NCBI C++ ToolKit
Classes | Functions | Variables
bam_ui_data_source.cpp File Reference
#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:

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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_ids_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_annots_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"
 

Function Documentation

◆ END_EVENT_TABLE()

END_EVENT_TABLE ( )

◆ s_GetAnnotName()

string s_GetAnnotName ( const CSeq_annot annot)

◆ s_GetRefSeq_id()

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

◆ s_GetTempSortedBamFile()

string s_GetTempSortedBamFile ( const string sorted_file,
int  file_i 
)

Definition at line 1045 of file bam_ui_data_source.cpp.

References NStr::IntToString().

Referenced by CBamLoadingJob::x_CreateDataLoader().

◆ s_GetTempSortedBamFileNew()

string s_GetTempSortedBamFileNew ( const string sorted_file,
int  file_i 
)

Definition at line 1054 of file bam_ui_data_source.cpp.

References NStr::IntToString().

Referenced by CBamLoadingJob::x_CreateDataLoader().

◆ s_LoadSeqAnnot()

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

◆ s_QuotedPath()

string s_QuotedPath ( const string path)
inline

Definition at line 1035 of file bam_ui_data_source.cpp.

Referenced by CBamLoadingJob::x_CreateDataLoader().

◆ USING_SCOPE()

USING_SCOPE ( objects  )

Variable Documentation

◆ kAppExpCmdExtPoint

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

Definition at line 313 of file bam_ui_data_source.cpp.

Referenced by CBamUIDataSource::Close(), and CBamUIDataSource::Open().

◆ kBAM_DS_Icon

const char* kBAM_DS_Icon = "icon::bam_data_source"
static

◆ kBamFile

const char* kBamFile = "files"
static

◆ kBamIndexFile

const char* kBamIndexFile = "index"
static

◆ kBamInputListTag

const char* kBamInputListTag = "BamInputList"
static

◆ kBamInputTag

const char* kBamInputTag = "BamInput2"
static

Definition at line 882 of file bam_ui_data_source.cpp.

Referenced by CBamUILoadManager::LoadSettings().

◆ kBamLoadOption

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

Definition at line 107 of file bam_ui_data_source.cpp.

Referenced by CBamDSEvtHandler::OnLoadBamFile().

◆ kBamPath

const char* kBamPath = "path"
static

◆ kCSraFile

const char* kCSraFile = "file"
static

◆ kLoaderDataType_CSra_File

const char* kLoaderDataType_CSra_File = "CSRA file"
static

◆ kLoaderDataType_File

const char* kLoaderDataType_File = "BAM file"
static

◆ kLoaderDataType_SRA

const char* kLoaderDataType_SRA = "SRA ACC"
static

◆ kLoaderDataType_SRZ

const char* kLoaderDataType_SRZ = "BAM SRZ"
static

◆ kLoaderPriority

const int kLoaderPriority = 90
static

◆ kProjectParamsTag

const char* kProjectParamsTag = "ProjectParams"
static

◆ kSamtoolsPathTag

const char* kSamtoolsPathTag = "SamtoolsPath"
static

◆ kSraAccession

const char* kSraAccession = "SRA"
static

◆ kSrzAccession

const char* kSrzAccession = "SRZ"
static

◆ kTargetAssm

const char* kTargetAssm = "context"
static
Modified on Tue Jun 25 13:31:55 2024 by modify_doxy.py rev. 669887