src/jalview/gui/AnnotationColourChooser.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
   3  * Copyright (C) 2015 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   JPanel jPanel1 = new JPanel();
  67
  68   JPanel jPanel2 = new JPanel();
  69
  70   BorderLayout borderLayout1 = new BorderLayout();
  71
  72   private JComboBox<String> threshold = new JComboBox<String>();
  73
  74   public AnnotationColourChooser(AlignViewport av, final AlignmentPanel ap)
  75   {
  76     super(av, ap);
  77     oldcs = av.getGlobalColourScheme();
  78     if (av.getAlignment().getGroups() != null)
  79     {
  80       oldgroupColours = new Hashtable<SequenceGroup, ColourSchemeI>();
  81       for (SequenceGroup sg : ap.av.getAlignment().getGroups())
  82       {
  83         if (sg.cs != null)
  84         {
  85           oldgroupColours.put(sg, sg.cs);
  86         }
  87       }
  88     }
  89     frame = new JInternalFrame();
  90     frame.setContentPane(this);
  91     frame.setLayer(JLayeredPane.PALETTE_LAYER);
  92     Desktop.addInternalFrame(frame,
  93             MessageManager.getString("label.colour_by_annotation"), 520,
  94             215);
  95
  96     addSliderChangeListener();
  97     addSliderMouseListeners();
  98
  99     if (av.getAlignment().getAlignmentAnnotation() == null)
 100     {
 101       return;
 102     }
 103
 104     // Always get default shading from preferences.
 105     setDefaultMinMax();
 106
 107     adjusting = true;
 108     if (oldcs instanceof AnnotationColourGradient)
 109     {
 110       AnnotationColourGradient acg = (AnnotationColourGradient) oldcs;
 111       currentColours.setSelected(acg.isPredefinedColours()
 112               || acg.getBaseColour() != null);
 113       if (!acg.isPredefinedColours() && acg.getBaseColour() == null)
 114       {
 115         minColour.setBackground(acg.getMinColour());
 116         maxColour.setBackground(acg.getMaxColour());
 117       }
 118       seqAssociated.setSelected(acg.isSeqAssociated());
 119
 120     }
 121     annotations = new JComboBox<String>(
 122             getAnnotationItems(seqAssociated.isSelected()));
 123
 124     populateThresholdComboBox(threshold);
 125
 126     if (oldcs instanceof AnnotationColourGradient)
 127     {
 128       AnnotationColourGradient acg = (AnnotationColourGradient) oldcs;
 129       annotations.setSelectedItem(acg.getAnnotation());
 130       switch (acg.getAboveThreshold())
 131       {
 132       case AnnotationColourGradient.NO_THRESHOLD:
 133         getThreshold().setSelectedIndex(0);
 134         break;
 135       case AnnotationColourGradient.ABOVE_THRESHOLD:
 136         getThreshold().setSelectedIndex(1);
 137         break;
 138       case AnnotationColourGradient.BELOW_THRESHOLD:
 139         getThreshold().setSelectedIndex(2);
 140         break;
 141       default:
 142         throw new Error(
 143                 MessageManager
 144                         .getString("error.implementation_error_dont_know_about_thereshold_setting"));
 145       }
 146       thresholdIsMin.setSelected(acg.thresholdIsMinMax);
 147       thresholdValue.setText("" + acg.getAnnotationThreshold());
 148     }
 149
 150     try
 151     {
 152       jbInit();
 153     } catch (Exception ex)
 154     {
 155     }
 156     adjusting = false;
 157
 158     updateView();
 159     frame.invalidate();
 160     frame.pack();
 161   }
 162
 163   public AnnotationColourChooser()
 164   {
 165     try
 166     {
 167       jbInit();
 168     } catch (Exception ex)
 169     {
 170       ex.printStackTrace();
 171     }
 172   }
 173
 174   private void jbInit() throws Exception
 175   {
 176     minColour.setFont(JvSwingUtils.getLabelFont());
 177     minColour.setBorder(BorderFactory.createEtchedBorder());
 178     minColour.setPreferredSize(new Dimension(40, 20));
 179     minColour.setToolTipText(MessageManager.getString("label.min_colour"));
 180     minColour.addMouseListener(new MouseAdapter()
 181     {
 182       @Override
 183       public void mousePressed(MouseEvent e)
 184       {
 185         if (minColour.isEnabled())
 186         {
 187           minColour_actionPerformed();
 188         }
 189       }
 190     });
 191     maxColour.setFont(JvSwingUtils.getLabelFont());
 192     maxColour.setBorder(BorderFactory.createEtchedBorder());
 193     maxColour.setPreferredSize(new Dimension(40, 20));
 194     maxColour.setToolTipText(MessageManager.getString("label.max_colour"));
 195     maxColour.addMouseListener(new MouseAdapter()
 196     {
 197       @Override
 198       public void mousePressed(MouseEvent e)
 199       {
 200         if (maxColour.isEnabled())
 201         {
 202           maxColour_actionPerformed();
 203         }
 204       }
 205     });
 206     ok.setOpaque(false);
 207     ok.setText(MessageManager.getString("action.ok"));
 208     ok.addActionListener(new ActionListener()
 209     {
 210       @Override
 211       public void actionPerformed(ActionEvent e)
 212       {
 213         ok_actionPerformed(e);
 214       }
 215     });
 216     cancel.setOpaque(false);
 217     cancel.setText(MessageManager.getString("action.cancel"));
 218     cancel.addActionListener(new ActionListener()
 219     {
 220       @Override
 221       public void actionPerformed(ActionEvent e)
 222       {
 223         cancel_actionPerformed(e);
 224       }
 225     });
 226     defColours.setOpaque(false);
 227     defColours.setText(MessageManager.getString("action.set_defaults"));
 228     defColours.setToolTipText(MessageManager
 229             .getString("label.reset_min_max_colours_to_defaults"));
 230     defColours.addActionListener(new ActionListener()
 231     {
 232
 233       @Override
 234       public void actionPerformed(ActionEvent arg0)
 235       {
 236         resetColours_actionPerformed(arg0);
 237       }
 238     });
 239
 240     annotations.addActionListener(new ActionListener()
 241     {
 242       @Override
 243       public void actionPerformed(ActionEvent e)
 244       {
 245         annotations_actionPerformed(e);
 246       }
 247     });
 248     getThreshold().addActionListener(new ActionListener()
 249     {
 250       @Override
 251       public void actionPerformed(ActionEvent e)
 252       {
 253         threshold_actionPerformed(e);
 254       }
 255     });
 256     thresholdValue.addActionListener(new ActionListener()
 257     {
 258       @Override
 259       public void actionPerformed(ActionEvent e)
 260       {
 261         thresholdValue_actionPerformed(e);
 262       }
 263     });
 264     slider.setPaintLabels(false);
 265     slider.setPaintTicks(true);
 266     slider.setBackground(Color.white);
 267     slider.setEnabled(false);
 268     slider.setOpaque(false);
 269     slider.setPreferredSize(new Dimension(100, 32));
 270     thresholdValue.setEnabled(false);
 271     thresholdValue.setColumns(7);
 272     currentColours.setFont(JvSwingUtils.getLabelFont());
 273     currentColours.setOpaque(false);
 274     currentColours.setText(MessageManager
 275             .getString("label.use_original_colours"));
 276     currentColours.addActionListener(new ActionListener()
 277     {
 278       @Override
 279       public void actionPerformed(ActionEvent e)
 280       {
 281         currentColours_actionPerformed(e);
 282       }
 283     });
 284     thresholdIsMin.setBackground(Color.white);
 285     thresholdIsMin.setFont(JvSwingUtils.getLabelFont());
 286     thresholdIsMin.setText(MessageManager
 287             .getString("label.threshold_minmax"));
 288     thresholdIsMin.addActionListener(new ActionListener()
 289     {
 290       @Override
 291       public void actionPerformed(ActionEvent actionEvent)
 292       {
 293         thresholdIsMin_actionPerformed(actionEvent);
 294       }
 295     });
 296     seqAssociated.setBackground(Color.white);
 297     seqAssociated.setFont(JvSwingUtils.getLabelFont());
 298     seqAssociated.setText(MessageManager
 299             .getString("label.per_sequence_only"));
 300     seqAssociated.addActionListener(new ActionListener()
 301     {
 302
 303       @Override
 304       public void actionPerformed(ActionEvent arg0)
 305       {
 306         seqAssociated_actionPerformed(arg0, annotations, seqAssociated);
 307       }
 308     });
 309
 310     this.setLayout(borderLayout1);
 311     jPanel2.setLayout(new MigLayout("", "[left][center][right]", "[][][]"));
 312     jPanel1.setBackground(Color.white);
 313     jPanel2.setBackground(Color.white);
 314
 315     jPanel1.add(ok);
 316     jPanel1.add(cancel);
 317     jPanel2.add(annotations, "grow, wrap");
 318     jPanel2.add(seqAssociated);
 319     jPanel2.add(currentColours);
 320     JPanel colpanel = new JPanel(new FlowLayout());
 321     colpanel.setBackground(Color.white);
 322     colpanel.add(minColour);
 323     colpanel.add(maxColour);
 324     jPanel2.add(colpanel, "wrap");
 325     jPanel2.add(getThreshold());
 326     jPanel2.add(defColours, "skip 1, wrap");
 327     jPanel2.add(thresholdIsMin);
 328     jPanel2.add(slider, "grow");
 329     jPanel2.add(thresholdValue, "grow");
 330     this.add(jPanel1, java.awt.BorderLayout.SOUTH);
 331     this.add(jPanel2, java.awt.BorderLayout.CENTER);
 332     this.validate();
 333   }
 334
 335   protected void resetColours_actionPerformed(ActionEvent arg0)
 336   {
 337     setDefaultMinMax();
 338     updateView();
 339   }
 340
 341   private void setDefaultMinMax()
 342   {
 343     minColour.setBackground(Cache.getDefaultColour("ANNOTATIONCOLOUR_MIN",
 344             Color.orange));
 345     maxColour.setBackground(Cache.getDefaultColour("ANNOTATIONCOLOUR_MAX",
 346             Color.red));
 347   }
 348
 349   public void minColour_actionPerformed()
 350   {
 351     Color col = JColorChooser.showDialog(this,
 352             MessageManager.getString("label.select_colour_minimum_value"),
 353             minColour.getBackground());
 354     if (col != null)
 355     {
 356       minColour.setBackground(col);
 357     }
 358     minColour.repaint();
 359     updateView();
 360   }
 361
 362   public void maxColour_actionPerformed()
 363   {
 364     Color col = JColorChooser.showDialog(this,
 365             MessageManager.getString("label.select_colour_maximum_value"),
 366             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 (slider.isEnabled())
 391     {
 392       if (currentColours.isSelected()
 393               && !(av.getGlobalColourScheme() instanceof AnnotationColourGradient))
 394       {
 395         updateView();
 396       }
 397       getCurrentAnnotation().threshold.value = slider.getValue() / 1000f;
 398       propagateSeqAssociatedThreshold(updateAllAnnotation,
 399               getCurrentAnnotation());
 400       ap.paintAlignment(false);
 401     }
 402   }
 403
 404   public JComboBox<String> getThreshold()
 405   {
 406     return threshold;
 407   }
 408
 409   public void setThreshold(JComboBox<String> threshold)
 410   {
 411     this.threshold = threshold;
 412   }
 413
 414   public void currentColours_actionPerformed(ActionEvent e)
 415   {
 416     if (currentColours.isSelected())
 417     {
 418       reset();
 419     }
 420     maxColour.setEnabled(!currentColours.isSelected());
 421     minColour.setEnabled(!currentColours.isSelected());
 422     updateView();
 423   }
 424
 425   @Override
 426   public void updateView()
 427   {
 428     // Check if combobox is still adjusting
 429     if (adjusting)
 430     {
 431       return;
 432     }
 433
 434     setCurrentAnnotation(av.getAlignment().getAlignmentAnnotation()[annmap[annotations
 435             .getSelectedIndex()]]);
 436
 437     int selectedThresholdItem = getSelectedThresholdItem(getThreshold()
 438             .getSelectedIndex());
 439
 440     slider.setEnabled(true);
 441     thresholdValue.setEnabled(true);
 442     thresholdIsMin.setEnabled(true);
 443
 444     if (selectedThresholdItem == AnnotationColourGradient.NO_THRESHOLD)
 445     {
 446       slider.setEnabled(false);
 447       thresholdValue.setEnabled(false);
 448       thresholdValue.setText("");
 449       thresholdIsMin.setEnabled(false);
 450     }
 451     else if (selectedThresholdItem != AnnotationColourGradient.NO_THRESHOLD
 452             && getCurrentAnnotation().threshold == null)
 453     {
 454       getCurrentAnnotation()
 455               .setThreshold(
 456                       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 }