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 java.util.*;
  24
  25 import java.awt.*;
  26 import java.awt.event.*;
  27
  28 import javax.swing.*;
  29 import javax.swing.event.*;
  30
  31 import net.miginfocom.swing.MigLayout;
  32
  33 import jalview.bin.Cache;
  34 import jalview.datamodel.*;
  35 import jalview.schemes.*;
  36 import jalview.util.MessageManager;
  37
  38 import java.awt.Dimension;
  39
  40 public class AnnotationColourChooser extends JPanel
  41 {
  42   JInternalFrame frame;
  43
  44   AlignViewport av;
  45
  46   AlignmentPanel ap;
  47
  48   ColourSchemeI oldcs;
  49
  50   Hashtable oldgroupColours;
  51
  52   jalview.datamodel.AlignmentAnnotation currentAnnotation;
  53
  54   boolean adjusting = false;
  55
  56   /**
  57    * enabled if the user is dragging the slider - try to keep updates to a
  58    * minimun
  59    */
  60   boolean sliderDragging = false;
  61
  62   public AnnotationColourChooser(AlignViewport av, final AlignmentPanel ap)
  63   {
  64     oldcs = av.getGlobalColourScheme();
  65     if (av.getAlignment().getGroups() != null)
  66     {
  67       oldgroupColours = new Hashtable();
  68       for (SequenceGroup sg : ap.av.getAlignment().getGroups())
  69       {
  70         if (sg.cs != null)
  71         {
  72           oldgroupColours.put(sg, sg.cs);
  73         }
  74       }
  75     }
  76     this.av = av;
  77     this.ap = ap;
  78     frame = new JInternalFrame();
  79     frame.setContentPane(this);
  80     frame.setLayer(JLayeredPane.PALETTE_LAYER);
  81     Desktop.addInternalFrame(frame,
  82             MessageManager.getString("label.colour_by_annotation"), 520,
  83             215);
  84
  85     slider.addChangeListener(new ChangeListener()
  86     {
  87       public void stateChanged(ChangeEvent evt)
  88       {
  89         if (!adjusting)
  90         {
  91           thresholdValue.setText(((float) slider.getValue() / 1000f) + "");
  92           valueChanged(!sliderDragging);
  93         }
  94       }
  95     });
  96     slider.addMouseListener(new MouseAdapter()
  97     {
  98       @Override
  99       public void mousePressed(MouseEvent e)
 100       {
 101         sliderDragging = true;
 102         super.mousePressed(e);
 103       }
 104
 105       @Override
 106       public void mouseDragged(MouseEvent e)
 107       {
 108         sliderDragging = true;
 109         super.mouseDragged(e);
 110       }
 111
 112       public void mouseReleased(MouseEvent evt)
 113       {
 114         if (sliderDragging)
 115         {
 116           sliderDragging = false;
 117           valueChanged(true);
 118         }
 119         ap.paintAlignment(true);
 120       }
 121     });
 122
 123     if (av.getAlignment().getAlignmentAnnotation() == null)
 124     {
 125       return;
 126     }
 127
 128     // Always get default shading from preferences.
 129     setDefaultMinMax();
 130
 131     adjusting = true;
 132     if (oldcs instanceof AnnotationColourGradient)
 133     {
 134       AnnotationColourGradient acg = (AnnotationColourGradient) oldcs;
 135       currentColours.setSelected(acg.isPredefinedColours()
 136               || acg.getBaseColour() != null);
 137       if (!acg.isPredefinedColours() && acg.getBaseColour() == null)
 138       {
 139         minColour.setBackground(acg.getMinColour());
 140         maxColour.setBackground(acg.getMaxColour());
 141       }
 142       seqAssociated.setSelected(acg.isSeqAssociated());
 143
 144     }
 145     annotations = new JComboBox(
 146             getAnnotationItems(seqAssociated.isSelected()));
 147
 148     threshold.addItem(MessageManager
 149             .getString("label.threshold_feature_no_thereshold"));
 150     threshold.addItem(MessageManager
 151             .getString("label.threshold_feature_above_thereshold"));
 152     threshold.addItem(MessageManager
 153             .getString("label.threshold_feature_below_thereshold"));
 154
 155     if (oldcs instanceof AnnotationColourGradient)
 156     {
 157       AnnotationColourGradient acg = (AnnotationColourGradient) oldcs;
 158       annotations.setSelectedItem(acg.getAnnotation());
 159       switch (acg.getAboveThreshold())
 160       {
 161       case AnnotationColourGradient.NO_THRESHOLD:
 162         threshold.setSelectedIndex(0);
 163         break;
 164       case AnnotationColourGradient.ABOVE_THRESHOLD:
 165         threshold.setSelectedIndex(1);
 166         break;
 167       case AnnotationColourGradient.BELOW_THRESHOLD:
 168         threshold.setSelectedIndex(2);
 169         break;
 170       default:
 171         throw new Error(MessageManager.getString("error.implementation_error_dont_know_about_thereshold_setting"));
 172       }
 173       thresholdIsMin.setSelected(acg.thresholdIsMinMax);
 174       thresholdValue.setText("" + acg.getAnnotationThreshold());
 175     }
 176
 177     try
 178     {
 179       jbInit();
 180     } catch (Exception ex)
 181     {
 182     }
 183
 184     adjusting = false;
 185
 186     changeColour();
 187     frame.invalidate();
 188     frame.pack();
 189
 190   }
 191
 192   private Vector<String> getAnnotationItems(boolean isSeqAssociated)
 193   {
 194     Vector<String> list = new Vector<String>();
 195     int index = 1;
 196     int[] anmap = new int[av.getAlignment().getAlignmentAnnotation().length];
 197     boolean enableSeqAss = false;
 198     for (int i = 0; i < av.getAlignment().getAlignmentAnnotation().length; i++)
 199     {
 200       if (av.getAlignment().getAlignmentAnnotation()[i].sequenceRef == null)
 201       {
 202         if (isSeqAssociated)
 203         {
 204           continue;
 205         }
 206       }
 207       else
 208       {
 209         enableSeqAss = true;
 210       }
 211       String label = av.getAlignment().getAlignmentAnnotation()[i].label;
 212       if (!list.contains(label))
 213       {
 214         anmap[list.size()] = i;
 215         list.addElement(label);
 216
 217       }
 218       else
 219       {
 220         if (!isSeqAssociated)
 221         {
 222           anmap[list.size()] = i;
 223           list.addElement(label + "_" + (index++));
 224         }
 225       }
 226     }
 227     seqAssociated.setEnabled(enableSeqAss);
 228     annmap = new int[list.size()];
 229     System.arraycopy(anmap, 0, annmap, 0, annmap.length);
 230     return list;
 231   }
 232
 233   private void setDefaultMinMax()
 234   {
 235     minColour.setBackground(Cache.getDefaultColour("ANNOTATIONCOLOUR_MIN",
 236             Color.orange));
 237     maxColour.setBackground(Cache.getDefaultColour("ANNOTATIONCOLOUR_MAX",
 238             Color.red));
 239   }
 240
 241   public AnnotationColourChooser()
 242   {
 243     try
 244     {
 245       jbInit();
 246     } catch (Exception ex)
 247     {
 248       ex.printStackTrace();
 249     }
 250   }
 251
 252   private void jbInit() throws Exception
 253   {
 254     minColour.setFont(JvSwingUtils.getLabelFont());
 255     minColour.setBorder(BorderFactory.createEtchedBorder());
 256     minColour.setPreferredSize(new Dimension(40, 20));
 257     minColour.setToolTipText(MessageManager.getString("label.min_colour"));
 258     minColour.addMouseListener(new MouseAdapter()
 259     {
 260       public void mousePressed(MouseEvent e)
 261       {
 262         if (minColour.isEnabled())
 263         {
 264           minColour_actionPerformed();
 265         }
 266       }
 267     });
 268     maxColour.setFont(JvSwingUtils.getLabelFont());
 269     maxColour.setBorder(BorderFactory.createEtchedBorder());
 270     maxColour.setPreferredSize(new Dimension(40, 20));
 271     maxColour.setToolTipText(MessageManager.getString("label.max_colour"));
 272     maxColour.addMouseListener(new MouseAdapter()
 273     {
 274       public void mousePressed(MouseEvent e)
 275       {
 276         if (maxColour.isEnabled())
 277         {
 278           maxColour_actionPerformed();
 279         }
 280       }
 281     });
 282     ok.setOpaque(false);
 283     ok.setText(MessageManager.getString("action.ok"));
 284     ok.addActionListener(new ActionListener()
 285     {
 286       public void actionPerformed(ActionEvent e)
 287       {
 288         ok_actionPerformed(e);
 289       }
 290     });
 291     cancel.setOpaque(false);
 292     cancel.setText(MessageManager.getString("action.cancel"));
 293     cancel.addActionListener(new ActionListener()
 294     {
 295       public void actionPerformed(ActionEvent e)
 296       {
 297         cancel_actionPerformed(e);
 298       }
 299     });
 300     defColours.setOpaque(false);
 301     defColours.setText(MessageManager.getString("action.set_defaults"));
 302     defColours.setToolTipText(MessageManager
 303             .getString("label.reset_min_max_colours_to_defaults"));
 304     defColours.addActionListener(new ActionListener()
 305     {
 306
 307       @Override
 308       public void actionPerformed(ActionEvent arg0)
 309       {
 310         resetColours_actionPerformed(arg0);
 311       }
 312     });
 313
 314     annotations.addActionListener(new ActionListener()
 315     {
 316       public void actionPerformed(ActionEvent e)
 317       {
 318         annotations_actionPerformed(e);
 319       }
 320     });
 321     threshold.addActionListener(new ActionListener()
 322     {
 323       public void actionPerformed(ActionEvent e)
 324       {
 325         threshold_actionPerformed(e);
 326       }
 327     });
 328     thresholdValue.addActionListener(new ActionListener()
 329     {
 330       public void actionPerformed(ActionEvent e)
 331       {
 332         thresholdValue_actionPerformed(e);
 333       }
 334     });
 335     slider.setPaintLabels(false);
 336     slider.setPaintTicks(true);
 337     slider.setBackground(Color.white);
 338     slider.setEnabled(false);
 339     slider.setOpaque(false);
 340     slider.setPreferredSize(new Dimension(100, 32));
 341     thresholdValue.setEnabled(false);
 342     thresholdValue.setColumns(7);
 343     currentColours.setFont(JvSwingUtils.getLabelFont());
 344     currentColours.setOpaque(false);
 345     currentColours.setText(MessageManager
 346             .getString("label.use_original_colours"));
 347     currentColours.addActionListener(new ActionListener()
 348     {
 349       public void actionPerformed(ActionEvent e)
 350       {
 351         currentColours_actionPerformed(e);
 352       }
 353     });
 354     thresholdIsMin.setBackground(Color.white);
 355     thresholdIsMin.setFont(JvSwingUtils.getLabelFont());
 356     thresholdIsMin.setText(MessageManager
 357             .getString("label.threshold_minmax"));
 358     thresholdIsMin.addActionListener(new ActionListener()
 359     {
 360       public void actionPerformed(ActionEvent actionEvent)
 361       {
 362         thresholdIsMin_actionPerformed(actionEvent);
 363       }
 364     });
 365     seqAssociated.setBackground(Color.white);
 366     seqAssociated.setFont(JvSwingUtils.getLabelFont());
 367     seqAssociated.setText(MessageManager
 368             .getString("label.per_sequence_only"));
 369     seqAssociated.addActionListener(new ActionListener()
 370     {
 371
 372       @Override
 373       public void actionPerformed(ActionEvent arg0)
 374       {
 375         seqAssociated_actionPerformed(arg0);
 376       }
 377     });
 378
 379     this.setLayout(borderLayout1);
 380     jPanel2.setLayout(new MigLayout("", "[left][center][right]", "[][][]"));
 381     jPanel1.setBackground(Color.white);
 382     jPanel2.setBackground(Color.white);
 383
 384     jPanel1.add(ok);
 385     jPanel1.add(cancel);
 386     jPanel2.add(annotations, "grow, wrap");
 387     jPanel2.add(seqAssociated);
 388     jPanel2.add(currentColours);
 389     JPanel colpanel = new JPanel(new FlowLayout());
 390     colpanel.setBackground(Color.white);
 391     colpanel.add(minColour);
 392     colpanel.add(maxColour);
 393     jPanel2.add(colpanel, "wrap");
 394     jPanel2.add(threshold);
 395     jPanel2.add(defColours, "skip 1, wrap");
 396     jPanel2.add(thresholdIsMin);
 397     jPanel2.add(slider, "grow");
 398     jPanel2.add(thresholdValue, "grow");
 399     this.add(jPanel1, java.awt.BorderLayout.SOUTH);
 400     this.add(jPanel2, java.awt.BorderLayout.CENTER);
 401     this.validate();
 402   }
 403
 404   protected void seqAssociated_actionPerformed(ActionEvent arg0)
 405   {
 406     adjusting = true;
 407     String cursel = (String) annotations.getSelectedItem();
 408     boolean isvalid = false, isseqs = seqAssociated.isSelected();
 409     this.annotations.removeAllItems();
 410     for (String anitem : getAnnotationItems(seqAssociated.isSelected()))
 411     {
 412       if (anitem.equals(cursel) || (isseqs && cursel.startsWith(anitem)))
 413       {
 414         isvalid = true;
 415         cursel = anitem;
 416       }
 417       this.annotations.addItem(anitem);
 418     }
 419     adjusting = false;
 420     if (isvalid)
 421     {
 422       this.annotations.setSelectedItem(cursel);
 423     }
 424     else
 425     {
 426       if (annotations.getItemCount() > 0)
 427       {
 428         annotations.setSelectedIndex(0);
 429       }
 430     }
 431   }
 432
 433   protected void resetColours_actionPerformed(ActionEvent arg0)
 434   {
 435     setDefaultMinMax();
 436     changeColour();
 437   }
 438
 439   JComboBox annotations;
 440
 441   int[] annmap;
 442
 443   JPanel minColour = new JPanel();
 444
 445   JPanel maxColour = new JPanel();
 446
 447   JButton defColours = new JButton();
 448
 449   JButton ok = new JButton();
 450
 451   JButton cancel = new JButton();
 452
 453   JPanel jPanel1 = new JPanel();
 454
 455   JPanel jPanel2 = new JPanel();
 456
 457   BorderLayout borderLayout1 = new BorderLayout();
 458
 459   JComboBox threshold = new JComboBox();
 460
 461   JSlider slider = new JSlider();
 462
 463   JTextField thresholdValue = new JTextField(20);
 464
 465   JCheckBox currentColours = new JCheckBox();
 466
 467   JCheckBox thresholdIsMin = new JCheckBox();
 468
 469   JCheckBox seqAssociated = new JCheckBox();
 470
 471   public void minColour_actionPerformed()
 472   {
 473     Color col = JColorChooser.showDialog(this,
 474             MessageManager.getString("label.select_colour_minimum_value"), minColour.getBackground());
 475     if (col != null)
 476     {
 477       minColour.setBackground(col);
 478     }
 479     minColour.repaint();
 480     changeColour();
 481   }
 482
 483   public void maxColour_actionPerformed()
 484   {
 485     Color col = JColorChooser.showDialog(this,
 486             MessageManager.getString("label.select_colour_maximum_value"), maxColour.getBackground());
 487     if (col != null)
 488     {
 489       maxColour.setBackground(col);
 490     }
 491     maxColour.repaint();
 492     changeColour();
 493   }
 494
 495   void changeColour()
 496   {
 497     // Check if combobox is still adjusting
 498     if (adjusting)
 499     {
 500       return;
 501     }
 502
 503     currentAnnotation = av.getAlignment().getAlignmentAnnotation()[annmap[annotations
 504             .getSelectedIndex()]];
 505
 506     int aboveThreshold = -1;
 507     if (threshold.getSelectedIndex() == 1)
 508     {
 509       aboveThreshold = AnnotationColourGradient.ABOVE_THRESHOLD;
 510     }
 511     else if (threshold.getSelectedIndex() == 2)
 512     {
 513       aboveThreshold = AnnotationColourGradient.BELOW_THRESHOLD;
 514     }
 515
 516     slider.setEnabled(true);
 517     thresholdValue.setEnabled(true);
 518     thresholdIsMin.setEnabled(true);
 519
 520     if (aboveThreshold == AnnotationColourGradient.NO_THRESHOLD)
 521     {
 522       slider.setEnabled(false);
 523       thresholdValue.setEnabled(false);
 524       thresholdValue.setText("");
 525       thresholdIsMin.setEnabled(false);
 526     }
 527     else if (aboveThreshold != AnnotationColourGradient.NO_THRESHOLD
 528             && currentAnnotation.threshold == null)
 529     {
 530       currentAnnotation
 531               .setThreshold(new jalview.datamodel.GraphLine(
 532                       (currentAnnotation.graphMax - currentAnnotation.graphMin) / 2f,
 533                       "Threshold", Color.black));
 534     }
 535
 536     if (aboveThreshold != AnnotationColourGradient.NO_THRESHOLD)
 537     {
 538       adjusting = true;
 539       float range = currentAnnotation.graphMax * 1000
 540               - currentAnnotation.graphMin * 1000;
 541
 542       slider.setMinimum((int) (currentAnnotation.graphMin * 1000));
 543       slider.setMaximum((int) (currentAnnotation.graphMax * 1000));
 544       slider.setValue((int) (currentAnnotation.threshold.value * 1000));
 545       thresholdValue.setText(currentAnnotation.threshold.value + "");
 546       slider.setMajorTickSpacing((int) (range / 10f));
 547       slider.setEnabled(true);
 548       thresholdValue.setEnabled(true);
 549       adjusting = false;
 550     }
 551
 552     AnnotationColourGradient acg = null;
 553     if (currentColours.isSelected())
 554     {
 555       acg = new AnnotationColourGradient(currentAnnotation,
 556               av.getGlobalColourScheme(), aboveThreshold);
 557     }
 558     else
 559     {
 560       acg = new AnnotationColourGradient(currentAnnotation,
 561               minColour.getBackground(), maxColour.getBackground(),
 562               aboveThreshold);
 563     }
 564     acg.setSeqAssociated(seqAssociated.isSelected());
 565
 566     if (currentAnnotation.graphMin == 0f
 567             && currentAnnotation.graphMax == 0f)
 568     {
 569       acg.setPredefinedColours(true);
 570     }
 571
 572     acg.thresholdIsMinMax = thresholdIsMin.isSelected();
 573
 574     av.setGlobalColourScheme(acg);
 575
 576     if (av.getAlignment().getGroups() != null)
 577     {
 578
 579       for (SequenceGroup sg : ap.av.getAlignment().getGroups())
 580       {
 581         if (sg.cs == null)
 582         {
 583           continue;
 584         }
 585
 586         if (currentColours.isSelected())
 587         {
 588           sg.cs = new AnnotationColourGradient(currentAnnotation, sg.cs,
 589                   aboveThreshold);
 590           ((AnnotationColourGradient) sg.cs).setSeqAssociated(seqAssociated
 591                   .isSelected());
 592
 593         }
 594         else
 595         {
 596           sg.cs = new AnnotationColourGradient(currentAnnotation,
 597                   minColour.getBackground(), maxColour.getBackground(),
 598                   aboveThreshold);
 599           ((AnnotationColourGradient) sg.cs).setSeqAssociated(seqAssociated
 600                   .isSelected());
 601         }
 602
 603       }
 604     }
 605     ap.alignmentChanged();
 606     // ensure all associated views (overviews, structures, etc) are notified of
 607     // updated colours.
 608     ap.paintAlignment(true);
 609   }
 610
 611   public void ok_actionPerformed(ActionEvent e)
 612   {
 613     changeColour();
 614     try
 615     {
 616       frame.setClosed(true);
 617     } catch (Exception ex)
 618     {
 619     }
 620   }
 621
 622   public void cancel_actionPerformed(ActionEvent e)
 623   {
 624     reset();
 625     // ensure all original colouring is propagated to listeners.
 626     ap.paintAlignment(true);
 627     try
 628     {
 629       frame.setClosed(true);
 630     } catch (Exception ex)
 631     {
 632     }
 633   }
 634
 635   void reset()
 636   {
 637     av.setGlobalColourScheme(oldcs);
 638     if (av.getAlignment().getGroups() != null)
 639     {
 640
 641       for (SequenceGroup sg : ap.av.getAlignment().getGroups())
 642       {
 643         sg.cs = (ColourSchemeI) oldgroupColours.get(sg);
 644       }
 645     }
 646   }
 647
 648   public void thresholdCheck_actionPerformed(ActionEvent e)
 649   {
 650     changeColour();
 651   }
 652
 653   public void annotations_actionPerformed(ActionEvent e)
 654   {
 655     changeColour();
 656   }
 657
 658   public void threshold_actionPerformed(ActionEvent e)
 659   {
 660     changeColour();
 661   }
 662
 663   public void thresholdValue_actionPerformed(ActionEvent e)
 664   {
 665     try
 666     {
 667       float f = Float.parseFloat(thresholdValue.getText());
 668       slider.setValue((int) (f * 1000));
 669     } catch (NumberFormatException ex)
 670     {
 671     }
 672   }
 673
 674   public void valueChanged(boolean updateAllAnnotation)
 675   {
 676     if (currentColours.isSelected()
 677             && !(av.getGlobalColourScheme() instanceof AnnotationColourGradient))
 678     {
 679       changeColour();
 680     }
 681     currentAnnotation.threshold.value = (float) slider.getValue() / 1000f;
 682     propagateSeqAssociatedThreshold(updateAllAnnotation);
 683     ap.paintAlignment(false);
 684   }
 685
 686   private void propagateSeqAssociatedThreshold(boolean allAnnotation)
 687   {
 688     if (currentAnnotation.sequenceRef == null
 689             || currentAnnotation.threshold == null)
 690     {
 691       return;
 692     }
 693     // TODO: JAL-1327 only update visible annotation thresholds if allAnnotation
 694     // is false, since we only need to provide a quick visual indicator
 695
 696     float thr = currentAnnotation.threshold.value;
 697     for (int i = 0; i < av.getAlignment().getAlignmentAnnotation().length; i++)
 698     {
 699       AlignmentAnnotation aa = av.getAlignment().getAlignmentAnnotation()[i];
 700       if (aa.label.equals(currentAnnotation.label))
 701       {
 702         aa.threshold.value = thr;
 703       }
 704     }
 705   }
 706
 707   public void currentColours_actionPerformed(ActionEvent e)
 708   {
 709     if (currentColours.isSelected())
 710     {
 711       reset();
 712     }
 713
 714     maxColour.setEnabled(!currentColours.isSelected());
 715     minColour.setEnabled(!currentColours.isSelected());
 716
 717     changeColour();
 718   }
 719
 720   public void thresholdIsMin_actionPerformed(ActionEvent actionEvent)
 721   {
 722     changeColour();
 723   }
 724
 725 }