#include <ncbi_pch.hpp>
#include <corelib/ncbiexec.hpp>
#include <corelib/ncbi_process.hpp>
#include <corelib/ncbi_system.hpp>
#include <corelib/ncbifile.hpp>
#include <serial/iterator.hpp>
#include <sra/readers/sra/csraread.hpp>
#include <gui/widgets/loaders/bam_indexing_panel.hpp>
#include <gui/widgets/loaders/bam_coverage_graph_panel.hpp>
#include <gui/widgets/loaders/assembly_sel_panel.hpp>
#include <gui/widgets/loaders/bam_ref_sequences_panel.hpp>
#include <gui/packages/pkg_sequence/bam_ui_data_source.hpp>
#include <gui/packages/pkg_sequence/bam_utils.hpp>
#include <gui/core/app_dialogs.hpp>
#include <gui/core/loading_app_job.hpp>
#include <gui/core/pt_data_source.hpp>
#include <gui/framework/workbench.hpp>
#include <gui/framework/app_task_service.hpp>
#include <gui/framework/app_job_task.hpp>
#include <gui/widgets/wx/wx_utils.hpp>
#include <gui/widgets/wx/fileartprov.hpp>
#include <gui/widgets/wx/ui_command.hpp>
#include <gui/widgets/wx/message_box.hpp>
#include <gui/objutils/registry.hpp>
#include <gui/objutils/label.hpp>
#include <gui/objutils/gencoll_svc.hpp>
#include <gui/objutils/id_mapper_num_assembly.hpp>
#include <gui/objutils/utils.hpp>
#include <gui/utils/extension_impl.hpp>
#include <wx/menu.h>
#include <objmgr/object_manager.hpp>
#include <objects/general/Object_id.hpp>
#include <objects/seq/Seq_annot.hpp>
#include <objects/seq/Annot_descr.hpp>
#include <objects/seq/Annotdesc.hpp>
#include <objects/seqloc/Seq_id.hpp>
#include <objects/seqres/Seq_graph.hpp>
#include <objects/gbproj/LoaderDescriptor.hpp>
#include <serial/objistr.hpp>
#include <serial/objostr.hpp>
#include <serial/serial.hpp>
#include <sra/data_loaders/bam/bamloader.hpp>
#include <sra/readers/bam/bamgraph.hpp>
#include <sra/readers/bam/bamread.hpp>
#include <sra/readers/ncbi_traces_path.hpp>
#include <objtools/readers/idmapper.hpp>
#include <sra/data_loaders/csra/csraloader.hpp>
#include <util/format_guess.hpp>
#include <sstream>
#include <mutex>
#include <util/thread_pool.hpp>

Include dependency graph for bam_ui_data_source.cpp:

Go to the SVN repository for this file.

Classes
class	CBamLoadingJob
	CBamLoadingJob. More...

struct	CBamLoadingJob::SBamFile

class	CBamDSEvtHandler
	CBamDSEvtHandler - wxEvtHandler-derived adapter for Bam data source. More...

Functions
	USING_SCOPE (objects)

static CRef< CSeq_id >	s_GetRefSeq_id (const string &id_str)

	END_EVENT_TABLE ()

string	s_QuotedPath (const string &path)

string	s_GetTempSortedBamFile (const string &sorted_file, int file_i)

string	s_GetTempSortedBamFileNew (const string &sorted_file, int file_i)

string	s_GetAnnotName (const CSeq_annot &annot)

CRef< CSeq_annot >	s_LoadSeqAnnot (const string &file, const string &annot_name)

Variables
static const char *	kLoaderDataType_File = "BAM file"

static const char *	kLoaderDataType_SRZ = "BAM SRZ"

static const char *	kLoaderDataType_SRA = "SRA ACC"

static const char *	kLoaderDataType_CSra_File = "CSRA file"

static const char *	kBamLoadOption = "BAM/CSRA files"

static const char *	kBamPath = "path"

static const char *	kBamFile = "files"

static const char *	kCSraFile = "file"

static const char *	kBamIndexFile = "index"

static const char *	kTargetAssm = "context"

static const char *	kSrzAccession = "SRZ"

static const char *	kSraAccession = "SRA"

static const int	kLoaderPriority = 90

static const char *	kBAM_DS_Icon = "icon::bam_data_source"
	CBamUIDataSource. More...

static const char *	kAppExpCmdExtPoint = "project_tree_view::context_menu::item_cmd_contributor"

static const char *	kBamInputTag = "BamInput2"

static const char *	kBamInputListTag = "BamInputList"

static const char *	kSamtoolsPathTag = "SamtoolsPath"

static const char *	kProjectParamsTag = "ProjectParams"