/usr/include/relion-1.4/src/gui_jobwindow.h is in librelion-dev-common 1.4+dfsg-2.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
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*
* Author: "Sjors H.W. Scheres"
* MRC Laboratory of Molecular Biology
*
* This program is free software; you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation; either version 2 of the License, or
* (at your option) any later version.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* This complete copyright notice must be included in any revised version of the
* source code. Additional authorship citations may be added, but existing
* author citations must be preserved.
***************************************************************************/
#ifndef GUI_JOBWINDOW_H_
#define GUI_JOBWINDOW_H_
#define MENUHEIGHT 30
#define TABHEIGHT 25
#define HAS_MPI true
#define HAS_NOT_MPI false
#define HAS_THREAD true
#define HAS_NOT_THREAD false
#define HAS_PARALLEL_DISCIO true
#define HAS_NOT_PARALLEL_DISCIO false
#define HAS_RUN true
#define HAS_NOT_RUN false
#include "src/gui_entries.h"
// Our own defaults at LMB are the hard-coded ones
#define DEFAULTQSUBLOCATION "/public/EM/RELION/relion/bin/qsub.csh"
#define DEFAULTCTFFINDLOCATION "\"/public/EM/ctffind/ctffind.exe --omp-num-threads 1 --old-school-input\""
#define DEFAULTRESMAPLOCATION "/public/EM/ResMap/ResMap-1.1.4-linux64"
#define DEFAULTMININIMUMDEDICATED 1
#define DEFAULTALLOWCHANGEMINDEDICATED true
static Fl_Menu_Item sampling_options[] = {
{"30 degrees"},
{"15 degrees"},
{"7.5 degrees"},
{"3.7 degrees"},
{"1.8 degrees"},
{"0.9 degrees"},
{"0.5 degrees"},
{"0.2 degrees"},
{"0.1 degrees"},
{0} // this should be the last entry
};
static int minimum_nr_dedicated;
static bool do_allow_change_minimum_dedicated;
class RelionJobWindow : public Fl_Box
{
public:
// Position of current cursor to place new elements
int start_y, current_y;
// Menu
Fl_Menu_Bar *menubar;
// Choice for new/continue
Fl_Choice *choice_continue;
Fl_Menu_ *menu_continue;
// Tabs
Fl_Tabs *tabs;
Fl_Group *tab1, *tab2, *tab3, *tab4, *tab5, *tab6, *runtab;
// Running
Fl_Group *queue_group;
SliderEntry nr_mpi;
SliderEntry nr_threads;
SliderEntry ram_per_thread;
BooleanEntry do_queue;
AnyEntry queuename;
AnyEntry qsub;
SliderEntry min_dedicated;
FileNameEntry qsubscript;
bool have_extra1, have_extra2;
AnyEntry qsub_extra1;
AnyEntry qsub_extra2;
AnyEntry other_args;
// Run buttons
Fl_Button *run_button, *print_CL_button, *cite_button;
// For the run tab
bool has_mpi;
bool has_thread;
bool is_continue;
public:
// Constructor with x, y, w, h and a title
RelionJobWindow(int nr_tabs, bool _has_mpi, bool _has_thread, bool _has_run = true,
int x = WCOL0, int y = MENUHEIGHT+10, int w = GUIWIDTH - WCOL0 - 10, int h = GUIHEIGHT-70, const char* title = "");
// Destructor
~RelionJobWindow() {};
void resetHeight();
void setupRunTab();
// by default nothing happens if you change continue old run radiobutton
void toggle_new_continue(bool is_continue);
// write/read settings to disc
void openWriteFile(std::string fn, std::ofstream &fh);
bool openReadFile(std::string fn, std::ifstream &fh);
void closeWriteFile(std::ofstream& fh);
void closeReadFile(std::ifstream& fh);
// Write the job submission script
void saveJobSubmissionScript(std::string newfilename, std::string outputname, std::vector<std::string> commands);
// Prepare the final (job submission or combined (mpi) command of possibly multiple lines)
void prepareFinalCommand(std::string &outputname, std::vector<std::string> &commands, std::string &final_command);
private:
static void cb_menu_continue(Fl_Widget*, void*);
inline void cb_menu_continue_i();
};
/*
class XXXXJobWindow : public RelionJobWindow
{
public:
// I/O
public:
// Constructor
XXXXJobWindow();
// Destructor
~XXXXJobWindow(){};
// write/read settings to disc
void write(std::string fn);
void read(std::string fn, bool &_is_continue);
// what happens if you change continue old run radiobutton
void toggle_new_continue(bool is_continue);
// Generate the correct commands
void getCommands(std::string &outputname, std::vector<std::string> &commands, std::string &final_command);
};
*/
class GeneralJobWindow : public RelionJobWindow
{
public:
// I/O
SliderEntry angpix, particle_diameter;
public:
// Constructor
GeneralJobWindow();
// Destructor
~GeneralJobWindow(){};
// write/read settings to disc
void write(std::string fn);
void read(std::string fn, bool &_is_continue);
// what happens if you change continue old run radiobutton
void toggle_new_continue(bool is_continue);
// Generate the correct commands
void getCommands(std::string &outputname, std::vector<std::string> &commands, std::string &final_command);
};
class CtffindJobWindow : public RelionJobWindow
{
public:
FileNameEntry mic_names;
AnyEntry output_star_ctf_mics;
FileNameEntry fn_ctffind_exe;
SliderEntry ctf_win;
SliderEntry cs, kv, q0, angpix, dstep, dast;
SliderEntry box, resmin, resmax, dfmin, dfmax, dfstep;
public:
// Constructor
CtffindJobWindow();
// Destructor
~CtffindJobWindow(){};
// write/read settings to disc
void write(std::string fn);
void read(std::string fn, bool &_is_continue);
// what happens if you change continue old run radiobutton
void toggle_new_continue(bool is_continue);
void getCommands(std::string &outputname, std::vector<std::string> &commands,
std::string &final_command, DOUBLE angpix);
};
class AutopickJobWindow : public RelionJobWindow
{
public:
FileNameEntry fn_input_autopick;
FileNameEntry fn_refs_autopick;
AnyEntry autopick_rootname;
BooleanEntry do_invert_refs;
BooleanEntry do_ctf_autopick;
BooleanEntry do_ignore_first_ctfpeak_autopick;
SliderEntry lowpass_autopick;
SliderEntry psi_sampling_autopick;
BooleanEntry do_write_fom_maps, do_read_fom_maps;
SliderEntry threshold_autopick;
SliderEntry mindist_autopick;
SliderEntry maxstddevnoise_autopick;
Fl_Group *autopick_ctf_group;
public:
// Constructor
AutopickJobWindow();
// Destructor
~AutopickJobWindow(){};
// write/read settings to disc
void write(std::string fn);
void read(std::string fn, bool &_is_continue);
// what happens if you change continue old run radiobutton
void toggle_new_continue(bool is_continue);
void getCommands(std::string &outputname, std::vector<std::string> &commands,
std::string &final_command, DOUBLE angpix, DOUBLE particle_diameter);
};
class ManualpickJobWindow : public RelionJobWindow
{
public:
FileNameEntry fn_in;
FileNameEntry fn_out;
AnyEntry manualpick_rootname;
SliderEntry lowpass;
SliderEntry micscale;
SliderEntry ctfscale;
SliderEntry sigma_contrast;
SliderEntry white_val;
SliderEntry black_val;
BooleanEntry do_color;
AnyEntry color_label;
FileNameEntry fn_color;
SliderEntry blue_value;
SliderEntry red_value;
Fl_Group *color_group;
public:
// Constructor
ManualpickJobWindow();
// Destructor
~ManualpickJobWindow(){};
// write/read settings to disc
void write(std::string fn);
void read(std::string fn, bool &_is_continue);
// what happens if you change continue old run radiobutton
void toggle_new_continue(bool is_continue);
void getCommands(std::string &outputname, std::vector<std::string> &commands,
std::string &final_command, DOUBLE angpix, DOUBLE particle_diameter);
};
class ExtractJobWindow : public RelionJobWindow
{
public:
// I/O
FileNameEntry star_mics;
AnyEntry pick_suffix;
AnyEntry extract_rootname;
// extract
BooleanEntry do_extract;
SliderEntry extract_size;
BooleanEntry do_rescale;
SliderEntry rescale;
BooleanEntry do_norm;
SliderEntry white_dust;
SliderEntry black_dust;
BooleanEntry do_invert;
// movies
BooleanEntry do_movie_extract;
AnyEntry movie_rootname;
SliderEntry first_movie_frame;
SliderEntry last_movie_frame;
Fl_Group *extract_group, *rescale_group, *norm_group, *movie_extract_group;
public:
// Constructor
ExtractJobWindow();
// Destructor
~ExtractJobWindow(){};
// write/read settings to disc
void write(std::string fn);
void read(std::string fn, bool &_is_continue);
// what happens if you change continue old run radiobutton
void toggle_new_continue(bool is_continue);
// Generate the correct commands
void getCommands(std::string &outputname, std::vector<std::string> &commands,
std::string &final_command, DOUBLE angpix, DOUBLE particle_diameter);
};
class SortJobWindow : public RelionJobWindow
{
public:
// I/O
FileNameEntry input_star;
FileNameEntry fn_refs;
BooleanEntry do_ctf;
BooleanEntry do_ignore_first_ctfpeak;
Fl_Group *ctf_group;
public:
// Constructor
SortJobWindow();
// Destructor
~SortJobWindow(){};
// write/read settings to disc
void write(std::string fn);
void read(std::string fn, bool &_is_continue);
// what happens if you change continue old run radiobutton
void toggle_new_continue(bool is_continue);
// Generate the correct commands
void getCommands(std::string &outputname, std::vector<std::string> &commands,
std::string &final_command, DOUBLE angpix, DOUBLE particle_diameter);
};
class Class2DJobWindow : public RelionJobWindow
{
public:
// I/O
AnyEntry fn_out;
FileNameEntry fn_cont;
FileNameEntry fn_img;
BooleanEntry do_parallel_discio;
// CTF
BooleanEntry do_ctf_correction;
BooleanEntry ctf_phase_flipped;
BooleanEntry ctf_intact_first_peak;
// Optimisation
SliderEntry nr_iter;
SliderEntry tau_fudge;
BooleanEntry do_zero_mask;
SliderEntry highres_limit;
// Sampling
SliderEntry nr_classes;
BooleanEntry dont_skip_align;
SliderEntry psi_sampling;
SliderEntry offset_range;
SliderEntry offset_step;
Fl_Group *ctf_group, *dont_skip_align_group;
public:
// Constructor
Class2DJobWindow();
// Destructor
~Class2DJobWindow(){};
// write/read settings to disc
void write(std::string fn);
void read(std::string fn, bool &_is_continue);
// what happens if you change continue old run radiobutton
void toggle_new_continue(bool is_continue);
// Generate the correct commands
void getCommands(std::string &outputname, std::vector<std::string> &commands,
std::string &final_command, DOUBLE angpix, DOUBLE particle_diameter);
};
class Class3DJobWindow : public RelionJobWindow
{
public:
// I/O
AnyEntry fn_out;
FileNameEntry fn_cont;
FileNameEntry fn_img;
SliderEntry nr_classes;
BooleanEntry do_parallel_discio;
// Reference
FileNameEntry fn_ref;
BooleanEntry ref_correct_greyscale;
SliderEntry ini_high;
AnyEntry sym_name;
// CTF
BooleanEntry do_ctf_correction;
BooleanEntry ctf_corrected_ref;
BooleanEntry ctf_phase_flipped;
BooleanEntry ctf_intact_first_peak;
// Optimisation
SliderEntry nr_iter;
SliderEntry tau_fudge;
BooleanEntry do_zero_mask;
FileNameEntry fn_mask;
SliderEntry highres_limit;
// Sampling
BooleanEntry dont_skip_align;
RadioEntry sampling;
SliderEntry offset_range;
SliderEntry offset_step;
BooleanEntry do_local_ang_searches;
SliderEntry sigma_angles;
Fl_Group *ctf_group, *dont_skip_align_group, *localsearch_group;
public:
// Constructor
Class3DJobWindow();
// Destructor
~Class3DJobWindow(){};
// write/read settings to disc
void write(std::string fn);
void read(std::string fn, bool &_is_continue);
// what happens if you change continue old run radiobutton
void toggle_new_continue(bool is_continue);
// Generate the correct commands
void getCommands(std::string &outputname, std::vector<std::string> &commands,
std::string &final_command, DOUBLE angpix, DOUBLE particle_diameter);
};
class Auto3DJobWindow : public RelionJobWindow
{
public:
// I/O
AnyEntry fn_out;
FileNameEntry fn_cont;
FileNameEntry fn_img;
BooleanEntry do_parallel_discio;
// Reference
FileNameEntry fn_ref;
BooleanEntry ref_correct_greyscale;
SliderEntry ini_high;
AnyEntry sym_name;
// CTF
BooleanEntry do_ctf_correction;
BooleanEntry ctf_corrected_ref;
BooleanEntry ctf_phase_flipped;
BooleanEntry ctf_intact_first_peak;
// Optimisation
BooleanEntry do_zero_mask;
FileNameEntry fn_mask;
// Sampling
textOnlyEntry autosample_text;
RadioEntry sampling;
SliderEntry offset_range;
SliderEntry offset_step;
RadioEntry auto_local_sampling;
// Movies
BooleanEntry do_movies;
FileNameEntry fn_movie_star;
SliderEntry movie_runavg_window;
SliderEntry movie_sigma_offset;
BooleanEntry do_alsorot_movies;
SliderEntry movie_sigma_angles;
Fl_Group *ctf_group, *movie_group, *alsorot_movie_group;
public:
// Constructor
Auto3DJobWindow();
// Destructor
~Auto3DJobWindow(){};
// write/read settings to disc
void write(std::string fn);
void read(std::string fn, bool &_is_continue);
// what happens if you change continue old run radiobutton
void toggle_new_continue(bool is_continue);
// Generate the correct commands
void getCommands(std::string &outputname, std::vector<std::string> &commands,
std::string &final_command, DOUBLE angpix, DOUBLE particle_diameter);
};
class PostJobWindow : public RelionJobWindow
{
public:
// I/O
FileNameEntry fn_in;
AnyEntry fn_out;
// Masking
BooleanEntry do_automask;
SliderEntry inimask_threshold;
SliderEntry extend_inimask;
SliderEntry width_mask_edge;
BooleanEntry do_usermask;
FileNameEntry fn_mask;
// Sharpening
BooleanEntry do_auto_bfac;
SliderEntry autob_lowres;
BooleanEntry do_adhoc_bfac;
SliderEntry adhoc_bfac;
FileNameEntry fn_mtf;
// Filtering
BooleanEntry do_skip_fsc_weighting;
SliderEntry low_pass;
Fl_Group *automask_group, *usermask_group, *autobfac_group, *adhocbfac_group, *skipweight_group;
public:
// Constructor
PostJobWindow();
// Destructor
~PostJobWindow(){};
// write/read settings to disc
void write(std::string fn);
void read(std::string fn, bool &_is_continue);
// what happens if you change continue old run radiobutton
void toggle_new_continue(bool is_continue);
// Generate the correct commands
void getCommands(std::string &outputname, std::vector<std::string> &commands, std::string &final_command,
DOUBLE angpix);
};
class PolishJobWindow : public RelionJobWindow
{
public:
// I/O
FileNameEntry fn_in;
AnyEntry fn_out;
// Movements
SliderEntry movie_runavg_window;
BooleanEntry do_fit_movement;
SliderEntry sigma_nb;
// Damage-model
BooleanEntry do_bfactor_weighting;
SliderEntry perframe_highres;
SliderEntry perframe_bfac_lowres;
FileNameEntry fn_mask;
AnyEntry sym_name;
Fl_Group *fit_group, *weight_group;
public:
// Constructor
PolishJobWindow();
// Destructor
~PolishJobWindow(){};
// write/read settings to disc
void write(std::string fn);
void read(std::string fn, bool &_is_continue);
// what happens if you change continue old run radiobutton
void toggle_new_continue(bool is_continue);
// Generate the correct commands
void getCommands(std::string &outputname, std::vector<std::string> &commands, std::string &final_command,
DOUBLE angpix, DOUBLE particle_diameter, DOUBLE black_dust, DOUBLE white_dust);
};
class ResmapJobWindow : public RelionJobWindow
{
public:
// I/O
FileNameEntry fn_resmap;
FileNameEntry fn_in;
// Params
SliderEntry pval;
SliderEntry minres;
SliderEntry maxres;
SliderEntry stepres;
FileNameEntry fn_mask;
public:
// Constructor
ResmapJobWindow();
// Destructor
~ResmapJobWindow(){};
// write/read settings to disc
void write(std::string fn);
void read(std::string fn, bool &_is_continue);
// what happens if you change continue old run radiobutton
void toggle_new_continue(bool is_continue);
// Generate the correct commands
void getCommands(std::string &outputname, std::vector<std::string> &commands, std::string &final_command,
DOUBLE angpix);
};
class PublishJobWindow : public RelionJobWindow
{
public:
// I/O
textOnlyEntry cite_text;
textOnlyEntry cite_external_text;
public:
// Constructor
PublishJobWindow();
// Destructor
~PublishJobWindow(){};
// what happens if you change continue old run radiobutton
void toggle_new_continue(bool is_continue);
// Generate the correct commands
void getCommands(std::string &outputname, std::vector<std::string> &commands, std::string &final_command);
};
#endif /* GUI_JOBWINDOW_H_ */
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