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