#include "ed4_ProteinViewer.hxx"
#include "ed4_edit_string.hxx"
#include "ed4_seq_colors.hxx"
#include "ed4_class.hxx"
#include <AP_pro_a_nucs.hxx>
#include <AP_codon_table.hxx>
#include <Translate.hxx>
#include <aw_question.hxx>
#include <aw_preset.hxx>
#include <aw_awars.hxx>
#include <aw_msg.hxx>
#include <aw_root.hxx>
#include <arbdbt.h>
#include <iostream>

Include dependency graph for ED4_ProteinViewer.cxx:

Macros
#define	FORWARD_STRAND 1

#define	COMPLEMENTARY_STRAND 2

#define	DB_FIELD_STRAND 3

#define	FORWARD_STRANDS 3

#define	COMPLEMENTARY_STRANDS 3

#define	DB_FIELD_STRANDS 1

Enumerations
enum	{ PV_MARKED = 0, PV_SELECTED, PV_CURSOR, PV_ALL }

Functions
static bool	PV_LookForNewTerminals (AW_root *root)

static void	PV_HideTerminal (ED4_orf_terminal *orfTerm)

static void	PV_UnHideTerminal (ED4_orf_terminal *orfTerm)

static void	PV_HideAllTerminals ()

static void	PV_ManageTerminalDisplay (AW_root root, ED4_orf_terminal orfTerm, long int DispMode)

static void	PV_ManageTerminals (AW_root *root)

void	PV_RefreshWindow (AW_root *root)

static GB_ERROR	PV_ComplementarySequence (char *sequence)

static void	PV_WriteTranslatedSequenceToDB (ED4_orf_terminal aaSeqTerm, const char spName)

static void	PV_SaveData (AW_window *)

static void	TranslateGeneToAminoAcidSequence (AW_root , ED4_orf_terminal seqTerm, const char *speciesName, int startPos4Translation, int translationMode)

static void	PV_PrintMissingDBentryInformation ()

static void	PV_DisplayAminoAcidNames (AW_root *root)

static void	PV_RefreshDisplay (AW_root *root)

static void	PV_RefreshProtViewDisplay (AW_window *aww)

void	PV_SequenceUpdate_CB (GB_CB_TYPE gbtype)

static void	PV_AddNewAAseqTerminals (ED4_sequence_terminal seqTerminal, ED4_species_manager speciesManager)

void	PV_AddCorrespondingOrfTerminals (ED4_species_name_terminal *spNameTerm)

void	PV_AddOrfTerminalsToLoadedSpecies ()

static void	PV_CreateAllTerminals (AW_root *root)

void	PV_CallBackFunction (AW_root *root)

static void	PV_AddCallBacks (AW_root *awr)

void	PV_CreateAwars (AW_root *root, AW_default aw_def)

AW_window *	ED4_CreateProteinViewer_window (AW_root *aw_root)

Variables
static bool	gTerminalsCreated = false

static int	PV_AA_Terminals4Species = 0

static int	gMissingTransTable = 0

static int	gMissingCodonStart = 0

static bool	gbWritingData = false

static int	giNewAlignments = 0

static AW_repeated_question *	ASKtoOverWriteData = NULp

Macro Definition Documentation

#define FORWARD_STRAND 1

Definition at line 33 of file ED4_ProteinViewer.cxx.

Referenced by PV_AddNewAAseqTerminals(), PV_ManageTerminalDisplay(), PV_WriteTranslatedSequenceToDB(), and TranslateGeneToAminoAcidSequence().

#define COMPLEMENTARY_STRAND 2

Definition at line 34 of file ED4_ProteinViewer.cxx.

Referenced by PV_AddNewAAseqTerminals(), PV_ManageTerminalDisplay(), PV_WriteTranslatedSequenceToDB(), and TranslateGeneToAminoAcidSequence().

#define DB_FIELD_STRAND 3

Definition at line 35 of file ED4_ProteinViewer.cxx.

Referenced by PV_AddNewAAseqTerminals(), PV_ManageTerminalDisplay(), PV_WriteTranslatedSequenceToDB(), and TranslateGeneToAminoAcidSequence().

#define FORWARD_STRANDS 3

Definition at line 37 of file ED4_ProteinViewer.cxx.

Referenced by PV_AddNewAAseqTerminals(), and PV_CreateAllTerminals().

#define COMPLEMENTARY_STRANDS 3

Definition at line 38 of file ED4_ProteinViewer.cxx.

Referenced by PV_AddNewAAseqTerminals(), and PV_CreateAllTerminals().

#define DB_FIELD_STRANDS 1

Definition at line 39 of file ED4_ProteinViewer.cxx.

Referenced by PV_CreateAllTerminals().

Enumeration Type Documentation

anonymous enum

Enumerator
PV_MARKED
PV_SELECTED
PV_CURSOR
PV_ALL

Definition at line 41 of file ED4_ProteinViewer.cxx.

Function Documentation

static bool PV_LookForNewTerminals ( AW_root * root )

static

Definition at line 58 of file ED4_ProteinViewer.cxx.

References arb_test::all(), AW_root::awar(), AWAR_PROTVIEW_COMPLEMENTARY_STRAND_1, AWAR_PROTVIEW_COMPLEMENTARY_STRAND_2, AWAR_PROTVIEW_COMPLEMENTARY_STRAND_3, AWAR_PROTVIEW_DEFINED_FIELDS, AWAR_PROTVIEW_FORWARD_STRAND_1, AWAR_PROTVIEW_FORWARD_STRAND_2, AWAR_PROTVIEW_FORWARD_STRAND_3, AWAR_PV_CURSOR, AWAR_PV_CURSOR_CS_1, AWAR_PV_CURSOR_CS_2, AWAR_PV_CURSOR_CS_3, AWAR_PV_CURSOR_DB, AWAR_PV_CURSOR_FS_1, AWAR_PV_CURSOR_FS_2, AWAR_PV_CURSOR_FS_3, AWAR_PV_DISPLAY_ALL, AWAR_PV_MARKED, AWAR_PV_MARKED_CS_1, AWAR_PV_MARKED_CS_2, AWAR_PV_MARKED_CS_3, AWAR_PV_MARKED_DB, AWAR_PV_MARKED_FS_1, AWAR_PV_MARKED_FS_2, AWAR_PV_MARKED_FS_3, AWAR_PV_SELECTED, AWAR_PV_SELECTED_CS_1, AWAR_PV_SELECTED_CS_2, AWAR_PV_SELECTED_CS_3, AWAR_PV_SELECTED_DB, AWAR_PV_SELECTED_FS_1, AWAR_PV_SELECTED_FS_2, AWAR_PV_SELECTED_FS_3, gTerminalsCreated, and AW_awar::read_int().

Referenced by PV_CreateAllTerminals().

static void PV_HideTerminal ( ED4_orf_terminal * orfTerm )

static

Definition at line 116 of file ED4_ProteinViewer.cxx.

References ED4_base::get_parent(), ED4_manager::hide_children(), and LEV_SEQUENCE.

Referenced by PV_HideAllTerminals(), and PV_ManageTerminalDisplay().

static void PV_UnHideTerminal ( ED4_orf_terminal * orfTerm )

static

Definition at line 121 of file ED4_ProteinViewer.cxx.

References ED4_base::get_parent(), LEV_SEQUENCE, and ED4_manager::unhide_children().

Referenced by PV_ManageTerminalDisplay().

static void PV_HideAllTerminals ( )

static

Definition at line 126 of file ED4_ProteinViewer.cxx.

References ED4_ROOT, ED4_manager::get_first_terminal(), ED4_base::get_next_terminal(), ED4_base::is_orf_terminal(), NULp, PV_HideTerminal(), and ED4_root::root_group_man.

Referenced by PV_ManageTerminals().

static void PV_ManageTerminalDisplay	(	AW_root *	root,
		ED4_orf_terminal *	orfTerm,
		long int	DispMode
	)

static

Definition at line 140 of file ED4_ProteinViewer.cxx.

References arb_test::all(), AW_root::awar(), AWAR_PROTVIEW_COMPLEMENTARY_STRAND_1, AWAR_PROTVIEW_COMPLEMENTARY_STRAND_2, AWAR_PROTVIEW_COMPLEMENTARY_STRAND_3, AWAR_PROTVIEW_DEFINED_FIELDS, AWAR_PROTVIEW_FORWARD_STRAND_1, AWAR_PROTVIEW_FORWARD_STRAND_2, AWAR_PROTVIEW_FORWARD_STRAND_3, AWAR_PV_CURSOR, AWAR_PV_CURSOR_CS_1, AWAR_PV_CURSOR_CS_2, AWAR_PV_CURSOR_CS_3, AWAR_PV_CURSOR_DB, AWAR_PV_CURSOR_FS_1, AWAR_PV_CURSOR_FS_2, AWAR_PV_CURSOR_FS_3, AWAR_PV_DISPLAY_ALL, AWAR_PV_MARKED, AWAR_PV_MARKED_CS_1, AWAR_PV_MARKED_CS_2, AWAR_PV_MARKED_CS_3, AWAR_PV_MARKED_DB, AWAR_PV_MARKED_FS_1, AWAR_PV_MARKED_FS_2, AWAR_PV_MARKED_FS_3, AWAR_PV_SELECTED, AWAR_PV_SELECTED_CS_1, AWAR_PV_SELECTED_CS_2, AWAR_PV_SELECTED_CS_3, AWAR_PV_SELECTED_DB, AWAR_PV_SELECTED_FS_1, AWAR_PV_SELECTED_FS_2, AWAR_PV_SELECTED_FS_3, COMPLEMENTARY_STRAND, DB_FIELD_STRAND, FORWARD_STRAND, ED4_orf_terminal::GET_aaStartPos(), ED4_orf_terminal::GET_aaStrandType(), PV_ALL, PV_CURSOR, PV_HideTerminal(), PV_MARKED, PV_SELECTED, PV_UnHideTerminal(), and AW_awar::read_int().

Referenced by PV_ManageTerminals().

static void PV_ManageTerminals ( AW_root * root )

static

void PV_RefreshWindow ( AW_root * root )

Definition at line 358 of file ED4_ProteinViewer.cxx.

References gTerminalsCreated, and PV_ManageTerminals().

Referenced by ED4_terminal::event_sent_by_parent(), PV_AddCorrespondingOrfTerminals(), PV_AddOrfTerminalsToLoadedSpecies(), PV_CallBackFunction(), PV_DisplayAminoAcidNames(), and PV_SequenceUpdate_CB().

static GB_ERROR PV_ComplementarySequence ( char * sequence )

static

Definition at line 367 of file ED4_ProteinViewer.cxx.

References ED4_root::alignment_type, ED4_ROOT, error(), GBT_complementNucSequence(), and GBT_determine_T_or_U().

Referenced by PV_WriteTranslatedSequenceToDB(), and TranslateGeneToAminoAcidSequence().

static void PV_WriteTranslatedSequenceToDB	(	ED4_orf_terminal *	aaSeqTerm,
		const char *	spName
	)

static

Definition at line 380 of file ED4_ProteinViewer.cxx.

References ASKtoOverWriteData, aw_message(), AWT_default_protein_type(), COMPLEMENTARY_STRAND, DB_FIELD_STRAND, e4_assert, ED4_ROOT, error(), FORWARD_STRAND, GB_await_error(), GB_begin_transaction(), GB_end_transaction_show_error(), GB_find_string(), GB_have_error(), GB_IGNORE_CASE, gb_main, GB_read_string(), GB_read_string_count(), GB_STRING, GB_write_string(), GBS_global_string(), GBS_global_string_copy(), GBT_add_alignment_changekeys(), GBT_add_data(), GBT_check_data(), GBT_create_alignment(), GBT_find_sequence(), GBT_find_species(), GBT_get_alignment(), GBT_get_alignment_len(), GBT_get_presets(), ED4_orf_terminal::GET_aaStartPos(), ED4_orf_terminal::GET_aaStrandType(), ED4_root::get_alignment_name(), ED4_root::get_gb_main(), NULp, PV_ComplementarySequence(), SEARCH_GRANDCHILD, and translate_nuc2aa().

Referenced by PV_SaveData().

static void PV_SaveData ( AW_window * )

static

Definition at line 470 of file ED4_ProteinViewer.cxx.

References ASKtoOverWriteData, aw_message(), ED4_ROOT, ED4_base::flag, GBS_global_string_copy(), gbWritingData, ED4_manager::get_first_terminal(), ED4_base::get_next_terminal(), gTerminalsCreated, ED4_base::hidden, PV_AA_Terminals4Species, PV_WriteTranslatedSequenceToDB(), and ED4_root::root_group_man.

Referenced by ED4_CreateProteinViewer_window().

static void TranslateGeneToAminoAcidSequence	(	AW_root *	,
		ED4_orf_terminal *	seqTerm,
		const char *	speciesName,
		int	startPos4Translation,
		int	translationMode
	)