indexed_export.cpp
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- /*
- * ===========================================================================
- * PRODUCTION $Log: indexed_export.cpp,v $
- * PRODUCTION Revision 1000.5 2004/06/01 20:58:04 gouriano
- * PRODUCTION PRODUCTION: UPGRADED [GCC34_MSVC7] Dev-tree R1.10
- * PRODUCTION
- * ===========================================================================
- */
- /* $Id: indexed_export.cpp,v 1000.5 2004/06/01 20:58:04 gouriano Exp $
- * ===========================================================================
- *
- * PUBLIC DOMAIN NOTICE
- * National Center for Biotechnology Information
- *
- * This software/database is a "United States Government Work" under the
- * terms of the United States Copyright Act. It was written as part of
- * the author's official duties as a United States Government employee and
- * thus cannot be copyrighted. This software/database is freely available
- * to the public for use. The National Library of Medicine and the U.S.
- * Government have not placed any restriction on its use or reproduction.
- *
- * Although all reasonable efforts have been taken to ensure the accuracy
- * and reliability of the software and data, the NLM and the U.S.
- * Government do not and cannot warrant the performance or results that
- * may be obtained by using this software or data. The NLM and the U.S.
- * Government disclaim all warranties, express or implied, including
- * warranties of performance, merchantability or fitness for any particular
- * purpose.
- *
- * Please cite the author in any work or product based on this material.
- *
- * ===========================================================================
- *
- * Authors: Mike DiCuccio
- *
- * File Description:
- * CDataPlugin_IndexedExport - save a sequence and all of its referenced components
- * into a directory
- */
- #include <ncbi_pch.hpp>
- #include "indexed_export.hpp"
- #include <corelib/ncbiapp.hpp>
- #include <corelib/ncbireg.hpp>
- #include <gui/core/idocument.hpp>
- #include <gui/core/plugin_utils.hpp>
- #include <gui/core/version.hpp>
- #include <gui/plugin/PluginCommandSet.hpp>
- #include <gui/plugin/PluginInfo.hpp>
- #include <gui/plugin/PluginValueConstraint.hpp>
- #include <gui/utils/message_box.hpp>
- #include <gui/dialogs/progress/progress_dlg_ex.hpp>
- #include <objects/seqset/Seq_entry.hpp>
- #include <objmgr/util/sequence.hpp>
- #include <objmgr/bioseq_ci.hpp>
- #include <objmgr/seq_map_ci.hpp>
- #include <serial/objostrasn.hpp>
- BEGIN_NCBI_SCOPE
- USING_SCOPE(objects);
- static const string sc_text_str ("Text ASN.1");
- static const string sc_binary_str("Binary ASN.1");
- static const string sc_xml_str ("XML");
- static const string sc_fasta_str ("FastA");
- static const string sc_flat_str ("GenBank Flat-File");
- void CDataPlugin_IndexedExport::GetInfo(CPluginInfo& info)
- {
- info.Reset();
- // version info macro
- info.SetInfo(CPluginVersion::eMajor, CPluginVersion::eMinor, 0,
- string(__DATE__) + " " + string(__TIME__),
- "CDataPlugin_IndexedExport", "Indexed Directory",
- "Save this record and all its components "
- "into a directory that can be indexed", "");
- // command info
- CPluginCommandSet& cmds = info.SetCommands();
- CPluginCommand& save_args = cmds.AddDataCommand(eDataCommand_save);
- save_args.AddArgument("seqid", "Sequence", CSeq_id::GetTypeInfo());
- save_args.AddDefaultArgument("fmt", "Format", CPluginArg::eString,
- sc_binary_str);
- save_args.SetConstraint("fmt",
- (*CPluginValueConstraint::CreateSet(),
- sc_text_str,
- sc_binary_str,
- sc_xml_str,
- sc_fasta_str
- ));
- save_args.AddArgument("file", "File name", CPluginArg::eFile);
- save_args.AddArgument("alias", "Alias", CPluginArg::eString);
- }
- class CCancelButtonException : EXCEPTION_VIRTUAL_BASE public CException
- {
- public:
- // Enumerated list of document management errors
- enum EErrCode {
- eCancelPressed
- };
- // Translate the specific error code into a string representations of
- // that error code.
- virtual const char* GetErrCodeString(void) const
- {
- switch (GetErrCode()) {
- case eCancelPressed: return "eCancelPressed";
- default: return CException::GetErrCodeString();
- }
- }
- NCBI_EXCEPTION_DEFAULT(CCancelButtonException, CException);
- };
- //
- // Save()
- // Save the information in a given document into a file
- //
- void CDataPlugin_IndexedExport::Save(CPluginMessage& msg)
- {
- const CPluginCommand& args = msg.GetRequest().GetCommand();
- CPluginReply& reply = msg.SetReply();
- const IDocument& doc = *args["seqid"].GetDocument();
- const CSeq_id* id = dynamic_cast<const CSeq_id*> (&args["seqid"].AsObject());
- if ( !id ) {
- reply.SetStatus(eMessageStatus_failed);
- return;
- }
- CProgressDlgEx dlg;
- dlg.Show();
- try {
- string fmt_str = args["fmt"].AsString();
- string file_base = args["file"].AsString();
- string alias = args["alias"].AsString();
- string path;
- string base;
- string sub_path;
- {{
- CDirEntry::SplitPath(file_base, &path, &base);
- sub_path = path;
- sub_path += base + ".data";
- sub_path += CDirEntry::GetPathSeparator();
- CDir dir(sub_path);
- if ( !dir.Exists() ) {
- dir.Create();
- }
- }}
- // find out what object to serialize
- // in general, we serialize precisely what the document contains
- // the exception to this is that we dereference any seq-id
- // to its largest component (= top-level seq-entry)
- CConstRef<CSerialObject> obj
- (dynamic_cast<const CSerialObject*> (doc.GetObject()));
- if (obj.GetPointer() &&
- obj->GetThisTypeInfo() == CSeq_id::GetTypeInfo()) {
- const CSeq_id& id =
- dynamic_cast<const CSeq_id&>(*doc.GetObject());
- CBioseq_Handle handle = doc.GetScope().GetBioseqHandle(id);
- obj.Reset(&handle.GetTopLevelSeqEntry());
- }
- //
- // format handling
- //
- EFormat fmt = eFormat_text_asn;
- if (fmt_str == sc_text_str) {
- // ASN.1 text
- fmt = eFormat_text_asn;
- } else if (fmt_str == sc_binary_str) {
- // ASN.1 binary
- fmt = eFormat_binary_asn;
- } else if (fmt_str == sc_xml_str) {
- // XML
- fmt = eFormat_xml;
- } else if (fmt_str == sc_fasta_str) {
- // FastA
- fmt = eFormat_fasta;
- }
- try {
- //
- // first, save the sequence of interest
- //
- set< CConstRef<CSeq_entry> > entries;
- list< CConstRef<CSeq_entry> > entries_for_products;
- dlg.SetMessage("Saving document...");
- CScope& scope = doc.GetScope();
- CBioseq_Handle handle = scope.GetBioseqHandle(*id);
- x_Save(scope, handle.GetTopLevelSeqEntry(), fmt, file_base);
- {{
- CConstRef<CSeq_entry> ref(&handle.GetTopLevelSeqEntry());
- entries.insert(ref);
- entries_for_products.push_back(ref);
- }}
- //
- // now, we iterate all sequences referred to by this sequence
- //
- int count = 0;
- const CSeqMap& seqmap = handle.GetSeqMap();
- CSeqMap::const_iterator map_iter =
- seqmap.begin_resolved(&scope, -1, CSeqMap::fFindRef);
- for ( ; map_iter; ++map_iter) {
- if (map_iter.GetType() != CSeqMap::eSeqRef) {
- continue;
- }
- CSeq_id_Handle idh = map_iter.GetRefSeqid();
- dlg.SetMessage("Retrieving sequence: " + idh.AsString());
- LOG_POST(Info << "retrieving " << idh.AsString());
- CBioseq_Handle h = scope.GetBioseqHandle(idh);
- const CSeq_entry& entry = h.GetTopLevelSeqEntry();
- CConstRef<CSeq_entry> ref(&entry);
- if ( !entries.insert(ref).second ) {
- continue;
- }
- entries_for_products.push_back(ref);
- dlg.SetMessage("Saving sequence: " + idh.AsString());
- LOG_POST(Info << "saving " << idh.AsString());
- string file_name =
- sub_path + base + "." + NStr::IntToString(++count);
- x_Save(scope, entry, fmt, file_name);
- Fl::check();
- if ( !dlg.IsShown() ) {
- NCBI_THROW(CCancelButtonException,
- eCancelPressed, "");
- }
- }
- //
- // now, iterate all products in all seq-entries
- //
- ITERATE (list< CConstRef<CSeq_entry> >, iter, entries_for_products) {
- CTypeConstIterator<CSeq_feat> feat_iter(**iter);
- for ( ; feat_iter; ++feat_iter) {
- const CSeq_feat& feat = *feat_iter;
- if ( !feat.IsSetProduct() ) {
- continue;
- }
- string id_label;
- sequence::GetId(feat.GetProduct()).GetLabel(&id_label);
- dlg.SetMessage("Retrieving product sequence: " + id_label);
- LOG_POST(Info << "retrieving " << id_label);
- CBioseq_Handle h = scope.GetBioseqHandle(feat.GetLocation());
- const CSeq_entry& entry = h.GetTopLevelSeqEntry();
- CConstRef<CSeq_entry> ref(&entry);
- if ( !entries.insert(ref).second ) {
- continue;
- }
- entries_for_products.push_back(ref);
- dlg.SetMessage("Saving product sequence: " + id_label);
- LOG_POST(Info << "saving " << id_label);
- string file_name =
- sub_path + base + "." + NStr::IntToString(++count);
- x_Save(scope, entry, fmt, file_name);
- Fl::check();
- if ( !dlg.IsShown() ) {
- NCBI_THROW(CCancelButtonException,
- eCancelPressed, "");
- }
- }
- }
- }
- catch (CCancelButtonException&) {
- }
- //
- // configure this path to be indexed at app start-up
- //
- CNcbiApplication* app = CNcbiApplication::Instance();
- _ASSERT(app);
- CNcbiRegistry& reg = app->GetConfig();
- string section_name = "LDS";
- {{
- list<string> sections;
- reg.EnumerateSections(§ions);
- size_t count = 0;
- ITERATE (list<string>, iter, sections) {
- if (iter->find("LDS") == 0) {
- ++count;
- }
- }
- section_name += NStr::IntToString(count + 1);
- }}
- reg.Set(section_name, "Path", path, CNcbiRegistry::ePersistent);
- reg.Set(section_name, "Alias", alias, CNcbiRegistry::ePersistent);
- reply.SetStatus(eMessageStatus_success);
- }
- catch (CException& e) {
- string msg("Failed to save file:n");
- msg += e.GetMsg();
- NcbiMessageBox(msg);
- reply.SetStatus(eMessageStatus_failed);
- }
- #ifndef _DEBUG
- catch (...) {
- NcbiMessageBox("Failed to save file:nUnknown errorn");
- reply.SetStatus(eMessageStatus_failed);
- }
- #endif
- }
- void CDataPlugin_IndexedExport::x_Save(CScope& scope, const CSeq_entry& entry,
- EFormat fmt, const string& file_name)
- {
- CNcbiOfstream ostr(file_name.c_str(), ios::binary);
- switch (fmt) {
- case eFormat_text_asn:
- {{
- auto_ptr<CObjectOStream> os
- (CObjectOStream::Open(eSerial_AsnText, ostr));
- *os << entry;
- }}
- break;
- case eFormat_binary_asn:
- {{
- auto_ptr<CObjectOStream> os
- (CObjectOStream::Open(eSerial_AsnBinary, ostr));
- *os << entry;
- }}
- break;
- case eFormat_xml:
- {{
- auto_ptr<CObjectOStream> os
- (CObjectOStream::Open(eSerial_Xml, ostr));
- *os << entry;
- }}
- break;
- case eFormat_fasta:
- {{
- CFastaOstream fasta_ostr(ostr);
- CBioseq_CI bioseq_iter(scope, entry);
- for ( ; bioseq_iter; ++bioseq_iter) {
- fasta_ostr.Write(*bioseq_iter);
- }
- }}
- break;
- }
- }
- END_NCBI_SCOPE
- /*
- * ===========================================================================
- * $Log: indexed_export.cpp,v $
- * Revision 1000.5 2004/06/01 20:58:04 gouriano
- * PRODUCTION: UPGRADED [GCC34_MSVC7] Dev-tree R1.10
- *
- * Revision 1.10 2004/05/25 17:21:59 dicuccio
- * Modified class names. Fonts to 12 point
- *
- * Revision 1.9 2004/05/21 22:27:48 gorelenk
- * Added PCH ncbi_pch.hpp
- *
- * Revision 1.8 2004/03/11 17:43:41 dicuccio
- * Use new file chooser dialog
- *
- * Revision 1.7 2004/02/05 18:05:07 dicuccio
- * Added better (GUI) handling of sequence download. Added saving of products as
- * well as main sequence.
- *
- * Revision 1.6 2004/01/27 18:44:25 dicuccio
- * Added progress dialog. Added missing headers. Added parameter handling of
- * fiel to save to. CHanged directory layout of indexed structure to show master
- * record in top-level directory
- *
- * Revision 1.5 2003/12/05 13:07:54 dicuccio
- * Split management interface into a separate plugin. Fixed linker error
- * introduced with status bar
- *
- * Revision 1.4 2003/11/24 15:45:37 dicuccio
- * Renamed CVersion to CPluginVersion
- *
- * Revision 1.3 2003/11/06 20:12:15 dicuccio
- * Cleaned up handling of USING_SCOPE - removed from all headers
- *
- * Revision 1.2 2003/11/04 17:49:25 dicuccio
- * Changed calling parameters for plugins - pass CPluginMessage instead of paired
- * CPluginCommand/CPluginReply
- *
- * Revision 1.1 2003/10/07 13:41:13 dicuccio
- * Added indexed export plugin
- *
- * Revision 1.1 2003/09/16 14:06:48 dicuccio
- * Initial revision - split from CFileLoader
- *
- * ===========================================================================
- */