#include <ncbi_pch.hpp>#include <objects/submit/Submit_block.hpp>#include <objects/seq/Pubdesc.hpp>#include <objects/pub/Pub.hpp>#include <objects/pub/Pub_equiv.hpp>#include <gui/utils/event_handler.hpp>#include <gui/utils/app_popup.hpp>#include <gui/objutils/cmd_create_desc.hpp>#include <gui/objutils/descriptor_change.hpp>#include <gui/packages/pkg_sequence_edit/subprep_util.hpp>#include <gui/packages/pkg_sequence_edit/subprepintropanel.hpp>#include <gui/packages/pkg_sequence_edit/submitblockdlg.hpp>#include <gui/widgets/wx/async_call.hpp>#include "subprep_event.hpp"#include <wx/msgdlg.h>
Include dependency graph for subprepintropanel.cpp:
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Functions | |
| static void | s_ShowStar (wxStaticText *star, bool show) |
Variables | |
| static const wxString | s_VectorScreenText |
| static const wxString | s_UnculturedSamplesIntroText |
| static const wxString | s_VirusesIntroText |
| static const wxString | s_rRNA_ITS_IGSIntroText |
| static const wxString | s_TSAIntroText |
| static const wxString | s_IGSIntroText |
| static const wxString | s_MicrosatelliteIntroText |
| static const wxString | s_DLoopIntroText |
| static const wxString | s_WGSIntroText |
| static const wxString | s_DefaultIntroText |
| static const string | kSubmitterInfoComplete = "All required fields present" |
Function Documentation
◆ s_ShowStar()
Definition at line 429 of file subprepintropanel.cpp.
References wxT.
Referenced by CSubPrepIntroPanel::OnSubmissionTypeSelected(), CSubPrepIntroPanel::RefreshSubmitterInfoStatus(), and CSubPrepIntroPanel::SetWizardTypeCtrl().
Variable Documentation
◆ kSubmitterInfoComplete
Definition at line 454 of file subprepintropanel.cpp.
Referenced by CSubPrepIntroPanel::IsComplete(), and CSubPrepIntroPanel::RefreshSubmitterInfoStatus().
◆ s_DefaultIntroText
|
static |
Initial value:
=
"\
Welcome to the Standard Submission Preparation Tool!\r\n\
\r\n\
The Standard Submission preparation tool may be used for any type of nucleotide sequence data except EST (expressed sequence tags), GSS (genome survey sequences), and STS (sequence tagged sites) submissions. Do not use this tool for EST, GSS, or STS submissions.\r\n\
\r\n\
Please review the GenBank data policies before proceeding:\r\n\
https://www.ncbi.nlm.nih.gov/genbank/submit_types \r\n\
\r\n\
"
Definition at line 398 of file subprepintropanel.cpp.
Referenced by CSubPrepIntroPanel::x_SetIntroText().
◆ s_DLoopIntroText
|
static |
Initial value:
=
"\
Welcome to the D-loop & Control Region Wizard!\r\n\
\r\n\
Use this tool for submitting D-loop or Control Region sequences.\r\n\
\r\n\
Requirements:\r\n\
- FASTA formatted nucleotide sequence text file\r\n\
- Organism names\r\n\
- Unique source information (such as isolate, haplotype, or specimen- voucher)\r\n\
\r\n\
"
Definition at line 367 of file subprepintropanel.cpp.
Referenced by CSubPrepIntroPanel::x_SetIntroText().
◆ s_IGSIntroText
|
static |
Initial value:
=
"\
Welcome to the Intergenic Spacer Submission Wizard!\r\n\
\r\n\
Use this tool for submitting intergenic spacer sequences.\r\n\
Do not use this tool for submitting complete genomes.\r\n\
\r\n\
Do not use this wizard if you are submitting rRNA-IGS sequences.\r\n\
If you are submitting rRNA-IGS sequences select the rRNA/ITS/IGS wizard instead.\r\n\
\r\n\
Requirements:\r\n\
- FASTA formatted nucleotide sequence text file or alignment file\r\n\
- Organism names\r\n\
- Unique Source information\r\n\
\r\n\
"
Definition at line 337 of file subprepintropanel.cpp.
Referenced by CSubPrepIntroPanel::x_SetIntroText().
◆ s_MicrosatelliteIntroText
|
static |
Initial value:
=
"\
Welcome to the Microsatellite Wizard!\r\n\
\r\n\
Use this tool for submitting Microsatellite sequences.\r\n\
\r\n\
Requirements:\r\n\
- FASTA formatted nucleotide sequence text file\r\n\
- Organism names\r\n\
- Unique microsatellite names or clone names\r\n\
\r\n\
"
Definition at line 354 of file subprepintropanel.cpp.
Referenced by CSubPrepIntroPanel::x_SetIntroText().
◆ s_rRNA_ITS_IGSIntroText
|
static |
Initial value:
=
"\
Welcome to the Cultured rRNA-ITS-IGS Submission Wizard!\r\n\
\r\n\
Use this tool for rRNA, ITS, or IGS sequences from:\r\n\
- Cultured, pure strains of Bacteria, Archaea, or Fungi\r\n\
- Vouchered Fungi\r\n\
- Plant, animal or other eukaryotic sequences\r\n\
\r\n\
This tool is NOT for uncultured samples. Use the uncultured sample wizard if you are submitting sequences from an uncultured source.\r\n\
\r\n\
Requirements:\r\n\
- FASTA formatted nucleotide sequence text file or alignment file\r\n\
- Organism names\r\n\
- Strain names for bacteria, and archaea\r\n\
- Strain or specimen-vouchers for fungi\r\n\
- Specimen vouchers or isolate codes for plants and animals\r\n\
\r\n\
Feature Annotation:\r\n\
Please use the wizard to annotate features in your sequences or annotate your submissions in the record viewer.\r\n\
If you do not provide feature annotation, assigning of Accession numbers will be delayed.\r\n\
\r\n\
"
Definition at line 294 of file subprepintropanel.cpp.
Referenced by CSubPrepIntroPanel::x_SetIntroText().
◆ s_TSAIntroText
|
static |
Initial value:
=
"\
Welcome to the TSA Submission Wizard!\r\n\
Use this tool for computationally assembled sequences from primary\r\n\
data such as ESTs, traces and Next Generation Sequencing\r\n\
Technologies. TSA sequence records differ from EST and GenBank\r\n\
records because there are no physical counterparts to the assemblies.\r\n\
\r\n\
Prior to preparing your TSA submission please make sure your\r\n\
assemblies conform to the following standards:\r\n\
\r\n\
-Screen your sequences for vector contamination and remove any\r\n\
vector sequence.\r\n\
-Remove any sequences less than 200bp in length.\r\n\
-Trim any sequences having more than 10% n's or containing greater\r\n\
than 14 n's in a row.\r\n\
\r\n\
"
Definition at line 318 of file subprepintropanel.cpp.
Referenced by CSubPrepIntroPanel::x_SetIntroText().
◆ s_UnculturedSamplesIntroText
|
static |
Initial value:
=
"\
Welcome to the Sequin Bulk DNA Sequence Submission Wizard!\r\n\
\r\n\
Use this tool if your sequences are from:\r\n\
-uncultured samples\r\n\
-the same gene region (for example: all 16S rRNA or all nifH)\r\n\
\r\n\
Requirements:\r\n\
-FASTA formatted nucleotide sequence text file or alignment file\r\n\
-Unique clone names\r\n\
-Isolation source (for example, freshwater lake at 100m depth)\r\n\
or hostname (for example, Cocos nucifera) \r\n\
\r\n\
"
Definition at line 260 of file subprepintropanel.cpp.
Referenced by CSubPrepIntroPanel::x_SetIntroText().
◆ s_VectorScreenText
|
static |
Initial value:
= "\
Vector Contamination:\r\n\
Vector contamination should be removed before submitting your sequences to GenBank.\r\n\
Click the Vector Trim Tool button below if you have not yet screened your sequences for vector.\r\n\
Please see: \r\n\
https://www.ncbi.nlm.nih.gov/Sequin/sequin.hlp.html#VectorScreen\r\n\
"
Definition at line 252 of file subprepintropanel.cpp.
Referenced by CSubPrepIntroPanel::x_SetIntroText().
◆ s_VirusesIntroText
|
static |
Initial value:
=
"\
Welcome to the Virus Sequence Submission Wizard!\r\n\
Use this tool if you are submitting:\r\n\
-virus sequences\r\n\
-viroid sequences\r\n\
\r\n\
Requirements\r\n\
-FASTA formatted nucleotide sequence text file or alignment file\r\n\
-Unique isolate/strain names\r\n\
-Country, host, collection-date, segment, genotype, and/or serotype may be required for certain viruses and is requested for all virus submissions\r\n\
\r\n\
Feature Annotation:\r\n\
Please use the assistance provided in the wizard to annotate the features your submission or annotate your submissions in the record viewer.\r\n\
If you do not provide feature annotation, assigning of Accession numbers will be delayed.\r\n\
\r\n\
"
Definition at line 276 of file subprepintropanel.cpp.
Referenced by CSubPrepIntroPanel::x_SetIntroText().
◆ s_WGSIntroText
|
static |
Initial value:
=
"\
Welcome to the WGS wizard!\r\n\
\n\
Use this tool for submitting Whole Genome Shotgun Submissions to NCBI. \r\n\
This tool is for microbial genomes without annotation. Your file should include sequences from one organism only.\r\n\
\r\n\
Prior to preparing your WGS submission, please make sure your sequences and file conform to the following standards:\r\n\
-WGS contigs should not have any Ns representing gaps. If there are gaps in your sequence, you will need to split the sequences at the gaps. \r\n\
-do not include terminal N's\r\n\
-do not include any sequences shorter than 200 nt \r\n\
-do not include sequences containing more than 10% N's or large regions of low quality sequence\r\n\
-file should not contain more than 10,000 sequences\r\n\
\n\
For more information about WGS submissions, please see: \r\n\
"
Definition at line 381 of file subprepintropanel.cpp.
