src/jalview/gui/AnnotationColourChooser.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
   3  * Copyright (C) 2014 The Jalview Authors
   4  *
   5  * This file is part of Jalview.
   6  *
   7  * Jalview is free software: you can redistribute it and/or
   8  * modify it under the terms of the GNU General Public License
   9  * as published by the Free Software Foundation, either version 3
  10  * of the License, or (at your option) any later version.
  11  *
  12  * Jalview is distributed in the hope that it will be useful, but
  13  * WITHOUT ANY WARRANTY; without even the implied warranty
  14  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  15  * PURPOSE.  See the GNU General Public License for more details.
  16  *
  17  * You should have received a copy of the GNU General Public License
  18  * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  19  * The Jalview Authors are detailed in the 'AUTHORS' file.
  20  */
  21 package jalview.gui;
  22
  23 import jalview.bin.Cache;
  24 import jalview.datamodel.SequenceGroup;
  25 import jalview.schemes.AnnotationColourGradient;
  26 import jalview.schemes.ColourSchemeI;
  27 import jalview.util.MessageManager;
  28
  29 import java.awt.BorderLayout;
  30 import java.awt.Color;
  31 import java.awt.Dimension;
  32 import java.awt.FlowLayout;
  33 import java.awt.event.ActionEvent;
  34 import java.awt.event.ActionListener;
  35 import java.awt.event.MouseAdapter;
  36 import java.awt.event.MouseEvent;
  37 import java.util.Hashtable;
  38
  39 import javax.swing.BorderFactory;
  40 import javax.swing.JButton;
  41 import javax.swing.JColorChooser;
  42 import javax.swing.JComboBox;
  43 import javax.swing.JInternalFrame;
  44 import javax.swing.JLayeredPane;
  45 import javax.swing.JPanel;
  46
  47 import net.miginfocom.swing.MigLayout;
  48
  49 @SuppressWarnings("serial")
  50 public class AnnotationColourChooser extends AnnotationRowFilter
  51 {
  52
  53   ColourSchemeI oldcs;
  54
  55   Hashtable<SequenceGroup, ColourSchemeI> oldgroupColours;
  56
  57   /**
  58    * enabled if the user is dragging the slider - try to keep updates to a
  59    * minimun
  60    */
  61
  62   JComboBox<String> annotations;
  63
  64   JButton defColours = new JButton();
  65
  66   JButton ok = new JButton();
  67
  68   JButton cancel = new JButton();
  69
  70   JPanel jPanel1 = new JPanel();
  71
  72   JPanel jPanel2 = new JPanel();
  73
  74   BorderLayout borderLayout1 = new BorderLayout();
  75
  76   private JComboBox<String> threshold = new JComboBox<String>();
  77
  78   public AnnotationColourChooser(AlignViewport av, final AlignmentPanel ap)
  79   {
  80     super(av, ap);
  81     oldcs = av.getGlobalColourScheme();
  82     if (av.getAlignment().getGroups() != null)
  83     {
  84       oldgroupColours = new Hashtable<SequenceGroup, ColourSchemeI>();
  85       for (SequenceGroup sg : ap.av.getAlignment().getGroups())
  86       {
  87         if (sg.cs != null)
  88         {
  89           oldgroupColours.put(sg, sg.cs);
  90         }
  91       }
  92     }
  93     frame = new JInternalFrame();
  94     frame.setContentPane(this);
  95     frame.setLayer(JLayeredPane.PALETTE_LAYER);
  96     Desktop.addInternalFrame(frame,
  97             MessageManager.getString("label.colour_by_annotation"), 520,
  98             215);
  99
 100     addSliderChangeListener();
 101     addSliderMouseListeners();
 102
 103     if (av.getAlignment().getAlignmentAnnotation() == null)
 104     {
 105       return;
 106     }
 107
 108     // Always get default shading from preferences.
 109     setDefaultMinMax();
 110
 111     adjusting = true;
 112     if (oldcs instanceof AnnotationColourGradient)
 113     {
 114       AnnotationColourGradient acg = (AnnotationColourGradient) oldcs;
 115       currentColours.setSelected(acg.isPredefinedColours()
 116               || acg.getBaseColour() != null);
 117       if (!acg.isPredefinedColours() && acg.getBaseColour() == null)
 118       {
 119         minColour.setBackground(acg.getMinColour());
 120         maxColour.setBackground(acg.getMaxColour());
 121       }
 122       seqAssociated.setSelected(acg.isSeqAssociated());
 123
 124     }
 125     annotations = new JComboBox<String>(
 126             getAnnotationItems(seqAssociated.isSelected()));
 127
 128     populateThresholdComboBox(threshold);
 129
 130     if (oldcs instanceof AnnotationColourGradient)
 131     {
 132       AnnotationColourGradient acg = (AnnotationColourGradient) oldcs;
 133       annotations.setSelectedItem(acg.getAnnotation());
 134       switch (acg.getAboveThreshold())
 135       {
 136       case AnnotationColourGradient.NO_THRESHOLD:
 137         getThreshold().setSelectedIndex(0);
 138         break;
 139       case AnnotationColourGradient.ABOVE_THRESHOLD:
 140         getThreshold().setSelectedIndex(1);
 141         break;
 142       case AnnotationColourGradient.BELOW_THRESHOLD:
 143         getThreshold().setSelectedIndex(2);
 144         break;
 145       default:
 146         throw new Error(MessageManager.getString("error.implementation_error_dont_know_about_thereshold_setting"));
 147       }
 148       thresholdIsMin.setSelected(acg.thresholdIsMinMax);
 149       thresholdValue.setText("" + acg.getAnnotationThreshold());
 150     }
 151
 152     try
 153     {
 154       jbInit();
 155     } catch (Exception ex)
 156     {
 157     }
 158     adjusting = false;
 159
 160     updateView();
 161     frame.invalidate();
 162     frame.pack();
 163   }
 164
 165   public AnnotationColourChooser()
 166   {
 167     try
 168     {
 169       jbInit();
 170     } catch (Exception ex)
 171     {
 172       ex.printStackTrace();
 173     }
 174   }
 175
 176   private void jbInit() throws Exception
 177   {
 178     minColour.setFont(JvSwingUtils.getLabelFont());
 179     minColour.setBorder(BorderFactory.createEtchedBorder());
 180     minColour.setPreferredSize(new Dimension(40, 20));
 181     minColour.setToolTipText(MessageManager.getString("label.min_colour"));
 182     minColour.addMouseListener(new MouseAdapter()
 183     {
 184       @Override
 185       public void mousePressed(MouseEvent e)
 186       {
 187         if (minColour.isEnabled())
 188         {
 189           minColour_actionPerformed();
 190         }
 191       }
 192     });
 193     maxColour.setFont(JvSwingUtils.getLabelFont());
 194     maxColour.setBorder(BorderFactory.createEtchedBorder());
 195     maxColour.setPreferredSize(new Dimension(40, 20));
 196     maxColour.setToolTipText(MessageManager.getString("label.max_colour"));
 197     maxColour.addMouseListener(new MouseAdapter()
 198     {
 199       @Override
 200       public void mousePressed(MouseEvent e)
 201       {
 202         if (maxColour.isEnabled())
 203         {
 204           maxColour_actionPerformed();
 205         }
 206       }
 207     });
 208     ok.setOpaque(false);
 209     ok.setText(MessageManager.getString("action.ok"));
 210     ok.addActionListener(new ActionListener()
 211     {
 212       @Override
 213       public void actionPerformed(ActionEvent e)
 214       {
 215         ok_actionPerformed(e);
 216       }
 217     });
 218     cancel.setOpaque(false);
 219     cancel.setText(MessageManager.getString("action.cancel"));
 220     cancel.addActionListener(new ActionListener()
 221     {
 222       @Override
 223       public void actionPerformed(ActionEvent e)
 224       {
 225         cancel_actionPerformed(e);
 226       }
 227     });
 228     defColours.setOpaque(false);
 229     defColours.setText(MessageManager.getString("action.set_defaults"));
 230     defColours.setToolTipText(MessageManager
 231             .getString("label.reset_min_max_colours_to_defaults"));
 232     defColours.addActionListener(new ActionListener()
 233     {
 234
 235       @Override
 236       public void actionPerformed(ActionEvent arg0)
 237       {
 238         resetColours_actionPerformed(arg0);
 239       }
 240     });
 241
 242     annotations.addActionListener(new ActionListener()
 243     {
 244       @Override
 245       public void actionPerformed(ActionEvent e)
 246       {
 247         annotations_actionPerformed(e);
 248       }
 249     });
 250     getThreshold().addActionListener(new ActionListener()
 251     {
 252       @Override
 253       public void actionPerformed(ActionEvent e)
 254       {
 255         threshold_actionPerformed(e);
 256       }
 257     });
 258     thresholdValue.addActionListener(new ActionListener()
 259     {
 260       @Override
 261       public void actionPerformed(ActionEvent e)
 262       {
 263         thresholdValue_actionPerformed(e);
 264       }
 265     });
 266     slider.setPaintLabels(false);
 267     slider.setPaintTicks(true);
 268     slider.setBackground(Color.white);
 269     slider.setEnabled(false);
 270     slider.setOpaque(false);
 271     slider.setPreferredSize(new Dimension(100, 32));
 272     thresholdValue.setEnabled(false);
 273     thresholdValue.setColumns(7);
 274     currentColours.setFont(JvSwingUtils.getLabelFont());
 275     currentColours.setOpaque(false);
 276     currentColours.setText(MessageManager
 277             .getString("label.use_original_colours"));
 278     currentColours.addActionListener(new ActionListener()
 279     {
 280       @Override
 281       public void actionPerformed(ActionEvent e)
 282       {
 283         currentColours_actionPerformed(e);
 284       }
 285     });
 286     thresholdIsMin.setBackground(Color.white);
 287     thresholdIsMin.setFont(JvSwingUtils.getLabelFont());
 288     thresholdIsMin.setText(MessageManager
 289             .getString("label.threshold_minmax"));
 290     thresholdIsMin.addActionListener(new ActionListener()
 291     {
 292       @Override
 293       public void actionPerformed(ActionEvent actionEvent)
 294       {
 295         thresholdIsMin_actionPerformed(actionEvent);
 296       }
 297     });
 298     seqAssociated.setBackground(Color.white);
 299     seqAssociated.setFont(JvSwingUtils.getLabelFont());
 300     seqAssociated.setText(MessageManager
 301             .getString("label.per_sequence_only"));
 302     seqAssociated.addActionListener(new ActionListener()
 303     {
 304
 305       @Override
 306       public void actionPerformed(ActionEvent arg0)
 307       {
 308         seqAssociated_actionPerformed(arg0, annotations, seqAssociated);
 309       }
 310     });
 311
 312     this.setLayout(borderLayout1);
 313     jPanel2.setLayout(new MigLayout("", "[left][center][right]", "[][][]"));
 314     jPanel1.setBackground(Color.white);
 315     jPanel2.setBackground(Color.white);
 316
 317     jPanel1.add(ok);
 318     jPanel1.add(cancel);
 319     jPanel2.add(annotations, "grow, wrap");
 320     jPanel2.add(seqAssociated);
 321     jPanel2.add(currentColours);
 322     JPanel colpanel = new JPanel(new FlowLayout());
 323     colpanel.setBackground(Color.white);
 324     colpanel.add(minColour);
 325     colpanel.add(maxColour);
 326     jPanel2.add(colpanel, "wrap");
 327     jPanel2.add(getThreshold());
 328     jPanel2.add(defColours, "skip 1, wrap");
 329     jPanel2.add(thresholdIsMin);
 330     jPanel2.add(slider, "grow");
 331     jPanel2.add(thresholdValue, "grow");
 332     this.add(jPanel1, java.awt.BorderLayout.SOUTH);
 333     this.add(jPanel2, java.awt.BorderLayout.CENTER);
 334     this.validate();
 335   }
 336
 337   protected void resetColours_actionPerformed(ActionEvent arg0)
 338   {
 339     setDefaultMinMax();
 340     updateView();
 341   }
 342
 343   private void setDefaultMinMax()
 344   {
 345     minColour.setBackground(Cache.getDefaultColour("ANNOTATIONCOLOUR_MIN",
 346             Color.orange));
 347     maxColour.setBackground(Cache.getDefaultColour("ANNOTATIONCOLOUR_MAX",
 348             Color.red));
 349   }
 350
 351   public void minColour_actionPerformed()
 352   {
 353     Color col = JColorChooser.showDialog(this,
 354             MessageManager.getString("label.select_colour_minimum_value"), minColour.getBackground());
 355     if (col != null)
 356     {
 357       minColour.setBackground(col);
 358     }
 359     minColour.repaint();
 360     updateView();
 361   }
 362
 363   public void maxColour_actionPerformed()
 364   {
 365     Color col = JColorChooser.showDialog(this,
 366             MessageManager.getString("label.select_colour_maximum_value"), maxColour.getBackground());
 367     if (col != null)
 368     {
 369       maxColour.setBackground(col);
 370     }
 371     maxColour.repaint();
 372     updateView();
 373   }
 374
 375   public void reset()
 376   {
 377     av.setGlobalColourScheme(oldcs);
 378     if (av.getAlignment().getGroups() != null)
 379     {
 380
 381       for (SequenceGroup sg : ap.av.getAlignment().getGroups())
 382       {
 383         sg.cs = oldgroupColours.get(sg);
 384       }
 385     }
 386   }
 387
 388   public void valueChanged(boolean updateAllAnnotation)
 389   {
 390     if (currentColours.isSelected()
 391             && !(av.getGlobalColourScheme() instanceof AnnotationColourGradient))
 392     {
 393       updateView();
 394     }
 395     getCurrentAnnotation().threshold.value = slider.getValue() / 1000f;
 396     propagateSeqAssociatedThreshold(updateAllAnnotation,
 397             getCurrentAnnotation());
 398     ap.paintAlignment(false);
 399   }
 400
 401   public JComboBox<String> getThreshold()
 402   {
 403     return threshold;
 404   }
 405
 406   public void setThreshold(JComboBox<String> threshold)
 407   {
 408     this.threshold = threshold;
 409   }
 410
 411   public void currentColours_actionPerformed(ActionEvent e)
 412   {
 413     if (currentColours.isSelected())
 414     {
 415       reset();
 416     }
 417     maxColour.setEnabled(!currentColours.isSelected());
 418     minColour.setEnabled(!currentColours.isSelected());
 419     updateView();
 420   }
 421
 422   @Override
 423   public void updateView()
 424   {
 425     changeColour();
 426   }
 427   void changeColour()
 428   {
 429     // Check if combobox is still adjusting
 430     if (adjusting)
 431     {
 432       return;
 433     }
 434
 435     setCurrentAnnotation(av.getAlignment().getAlignmentAnnotation()[annmap[annotations
 436             .getSelectedIndex()]]);
 437
 438     int selectedThresholdItem = getSelectedThresholdItem(getThreshold()
 439             .getSelectedIndex());
 440
 441     slider.setEnabled(true);
 442     thresholdValue.setEnabled(true);
 443     thresholdIsMin.setEnabled(true);
 444
 445     if (selectedThresholdItem == AnnotationColourGradient.NO_THRESHOLD)
 446     {
 447       slider.setEnabled(false);
 448       thresholdValue.setEnabled(false);
 449       thresholdValue.setText("");
 450       thresholdIsMin.setEnabled(false);
 451     }
 452     else if (selectedThresholdItem != AnnotationColourGradient.NO_THRESHOLD
 453             && getCurrentAnnotation().threshold == null)
 454     {
 455       getCurrentAnnotation()
 456               .setThreshold(new jalview.datamodel.GraphLine(
 457                       (getCurrentAnnotation().graphMax - getCurrentAnnotation().graphMin) / 2f,
 458                       "Threshold", Color.black));
 459     }
 460
 461     if (selectedThresholdItem != AnnotationColourGradient.NO_THRESHOLD)
 462     {
 463       adjusting = true;
 464       float range = getCurrentAnnotation().graphMax * 1000
 465               - getCurrentAnnotation().graphMin * 1000;
 466
 467       slider.setMinimum((int) (getCurrentAnnotation().graphMin * 1000));
 468       slider.setMaximum((int) (getCurrentAnnotation().graphMax * 1000));
 469       slider.setValue((int) (getCurrentAnnotation().threshold.value * 1000));
 470       thresholdValue.setText(getCurrentAnnotation().threshold.value + "");
 471       slider.setMajorTickSpacing((int) (range / 10f));
 472       slider.setEnabled(true);
 473       thresholdValue.setEnabled(true);
 474       adjusting = false;
 475     }
 476     colorAlignmContaining(getCurrentAnnotation(), selectedThresholdItem);
 477
 478     ap.alignmentChanged();
 479     // ensure all associated views (overviews, structures, etc) are notified of
 480     // updated colours.
 481     ap.paintAlignment(true);
 482   }
 483
 484 }