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(
 172                 "Implementation error: don't know about threshold setting for current AnnotationColourGradient.");
 173       }
 174       thresholdIsMin.setSelected(acg.thresholdIsMinMax);
 175       thresholdValue.setText("" + acg.getAnnotationThreshold());
 176     }
 177
 178     try
 179     {
 180       jbInit();
 181     } catch (Exception ex)
 182     {
 183     }
 184
 185     adjusting = false;
 186
 187     changeColour();
 188     frame.invalidate();
 189     frame.pack();
 190
 191   }
 192
 193   private Vector<String> getAnnotationItems(boolean isSeqAssociated)
 194   {
 195     Vector<String> list = new Vector<String>();
 196     int index = 1;
 197     int[] anmap = new int[av.getAlignment().getAlignmentAnnotation().length];
 198     boolean enableSeqAss = false;
 199     for (int i = 0; i < av.getAlignment().getAlignmentAnnotation().length; i++)
 200     {
 201       if (av.getAlignment().getAlignmentAnnotation()[i].sequenceRef == null)
 202       {
 203         if (isSeqAssociated)
 204         {
 205           continue;
 206         }
 207       }
 208       else
 209       {
 210         enableSeqAss = true;
 211       }
 212       String label = av.getAlignment().getAlignmentAnnotation()[i].label;
 213       if (!list.contains(label))
 214       {
 215         anmap[list.size()] = i;
 216         list.addElement(label);
 217
 218       }
 219       else
 220       {
 221         if (!isSeqAssociated)
 222         {
 223           anmap[list.size()] = i;
 224           list.addElement(label + "_" + (index++));
 225         }
 226       }
 227     }
 228     seqAssociated.setEnabled(enableSeqAss);
 229     annmap = new int[list.size()];
 230     System.arraycopy(anmap, 0, annmap, 0, annmap.length);
 231     return list;
 232   }
 233
 234   private void setDefaultMinMax()
 235   {
 236     minColour.setBackground(Cache.getDefaultColour("ANNOTATIONCOLOUR_MIN",
 237             Color.orange));
 238     maxColour.setBackground(Cache.getDefaultColour("ANNOTATIONCOLOUR_MAX",
 239             Color.red));
 240   }
 241
 242   public AnnotationColourChooser()
 243   {
 244     try
 245     {
 246       jbInit();
 247     } catch (Exception ex)
 248     {
 249       ex.printStackTrace();
 250     }
 251   }
 252
 253   private void jbInit() throws Exception
 254   {
 255     minColour.setFont(JvSwingUtils.getLabelFont());
 256     minColour.setBorder(BorderFactory.createEtchedBorder());
 257     minColour.setPreferredSize(new Dimension(40, 20));
 258     minColour.setToolTipText(MessageManager.getString("label.min_colour"));
 259     minColour.addMouseListener(new MouseAdapter()
 260     {
 261       public void mousePressed(MouseEvent e)
 262       {
 263         if (minColour.isEnabled())
 264         {
 265           minColour_actionPerformed();
 266         }
 267       }
 268     });
 269     maxColour.setFont(JvSwingUtils.getLabelFont());
 270     maxColour.setBorder(BorderFactory.createEtchedBorder());
 271     maxColour.setPreferredSize(new Dimension(40, 20));
 272     maxColour.setToolTipText(MessageManager.getString("label.max_colour"));
 273     maxColour.addMouseListener(new MouseAdapter()
 274     {
 275       public void mousePressed(MouseEvent e)
 276       {
 277         if (maxColour.isEnabled())
 278         {
 279           maxColour_actionPerformed();
 280         }
 281       }
 282     });
 283     ok.setOpaque(false);
 284     ok.setText(MessageManager.getString("action.ok"));
 285     ok.addActionListener(new ActionListener()
 286     {
 287       public void actionPerformed(ActionEvent e)
 288       {
 289         ok_actionPerformed(e);
 290       }
 291     });
 292     cancel.setOpaque(false);
 293     cancel.setText(MessageManager.getString("action.cancel"));
 294     cancel.addActionListener(new ActionListener()
 295     {
 296       public void actionPerformed(ActionEvent e)
 297       {
 298         cancel_actionPerformed(e);
 299       }
 300     });
 301     defColours.setOpaque(false);
 302     defColours.setText(MessageManager.getString("action.set_defaults"));
 303     defColours.setToolTipText(MessageManager
 304             .getString("label.reset_min_max_colours_to_defaults"));
 305     defColours.addActionListener(new ActionListener()
 306     {
 307
 308       @Override
 309       public void actionPerformed(ActionEvent arg0)
 310       {
 311         resetColours_actionPerformed(arg0);
 312       }
 313     });
 314
 315     annotations.addActionListener(new ActionListener()
 316     {
 317       public void actionPerformed(ActionEvent e)
 318       {
 319         annotations_actionPerformed(e);
 320       }
 321     });
 322     threshold.addActionListener(new ActionListener()
 323     {
 324       public void actionPerformed(ActionEvent e)
 325       {
 326         threshold_actionPerformed(e);
 327       }
 328     });
 329     thresholdValue.addActionListener(new ActionListener()
 330     {
 331       public void actionPerformed(ActionEvent e)
 332       {
 333         thresholdValue_actionPerformed(e);
 334       }
 335     });
 336     slider.setPaintLabels(false);
 337     slider.setPaintTicks(true);
 338     slider.setBackground(Color.white);
 339     slider.setEnabled(false);
 340     slider.setOpaque(false);
 341     slider.setPreferredSize(new Dimension(100, 32));
 342     thresholdValue.setEnabled(false);
 343     thresholdValue.setColumns(7);
 344     currentColours.setFont(JvSwingUtils.getLabelFont());
 345     currentColours.setOpaque(false);
 346     currentColours.setText(MessageManager
 347             .getString("label.use_original_colours"));
 348     currentColours.addActionListener(new ActionListener()
 349     {
 350       public void actionPerformed(ActionEvent e)
 351       {
 352         currentColours_actionPerformed(e);
 353       }
 354     });
 355     thresholdIsMin.setBackground(Color.white);
 356     thresholdIsMin.setFont(JvSwingUtils.getLabelFont());
 357     thresholdIsMin.setText(MessageManager
 358             .getString("label.threshold_minmax"));
 359     thresholdIsMin.addActionListener(new ActionListener()
 360     {
 361       public void actionPerformed(ActionEvent actionEvent)
 362       {
 363         thresholdIsMin_actionPerformed(actionEvent);
 364       }
 365     });
 366     seqAssociated.setBackground(Color.white);
 367     seqAssociated.setFont(JvSwingUtils.getLabelFont());
 368     seqAssociated.setText(MessageManager
 369             .getString("label.per_sequence_only"));
 370     seqAssociated.addActionListener(new ActionListener()
 371     {
 372
 373       @Override
 374       public void actionPerformed(ActionEvent arg0)
 375       {
 376         seqAssociated_actionPerformed(arg0);
 377       }
 378     });
 379
 380     this.setLayout(borderLayout1);
 381     jPanel2.setLayout(new MigLayout("", "[left][center][right]", "[][][]"));
 382     jPanel1.setBackground(Color.white);
 383     jPanel2.setBackground(Color.white);
 384
 385     jPanel1.add(ok);
 386     jPanel1.add(cancel);
 387     jPanel2.add(annotations, "grow, wrap");
 388     jPanel2.add(seqAssociated);
 389     jPanel2.add(currentColours);
 390     JPanel colpanel = new JPanel(new FlowLayout());
 391     colpanel.setBackground(Color.white);
 392     colpanel.add(minColour);
 393     colpanel.add(maxColour);
 394     jPanel2.add(colpanel, "wrap");
 395     jPanel2.add(threshold);
 396     jPanel2.add(defColours, "skip 1, wrap");
 397     jPanel2.add(thresholdIsMin);
 398     jPanel2.add(slider, "grow");
 399     jPanel2.add(thresholdValue, "grow");
 400     this.add(jPanel1, java.awt.BorderLayout.SOUTH);
 401     this.add(jPanel2, java.awt.BorderLayout.CENTER);
 402     this.validate();
 403   }
 404
 405   protected void seqAssociated_actionPerformed(ActionEvent arg0)
 406   {
 407     adjusting = true;
 408     String cursel = (String) annotations.getSelectedItem();
 409     boolean isvalid = false, isseqs = seqAssociated.isSelected();
 410     this.annotations.removeAllItems();
 411     for (String anitem : getAnnotationItems(seqAssociated.isSelected()))
 412     {
 413       if (anitem.equals(cursel) || (isseqs && cursel.startsWith(anitem)))
 414       {
 415         isvalid = true;
 416         cursel = anitem;
 417       }
 418       this.annotations.addItem(anitem);
 419     }
 420     adjusting = false;
 421     if (isvalid)
 422     {
 423       this.annotations.setSelectedItem(cursel);
 424     }
 425     else
 426     {
 427       if (annotations.getItemCount() > 0)
 428       {
 429         annotations.setSelectedIndex(0);
 430       }
 431     }
 432   }
 433
 434   protected void resetColours_actionPerformed(ActionEvent arg0)
 435   {
 436     setDefaultMinMax();
 437     changeColour();
 438   }
 439
 440   JComboBox annotations;
 441
 442   int[] annmap;
 443
 444   JPanel minColour = new JPanel();
 445
 446   JPanel maxColour = new JPanel();
 447
 448   JButton defColours = new JButton();
 449
 450   JButton ok = new JButton();
 451
 452   JButton cancel = new JButton();
 453
 454   JPanel jPanel1 = new JPanel();
 455
 456   JPanel jPanel2 = new JPanel();
 457
 458   BorderLayout borderLayout1 = new BorderLayout();
 459
 460   JComboBox threshold = new JComboBox();
 461
 462   JSlider slider = new JSlider();
 463
 464   JTextField thresholdValue = new JTextField(20);
 465
 466   JCheckBox currentColours = new JCheckBox();
 467
 468   JCheckBox thresholdIsMin = new JCheckBox();
 469
 470   JCheckBox seqAssociated = new JCheckBox();
 471
 472   public void minColour_actionPerformed()
 473   {
 474     Color col = JColorChooser.showDialog(this,
 475             "Select Colour for Minimum Value", minColour.getBackground());
 476     if (col != null)
 477     {
 478       minColour.setBackground(col);
 479     }
 480     minColour.repaint();
 481     changeColour();
 482   }
 483
 484   public void maxColour_actionPerformed()
 485   {
 486     Color col = JColorChooser.showDialog(this,
 487             "Select Colour for Maximum Value", maxColour.getBackground());
 488     if (col != null)
 489     {
 490       maxColour.setBackground(col);
 491     }
 492     maxColour.repaint();
 493     changeColour();
 494   }
 495
 496   void changeColour()
 497   {
 498     // Check if combobox is still adjusting
 499     if (adjusting)
 500     {
 501       return;
 502     }
 503
 504     currentAnnotation = av.getAlignment().getAlignmentAnnotation()[annmap[annotations
 505             .getSelectedIndex()]];
 506
 507     int aboveThreshold = -1;
 508     if (threshold.getSelectedIndex() == 1)
 509     {
 510       aboveThreshold = AnnotationColourGradient.ABOVE_THRESHOLD;
 511     }
 512     else if (threshold.getSelectedIndex() == 2)
 513     {
 514       aboveThreshold = AnnotationColourGradient.BELOW_THRESHOLD;
 515     }
 516
 517     slider.setEnabled(true);
 518     thresholdValue.setEnabled(true);
 519     thresholdIsMin.setEnabled(true);
 520
 521     if (aboveThreshold == AnnotationColourGradient.NO_THRESHOLD)
 522     {
 523       slider.setEnabled(false);
 524       thresholdValue.setEnabled(false);
 525       thresholdValue.setText("");
 526       thresholdIsMin.setEnabled(false);
 527     }
 528     else if (aboveThreshold != AnnotationColourGradient.NO_THRESHOLD
 529             && currentAnnotation.threshold == null)
 530     {
 531       currentAnnotation
 532               .setThreshold(new jalview.datamodel.GraphLine(
 533                       (currentAnnotation.graphMax - currentAnnotation.graphMin) / 2f,
 534                       "Threshold", Color.black));
 535     }
 536
 537     if (aboveThreshold != AnnotationColourGradient.NO_THRESHOLD)
 538     {
 539       adjusting = true;
 540       float range = currentAnnotation.graphMax * 1000
 541               - currentAnnotation.graphMin * 1000;
 542
 543       slider.setMinimum((int) (currentAnnotation.graphMin * 1000));
 544       slider.setMaximum((int) (currentAnnotation.graphMax * 1000));
 545       slider.setValue((int) (currentAnnotation.threshold.value * 1000));
 546       thresholdValue.setText(currentAnnotation.threshold.value + "");
 547       slider.setMajorTickSpacing((int) (range / 10f));
 548       slider.setEnabled(true);
 549       thresholdValue.setEnabled(true);
 550       adjusting = false;
 551     }
 552
 553     AnnotationColourGradient acg = null;
 554     if (currentColours.isSelected())
 555     {
 556       acg = new AnnotationColourGradient(currentAnnotation,
 557               av.getGlobalColourScheme(), aboveThreshold);
 558     }
 559     else
 560     {
 561       acg = new AnnotationColourGradient(currentAnnotation,
 562               minColour.getBackground(), maxColour.getBackground(),
 563               aboveThreshold);
 564     }
 565     acg.setSeqAssociated(seqAssociated.isSelected());
 566
 567     if (currentAnnotation.graphMin == 0f
 568             && currentAnnotation.graphMax == 0f)
 569     {
 570       acg.setPredefinedColours(true);
 571     }
 572
 573     acg.thresholdIsMinMax = thresholdIsMin.isSelected();
 574
 575     av.setGlobalColourScheme(acg);
 576
 577     if (av.getAlignment().getGroups() != null)
 578     {
 579
 580       for (SequenceGroup sg : ap.av.getAlignment().getGroups())
 581       {
 582         if (sg.cs == null)
 583         {
 584           continue;
 585         }
 586
 587         if (currentColours.isSelected())
 588         {
 589           sg.cs = new AnnotationColourGradient(currentAnnotation, sg.cs,
 590                   aboveThreshold);
 591           ((AnnotationColourGradient) sg.cs).setSeqAssociated(seqAssociated
 592                   .isSelected());
 593
 594         }
 595         else
 596         {
 597           sg.cs = new AnnotationColourGradient(currentAnnotation,
 598                   minColour.getBackground(), maxColour.getBackground(),
 599                   aboveThreshold);
 600           ((AnnotationColourGradient) sg.cs).setSeqAssociated(seqAssociated
 601                   .isSelected());
 602         }
 603
 604       }
 605     }
 606     ap.alignmentChanged();
 607     // ensure all associated views (overviews, structures, etc) are notified of
 608     // updated colours.
 609     ap.paintAlignment(true);
 610   }
 611
 612   public void ok_actionPerformed(ActionEvent e)
 613   {
 614     changeColour();
 615     try
 616     {
 617       frame.setClosed(true);
 618     } catch (Exception ex)
 619     {
 620     }
 621   }
 622
 623   public void cancel_actionPerformed(ActionEvent e)
 624   {
 625     reset();
 626     // ensure all original colouring is propagated to listeners.
 627     ap.paintAlignment(true);
 628     try
 629     {
 630       frame.setClosed(true);
 631     } catch (Exception ex)
 632     {
 633     }
 634   }
 635
 636   void reset()
 637   {
 638     av.setGlobalColourScheme(oldcs);
 639     if (av.getAlignment().getGroups() != null)
 640     {
 641
 642       for (SequenceGroup sg : ap.av.getAlignment().getGroups())
 643       {
 644         sg.cs = (ColourSchemeI) oldgroupColours.get(sg);
 645       }
 646     }
 647   }
 648
 649   public void thresholdCheck_actionPerformed(ActionEvent e)
 650   {
 651     changeColour();
 652   }
 653
 654   public void annotations_actionPerformed(ActionEvent e)
 655   {
 656     changeColour();
 657   }
 658
 659   public void threshold_actionPerformed(ActionEvent e)
 660   {
 661     changeColour();
 662   }
 663
 664   public void thresholdValue_actionPerformed(ActionEvent e)
 665   {
 666     try
 667     {
 668       float f = Float.parseFloat(thresholdValue.getText());
 669       slider.setValue((int) (f * 1000));
 670     } catch (NumberFormatException ex)
 671     {
 672     }
 673   }
 674
 675   public void valueChanged(boolean updateAllAnnotation)
 676   {
 677     if (currentColours.isSelected()
 678             && !(av.getGlobalColourScheme() instanceof AnnotationColourGradient))
 679     {
 680       changeColour();
 681     }
 682     currentAnnotation.threshold.value = (float) slider.getValue() / 1000f;
 683     propagateSeqAssociatedThreshold(updateAllAnnotation);
 684     ap.paintAlignment(false);
 685   }
 686
 687   private void propagateSeqAssociatedThreshold(boolean allAnnotation)
 688   {
 689     if (currentAnnotation.sequenceRef == null
 690             || currentAnnotation.threshold == null)
 691     {
 692       return;
 693     }
 694     // TODO: JAL-1327 only update visible annotation thresholds if allAnnotation
 695     // is false, since we only need to provide a quick visual indicator
 696
 697     float thr = currentAnnotation.threshold.value;
 698     for (int i = 0; i < av.getAlignment().getAlignmentAnnotation().length; i++)
 699     {
 700       AlignmentAnnotation aa = av.getAlignment().getAlignmentAnnotation()[i];
 701       if (aa.label.equals(currentAnnotation.label))
 702       {
 703         aa.threshold.value = thr;
 704       }
 705     }
 706   }
 707
 708   public void currentColours_actionPerformed(ActionEvent e)
 709   {
 710     if (currentColours.isSelected())
 711     {
 712       reset();
 713     }
 714
 715     maxColour.setEnabled(!currentColours.isSelected());
 716     minColour.setEnabled(!currentColours.isSelected());
 717
 718     changeColour();
 719   }
 720
 721   public void thresholdIsMin_actionPerformed(ActionEvent actionEvent)
 722   {
 723     changeColour();
 724   }
 725
 726 }