#include "NT_local.h"
#include <ColumnStat.hxx>
#include <AP_filter.hxx>
#include <awt_filter.hxx>
#include <aw_awars.hxx>
#include <aw_file.hxx>
#include <aw_msg.hxx>
#include <aw_root.hxx>
#include <aw_select.hxx>
#include <arbdbt.h>
#include <arb_file.h>
#include <unistd.h>

Include dependency graph for ColumnStat_2_gnuplot.cxx:

Classes
class	SortedFreq

class	Smoother

struct	PlotParam

Macros
#define	AWAR_CS2GP "tmp/ntree/colstat_2_gnuplot"

#define	AWAR_CS2GP_NAME AWAR_CS2GP "/name"

#define	AWAR_CS2GP_SUFFIX AWAR_CS2GP "/filter"

#define	AWAR_CS2GP_DIRECTORY AWAR_CS2GP "/directory"

#define	AWAR_CS2GP_FILENAME AWAR_CS2GP "/file_name"

#define	AWAR_CS2GP_SMOOTH_VALUES AWAR_CS2GP "/smooth_values"

#define	AWAR_CS2GP_SMOOTH_GNUPLOT AWAR_CS2GP "/smooth_gnuplot"

#define	AWAR_CS2GP_GNUPLOT_OVERLAY_PREFIX AWAR_CS2GP "/gnuplot_overlay_prefix"

#define	AWAR_CS2GP_GNUPLOT_OVERLAY_POSTFIX AWAR_CS2GP "/gnuplot_overlay_postfix"

#define	AWAR_CS2GP_FILTER_NAME AWAR_CS2GP "/ap_filter/name"

Enumerations
enum	PlotType { PT_GC_RATIO, PT_GA_RATIO, PT_RATE, PT_TT_RATIO, PT_MOST_FREQUENT_BASE, PT_SECOND_FREQUENT_BASE, PT_THIRD_FREQUENT_BASE, PT_LEAST_FREQUENT_BASE, PT_BASE_A, PT_BASE_C, PT_BASE_G, PT_BASE_TU, PT_HELIX, PT_PLOT_TYPES, PT_UNKNOWN }

enum	PlotMode { PLOT, PLOT_AND_VIEW, PLOT_CLEANUP }

Functions
static GB_ERROR	split_stat_filename (const char fname, char dirPtr, char name_prefixPtr, char *name_postfixPtr)

static char *	get_overlay_files (AW_root awr, const char fname, GB_ERROR &error)

static PlotType	string2PlotType (const char *type)

static const char *	makeTitle (const char *fname)

static void	colstat_2_gnuplot_cb (AW_window aww, PlotParam param, PlotMode mode)

static void	colstat_ali_changed_cb (AW_root root, AW_awar awar_ali)

AW_window *	NT_create_colstat_2_gnuplot_window (AW_root *root)

Variables
static const char *	plotTypeName [PT_PLOT_TYPES]

static const char *	plotTypeDescription [PT_PLOT_TYPES]

Macro Definition Documentation

#define AWAR_CS2GP "tmp/ntree/colstat_2_gnuplot"

Definition at line 26 of file ColumnStat_2_gnuplot.cxx.

Referenced by NT_create_colstat_2_gnuplot_window().

#define AWAR_CS2GP_NAME AWAR_CS2GP "/name"

Definition at line 28 of file ColumnStat_2_gnuplot.cxx.

Referenced by NT_create_colstat_2_gnuplot_window().

#define AWAR_CS2GP_SUFFIX AWAR_CS2GP "/filter"

Definition at line 29 of file ColumnStat_2_gnuplot.cxx.

Referenced by colstat_2_gnuplot_cb(), and NT_create_colstat_2_gnuplot_window().

#define AWAR_CS2GP_DIRECTORY AWAR_CS2GP "/directory"

Definition at line 30 of file ColumnStat_2_gnuplot.cxx.

Referenced by colstat_2_gnuplot_cb().

#define AWAR_CS2GP_FILENAME AWAR_CS2GP "/file_name"

Definition at line 31 of file ColumnStat_2_gnuplot.cxx.

Referenced by colstat_2_gnuplot_cb().

#define AWAR_CS2GP_SMOOTH_VALUES AWAR_CS2GP "/smooth_values"

Definition at line 33 of file ColumnStat_2_gnuplot.cxx.

Referenced by colstat_2_gnuplot_cb(), colstat_ali_changed_cb(), and NT_create_colstat_2_gnuplot_window().

#define AWAR_CS2GP_SMOOTH_GNUPLOT AWAR_CS2GP "/smooth_gnuplot"

Definition at line 34 of file ColumnStat_2_gnuplot.cxx.

Referenced by colstat_2_gnuplot_cb(), and NT_create_colstat_2_gnuplot_window().

#define AWAR_CS2GP_GNUPLOT_OVERLAY_PREFIX AWAR_CS2GP "/gnuplot_overlay_prefix"

Definition at line 35 of file ColumnStat_2_gnuplot.cxx.

Referenced by get_overlay_files(), and NT_create_colstat_2_gnuplot_window().

#define AWAR_CS2GP_GNUPLOT_OVERLAY_POSTFIX AWAR_CS2GP "/gnuplot_overlay_postfix"

Definition at line 36 of file ColumnStat_2_gnuplot.cxx.

Referenced by get_overlay_files(), and NT_create_colstat_2_gnuplot_window().

#define AWAR_CS2GP_FILTER_NAME AWAR_CS2GP "/ap_filter/name"

Definition at line 37 of file ColumnStat_2_gnuplot.cxx.

Referenced by NT_create_colstat_2_gnuplot_window().

Enumeration Type Documentation

enum PlotType

Enumerator
PT_GC_RATIO
PT_GA_RATIO
PT_RATE
PT_TT_RATIO
PT_MOST_FREQUENT_BASE
PT_SECOND_FREQUENT_BASE
PT_THIRD_FREQUENT_BASE
PT_LEAST_FREQUENT_BASE
PT_BASE_A
PT_BASE_C
PT_BASE_G
PT_BASE_TU
PT_HELIX
PT_PLOT_TYPES
PT_UNKNOWN

Definition at line 136 of file ColumnStat_2_gnuplot.cxx.

enum PlotMode

Enumerator
PLOT
PLOT_AND_VIEW
PLOT_CLEANUP

Definition at line 332 of file ColumnStat_2_gnuplot.cxx.

Function Documentation

static GB_ERROR split_stat_filename	(	const char *	fname,
		char **	dirPtr,
		char **	name_prefixPtr,
		char **	name_postfixPtr
	)

static

Definition at line 39 of file ColumnStat_2_gnuplot.cxx.

References ARB_strdup(), GB_export_errorf(), nt_assert, and NULp.

Referenced by get_overlay_files().

static char* get_overlay_files	(	AW_root *	awr,
		const char *	fname,
		GB_ERROR &	error
	)

static

Definition at line 76 of file ColumnStat_2_gnuplot.cxx.

References AW_root::awar(), AWAR_CS2GP_GNUPLOT_OVERLAY_POSTFIX, AWAR_CS2GP_GNUPLOT_OVERLAY_PREFIX, GB_find_all_files(), GB_get_error(), GBS_global_string_copy(), nt_assert, NULp, AW_awar::read_int(), and split_stat_filename().

Referenced by colstat_2_gnuplot_cb().

static PlotType string2PlotType ( const char * type )

static

Definition at line 187 of file ColumnStat_2_gnuplot.cxx.

References PT_PLOT_TYPES, and PT_UNKNOWN.

Referenced by colstat_2_gnuplot_cb(), and makeTitle().

static const char* makeTitle ( const char * fname )

static

Definition at line 197 of file ColumnStat_2_gnuplot.cxx.

References ARB_strdup(), GBS_global_string_copy(), NULp, PT_UNKNOWN, string2PlotType(), and title.

Referenced by colstat_2_gnuplot_cb().

static void colstat_2_gnuplot_cb	(	AW_window *	aww,
		PlotParam *	param,
		PlotMode	mode
	)

static

Definition at line 348 of file ColumnStat_2_gnuplot.cxx.

References A, alignment_name, aw_message(), AW_root::awar(), AWAR_CS2GP_DIRECTORY, AWAR_CS2GP_FILENAME, AWAR_CS2GP_SMOOTH_GNUPLOT, AWAR_CS2GP_SMOOTH_VALUES, AWAR_CS2GP_SUFFIX, C, ColumnStat::calculate(), PlotParam::colstat, adfiltercbstruct::def_alignment, adfiltercbstruct::def_filter, error(), PlotParam::filterdef, G, GB_await_error(), GB_clear_error(), GB_export_errorf(), GB_fopen_tempfile(), NT_global::gb_main, GB_unique_filename(), GB_xcmd(), GBS_global_string_copy(), GBT_get_alignment_len(), ColumnStat::get_frequencies(), ColumnStat::get_is_helix(), ColumnStat::get_length(), get_overlay_files(), ColumnStat::get_rates(), AW_window::get_root(), ColumnStat::get_ttratio(), ColumnStat::get_weights(), GLOBAL, makeTitle(), nt_assert, NULp, PLOT, PLOT_AND_VIEW, PLOT_CLEANUP, Smoother::print(), PT_BASE_A, PT_BASE_C, PT_BASE_G, PT_BASE_TU, PT_GA_RATIO, PT_GC_RATIO, PT_HELIX, PT_LEAST_FREQUENT_BASE, PT_MOST_FREQUENT_BASE, PT_PLOT_TYPES, PT_RATE, PT_SECOND_FREQUENT_BASE, PT_THIRD_FREQUENT_BASE, PT_TT_RATIO, PT_UNKNOWN, AW_awar::read_int(), AW_awar::read_string(), string2PlotType(), ta, AW_awar::touch(), type, weights, and XCMD_ASYNC_WAIT_ON_ERROR.

Referenced by NT_create_colstat_2_gnuplot_window().

static void colstat_ali_changed_cb	(	AW_root *	root,
		AW_awar *	awar_ali
	)

static

Definition at line 577 of file ColumnStat_2_gnuplot.cxx.

References AW_root::awar(), AWAR_CS2GP_SMOOTH_VALUES, GB_clear_error(), NT_global::gb_main, GBT_get_alignment_len(), GLOBAL, AW_awar::read_char_pntr(), and AW_awar::set_minmax().

Referenced by NT_create_colstat_2_gnuplot_window().

AW_window* NT_create_colstat_2_gnuplot_window ( AW_root * root )

Definition at line 588 of file ColumnStat_2_gnuplot.cxx.

References AW_awar::add_callback(), AW_create_fileselection_awars(), AW_create_standard_fileselection(), AW_HORIZONTAL, AW_POPDOWN(), AW_ROOT_DEFAULT, AW_root::awar(), AWAR_CS2GP, AWAR_CS2GP_FILTER_NAME, AWAR_CS2GP_GNUPLOT_OVERLAY_POSTFIX, AWAR_CS2GP_GNUPLOT_OVERLAY_PREFIX, AWAR_CS2GP_NAME, AWAR_CS2GP_SMOOTH_GNUPLOT, AWAR_CS2GP_SMOOTH_VALUES, AWAR_CS2GP_SUFFIX, AWAR_DEFAULT_ALIGNMENT, AW_root::awar_int(), AW_root::awar_string(), awt_create_filter_awars(), awt_create_select_filter(), awt_create_select_filter_win(), colstat_2_gnuplot_cb(), colstat_ali_changed_cb(), COLSTAT_create_selection_list(), adfiltercbstruct::def_alignment, NT_global::gb_main, GLOBAL, AW_selection_list::insert(), AW_selection_list::insert_default(), makeHelpCallback(), PLOT, PLOT_AND_VIEW, PLOT_CLEANUP, PT_PLOT_TYPES, ta, AW_awar::touch(), and AW_selection_list::update().

Referenced by popup_new_main_window().

Variable Documentation

const char* plotTypeName[PT_PLOT_TYPES]

static

Initial value:

= {
    "gc_gnu",
    "ga_gnu",
    "rate_gnu",
    "tt_gnu",
    "f1_gnu",
    "f2_gnu",
    "f3_gnu",
    "f4_gnu",
    "a_gnu",
    "c_gnu",
    "g_gnu",
    "tu_gnu",
    "helix_gnu"
}

Definition at line 155 of file ColumnStat_2_gnuplot.cxx.

const char* plotTypeDescription[PT_PLOT_TYPES]

static

Initial value:

= {
    "G+C ratio",
    "G+A ratio",
    "Rate",
    "TT Ratio",
    "Most frequent base",
    "2nd frequent base",
    "3rd frequent base",
    "Least frequent base",
    "A ratio",
    "C ratio",
    "G ratio",
    "T/U ratio",
    "Helix"
}

Definition at line 171 of file ColumnStat_2_gnuplot.cxx.

Classes

Macros

Enumerations

Functions

Variables

Macro Definition Documentation

Enumeration Type Documentation

Function Documentation

Variable Documentation