SettingsData.h

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/**
 *  \file IMP/multifit/SettingsData.h
 *  \brief stored multifit settings data
 *
 *  Copyright 2007-2016 IMP Inventors. All rights reserved.
 *
 */

#ifndef IMPMULTIFIT_SETTINGS_DATA_H
#define IMPMULTIFIT_SETTINGS_DATA_H
#include <IMP/multifit/multifit_config.h>
#include <IMP/base_types.h>
#include <IMP/container_macros.h>
#include <IMP/Pointer.h>
#include <IMP/Model.h>
#include <IMP/Pointer.h>
#include <IMP/algebra/Transformation3D.h>

IMPMULTIFIT_BEGIN_NAMESPACE

//! Holds data about a component needed for optimization
class IMPMULTIFITEXPORT ComponentHeader : public IMP::Object {
 public:
  ComponentHeader() : Object("ComponentHeader%1%") {
    name_ = "";
    filename_ = "";
    surface_fn_ = "";
    pdb_ap_fn_ = "";
    pdb_fine_ap_fn_ = "";
    num_ap_ = 0;
    transformations_fn_ = "";
    reference_fn_ = "";
  }
  void set_name(const std::string &name) { name_ = name; }
  inline std::string get_name() const { return name_; }
  inline std::string get_filename() const { return filename_; }
  void set_filename(const std::string &filename) { filename_ = filename; }
  inline std::string get_surface_fn() const { return surface_fn_; }
  void set_surface_fn(const std::string &fn) { surface_fn_ = fn; }
  void set_txt_ap_fn(const std::string &pdb_ap_fn) { pdb_ap_fn_ = pdb_ap_fn; }
  inline std::string get_txt_ap_fn() const { return pdb_ap_fn_; }
  void set_txt_fine_ap_fn(const std::string &pdb_ap_fn) {
    pdb_fine_ap_fn_ = pdb_ap_fn;
  }
  inline std::string get_txt_fine_ap_fn() const { return pdb_fine_ap_fn_; }
  void set_num_ap(int num_ap) { num_ap_ = num_ap; }
  inline int get_num_ap() const { return num_ap_; }
  void set_num_fine_ap(int num_ap) { num_fine_ap_ = num_ap; }
  inline int get_num_fine_ap() const { return num_fine_ap_; }
  void set_transformations_fn(std::string transformations_fn) {
    transformations_fn_ = transformations_fn;
  }
  std::string get_transformations_fn() const { return transformations_fn_; }
  void set_reference_fn(const std::string &ref_fn) { reference_fn_ = ref_fn; }
  std::string get_reference_fn() const { return reference_fn_; }
  IMP_OBJECT_METHODS(ComponentHeader);
  /*IMP_OBJECT_INLINE(ComponentHeader, {
      out<<name_<<"|"<<filename_<<"|"<<surface_fn_<<"|";
      out<<pdb_ap_fn_<<"|"<<num_ap_<<"|";
      out<<pdb_fine_ap_fn_<<"|"<<num_fine_ap_<<"|";
      out<<transformations_fn_<<"|"<<reference_fn_<<"|"<<std::endl; }, {});*/
 protected:
  std::string name_;
  std::string filename_;
  std::string surface_fn_;
  std::string pdb_ap_fn_;
  int num_ap_;
  std::string pdb_fine_ap_fn_;
  int num_fine_ap_;
  std::string transformations_fn_;
  std::string reference_fn_;
};
IMP_OBJECTS(ComponentHeader, ComponentHeaders);

//! Holds data about the assembly density needed for optimization
class IMPMULTIFITEXPORT AssemblyHeader : public IMP::Object {
 public:
  AssemblyHeader() : Object("AssemblyHeader%1%") {
    dens_fn_ = "";
    resolution_ = 0.;
    spacing_ = 0.;
    threshold_ = 0.;
    coarse_ap_fn_ = "";
    coarse_over_sampled_ap_fn_ = "";
    fine_ap_fn_ = "";
    fine_over_sampled_ap_fn_ = "";
  }
  void set_dens_fn(const std::string &dens_fn) { dens_fn_ = dens_fn; }
  std::string get_dens_fn() const { return dens_fn_; }
  void set_resolution(float res) { resolution_ = res; }
  float get_resolution() const { return resolution_; }
  float get_spacing() const { return spacing_; }
  void set_spacing(float spacing) { spacing_ = spacing; }
  void set_threshold(float t) { threshold_ = t; }
  float get_threshold() const { return threshold_; }
  algebra::Vector3D get_origin() const { return origin_; }
  void set_origin(algebra::Vector3D origin) { origin_ = origin; }
  std::string get_coarse_ap_fn() const { return coarse_ap_fn_; }
  void set_coarse_ap_fn(const std::string &new_fn) { coarse_ap_fn_ = new_fn; }
  std::string get_coarse_over_sampled_ap_fn() const {
    return coarse_over_sampled_ap_fn_;
  }
  void set_coarse_over_sampled_ap_fn(const std::string &new_fn) {
    coarse_over_sampled_ap_fn_ = new_fn;
  }
  std::string get_fine_ap_fn() const { return fine_ap_fn_; }
  void set_fine_ap_fn(const std::string &new_fn) { fine_ap_fn_ = new_fn; }
  std::string get_fine_over_sampled_ap_fn() const {
    return fine_over_sampled_ap_fn_;
  }
  void set_fine_over_sampled_ap_fn(const std::string &new_fn) {
    fine_over_sampled_ap_fn_ = new_fn;
  }
  IMP_OBJECT_METHODS(AssemblyHeader);
  /*IMP_OBJECT_INLINE(AssemblyHeader, {
      out<<dens_fn_<<"|"<<resolution_<<"|"<<spacing_<<"|"<<threshold_
         <<"|"<<origin_[0]<<"|";
      out<<origin_[1]<<"|"<<origin_[2]<<"|"<<coarse_ap_fn_;
      out<<"|"<<coarse_over_sampled_ap_fn_<<"|";
      out<<fine_ap_fn_<<"|"<<fine_over_sampled_ap_fn_<<"|\n";
      }, {});*/
 protected:
  std::string dens_fn_;
  float resolution_;
  float spacing_;
  float threshold_;
  algebra::Vector3D origin_;
  std::string coarse_ap_fn_;
  std::string coarse_over_sampled_ap_fn_;
  std::string fine_ap_fn_;
  std::string fine_over_sampled_ap_fn_;
};

//! Holds header data for optimization
class IMPMULTIFITEXPORT SettingsData : public IMP::Object {
 public:
  SettingsData() : Object("SettingsData%1%") { data_path_ = "./"; }
  static void show_component_header_line(std::ostream &out = std::cout) {
    out << get_component_header_line();
  }
  static std::string get_component_header_line() {
    std::stringstream ss;
    ss << "name|protein|surface|pdb_anchor_points|number of anchor points|"
       << "fine pdb_anchor_points|number of fine anchor points|"
       << "transformations|ref filename|" << std::endl;
    return ss.str();
  }
  static void show_density_header_line(std::ostream &out = std::cout) {
    out << get_density_header_line();
  }
  static std::string get_density_header_line() {
    std::stringstream ss;
    ss << "map| resolution| spacing| threshold|x-origin| y-origin| z-origin|";
    ss << "coarse anchor points|coarse over sampled anchor points|";
    ss << "fine anchor points|fine over sampled anchor points|" << std::endl;
    return ss.str();
  }
  void set_assembly_filename(const std::string &fn) { asmb_fn_ = fn; }
  const char *get_assembly_filename() const { return asmb_fn_.c_str(); }
  void set_assembly_header(AssemblyHeader *h) { dens_data_ = h; }
  AssemblyHeader *get_assembly_header() const { return dens_data_; }
  void set_data_path(const std::string &fn) { data_path_ = fn; }
  std::string get_data_path() const { return data_path_; }

  IMP_OBJECT_METHODS(SettingsData);

  IMP_LIST_ACTION(public, ComponentHeader, ComponentHeaders, component_header,
                  component_headers, ComponentHeader *, ComponentHeaders,
                  obj->set_was_used(true);
                  , , );

 protected:
  IMP::PointerMember<AssemblyHeader> dens_data_;
  std::string asmb_fn_;
  std::string data_path_;
};

IMPMULTIFITEXPORT SettingsData *read_settings(const char *filename);
IMPMULTIFITEXPORT void write_settings(const char *filename,
                                      const SettingsData *sd);
IMPMULTIFIT_END_NAMESPACE
#endif /* IMPMULTIFIT_SETTINGS_DATA_H */