src/jalview/gui/AnnotationColourChooser.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
   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 of the License, or (at your option) any later version.
  10  *
  11  * Jalview is distributed in the hope that it will be useful, but
  12  * WITHOUT ANY WARRANTY; without even the implied warranty
  13  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  14  * PURPOSE.  See the GNU General Public License for more details.
  15  *
  16  * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  17  * The Jalview Authors are detailed in the 'AUTHORS' file.
  18  */
  19 package jalview.gui;
  20
  21 import java.util.*;
  22
  23 import java.awt.*;
  24 import java.awt.event.*;
  25
  26 import javax.swing.*;
  27 import javax.swing.event.*;
  28
  29 import net.miginfocom.swing.MigLayout;
  30
  31 import jalview.bin.Cache;
  32 import jalview.datamodel.*;
  33 import jalview.schemes.*;
  34 import java.awt.Dimension;
  35
  36 public class AnnotationColourChooser extends JPanel
  37 {
  38   JInternalFrame frame;
  39
  40   AlignViewport av;
  41
  42   AlignmentPanel ap;
  43
  44   ColourSchemeI oldcs;
  45
  46   Hashtable oldgroupColours;
  47
  48   jalview.datamodel.AlignmentAnnotation currentAnnotation;
  49
  50   boolean adjusting = false;
  51   /**
  52    * enabled if the user is dragging the slider - try to keep updates to a minimun
  53    */
  54   boolean sliderDragging = false;
  55
  56   public AnnotationColourChooser(AlignViewport av, final AlignmentPanel ap)
  57   {
  58     oldcs = av.getGlobalColourScheme();
  59     if (av.getAlignment().getGroups() != null)
  60     {
  61       oldgroupColours = new Hashtable();
  62       for (SequenceGroup sg : ap.av.getAlignment().getGroups())
  63       {
  64         if (sg.cs != null)
  65         {
  66           oldgroupColours.put(sg, sg.cs);
  67         }
  68       }
  69     }
  70     this.av = av;
  71     this.ap = ap;
  72     frame = new JInternalFrame();
  73     frame.setContentPane(this);
  74     frame.setLayer(JLayeredPane.PALETTE_LAYER);
  75     Desktop.addInternalFrame(frame, "Colour by Annotation", 520, 215);
  76
  77     slider.addChangeListener(new ChangeListener()
  78     {
  79       public void stateChanged(ChangeEvent evt)
  80       {
  81         if (!adjusting)
  82         {
  83           thresholdValue.setText(((float) slider.getValue() / 1000f) + "");
  84           valueChanged(!sliderDragging);
  85         }
  86       }
  87     });
  88     slider.addMouseListener(new MouseAdapter()
  89     {
  90       @Override
  91       public void mousePressed(MouseEvent e)
  92       {
  93         sliderDragging=true;
  94         super.mousePressed(e);
  95       }
  96
  97       @Override
  98       public void mouseDragged(MouseEvent e)
  99       {
 100         sliderDragging=true;
 101         super.mouseDragged(e);
 102       }
 103       public void mouseReleased(MouseEvent evt)
 104       {
 105         if (sliderDragging)
 106         {
 107           sliderDragging=false;
 108           valueChanged(true);
 109         }
 110         ap.paintAlignment(true);
 111       }
 112     });
 113
 114     if (av.getAlignment().getAlignmentAnnotation() == null)
 115     {
 116       return;
 117     }
 118
 119     // Always get default shading from preferences.
 120     setDefaultMinMax();
 121
 122     if (oldcs instanceof AnnotationColourGradient)
 123     {
 124       AnnotationColourGradient acg = (AnnotationColourGradient) oldcs;
 125       currentColours.setSelected(acg.predefinedColours);
 126       if (!acg.predefinedColours)
 127       {
 128         minColour.setBackground(acg.getMinColour());
 129         maxColour.setBackground(acg.getMaxColour());
 130       }
 131       seqAssociated.setSelected(acg.isSeqAssociated());
 132     }
 133     adjusting = true;
 134     annotations = new JComboBox(
 135             getAnnotationItems(seqAssociated.isSelected()));
 136
 137     threshold.addItem("No Threshold");
 138     threshold.addItem("Above Threshold");
 139     threshold.addItem("Below Threshold");
 140
 141     if (oldcs instanceof AnnotationColourGradient)
 142     {
 143       AnnotationColourGradient acg = (AnnotationColourGradient) oldcs;
 144       annotations.setSelectedItem(acg.getAnnotation());
 145       switch (acg.getAboveThreshold())
 146       {
 147       case AnnotationColourGradient.NO_THRESHOLD:
 148         threshold.setSelectedItem("No Threshold");
 149         break;
 150       case AnnotationColourGradient.ABOVE_THRESHOLD:
 151         threshold.setSelectedItem("Above Threshold");
 152         break;
 153       case AnnotationColourGradient.BELOW_THRESHOLD:
 154         threshold.setSelectedItem("Below Threshold");
 155         break;
 156       default:
 157         throw new Error(
 158                 "Implementation error: don't know about threshold setting for current AnnotationColourGradient.");
 159       }
 160       thresholdIsMin.setSelected(acg.thresholdIsMinMax);
 161       thresholdValue.setText("" + acg.getAnnotationThreshold());
 162     }
 163
 164     try
 165     {
 166       jbInit();
 167     } catch (Exception ex)
 168     {
 169     }
 170
 171     adjusting = false;
 172
 173     changeColour();
 174     frame.invalidate();
 175     frame.pack();
 176
 177   }
 178
 179   private Vector<String> getAnnotationItems(boolean isSeqAssociated)
 180   {
 181     Vector<String> list = new Vector<String>();
 182     int index = 1;
 183     int[] anmap = new int[av.getAlignment().getAlignmentAnnotation().length];
 184     boolean enableSeqAss = false;
 185     for (int i = 0; i < av.getAlignment().getAlignmentAnnotation().length; i++)
 186     {
 187       if (av.getAlignment().getAlignmentAnnotation()[i].sequenceRef == null)
 188       {
 189         if (isSeqAssociated)
 190         {
 191           continue;
 192         }
 193       }
 194       else
 195       {
 196         enableSeqAss = true;
 197       }
 198       String label = av.getAlignment().getAlignmentAnnotation()[i].label;
 199       if (!list.contains(label))
 200       {
 201         anmap[list.size()] = i;
 202         list.addElement(label);
 203
 204       }
 205       else
 206       {
 207         if (!isSeqAssociated)
 208         {
 209           anmap[list.size()] = i;
 210           list.addElement(label + "_" + (index++));
 211         }
 212       }
 213     }
 214     seqAssociated.setEnabled(enableSeqAss);
 215     annmap = new int[list.size()];
 216     System.arraycopy(anmap, 0, annmap, 0, annmap.length);
 217     return list;
 218   }
 219   private void setDefaultMinMax()
 220   {
 221     minColour.setBackground(Cache.getDefaultColour("ANNOTATIONCOLOUR_MIN",
 222             Color.orange));
 223     maxColour.setBackground(Cache.getDefaultColour("ANNOTATIONCOLOUR_MAX",
 224             Color.red));
 225   }
 226
 227   public AnnotationColourChooser()
 228   {
 229     try
 230     {
 231       jbInit();
 232     } catch (Exception ex)
 233     {
 234       ex.printStackTrace();
 235     }
 236   }
 237
 238   private void jbInit() throws Exception
 239   {
 240     minColour.setFont(JvSwingUtils.getLabelFont());
 241     minColour.setBorder(BorderFactory.createEtchedBorder());
 242     minColour.setPreferredSize(new Dimension(40, 20));
 243     minColour.setToolTipText("Minimum Colour");
 244     minColour.addMouseListener(new MouseAdapter()
 245     {
 246       public void mousePressed(MouseEvent e)
 247       {
 248         if (minColour.isEnabled())
 249         {
 250           minColour_actionPerformed();
 251         }
 252       }
 253     });
 254     maxColour.setFont(JvSwingUtils.getLabelFont());
 255     maxColour.setBorder(BorderFactory.createEtchedBorder());
 256     maxColour.setPreferredSize(new Dimension(40, 20));
 257     maxColour.setToolTipText("Maximum Colour");
 258     maxColour.addMouseListener(new MouseAdapter()
 259     {
 260       public void mousePressed(MouseEvent e)
 261       {
 262         if (maxColour.isEnabled())
 263         {
 264           maxColour_actionPerformed();
 265         }
 266       }
 267     });
 268     ok.setOpaque(false);
 269     ok.setText("OK");
 270     ok.addActionListener(new ActionListener()
 271     {
 272       public void actionPerformed(ActionEvent e)
 273       {
 274         ok_actionPerformed(e);
 275       }
 276     });
 277     cancel.setOpaque(false);
 278     cancel.setText("Cancel");
 279     cancel.addActionListener(new ActionListener()
 280     {
 281       public void actionPerformed(ActionEvent e)
 282       {
 283         cancel_actionPerformed(e);
 284       }
 285     });
 286     defColours.setOpaque(false);
 287     defColours.setText("Defaults");
 288     defColours
 289             .setToolTipText("Reset min and max colours to defaults from user preferences.");
 290     defColours.addActionListener(new ActionListener()
 291     {
 292
 293       @Override
 294       public void actionPerformed(ActionEvent arg0)
 295       {
 296         resetColours_actionPerformed(arg0);
 297       }
 298     });
 299
 300     annotations.addActionListener(new ActionListener()
 301     {
 302       public void actionPerformed(ActionEvent e)
 303       {
 304         annotations_actionPerformed(e);
 305       }
 306     });
 307     threshold.addActionListener(new ActionListener()
 308     {
 309       public void actionPerformed(ActionEvent e)
 310       {
 311         threshold_actionPerformed(e);
 312       }
 313     });
 314     thresholdValue.addActionListener(new ActionListener()
 315     {
 316       public void actionPerformed(ActionEvent e)
 317       {
 318         thresholdValue_actionPerformed(e);
 319       }
 320     });
 321     slider.setPaintLabels(false);
 322     slider.setPaintTicks(true);
 323     slider.setBackground(Color.white);
 324     slider.setEnabled(false);
 325     slider.setOpaque(false);
 326     slider.setPreferredSize(new Dimension(100, 32));
 327     thresholdValue.setEnabled(false);
 328     thresholdValue.setColumns(7);
 329     currentColours.setFont(JvSwingUtils.getLabelFont());
 330     currentColours.setOpaque(false);
 331     currentColours.setText("Use Original Colours");
 332     currentColours.addActionListener(new ActionListener()
 333     {
 334       public void actionPerformed(ActionEvent e)
 335       {
 336         currentColours_actionPerformed(e);
 337       }
 338     });
 339     thresholdIsMin.setBackground(Color.white);
 340     thresholdIsMin.setFont(JvSwingUtils.getLabelFont());
 341     thresholdIsMin.setText("Threshold is Min/Max");
 342     thresholdIsMin.addActionListener(new ActionListener()
 343     {
 344       public void actionPerformed(ActionEvent actionEvent)
 345       {
 346         thresholdIsMin_actionPerformed(actionEvent);
 347       }
 348     });
 349     seqAssociated.setBackground(Color.white);
 350     seqAssociated.setFont(JvSwingUtils.getLabelFont());
 351     seqAssociated.setText("Per-sequence only");
 352     seqAssociated.addActionListener(new ActionListener()
 353     {
 354
 355       @Override
 356       public void actionPerformed(ActionEvent arg0)
 357       {
 358         seqAssociated_actionPerformed(arg0);
 359       }
 360     });
 361
 362     this.setLayout(borderLayout1);
 363     jPanel2.setLayout(new MigLayout("", "[left][center][right]", "[][][]"));
 364     jPanel1.setBackground(Color.white);
 365     jPanel2.setBackground(Color.white);
 366
 367     jPanel1.add(ok);
 368     jPanel1.add(cancel);
 369     jPanel2.add(annotations, "grow, wrap");
 370     jPanel2.add(seqAssociated);
 371     jPanel2.add(currentColours);
 372     JPanel colpanel = new JPanel(new FlowLayout());
 373     colpanel.setBackground(Color.white);
 374     colpanel.add(minColour);
 375     colpanel.add(maxColour);
 376     jPanel2.add(colpanel, "wrap");
 377     jPanel2.add(threshold);
 378     jPanel2.add(defColours, "skip 1, wrap");
 379     jPanel2.add(thresholdIsMin);
 380     jPanel2.add(slider, "grow");
 381     jPanel2.add(thresholdValue, "grow");
 382     this.add(jPanel1, java.awt.BorderLayout.SOUTH);
 383     this.add(jPanel2, java.awt.BorderLayout.CENTER);
 384     this.validate();
 385   }
 386
 387   protected void seqAssociated_actionPerformed(ActionEvent arg0)
 388   {
 389     adjusting = true;
 390     String cursel = (String) annotations.getSelectedItem();
 391     boolean isvalid = false, isseqs = seqAssociated.isSelected();
 392     this.annotations.removeAllItems();
 393     for (String anitem : getAnnotationItems(seqAssociated.isSelected()))
 394     {
 395       if (anitem.equals(cursel) || (isseqs && cursel.startsWith(anitem)))
 396       {
 397         isvalid = true;
 398         cursel = anitem;
 399       }
 400       this.annotations.addItem(anitem);
 401     }
 402     adjusting = false;
 403     if (isvalid)
 404     {
 405       this.annotations.setSelectedItem(cursel);
 406     }
 407     else
 408     {
 409       if (annotations.getItemCount() > 0)
 410       {
 411         annotations.setSelectedIndex(0);
 412       }
 413     }
 414   }
 415
 416   protected void resetColours_actionPerformed(ActionEvent arg0)
 417   {
 418     setDefaultMinMax();
 419     changeColour();
 420   }
 421
 422   JComboBox annotations;
 423
 424   int[] annmap;
 425
 426   JPanel minColour = new JPanel();
 427
 428   JPanel maxColour = new JPanel();
 429
 430   JButton defColours = new JButton();
 431
 432   JButton ok = new JButton();
 433
 434   JButton cancel = new JButton();
 435
 436   JPanel jPanel1 = new JPanel();
 437
 438   JPanel jPanel2 = new JPanel();
 439
 440   BorderLayout borderLayout1 = new BorderLayout();
 441
 442   JComboBox threshold = new JComboBox();
 443
 444   JSlider slider = new JSlider();
 445
 446   JTextField thresholdValue = new JTextField(20);
 447
 448   JCheckBox currentColours = new JCheckBox();
 449
 450   JCheckBox thresholdIsMin = new JCheckBox();
 451
 452   JCheckBox seqAssociated = new JCheckBox();
 453
 454   public void minColour_actionPerformed()
 455   {
 456     Color col = JColorChooser.showDialog(this,
 457             "Select Colour for Minimum Value", minColour.getBackground());
 458     if (col != null)
 459     {
 460       minColour.setBackground(col);
 461     }
 462     minColour.repaint();
 463     changeColour();
 464   }
 465
 466   public void maxColour_actionPerformed()
 467   {
 468     Color col = JColorChooser.showDialog(this,
 469             "Select Colour for Maximum Value", maxColour.getBackground());
 470     if (col != null)
 471     {
 472       maxColour.setBackground(col);
 473     }
 474     maxColour.repaint();
 475     changeColour();
 476   }
 477
 478   void changeColour()
 479   {
 480     // Check if combobox is still adjusting
 481     if (adjusting)
 482     {
 483       return;
 484     }
 485
 486     currentAnnotation = av.getAlignment().getAlignmentAnnotation()[annmap[annotations
 487             .getSelectedIndex()]];
 488
 489     int aboveThreshold = -1;
 490     if (threshold.getSelectedItem().equals("Above Threshold"))
 491     {
 492       aboveThreshold = AnnotationColourGradient.ABOVE_THRESHOLD;
 493     }
 494     else if (threshold.getSelectedItem().equals("Below Threshold"))
 495     {
 496       aboveThreshold = AnnotationColourGradient.BELOW_THRESHOLD;
 497     }
 498
 499     slider.setEnabled(true);
 500     thresholdValue.setEnabled(true);
 501     thresholdIsMin.setEnabled(true);
 502
 503     if (aboveThreshold == AnnotationColourGradient.NO_THRESHOLD)
 504     {
 505       slider.setEnabled(false);
 506       thresholdValue.setEnabled(false);
 507       thresholdValue.setText("");
 508       thresholdIsMin.setEnabled(false);
 509     }
 510     else if (aboveThreshold != AnnotationColourGradient.NO_THRESHOLD
 511             && currentAnnotation.threshold == null)
 512     {
 513       currentAnnotation
 514               .setThreshold(new jalview.datamodel.GraphLine(
 515                       (currentAnnotation.graphMax - currentAnnotation.graphMin) / 2f,
 516                       "Threshold", Color.black));
 517     }
 518
 519     if (aboveThreshold != AnnotationColourGradient.NO_THRESHOLD)
 520     {
 521       adjusting = true;
 522       float range = currentAnnotation.graphMax * 1000
 523               - currentAnnotation.graphMin * 1000;
 524
 525       slider.setMinimum((int) (currentAnnotation.graphMin * 1000));
 526       slider.setMaximum((int) (currentAnnotation.graphMax * 1000));
 527       slider.setValue((int) (currentAnnotation.threshold.value * 1000));
 528       thresholdValue.setText(currentAnnotation.threshold.value + "");
 529       slider.setMajorTickSpacing((int) (range / 10f));
 530       slider.setEnabled(true);
 531       thresholdValue.setEnabled(true);
 532       adjusting = false;
 533     }
 534
 535     AnnotationColourGradient acg = null;
 536     if (currentColours.isSelected())
 537     {
 538       acg = new AnnotationColourGradient(currentAnnotation,
 539               av.getGlobalColourScheme(), aboveThreshold);
 540     }
 541     else
 542     {
 543       acg = new AnnotationColourGradient(currentAnnotation,
 544               minColour.getBackground(), maxColour.getBackground(),
 545               aboveThreshold);
 546     }
 547     acg.setSeqAssociated(seqAssociated.isSelected());
 548
 549     if (currentAnnotation.graphMin == 0f
 550             && currentAnnotation.graphMax == 0f)
 551     {
 552       acg.predefinedColours = true;
 553     }
 554
 555     acg.thresholdIsMinMax = thresholdIsMin.isSelected();
 556
 557     av.setGlobalColourScheme(acg);
 558
 559     if (av.getAlignment().getGroups() != null)
 560     {
 561
 562       for (SequenceGroup sg : ap.av.getAlignment().getGroups())
 563       {
 564         if (sg.cs == null)
 565         {
 566           continue;
 567         }
 568
 569         if (currentColours.isSelected())
 570         {
 571           sg.cs = new AnnotationColourGradient(currentAnnotation, sg.cs,
 572                   aboveThreshold);
 573           ((AnnotationColourGradient) sg.cs).setSeqAssociated(seqAssociated
 574                   .isSelected());
 575
 576         }
 577         else
 578         {
 579           sg.cs = new AnnotationColourGradient(currentAnnotation,
 580                   minColour.getBackground(), maxColour.getBackground(),
 581                   aboveThreshold);
 582           ((AnnotationColourGradient) sg.cs).setSeqAssociated(seqAssociated
 583                   .isSelected());
 584         }
 585
 586       }
 587     }
 588     ap.alignmentChanged();
 589     // ensure all associated views (overviews, structures, etc) are notified of
 590     // updated colours.
 591     ap.paintAlignment(true);
 592   }
 593
 594   public void ok_actionPerformed(ActionEvent e)
 595   {
 596     changeColour();
 597     try
 598     {
 599       frame.setClosed(true);
 600     } catch (Exception ex)
 601     {
 602     }
 603   }
 604
 605   public void cancel_actionPerformed(ActionEvent e)
 606   {
 607     reset();
 608     // ensure all original colouring is propagated to listeners.
 609     ap.paintAlignment(true);
 610     try
 611     {
 612       frame.setClosed(true);
 613     } catch (Exception ex)
 614     {
 615     }
 616   }
 617
 618   void reset()
 619   {
 620     av.setGlobalColourScheme(oldcs);
 621     if (av.getAlignment().getGroups() != null)
 622     {
 623
 624       for (SequenceGroup sg : ap.av.getAlignment().getGroups())
 625       {
 626         sg.cs = (ColourSchemeI) oldgroupColours.get(sg);
 627       }
 628     }
 629   }
 630
 631   public void thresholdCheck_actionPerformed(ActionEvent e)
 632   {
 633     changeColour();
 634   }
 635
 636   public void annotations_actionPerformed(ActionEvent e)
 637   {
 638     changeColour();
 639   }
 640
 641   public void threshold_actionPerformed(ActionEvent e)
 642   {
 643     changeColour();
 644   }
 645
 646   public void thresholdValue_actionPerformed(ActionEvent e)
 647   {
 648     try
 649     {
 650       float f = Float.parseFloat(thresholdValue.getText());
 651       slider.setValue((int) (f * 1000));
 652     } catch (NumberFormatException ex)
 653     {
 654     }
 655   }
 656
 657   public void valueChanged(boolean updateAllAnnotation)
 658   {
 659     if (currentColours.isSelected()
 660             && !(av.getGlobalColourScheme() instanceof AnnotationColourGradient))
 661     {
 662       changeColour();
 663     }
 664     currentAnnotation.threshold.value = (float) slider.getValue() / 1000f;
 665     propagateSeqAssociatedThreshold(updateAllAnnotation);
 666     ap.paintAlignment(false);
 667   }
 668
 669   private void propagateSeqAssociatedThreshold(boolean allAnnotation)
 670   {
 671     if (currentAnnotation.sequenceRef == null
 672             || currentAnnotation.threshold == null)
 673     {
 674       return;
 675     }
 676     // TODO: JAL-1327 only update visible annotation thresholds if allAnnotation is false, since we only need to provide a quick visual indicator
 677
 678     float thr = currentAnnotation.threshold.value;
 679     for (int i = 0; i < av.getAlignment().getAlignmentAnnotation().length; i++)
 680     {
 681       AlignmentAnnotation aa = av.getAlignment().getAlignmentAnnotation()[i];
 682       if (aa.label.equals(currentAnnotation.label))
 683       {
 684         aa.threshold.value = thr;
 685       }
 686     }
 687   }
 688
 689   public void currentColours_actionPerformed(ActionEvent e)
 690   {
 691     if (currentColours.isSelected())
 692     {
 693       reset();
 694     }
 695
 696     maxColour.setEnabled(!currentColours.isSelected());
 697     minColour.setEnabled(!currentColours.isSelected());
 698
 699     changeColour();
 700   }
 701
 702   public void thresholdIsMin_actionPerformed(ActionEvent actionEvent)
 703   {
 704     changeColour();
 705   }
 706
 707 }