/**
 *  \file anchor_utilities.cpp
 *  \brief Tools for handling anchors.
 *
 *  Copyright 2007-2013 IMP Inventors. All rights reserved.
 */

#include <IMP/multifit/anchor_utilities.h>
#include <IMP/statistics/internal/VQClustering.h>
#include <IMP/algebra/vector_search.h>
#include <IMP/atom/Atom.h>
#include <IMP/atom/SecondaryStructureResidue.h>
#include <boost/graph/metric_tsp_approx.hpp>
#include <boost/graph/adjacency_list.hpp>
#include <boost/graph/adjacency_matrix.hpp>
#include <boost/graph/graphviz.hpp>

IMPMULTIFIT_BEGIN_NAMESPACE

void get_anchors_for_density(em::DensityMap *dmap, int number_of_means,
                             float density_threshold,
                             std::string pdb_filename,
                             std::string cmm_filename,
                             std::string seg_filename,
                             std::string txt_filename)
{
  dmap->set_was_used(true);
  IMP_NEW(multifit::DensityDataPoints, ddp, (dmap,density_threshold));
  IMP::statistics::internal::VQClustering vq(ddp, number_of_means);
  ddp->set_was_used(true);
  vq.run();
  multifit::DataPointsAssignment assignment(ddp, &vq);
  multifit::AnchorsData ad(assignment.get_centers(),
                           *(assignment.get_edges()));
  multifit::write_pdb(pdb_filename, assignment);
  //also write cmm string into a file:
  if (cmm_filename != "") {
    multifit::write_cmm(cmm_filename, "anchor_graph", ad);
  }
  if (seg_filename != "") {
    float apix = dmap->get_spacing();
    multifit::write_segments_as_mrc(dmap, assignment, apix, apix,
                                    density_threshold, seg_filename);
  }
  if (txt_filename != "") {
    multifit::write_txt(txt_filename, ad);
  }
}

IMPMULTIFITEXPORT
IntsList get_anchor_indices_matching_secondary_structure(
                            const AnchorsData &ad,
                            const atom::SecondaryStructureResidues &match_ssrs,
                            Float max_rmsd){

  atom::SecondaryStructureResidues anchor_ssrs=
    ad.get_secondary_structure_particles();
  IMP_USAGE_CHECK(anchor_ssrs.size()==ad.points_.size(),
                  "Anchors do not have enough SSEs set");

  //double loop unfortunately: for each match_ps check all anchors
  IntsList all_matches;
  for (atom::SecondaryStructureResidues::const_iterator it_match=
         match_ssrs.begin();it_match!=match_ssrs.end();++it_match){
    Ints matches;
    int count=0;
    for(atom::SecondaryStructureResidues::const_iterator
          it_anchor=anchor_ssrs.begin();
        it_anchor!=anchor_ssrs.end();++it_anchor){
      float match_score=
        atom::get_secondary_structure_match_score(
                    *it_anchor,*it_match);
      if (match_score<max_rmsd) matches.push_back(count);
      count++;
    }
    all_matches.push_back(matches);
  }
  return all_matches;
}

IMPMULTIFIT_END_NAMESPACE