root/trunk/FRII/cartwheel-interface/AlignmentCloseupView.cc

/*
 * This file is part of the FamilyRelations II source distribution.
 *
 * FamilyRelations II is part of the FamilyJewels package for comparative
 * sequence analysis: http://family.caltech.edu/.
 *
 * Contact author: C. Titus Brown, titus@caltech.edu.
 *
 * This program and all associated source code files are Copyright (C) 2003,
 * 2004 the California Institute of Technology, Pasadena, CA, 91125 USA.  It
 * is under the Lesser GNU Public License; please see the included
 * LICENSE.txt file for more information, or contact Titus directly.
 *
 */

#include <iostream>
#include "AlignmentCloseupView.hh"
#include "SequenceZoomCoordinator.hh"
#include "FeatureInfoDisplayWindow.hh"

// An internal class to deal with highlighting features in the pairwise map
// display alignments between the two sequences.

class _HighlightedFeatureList : public gui::SimpleMappingContainer {
protected:
  gui::FeaturesContainer * _orig_c;
public:
  _HighlightedFeatureList(gui::FeaturesContainer* c) :_orig_c(c) {
    select_feature(NULL);
  }

  void select_feature(const gui::Feature * f) {
    delete _c;
    gui::FeatureList * new_l = new gui::FeatureList();
    if (f) { new_l->add_feature(f->copy_me()); }
    _c = new gui::SimpleFeaturesContainer(new_l);

    notify_changed();
  }
};

static void feature_select_cb(const gui::Feature * f, void * passthru)
{
  AlignmentCloseupView * aln_obj;
  aln_obj = (AlignmentCloseupView *) passthru;

  aln_obj->change_viewed_feature(f);
}

static void feature_info_cb(Fl_Widget * w, void * passthru)
{
  gui::Feature * f = (gui::Feature*) passthru;
  if (f && f->has_info()) {
    FeatureInfoDisplayWindow * disp = new FeatureInfoDisplayWindow(300, 400,
                                                                   f);
    disp->show();
  }
}

static void del_window_cb(Fl_Widget * w, void * p)
{
  Fl_Window * window = (Fl_Window *) w;

  w->hide();
  delete window;
}

AlignmentCloseupView::AlignmentCloseupView(const gui::SimpleMappingContainer * map,
                                           const gui::MappingView * view,
                                           unsigned int w, unsigned int h) :
  Fl_Double_Window(w, h)
{
  callback(del_window_cb);

  gui::SequenceView * old_top_view = view->get_top_seq_view();
  gui::SequenceView * old_bot_view = view->get_bot_seq_view();

  std::string top_name = old_top_view->sequence_name();
  std::string top_seq = old_top_view->sequence_text();
  std::string bot_name = old_top_view->sequence_name();
  std::string bot_seq = old_bot_view->sequence_text();

  // tile this window
  tiling = new Fl_Pack(0, 0, w, h);
  add(tiling);

  // Also create two separate sequence lines showing the features.
  line_view_a = new gui::HorizontalSequenceView(0, 100, w, top_seq.length());
  line_view_a->sequence_text(top_seq);

  line_view_b = new gui::ClickableFeaturesSequenceView(0, 0, w, top_seq.length(), map->get_features_container());
  line_view_b->sequence_text(top_seq);
  line_view_b->show_sequence_line(false);
  line_view_b->select_feature_handler(feature_select_cb, this);

  gui::SequenceZoomCoordinator* top_coord = new gui::SequenceZoomCoordinator();
  gui::SequenceZoomCoordinator* bot_coord = new gui::SequenceZoomCoordinator();
  line_view_a->zoom_coordinator(top_coord);
  line_view_b->zoom_coordinator(top_coord);

  // create a new alignment map
  gui::SimpleMappingContainer * new_map = map->copy_me();

  // create a new view with that map.
  new_view = new gui::PairwiseMappingView(0, 200, w, 250,
                                          top_name, top_seq,
                                          bot_name, bot_seq);
  
  new_view->get_top_seq_view()->zoom_coordinator(top_coord);
  new_view->get_bot_seq_view()->zoom_coordinator(bot_coord);

  new_view->add_map(new_map);

  hilite = new _HighlightedFeatureList(map->get_features_container());
  hilite->color(FL_RED);
  new_view->add_map(hilite);

  //
  // Devote the lower half of the window to display the alignment
  // and associated information.
  //

  aln_label = new gui::TextLabel(0, 0, w - 120, 40, "Alignment:");
  aln_label->align(FL_ALIGN_LEFT);
  aln_label->color(FL_WHITE);
  aln_label->bold(true);
  aln_label->box(FL_THIN_DOWN_FRAME);

  aln_info_pack = new Fl_Pack(0, 0, w, 40);
  aln_info_pack->type(Fl_Pack::HORIZONTAL);
  aln_info_pack->add(aln_label);

  view_info = new Fl_Button(w - 120, 0, 120, 40);
  view_info->label("View feature info");
  view_info->callback(feature_info_cb);
  aln_info_pack->add(view_info);
  
  aln_view = new gui::AlignedSequencePairWidget(0, 0, w, h);

  tiling->add(line_view_a);
  tiling->add(line_view_b);
  tiling->add(new_view);
  tiling->add(aln_info_pack);
  tiling->add(aln_view);

  //
  // Set the basic viewing boundaries of the maps.
  //

  unsigned int top_sel_start = old_top_view->start_sel_base();
  unsigned int top_sel_end = old_top_view->end_sel_base();
  
  unsigned int bot_sel_start = old_bot_view->start_sel_base();
  unsigned int bot_sel_end = old_bot_view->end_sel_base();

  line_view_a->set_visible_bases(top_sel_start, top_sel_end);
  line_view_b->set_visible_bases(top_sel_start, top_sel_end);
  new_view->get_top_seq_view()->set_visible_bases(top_sel_start,
                                                  top_sel_end);

  new_view->get_bot_seq_view()->set_visible_bases(bot_sel_start, bot_sel_end);

  //
  // Select a feature.
  //

  const gui::FeatureList * l = map->get_features_container()->getFeatureList();
  const gui::Feature * f = NULL;
  for (unsigned int i = 0; i < l->n_features(); i++) {
    f = l->get(i);
    if (f->has_alignment() &&
        f->end > top_sel_start && // overlaps
        f->start < top_sel_end) {
      break;
    }
  }

  // this calls the select_feature callback, which in turn sets the aln_view
  // current feature.
  if (f) {
    line_view_b->select_feature(f);
  }

  //
  // Finalize.
  //

  resizable(this);
  end();
}

AlignmentCloseupView::~AlignmentCloseupView()
{
  // delete hilite;
  // delete new_view;
  // delete aln_view;
  // delete line_view_a;
  // delete line_view_b;
  // delete aln_label;
  // delete aln_pair;
}

void AlignmentCloseupView::change_viewed_feature(const gui::Feature * f)
{
  aln_view->change_feature(f);
  ((_HighlightedFeatureList *) hilite)->select_feature(f);

  gui::Feature * new_f = f->copy_me();
  gui::Feature * old_f = (gui::Feature *) view_info->user_data();
  if (old_f) { delete old_f; }

  if (f->has_info()) {
    view_info->label("View info...");
    view_info->user_data(new_f);        // so the "view info" button has access to it.
  } else {
    view_info->label("no info");
    view_info->user_data(NULL);
  }
  redraw();
}