Something went wrong on our end
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Studer Gabriel authored
Compilation was broken for years when IMG has been disabled. IMG is now always built.
Studer Gabriel authoredCompilation was broken for years when IMG has been disabled. IMG is now always built.
io_manager.cc 12.49 KiB
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
// Copyright (C) 2008-2020 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
//------------------------------------------------------------------------------
#include <ost/io/io_manager.hh>
#include <ost/io/mol/entity_io_pdb_handler.hh>
#include <ost/io/mol/entity_io_crd_handler.hh>
#include <ost/io/mol/entity_io_sdf_handler.hh>
#include <ost/io/mol/entity_io_mae_handler.hh>
#include <ost/io/mol/entity_io_mmcif_handler.hh>
#include <ost/io/seq/fasta_io_handler.hh>
#include <ost/io/seq/pir_io_handler.hh>
#include <ost/io/seq/promod_io_handler.hh>
#include <ost/io/seq/hhm_io_handler.hh>
#include <ost/io/seq/pssm_io_handler.hh>
#include <ost/io/mol/surface_io_msms_handler.hh>
#include <ost/io/seq/clustal_io_handler.hh>
#include <ost/io/img/map_io_dx_handler.hh>
#include <ost/io/img/map_io_spi_handler.hh>
#include <ost/io/img/map_io_mrc_handler.hh>
#include <ost/io/img/map_io_dm3_handler.hh>
#include <ost/io/img/map_io_situs_handler.hh>
#include <ost/io/img/map_io_tiff_handler.hh>
#include <ost/io/img/map_io_png_handler.hh>
#include <ost/io/img/map_io_dat_handler.hh>
#include <ost/io/img/map_io_jpk_handler.hh>
#include <ost/io/img/map_io_nanoscope_handler.hh>
#include <ost/io/img/map_io_df3_handler.hh>
#include <ost/io/img/map_io_ipl_handler.hh>
namespace ost { namespace io {
IOManager::IOManager()
{
RegisterFactory(EntityIOHandlerFactoryBaseP(new EntityIOMMCIFHandlerFactory));
RegisterFactory(EntityIOHandlerFactoryBaseP(new EntityIOPDBHandlerFactory));
RegisterFactory(EntityIOHandlerFactoryBaseP(new EntityIOCRDHandlerFactory));
RegisterFactory(EntityIOHandlerFactoryBaseP(new EntityIOSDFHandlerFactory));
RegisterFactory(EntityIOHandlerFactoryBaseP(new EntityIOMAEHandlerFactory));
RegisterFactory(SequenceIOHandlerFactoryBasePtr(new FastaIOHandlerFactory));
RegisterFactory(SequenceIOHandlerFactoryBasePtr(new PirIOHandlerFactory));
RegisterFactory(SequenceIOHandlerFactoryBasePtr(new ClustalIOHandlerFactory));
RegisterFactory(SequenceIOHandlerFactoryBasePtr(new PromodIOHandlerFactory));
RegisterFactory(ProfileIOHandlerFactoryBasePtr(new HhmIOHandlerFactory));
RegisterFactory(ProfileIOHandlerFactoryBasePtr(new PssmIOHandlerFactory));
RegisterFactory(SurfaceIOHandlerFactoryBasePtr(new SurfaceIOMSMSHandlerFactory));
RegisterFactory(MapIOHandlerFactoryBasePtr(new MapIODxHandlerFactory));
RegisterFactory(MapIOHandlerFactoryBasePtr(new MapIOSpiHandlerFactory));
RegisterFactory(MapIOHandlerFactoryBasePtr(new MapIOSitusHandlerFactory));
RegisterFactory(MapIOHandlerFactoryBasePtr(new MapIOMrcHandlerFactory));
RegisterFactory(MapIOHandlerFactoryBasePtr(new MapIODm3HandlerFactory));
RegisterFactory(MapIOHandlerFactoryBasePtr(new MapIOTiffHandlerFactory));
RegisterFactory(MapIOHandlerFactoryBasePtr(new MapIOPngHandlerFactory));
RegisterFactory(MapIOHandlerFactoryBasePtr(new MapIOJpkHandlerFactory));
RegisterFactory(MapIOHandlerFactoryBasePtr(new MapIODatHandlerFactory));
RegisterFactory(MapIOHandlerFactoryBasePtr(new MapIONanoscopeHandlerFactory)); RegisterFactory(MapIOHandlerFactoryBasePtr(new MapIODF3HandlerFactory));
RegisterFactory(MapIOHandlerFactoryBasePtr(new MapIOIPLHandlerFactory));
}
IOManager& IOManager::Instance()
{
static IOManager iom;
return iom;
}
EntityIOHandlerP IOManager::FindEntityImportHandler(const String& filename,
const String& format)
{
for(EntityIOHFList::const_iterator it=entity_iohf_list_.begin();
it!=entity_iohf_list_.end();++it) {
if( (*it)->ProvidesImport(filename,format)) {
return (*it)->Create();
}
}
throw IOUnknownFormatException("no suitable entity io handler found for "+filename);
}
EntityIOHandlerP IOManager::FindEntityExportHandler(const String& filename,
const String& format)
{
for (EntityIOHFList::const_iterator it=entity_iohf_list_.begin();
it!=entity_iohf_list_.end();++it) {
if ((*it)->ProvidesExport(filename, format)) {
return (*it)->Create();
}
}
throw IOUnknownFormatException("no suitable handler found for "+filename);
}
SequenceIOHandlerPtr IOManager::FindAlignmentImportHandler(const String& filename,
const String& format) {
for(AlignmentIOFList::const_iterator it=alignment_io_list_.begin();
it!=alignment_io_list_.end();++it) {
if( (*it)->ProvidesImport(filename,format)) {
return (*it)->Create();
}
}
throw IOUnknownFormatException("no suitable alignment io handler found for "+filename);
}
SequenceIOHandlerPtr IOManager::FindAlignmentExportHandler(const String& filename,
const String& format)
{
for(AlignmentIOFList::const_iterator it=alignment_io_list_.begin();
it!=alignment_io_list_.end();++it) {
if( (*it)->ProvidesExport(filename,format)) {
return (*it)->Create();
}
}
throw IOUnknownFormatException("no suitable alignment io handler found for "+filename);
}
ProfileIOHandlerPtr IOManager::FindProfileImportHandler(const String& filename,
const String& format) {
for(ProfileIOFList::const_iterator it=profile_io_list_.begin();
it!=profile_io_list_.end();++it) {
if( (*it)->ProvidesImport(filename,format)) {
return (*it)->Create();
}
}
throw IOUnknownFormatException("no suitable profile io handler found for "+filename);
}
ProfileIOHandlerPtr IOManager::FindProfileExportHandler(const String& filename, const String& format)
{
for(ProfileIOFList::const_iterator it=profile_io_list_.begin();
it!=profile_io_list_.end();++it) {
if( (*it)->ProvidesExport(filename,format)) {
return (*it)->Create();
}
}
throw IOUnknownFormatException("no suitable profile io handler found for "+filename);
}
SurfaceIOHandlerPtr IOManager::FindSurfaceImportHandler(const String& filename,
const String& format)
{
for(SurfaceIOFList::const_iterator it=surface_io_list_.begin();
it!=surface_io_list_.end();++it) {
if( (*it)->ProvidesImport(filename,format)) {
return (*it)->Create();
}
}
throw IOUnknownFormatException("no suitable surface io handler found for "+filename);
}
MapIOHandlerPtr IOManager::FindMapImportHandlerFile(const boost::filesystem::path& loc,
const ImageFormatBase& formatstruct)
{
if(formatstruct.GetFormatString()!="undefined" ){
for(MapIOFList::const_iterator it=map_io_list_.begin(); it!=map_io_list_.end();++it) {
if((*it)->ProvidesImport() && (*it)->MatchType(formatstruct)) {
return (*it)->Create();
}
}
throw IOUnknownFormatException("Unsupported type in FindMapImportHandle.");
}else{
String match_suf_string=loc.string();
std::transform(match_suf_string.begin(),match_suf_string.end(),match_suf_string.begin(),tolower);
for(MapIOFList::const_iterator it=map_io_list_.begin(); it!=map_io_list_.end();++it) {
if((*it)->ProvidesImport() && (*it)->MatchSuffix(match_suf_string)) {
return (*it)->Create();
}
}
unsigned char header[256];
boost::filesystem::ifstream infile(loc, std::ios::binary);
if(!infile)
{
throw IOException("could not open "+loc.string());
}
infile.read(reinterpret_cast<char*>(&header),256);
infile.close();
for(MapIOFList::const_iterator it=map_io_list_.begin(); it!=map_io_list_.end();++it) {
if((*it)->ProvidesImport() && (*it)->MatchContent(header)) {
return (*it)->Create();
}
}
throw IOUnknownFormatException("No file suffix given for " + loc.string()+", and could not detect automatically, please indicate file type.");
}
return MapIOHandlerPtr(); // removes warning
}
MapIOHandlerPtr IOManager::FindMapImportHandlerStream(std::istream& stream,
const ImageFormatBase& formatstruct)
{
if(formatstruct.GetFormatString()!="undefined" ){
for(MapIOFList::const_iterator it=map_io_list_.begin(); it!=map_io_list_.end();++it) {
if((*it)->ProvidesImport() && (*it)->MatchType(formatstruct)) {
return (*it)->Create();;
}
} throw IOUnknownFormatException("Unsuspported type in FindMapImportHandle.");
}else{
unsigned char header[256];
stream.read(reinterpret_cast<char*>(&header),256);
stream.seekg(0,std::ios::beg);
for(MapIOFList::const_iterator it=map_io_list_.begin(); it!=map_io_list_.end();++it) {
if((*it)->ProvidesImport() && (*it)->MatchContent(header)) {
return (*it)->Create();;
}
}
throw IOUnknownFormatException("No type given for stream, and could not detect automatically, please indicate file type.");
}
return MapIOHandlerPtr(); //removes warning
}
MapIOHandlerPtr IOManager::FindMapExportHandlerFile(const boost::filesystem::path& loc,
const ImageFormatBase& formatstruct)
{
if(formatstruct.GetFormatString()!="undefined" ){
for(MapIOFList::const_iterator it=map_io_list_.begin(); it!=map_io_list_.end();++it) {
if((*it)->ProvidesExport() && (*it)->MatchType(formatstruct)) {
return (*it)->Create();
}
}
throw IOUnknownFormatException("Unsupported type in FindMapExportHandle.");
}else{
String filename=loc.string();
String::size_type pos = filename.rfind(".");
if (pos == String::npos){
throw IOUnknownFormatException("No file suffix given for " + filename+", please indicate file type.");
}
String match_suf_string=loc.string();
std::transform(match_suf_string.begin(),match_suf_string.end(),match_suf_string.begin(),tolower);
for(MapIOFList::const_iterator it=map_io_list_.begin(); it!=map_io_list_.end();++it) {
if((*it)->ProvidesExport() && (*it)->MatchSuffix(match_suf_string)) {
return(*it)->Create();
}
}
throw IOUnknownFormatException("could not find io-plugin for " + filename);
}
return MapIOHandlerPtr(); // removes the warning
}
MapIOHandlerPtr IOManager::FindMapExportHandlerStream(std::istream& stream, const ImageFormatBase& formatstruct)
{
if(formatstruct.GetFormatString()!="undefined" ){
for(MapIOFList::const_iterator it=map_io_list_.begin(); it!=map_io_list_.end();++it) {
if((*it)->ProvidesExport() && (*it)->MatchType(formatstruct)) {
return (*it)->Create();
}
}
throw IOUnknownFormatException("Unsupported type in FindMapExportHandlerStream");
} else {
throw IOUnknownFormatException("No type given. Please indicate stream type");
}
return MapIOHandlerPtr(); // removes the warning
}
void IOManager::RegisterFactory(const MapIOHandlerFactoryBasePtr& f)
{
map_io_list_.push_back(f);
}
const MapIOFList& IOManager::GetAvailableMapHandler() const
{
return map_io_list_;
}
void IOManager::RegisterFactory(const EntityIOHandlerFactoryBaseP& f)
{
entity_iohf_list_.push_back(f);
}
void IOManager::RegisterFactory(const SequenceIOHandlerFactoryBasePtr& f)
{
alignment_io_list_.push_back(f);
}
void IOManager::RegisterFactory(const ProfileIOHandlerFactoryBasePtr& f)
{
profile_io_list_.push_back(f);
}
void IOManager::RegisterFactory(const SurfaceIOHandlerFactoryBasePtr& f)
{
surface_io_list_.push_back(f);
}
const EntityIOHFList& IOManager::GetAvailableEntityHandler() const
{
return entity_iohf_list_;
}
const AlignmentIOFList& IOManager::GetAvailableAlignmentHandler() const
{
return alignment_io_list_;
}
const ProfileIOFList& IOManager::GetAvailableProfileHandler() const
{
return profile_io_list_;
}
const SurfaceIOFList& IOManager::GetAvailableSurfaceHandler() const
{
return surface_io_list_;
}
}} // ns