/base/src/impl/residue_impl.cc | 2 --
modules/mol/base/src/residue_view.cc | 9 ++++-----
modules/seq/base/src/sequence_op.cc | 2 --
13 files changed, 32 insertions(+), 44 deletions(-)
diff --git a/modules/gfx/src/gfx_node.cc b/modules/gfx/src/gfx_node.cc
index 716523f1d..3923eb735 100644
--- a/modules/gfx/src/gfx_node.cc
+++ b/modules/gfx/src/gfx_node.cc
@@ -16,7 +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 <boost/bind.hpp>
+#include <boost/bind/bind.hpp>
#include <ost/dyn_cast.hh>
#include "gfx_node.hh"
@@ -156,7 +156,7 @@ void GfxNode::Remove(GfxObjP obj)
obj->parent_.reset();
if (this->IsAttachedToScene()) {
Scene::Instance().NotifyObservers(bind(&SceneObserver::NodeRemoved,
- _1, obj));
+ boost::placeholders::_1, obj));
}
}
@@ -174,7 +174,7 @@ void GfxNode::RemoveAll()
if (!attached)
continue;
Scene::Instance().NotifyObservers(bind(&SceneObserver::NodeRemoved,
- _1, *i));
+ boost::placeholders::_1, *i));
}
node_vector_.clear();
}
@@ -211,7 +211,7 @@ void GfxNode::Remove(GfxNodeP node)
}
if (this->IsAttachedToScene()) {
Scene::Instance().NotifyObservers(bind(&SceneObserver::NodeRemoved,
- _1, node));
+ boost::placeholders::_1, node));
}
}
diff --git a/modules/gfx/src/scene.cc b/modules/gfx/src/scene.cc
index a6fbd0d68..1774cb72f 100644
--- a/modules/gfx/src/scene.cc
+++ b/modules/gfx/src/scene.cc
@@ -30,7 +30,7 @@
#include <sys/time.h>
#endif
-#include <boost/bind.hpp>
+#include <boost/bind/bind.hpp>
#include <boost/shared_array.hpp>
#include <boost/filesystem/operations.hpp>
#include <boost/filesystem/fstream.hpp>
@@ -995,7 +995,7 @@ bool Scene::IsNameAvailable(const String& name) const
void Scene::NodeAdded(const GfxNodeP& node)
{
- this->NotifyObservers(bind(&SceneObserver::NodeAdded, _1, node));
+ this->NotifyObservers(bind(&SceneObserver::NodeAdded, boost::placeholders::_1, node));
}
void Scene::ObjectChanged(const String& name)
@@ -1003,13 +1003,13 @@ void Scene::ObjectChanged(const String& name)
FindObj fn(name);
Apply(fn);
if(fn.node) {
- this->NotifyObservers(bind(&SceneObserver::NodeChanged, _1, fn.node));
+ this->NotifyObservers(bind(&SceneObserver::NodeChanged, boost::placeholders::_1, fn.node));
}
}
void Scene::NodeTransformed(const GfxObjP& object)
{
- this->NotifyObservers(bind(&SceneObserver::NodeTransformed, _1, object));
+ this->NotifyObservers(bind(&SceneObserver::NodeTransformed, boost::placeholders::_1, object));
}
void Scene::SelectionChanged(const String& name, const mol::EntityView& sel)
@@ -1017,7 +1017,7 @@ void Scene::SelectionChanged(const String& name, const mol::EntityView& sel)
FindObj fn(name);
Apply(fn);
if(fn.node) {
- this->NotifyObservers(bind(&SceneObserver::SelectionChanged, _1, fn.node, sel));
+ this->NotifyObservers(bind(&SceneObserver::SelectionChanged, boost::placeholders::_1, fn.node, sel));
}
}
@@ -1026,7 +1026,7 @@ void Scene::RenderModeChanged(const String& name)
FindObj fn(name);
Apply(fn);
if(fn.node) {
- this->NotifyObservers(bind(&SceneObserver::RenderModeChanged, _1, fn.node));
+ this->NotifyObservers(bind(&SceneObserver::RenderModeChanged, boost::placeholders::_1, fn.node));
}
}
@@ -1034,7 +1034,7 @@ void Scene::Remove(const GfxNodeP& go)
{
if(!go) return;
root_node_->Remove(go);
- this->NotifyObservers(bind(&SceneObserver::NodeRemoved, _1,go));
+ this->NotifyObservers(bind(&SceneObserver::NodeRemoved, boost::placeholders::_1,go));
}
void Scene::RemoveAll()
@@ -1050,7 +1050,7 @@ void Scene::Remove(const String& name)
if(fn.node) {
root_node_->Remove(name);
if(GfxObjP go = dyn_cast<GfxObj>(fn.node)) {
- this->NotifyObservers(bind(&SceneObserver::NodeRemoved, _1, go));
+ this->NotifyObservers(bind(&SceneObserver::NodeRemoved, boost::placeholders::_1, go));
}
}
}
@@ -1610,7 +1610,7 @@ void Scene::SetSelectionMode(uint m)
{
if (selection_mode_!=m) {
selection_mode_=m;
- this->NotifyObservers(bind(&SceneObserver::SelectionModeChanged, _1,
+ this->NotifyObservers(bind(&SceneObserver::SelectionModeChanged, boost::placeholders::_1,
selection_mode_));
}
diff --git a/modules/io/src/img/map_io_jpk_handler.cc b/modules/io/src/img/map_io_jpk_handler.cc
index 3225ef871..58922e541 100644
--- a/modules/io/src/img/map_io_jpk_handler.cc
+++ b/modules/io/src/img/map_io_jpk_handler.cc
@@ -32,7 +32,6 @@
#include <ost/io/io_exception.hh>
#include <boost/function.hpp>
-#include <boost/bind.hpp>
#include "jpk_util.hh"
#include "tiff_util.hh"
diff --git a/modules/io/src/img/map_io_tiff_handler.cc b/modules/io/src/img/map_io_tiff_handler.cc
index d88fc01d7..fbabb0cf6 100644
--- a/modules/io/src/img/map_io_tiff_handler.cc
+++ b/modules/io/src/img/map_io_tiff_handler.cc
@@ -29,7 +29,6 @@
#include <stdarg.h>
#include <boost/function.hpp>
-#include <boost/bind.hpp>
#include <ost/img/image_state.hh>
#include <ost/img/progress.hh>
diff --git a/modules/io/src/mol/sdf_writer.cc b/modules/io/src/mol/sdf_writer.cc
index ff14d0fd5..8deaf9a78 100644
--- a/modules/io/src/mol/sdf_writer.cc
+++ b/modules/io/src/mol/sdf_writer.cc
@@ -28,7 +28,7 @@
#include <ost/mol/chain_view.hh>
#include <ost/mol/bond_handle.hh>
#include <boost/regex.hpp>
-#include <boost/bind.hpp>
+#include <boost/bind/bind.hpp>
namespace ost { namespace io {
@@ -100,7 +100,8 @@ namespace {
// get all neighboring atoms and sort them according to their atom index
mol::AtomViewList atoms = atom.GetBondPartners();
std::sort(atoms.begin(), atoms.end(), bind(&SDFBondWriter::CompareAtomIdx,
- this, _1, _2));
+ this, boost::placeholders::_1,
+ boost::placeholders::_2));
// iterate all neighboring atoms and print bonds to all atoms with index
// larger than current atom index
diff --git a/modules/mol/alg/src/svd_superpose.cc b/modules/mol/alg/src/svd_superpose.cc
index 6780213cf..bbf35c24d 100644
--- a/modules/mol/alg/src/svd_superpose.cc
+++ b/modules/mol/alg/src/svd_superpose.cc
@@ -19,7 +19,6 @@
#include <stdexcept>
#include <iostream>
-#include <boost/bind.hpp>
#include <Eigen/SVD>
#include <Eigen/Geometry>
@@ -39,7 +38,6 @@
namespace ost { namespace mol { namespace alg {
-using boost::bind;
typedef Eigen::Matrix<Real,3,1> EVec3;
typedef Eigen::Matrix<Real,3,3> EMat3;
typedef Eigen::Matrix<Real,4,4> EMat4;
diff --git a/modules/mol/base/src/chain_view.cc b/modules/mol/base/src/chain_view.cc
index 96c038460..e0c5b5dce 100644
--- a/modules/mol/base/src/chain_view.cc
+++ b/modules/mol/base/src/chain_view.cc
@@ -18,7 +18,7 @@
//------------------------------------------------------------------------------
#include <algorithm>
#include <limits>
-#include <boost/bind.hpp>
+#include <boost/bind/bind.hpp>
#include <ost/log.hh>
#include <ost/mol/bond_handle.hh>
#include <ost/mol/residue_handle.hh>
@@ -31,7 +31,6 @@
#include <ost/mol/impl/chain_impl.hh>
#include <ost/mol/entity_handle.hh>
-using boost::bind;
namespace ost { namespace mol {
@@ -182,7 +181,7 @@ ResidueView ChainView::FindResidue(const ResNum& number) const {
return ResidueView();
} else {
i=std::find_if(l.begin(), l.end(),
- bind(&ResidueView::GetNumber, _1)==number);
+ bind(&ResidueView::GetNumber, boost::placeholders::_1)==number);
return i==data_->residues.end() ? ResidueView() : *i;
}
}
@@ -310,7 +309,7 @@ ResidueView ChainView::AddResidue(const ResidueView& residue_view,
void ChainView::RemoveResidues() {
this->CheckValidity();
std::for_each(data_->residues.begin(), data_->residues.end(),
- bind(&ResidueView::RemoveAtoms, _1));
+ bind(&ResidueView::RemoveAtoms, boost::placeholders::_1));
data_->residues.clear();
data_->handle_to_view.clear();
}
@@ -340,7 +339,7 @@ int ChainView::GetResidueIndex(const ResNum& number) const
i=p.first;
} else {
i=std::find_if(data_->residues.begin(), data_->residues.end(),
- bind(&ResidueView::GetNumber, _1)==number);
+ bind(&ResidueView::GetNumber, boost::placeholders::_1)==number);
}
return i==data_->residues.end() ? -1 : i-data_->residues.begin();
diff --git a/modules/mol/base/src/entity_view.cc b/modules/mol/base/src/entity_view.cc
index 26cfa75e3..c28b7aae5 100644
--- a/modules/mol/base/src/entity_view.cc
+++ b/modules/mol/base/src/entity_view.cc
@@ -22,7 +22,7 @@
*/
#include <algorithm>
-#include <boost/bind.hpp>
+#include <boost/bind/bind.hpp>
#include <boost/logic/tribool.hpp>
#include <ost/log.hh>
@@ -44,7 +44,6 @@
using boost::logic::tribool;
using boost::logic::indeterminate;
-using boost::bind;
@@ -266,7 +265,7 @@ ChainView EntityView::FindChain(const String& chain_name) const{
this->CheckValidity();
ChainViewList::const_iterator i;
i=std::find_if(data_->chains.begin(), data_->chains.end(),
- boost::bind(&ChainView::GetName, _1)==chain_name);
+ boost::bind(&ChainView::GetName, boost::placeholders::_1)==chain_name);
return (i!=data_->chains.end()) ? *i : ChainView();
}
@@ -428,7 +427,7 @@ ChainView EntityView::ViewForHandle(const ChainHandle& chain) const {
this->CheckValidity();
ChainViewList::const_iterator i;
i=std::find_if(data_->chains.begin(), data_->chains.end(),
- bind(&ChainView::GetHandle, _1)==chain);
+ bind(&ChainView::GetHandle, boost::placeholders::_1)==chain);
return (i!=data_->chains.end()) ? *i : ChainView();
}
diff --git a/modules/mol/base/src/impl/atom_impl.cc b/modules/mol/base/src/impl/atom_impl.cc
index 73d0d5e6a..9c5642eaf 100644
--- a/modules/mol/base/src/impl/atom_impl.cc
+++ b/modules/mol/base/src/impl/atom_impl.cc
@@ -29,10 +29,9 @@
#include "chain_impl.hh"
#include "torsion_impl.hh"
#include <ost/mol/entity_visitor.hh>
-#include <boost/bind.hpp>
+#include <boost/bind/bind.hpp>
#include <algorithm>
-using boost::bind;
namespace ost { namespace mol { namespace impl {
@@ -375,7 +374,7 @@ void AtomImpl::DeleteAllTorsions() {
TorsionImplList& l = (*i)->GetTorsionList();
TorsionImplList::iterator j;
j=std::remove_if(l.begin(), l.end(),
- bind(&TorsionImpl::IsAtomInvolved, _1, shared_from_this()));
+ bind(&TorsionImpl::IsAtomInvolved, boost::placeholders::_1, shared_from_this()));
l.erase(j, l.end());
}
}
diff --git a/modules/mol/base/src/impl/chain_impl.cc b/modules/mol/base/src/impl/chain_impl.cc
index d07bc6436..ca2aeaad7 100644
--- a/modules/mol/base/src/impl/chain_impl.cc
+++ b/modules/mol/base/src/impl/chain_impl.cc
@@ -23,11 +23,10 @@
#include "entity_impl.hh"
#include <ost/mol/impl/atom_impl.hh>
#include <ost/mol/entity_visitor.hh>
-#include <boost/bind.hpp>
+#include <boost/bind/bind.hpp>
#include <algorithm>
#include <numeric>
-using boost::bind;
using std::accumulate;
namespace ost { namespace mol { namespace impl {
@@ -380,7 +379,7 @@ int ChainImpl::GetIndexForResNum(const ResNum& number) const
ResidueImplList::const_iterator k;
k=std::find_if(residue_list_.begin(),
residue_list_.end(),
- bind(&ResidueImpl::GetNumber, _1)==number);
+ bind(&ResidueImpl::GetNumber, boost::placeholders::_1)==number);
if (k==residue_list_.end())
return -1;
@@ -426,7 +425,7 @@ int ChainImpl::GetIndex(const ResidueImplPtr& res) const
ResidueImplList::const_iterator k=residue_list_.begin()-1;
do {
k=std::find_if(k+1, residue_list_.end(),
- bind(&ResidueImpl::GetNumber, _1)==number);
+ bind(&ResidueImpl::GetNumber, boost::placeholders::_1)==number);
} while(k!=residue_list_.end() && (*k)!=res);
if (k==residue_list_.end())
diff --git a/modules/mol/base/src/impl/residue_impl.cc b/modules/mol/base/src/impl/residue_impl.cc
index c4ddfbe36..819c7294d 100644
--- a/modules/mol/base/src/impl/residue_impl.cc
+++ b/modules/mol/base/src/impl/residue_impl.cc
@@ -23,12 +23,10 @@
#include "residue_impl.hh"
#include "atom_impl.hh"
#include "entity_impl.hh"
-#include <boost/bind.hpp>
#include <algorithm>
#include "torsion_impl.hh"
#include <ost/mol/impl/connector_impl.hh>
-using boost::bind;
namespace ost { namespace mol { namespace impl {
diff --git a/modules/mol/base/src/residue_view.cc b/modules/mol/base/src/residue_view.cc
index ee463fe1a..db5503407 100644
--- a/modules/mol/base/src/residue_view.cc
+++ b/modules/mol/base/src/residue_view.cc
@@ -19,7 +19,7 @@
#include <algorithm>
#include <limits>
-#include <boost/bind.hpp>
+#include <boost/bind/bind.hpp>
#include <ost/log.hh>
#include <ost/mol/bond_handle.hh>
#include <ost/mol/chain_view.hh>
@@ -32,7 +32,6 @@
#include "residue_view.hh"
#include "residue_handle.hh"
-using boost::bind;
namespace ost { namespace mol {
@@ -114,7 +113,7 @@ AtomView ResidueView::FindAtom(const String& atom_name) const {
this->CheckValidity();
const AtomViewList& l=data_->atoms;
AtomViewList::const_iterator i;
- i=std::find_if(l.begin(), l.end(), boost::bind(&AtomView::GetName, _1)==atom_name);
+ i=std::find_if(l.begin(), l.end(), boost::bind(&AtomView::GetName, boost::placeholders::_1)==atom_name);
return i==data_->atoms.end() ? AtomView() : *i;
}
@@ -122,7 +121,7 @@ AtomView ResidueView::ViewForHandle(const AtomHandle& handle) const {
this->CheckValidity();
const AtomViewList& l=data_->atoms;
AtomViewList::const_iterator i;
- i=std::find_if(l.begin(), l.end(), bind(&AtomView::GetHandle, _1)==handle);
+ i=std::find_if(l.begin(), l.end(), bind(&AtomView::GetHandle, boost::placeholders::_1)==handle);
return i==data_->atoms.end() ? AtomView() : *i;
}
@@ -166,7 +165,7 @@ void ResidueView::RemoveAtoms()
{
this->CheckValidity();
std::for_each(data_->atoms.begin(), data_->atoms.end(),
- bind(&AtomView::RemoveBonds, _1));
+ bind(&AtomView::RemoveBonds, boost::placeholders::_1));
AtomViewList::iterator i;
EntityView ev=this->GetEntity();
for (i=data_->atoms.begin(); i!=data_->atoms.end(); ++i) {
diff --git a/modules/seq/base/src/sequence_op.cc b/modules/seq/base/src/sequence_op.cc
index b6a5dfda5..3bf3efaab 100644
--- a/modules/seq/base/src/sequence_op.cc
+++ b/modules/seq/base/src/sequence_op.cc
@@ -19,14 +19,12 @@
#include <sstream>
#include <numeric>
-#include <boost/bind.hpp>
#include <ost/mol/mol.hh>
#include "sequence_op.hh"
-using boost::bind;
namespace ost { namespace seq {
--
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