create_gene_model_tool_manager.cpp File Reference

#include <ncbi_pch.hpp>
#include <gui/packages/pkg_alignment/create_gene_model_tool_manager.hpp>
#include <gui/widgets/wx/message_box.hpp>
#include <gui/widgets/loaders/job_results_dlg.hpp>
#include <gui/core/document.hpp>
#include <gui/core/prefetch_seq_descr.hpp>
#include <gui/objutils/cmd_composite.hpp>
#include <gui/objutils/cmd_add_seq_annot.hpp>
#include <gui/objutils/cmd_change_seq_feat.hpp>
#include <gui/objutils/cmd_del_seq_feat.hpp>
#include <gui/objutils/label.hpp>
#include <objects/gbproj/ProjectItem.hpp>
#include <algo/sequence/align_group.hpp>
#include <objects/seq/Annot_descr.hpp>
#include <objects/seq/Annotdesc.hpp>
#include <objects/seqalign/Seq_align.hpp>
#include <algo/sequence/gene_model.hpp>
#include <objmgr/object_manager.hpp>
#include <objmgr/util/sequence.hpp>
#include <objects/general/Dbtag.hpp>
#include <objects/seqfeat/Feat_id.hpp>
#include <objects/misc/sequence_macros.hpp>

Include dependency graph for create_gene_model_tool_manager.cpp:

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Functions
	USING_SCOPE (objects)
static string	s_RetrieveMessage (const string &msg)
static CConstRef< CSeq_feat >	s_GetCDSformRNA (const CSeq_feat &mrna, CScope &scope)

Function Documentation

s_GetCDSformRNA()

static CConstRef<CSeq_feat> s_GetCDSformRNA ( const CSeq_feat &  mrna, CScope &  scope  )

static

Definition at line 767 of file create_gene_model_tool_manager.cpp.

References eOverlap_CheckIntervals, CSeqFeatData::eSubtype_cdregion, FOR_EACH_SEQFEATXREF_ON_SEQFEAT, GetBestOverlappingFeat(), CScope::GetBioseqHandle(), CTSE_Handle::GetFeatureWithId(), CSeq_feat_Base::GetLocation(), CSeq_feat_Handle::GetSeq_feat(), CBioseq_Handle::GetTSE_Handle(), and CSeq_feat_Base::IsSetXref().

Referenced by CCreateGeneModelTask::x_AssignIDsAndUpdateGenes().

s_RetrieveMessage()

static string s_RetrieveMessage ( const string &  msg )

static

Definition at line 317 of file create_gene_model_tool_manager.cpp.

References NStr::fSS_punct, NStr::fSS_Reject, isalpha(), NStr::IsBlank(), islower(), NStr::Sanitize(), NStr::StartsWith(), and Upcase().

Referenced by CCreateGeneModelTask::x_GetCommand().

USING_SCOPE()

USING_SCOPE

(

objects

)