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