root/trunk/FRII/cartwheel-interface/PairView.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 "PairView.hh"
#include <FL/Fl_Menu_Item.H>
#include <FL/Fl_Menu_Button.H>
#include <FL/fl_ask.H>
#include "MotifSearchView.hh"
#include "SingleView.hh"

#include <iostream>
#include <vector>

#include <FL/Fl.H>
#include <FL/Fl_Window.H>
#include <FL/Fl_Double_Window.H>
#include <FL/Fl_Tabs.H>
#include <FL/Fl_Button.H>
#include <FL/Fl_Check_Button.H>
#include <FL/Fl_Tile.H>
#include <FL/Fl_Pack.H>
#include <FL/Fl_Menu_Bar.H>
#include <FL/Fl_Menu_Item.H>
#include <FL/Fl_Menu_Button.H>
#include <FL/Fl_Scroll.H>

#include "ParsedSingleAnalysis.hh"
#include "ParsedPairwiseAnalysis.hh"
#include "parsed_analyses.hh"

#include "SeqcompMappingContainer.hh"
#include "SimpleMappingContainer.hh"
#include "BlastMappingContainer.hh"
#include "PairwiseMappingView.hh"
#include "DotPlotMappingView.hh"
#include "TripleMappingView.hh"
#include "SeqcompThresholdSlider.hh"
#include "SimpleFeaturesContainer.hh"
#include "SequenceView.hh"
#include "HorizontalSequenceView.hh"

#include "BlastFeaturesContainer.hh"
#include "BlastThresholdSlider.hh"
#include "SequenceZoomCoordinator.hh"
#include "TextLabel.hh"
#include "SlavedHorizontalSequenceView.hh"
#include "TextSequenceView.hh"
#include "ColorPatch.hh"

#include "SearchPlug.hh"

#define N_ROTATING_COLORS 5
static Fl_Color rotating_colors[N_ROTATING_COLORS] =
     { FL_RED, FL_BLUE, FL_GREEN, FL_CYAN, FL_MAGENTA };

// forward-declare callback to pop up the menu attached to the sequence bar.
static int toplevel_sequence_popup_menu(gui::SequenceView * seq_view,
                                        int x, int y, void * passthru);

// menu item callbacks:
static void new_cb(Fl_Widget * w, void * p);
static void close_cb(Fl_Widget * w, void * p);
static void quit_cb(Fl_Widget * w, void * p);

static Fl_Menu_Item menuitems[] = {
  { "&File",              0, 0, 0, FL_SUBMENU },
     { "&New analysis window", FL_CTRL + 'n', new_cb, 0 },
     { "&Close analysis window", FL_CTRL + 'w', close_cb, 0 },
     { "E&xit", FL_CTRL + 'q', quit_cb, 0 },
     { 0 },
  { 0 }
};

PairView::PairView(iff::PairAnalysisGroup* g, unsigned int w, unsigned int h) :
  Fl_Double_Window(w, h)
{
  _parent_window = NULL;

  int controls_x;
  int controls_y;
  int controls_width;

  Fl_Color color;

  //
  // Get the two sequences.
  //

  iff::Sequence* top_seq = g->get_top_group()->sequence();
  iff::Sequence* bot_seq = g->get_bot_group()->sequence();

  //
  // Set up the window a bit.
  //

  window_name = std::string("Pairwise comparison: ");
  
  std::string top_trunc(top_seq->name(), 0, 12);
  if (top_seq->name().length() > 12) {
    top_trunc += "...";
  }
  std::string bot_trunc(bot_seq->name(), 0, 12);
  if (bot_seq->name().length() > 12) {
    bot_trunc += "...";
  }

  window_name += top_trunc + " against " + bot_trunc;
  this->label(window_name.c_str());

  this->color(FL_WHITE);
  this->end();

  //
  // Create the basic views in the center.
  //

  Fl_Group* view1 = new Fl_Group(0, 60, 480, 570);
  Fl_Group* view2 = new Fl_Group(0, 60, 480, 570);

  //
  // Also create the sidebar that contains controls for the comparisons.
  //

  Fl_Scroll * cmp_scroll = new Fl_Scroll(485, 60, 212, 570);
  cmp_scroll->label("Comparisons");
  cmp_scroll->color(FL_WHITE);

  //
  // Create the two main views.
  //

  gui::PairwiseMappingView* pair_view1;
  gui::DotPlotMappingView* pair_view2;

  pair_view1 = new gui::PairwiseMappingView(0, 60, 485, 570,
                                            top_seq->name(),
                                            top_seq->sequence(),
                                            bot_seq->name(),
                                            bot_seq->sequence());
  view1->add(pair_view1);
  view1->label("Pair View");
  view1->color(FL_WHITE);

  pair_view2 = new gui::DotPlotMappingView(0, 60, 485, 570,
                                           top_seq->name(),
                                           top_seq->sequence(),
                                           bot_seq->name(),
                                           bot_seq->sequence());
  view2->add(pair_view2);
  view2->label("Dot Plot");
  view2->color(FL_WHITE);

  //
  // Now run through all of the feature lists & add control widgets to
  // the sidebar.
  //

  controls_x = 485 + 5;
  controls_y = 60;
  controls_width = 210 - 20;

  // get the feature lists
  std::vector<iff::FeatureList*> comparisons = g->get_feature_lists();

  unsigned int color_n = 0;
  for (unsigned int i = 0; i < comparisons.size(); i++) {
    iff::FeatureList* fl = comparisons[i];
    ParsedPairwiseAnalysis * pair_analysis = make_pairwise_analysis(fl, pair_view1);

    if (pair_analysis == NULL) continue;

    gui::MappingContainer * map = pair_analysis->get_mapping_container();

    color = rotating_colors[color_n % N_ROTATING_COLORS];
    color_n++;

    map->color(color);

    pair_view1->add_map(map);
    pair_view2->add_map(map);

    pair_analysis->add_control_panel(cmp_scroll, controls_x, controls_y,
                                     controls_width);
  }

  // Create two SequenceZoomCoordinators to coordinate the zooms between
  // the sequences for maps 1 & 2.

  gui::SequenceZoomCoordinator* top_coord = new gui::SequenceZoomCoordinator();
  gui::SequenceZoomCoordinator* bot_coord = new gui::SequenceZoomCoordinator();

  // First add the dotplot in...
  pair_view2->top_zoom_coordinator(top_coord);
  pair_view2->bot_zoom_coordinator(bot_coord);

  //////////////////////

  //
  // Run through all of the feature lists on the top/bottom sequences.
  //

  Fl_Group* top_scroll = new Fl_Scroll(485, 60, 212, 570);
  top_scroll->color(FL_WHITE);
  top_scroll->label("Top");

  iff::SingleAnalysisGroup* top = g->get_top_group();
  gui::SequenceView * top_view1 = pair_view1->get_top_seq_view();
  gui::SequenceView * top_view2 = pair_view2->get_top_seq_view();

  top_view1->popup_menu_handler(toplevel_sequence_popup_menu, top);
  top_view2->popup_menu_handler(toplevel_sequence_popup_menu, top);

#if 0
  for (unsigned int i = 0; i < plugs.size(); i++) {
    SearchPlug * p = plugs[i];
    p->add_view(top_view1);
    p->add_view(top_view2);
  }
#endif // 0

  top_view1->zoom_coordinator(top_coord);
  top_view2->zoom_coordinator(top_coord);

  // Top group stuff.

  std::vector<iff::FeatureList*> featureLists = top->get_feature_lists();

  color_n = 0;

  controls_y = 60;
  for (unsigned int i = 0; i < featureLists.size(); i++) {
    iff::FeatureList* fl = featureLists[i];
    ParsedSingleAnalysis * single_analysis = make_single_analysis(fl,
                                                                  top_view1);
    if (single_analysis == NULL) continue;

    gui::FeaturesContainer* cont;
    cont = single_analysis->get_features_container();

    color = rotating_colors[color_n % N_ROTATING_COLORS];
    color_n++;

    cont->color(color);

    top_view1->add_feature_list(cont);
    top_view2->add_feature_list(cont);

    single_analysis->add_control_panel(top_scroll, controls_x, controls_y,
                                       controls_width);
  }

  //
  // Transfer over the bottom group stuff, too.
  //

  Fl_Group* bot_scroll = new Fl_Scroll(485, 60, 212, 570);
  bot_scroll->label("Bottom");
  bot_scroll->color(FL_WHITE);

  iff::SingleAnalysisGroup* bot = g->get_bot_group();
  gui::SequenceView * bot_view1 = pair_view1->get_bot_seq_view();
  gui::SequenceView * bot_view2 = pair_view2->get_bot_seq_view();

  bot_view1->popup_menu_handler(toplevel_sequence_popup_menu, bot);
  bot_view2->popup_menu_handler(toplevel_sequence_popup_menu, bot);

#if 0
  for (unsigned int i = 0; i < plugs.size(); i++) {
    SearchPlug * p = plugs[i];
    p->add_view(bot_view1);
    p->add_view(bot_view2);
  }
#endif // 0

  bot_view1->zoom_coordinator(bot_coord);
  bot_view2->zoom_coordinator(bot_coord);

  featureLists = bot->get_feature_lists();

  controls_y = 60;
  for (unsigned int i = 0; i < featureLists.size(); i++) {
    iff::FeatureList* fl = featureLists[i];
    ParsedSingleAnalysis * single_analysis = make_single_analysis(fl,
                                                                  bot_view1);
    if (single_analysis == NULL) continue;

    gui::FeaturesContainer* cont;
    cont = single_analysis->get_features_container();

    color = rotating_colors[color_n % N_ROTATING_COLORS];
    color_n++;

    cont->color(color);

    bot_view1->add_feature_list(cont);
    bot_view2->add_feature_list(cont);

    single_analysis->add_control_panel(bot_scroll, controls_x, controls_y,
                                       controls_width);
  }

  //
  // Finalize everything.
  //

  // Menu bar

  Fl_Menu_Bar *m = new Fl_Menu_Bar(0, 0, w, 30);
  m->copy(menuitems);
  m->user_data(this);           // attach the PairView to the menu bar for cb

  this->add(m);

  // Add the two different pairwise views.
  Fl_Tabs* view_tabs = new Fl_Tabs(0, 30, 480, 600);
  view_tabs->add(view1);
  view_tabs->add(view2);

  view1->selection_color(FL_LIGHT1);
  view2->selection_color(FL_LIGHT1);
  view_tabs->selection_color(FL_WHITE);
  view_tabs->color(FL_WHITE);

  this->add(view_tabs);
  //this->resizable(view_tabs);

  // default to dotplot view for the moment.
  view_tabs->value(view2);

  // Also add the sidebar views.
  Fl_Box* ctrl_tabs_box = new Fl_Box(480, 30, 220, 600);
  ctrl_tabs_box->box(FL_UP_BOX);
  ctrl_tabs_box->color(FL_WHITE);

  Fl_Tabs* ctrl_tabs = new Fl_Tabs(482, 30, 212, 600);
  ctrl_tabs->add(cmp_scroll);
  ctrl_tabs->add(top_scroll);
  ctrl_tabs->add(bot_scroll);

  cmp_scroll->selection_color(FL_LIGHT1);
  top_scroll->selection_color(FL_LIGHT1);
  bot_scroll->selection_color(FL_LIGHT1);
  ctrl_tabs->selection_color(FL_WHITE);
  ctrl_tabs->color(FL_WHITE);

  this->add(ctrl_tabs_box);
  this->add(ctrl_tabs);

  resizable(this);
}

//////////////

//
// popup_menu -- display a popup menu
//

static Fl_Menu_Item _popup[] = {
  {"&view features", 0, 0 },
  {"&zoom", 0, 0 },
  {"&unzoom", 0, 0 },
  {"&copy sequence", 0, 0 },
  {"search for &motifs...", 0, 0 },
  { 0 }
};

static int toplevel_sequence_popup_menu(gui::SequenceView * seq_view,
                                        int x, int y, void * passthru)
{
  Fl_Menu_Button * w = new Fl_Menu_Button(0, 0, 100, 300);
  gui::MotifSearchView * motif_view;
  SingleView * new_view;
  iff::SingleAnalysisGroup * group = (iff::SingleAnalysisGroup *) passthru;

  x = Fl::event_x();
  y = Fl::event_y();

  w->copy(_popup);

  // I don't know why I have to do this, exactly, but there's some weird
  // code in Fl_Menu that runs through and systematically screws up the
  // position of the popup.  So I'm setting it manually.

  const Fl_Menu_Item * m = w->menu()->popup(x, y, w->label(), NULL, w);
  if (m != NULL) {      // picked an item
    w->picked(m);
    int v = w->value();
    switch(v) {
    case 0:
      new_view = new SingleView(group, 600, 400);
      new_view->show();
      break;
    case 1:                     // zoom
      seq_view->zoom();
      break;
    case 2:                     // unzoom
      seq_view->unzoom();
      break;
    case 3:                     // copy selected or displayed region
      seq_view->copy_to_clipboard();
      break;
    case 4:                     // bring up motif search window
      motif_view = new gui::MotifSearchView(seq_view);
      break;
    default:
      break;
    }
  }
  delete w;

  return 1;
}

//
// menu bar callbacks
//

// unhide parent (==> new analysis?)
static void new_cb(Fl_Widget * w, void * p)
{
  Fl_Menu_Bar * m = (Fl_Menu_Bar *) w;
  PairView * pv = (PairView *) m->user_data();

  Fl_Window * parent = pv->parent_window();
  if (parent != NULL) {
    parent->show();
  } else {
    fl_alert("I'm sorry, I have no way of bringing up a new analysis.");
  }
}

// close?
static void close_cb(Fl_Widget * w, void * p)
{
  Fl_Menu_Bar * m = (Fl_Menu_Bar *) w;
  Fl_Window * win = (Fl_Window *) m->user_data();
  win->hide();
}

// quit?
static void quit_cb(Fl_Widget * w, void * p)
{
  int choice = fl_choice("Close all windows and exit?",
                             "No", "Yes", 0);
  if (choice == 1) {
    exit(0);
  }
}