src/jalview/gui/AnnotationColourChooser.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
   3  * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
   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  */
  18 package jalview.gui;
  19
  20 import java.util.*;
  21
  22 import java.awt.*;
  23 import java.awt.event.*;
  24
  25 import javax.swing.*;
  26 import javax.swing.event.*;
  27
  28 import net.miginfocom.swing.MigLayout;
  29
  30 import jalview.bin.Cache;
  31 import jalview.datamodel.*;
  32 import jalview.schemes.*;
  33 import java.awt.Dimension;
  34
  35 public class AnnotationColourChooser extends JPanel
  36 {
  37   JInternalFrame frame;
  38
  39   AlignViewport av;
  40
  41   AlignmentPanel ap;
  42
  43   ColourSchemeI oldcs;
  44
  45   Hashtable oldgroupColours;
  46
  47   jalview.datamodel.AlignmentAnnotation currentAnnotation;
  48
  49   boolean adjusting = false;
  50
  51   public AnnotationColourChooser(AlignViewport av, final AlignmentPanel ap)
  52   {
  53     oldcs = av.getGlobalColourScheme();
  54     if (av.getAlignment().getGroups() != null)
  55     {
  56       oldgroupColours = new Hashtable();
  57       for (SequenceGroup sg : ap.av.getAlignment().getGroups())
  58       {
  59         if (sg.cs != null)
  60         {
  61           oldgroupColours.put(sg, sg.cs);
  62         }
  63       }
  64     }
  65     this.av = av;
  66     this.ap = ap;
  67     frame = new JInternalFrame();
  68     frame.setContentPane(this);
  69     frame.setLayer(JLayeredPane.PALETTE_LAYER);
  70     Desktop.addInternalFrame(frame, "Colour by Annotation", 520, 215);
  71
  72     slider.addChangeListener(new ChangeListener()
  73     {
  74       public void stateChanged(ChangeEvent evt)
  75       {
  76         if (!adjusting)
  77         {
  78           thresholdValue.setText(((float) slider.getValue() / 1000f) + "");
  79           valueChanged();
  80         }
  81       }
  82     });
  83     slider.addMouseListener(new MouseAdapter()
  84     {
  85       public void mouseReleased(MouseEvent evt)
  86       {
  87         ap.paintAlignment(true);
  88       }
  89     });
  90
  91     if (av.getAlignment().getAlignmentAnnotation() == null)
  92     {
  93       return;
  94     }
  95
  96     // Always get default shading from preferences.
  97     setDefaultMinMax();
  98
  99     if (oldcs instanceof AnnotationColourGradient)
 100     {
 101       AnnotationColourGradient acg = (AnnotationColourGradient) oldcs;
 102       currentColours.setSelected(acg.predefinedColours);
 103       if (!acg.predefinedColours)
 104       {
 105         minColour.setBackground(acg.getMinColour());
 106         maxColour.setBackground(acg.getMaxColour());
 107       }
 108       seqAssociated.setSelected(acg.isSeqAssociated());
 109     }
 110     adjusting = true;
 111     annotations = new JComboBox(
 112             getAnnotationItems(seqAssociated.isSelected()));
 113
 114     threshold.addItem("No Threshold");
 115     threshold.addItem("Above Threshold");
 116     threshold.addItem("Below Threshold");
 117
 118     if (oldcs instanceof AnnotationColourGradient)
 119     {
 120       AnnotationColourGradient acg = (AnnotationColourGradient) oldcs;
 121       annotations.setSelectedItem(acg.getAnnotation());
 122       switch (acg.getAboveThreshold())
 123       {
 124       case AnnotationColourGradient.NO_THRESHOLD:
 125         threshold.setSelectedItem("No Threshold");
 126         break;
 127       case AnnotationColourGradient.ABOVE_THRESHOLD:
 128         threshold.setSelectedItem("Above Threshold");
 129         break;
 130       case AnnotationColourGradient.BELOW_THRESHOLD:
 131         threshold.setSelectedItem("Below Threshold");
 132         break;
 133       default:
 134         throw new Error(
 135                 "Implementation error: don't know about threshold setting for current AnnotationColourGradient.");
 136       }
 137       thresholdIsMin.setSelected(acg.thresholdIsMinMax);
 138       thresholdValue.setText("" + acg.getAnnotationThreshold());
 139     }
 140
 141     try
 142     {
 143       jbInit();
 144     } catch (Exception ex)
 145     {
 146     }
 147
 148     adjusting = false;
 149
 150     changeColour();
 151     frame.invalidate();
 152     frame.pack();
 153
 154   }
 155
 156   private Vector<String> getAnnotationItems(boolean isSeqAssociated)
 157   {
 158     Vector<String> list = new Vector<String>();
 159     int index = 1;
 160     int[] anmap = new int[av.getAlignment().getAlignmentAnnotation().length];
 161     boolean enableSeqAss = false;
 162     for (int i = 0; i < av.getAlignment().getAlignmentAnnotation().length; i++)
 163     {
 164       if (av.getAlignment().getAlignmentAnnotation()[i].sequenceRef == null)
 165       {
 166         if (isSeqAssociated)
 167         {
 168           continue;
 169         }
 170       }
 171       else
 172       {
 173         enableSeqAss = true;
 174       }
 175       String label = av.getAlignment().getAlignmentAnnotation()[i].label;
 176       if (!list.contains(label))
 177       {
 178         anmap[list.size()] = i;
 179         list.addElement(label);
 180
 181       }
 182       else
 183       {
 184         if (!isSeqAssociated)
 185         {
 186           anmap[list.size()] = i;
 187           list.addElement(label + "_" + (index++));
 188         }
 189       }
 190     }
 191     seqAssociated.setEnabled(enableSeqAss);
 192     annmap = new int[list.size()];
 193     System.arraycopy(anmap, 0, annmap, 0, annmap.length);
 194     return list;
 195   }
 196
 197   private void setDefaultMinMax()
 198   {
 199     minColour.setBackground(Cache.getDefaultColour("ANNOTATIONCOLOUR_MIN",
 200             Color.orange));
 201     maxColour.setBackground(Cache.getDefaultColour("ANNOTATIONCOLOUR_MAX",
 202             Color.red));
 203   }
 204
 205   public AnnotationColourChooser()
 206   {
 207     try
 208     {
 209       jbInit();
 210     } catch (Exception ex)
 211     {
 212       ex.printStackTrace();
 213     }
 214   }
 215
 216   private void jbInit() throws Exception
 217   {
 218     minColour.setFont(JvSwingUtils.getLabelFont());
 219     minColour.setBorder(BorderFactory.createEtchedBorder());
 220     minColour.setPreferredSize(new Dimension(40, 20));
 221     minColour.setToolTipText("Minimum Colour");
 222     minColour.addMouseListener(new MouseAdapter()
 223     {
 224       public void mousePressed(MouseEvent e)
 225       {
 226         if (minColour.isEnabled())
 227         {
 228           minColour_actionPerformed();
 229         }
 230       }
 231     });
 232     maxColour.setFont(JvSwingUtils.getLabelFont());
 233     maxColour.setBorder(BorderFactory.createEtchedBorder());
 234     maxColour.setPreferredSize(new Dimension(40, 20));
 235     maxColour.setToolTipText("Maximum Colour");
 236     maxColour.addMouseListener(new MouseAdapter()
 237     {
 238       public void mousePressed(MouseEvent e)
 239       {
 240         if (maxColour.isEnabled())
 241         {
 242           maxColour_actionPerformed();
 243         }
 244       }
 245     });
 246     ok.setOpaque(false);
 247     ok.setText("OK");
 248     ok.addActionListener(new ActionListener()
 249     {
 250       public void actionPerformed(ActionEvent e)
 251       {
 252         ok_actionPerformed(e);
 253       }
 254     });
 255     cancel.setOpaque(false);
 256     cancel.setText("Cancel");
 257     cancel.addActionListener(new ActionListener()
 258     {
 259       public void actionPerformed(ActionEvent e)
 260       {
 261         cancel_actionPerformed(e);
 262       }
 263     });
 264     defColours.setOpaque(false);
 265     defColours.setText("Defaults");
 266     defColours
 267             .setToolTipText("Reset min and max colours to defaults from user preferences.");
 268     defColours.addActionListener(new ActionListener()
 269     {
 270
 271       @Override
 272       public void actionPerformed(ActionEvent arg0)
 273       {
 274         resetColours_actionPerformed(arg0);
 275       }
 276     });
 277
 278     annotations.addActionListener(new ActionListener()
 279     {
 280       public void actionPerformed(ActionEvent e)
 281       {
 282         annotations_actionPerformed(e);
 283       }
 284     });
 285     threshold.addActionListener(new ActionListener()
 286     {
 287       public void actionPerformed(ActionEvent e)
 288       {
 289         threshold_actionPerformed(e);
 290       }
 291     });
 292     thresholdValue.addActionListener(new ActionListener()
 293     {
 294       public void actionPerformed(ActionEvent e)
 295       {
 296         thresholdValue_actionPerformed(e);
 297       }
 298     });
 299     slider.setPaintLabels(false);
 300     slider.setPaintTicks(true);
 301     slider.setBackground(Color.white);
 302     slider.setEnabled(false);
 303     slider.setOpaque(false);
 304     slider.setPreferredSize(new Dimension(100, 32));
 305     thresholdValue.setEnabled(false);
 306     thresholdValue.setColumns(7);
 307     currentColours.setFont(JvSwingUtils.getLabelFont());
 308     currentColours.setOpaque(false);
 309     currentColours.setText("Use Original Colours");
 310     currentColours.addActionListener(new ActionListener()
 311     {
 312       public void actionPerformed(ActionEvent e)
 313       {
 314         currentColours_actionPerformed(e);
 315       }
 316     });
 317     thresholdIsMin.setBackground(Color.white);
 318     thresholdIsMin.setFont(JvSwingUtils.getLabelFont());
 319     thresholdIsMin.setText("Threshold is Min/Max");
 320     thresholdIsMin.addActionListener(new ActionListener()
 321     {
 322       public void actionPerformed(ActionEvent actionEvent)
 323       {
 324         thresholdIsMin_actionPerformed(actionEvent);
 325       }
 326     });
 327     seqAssociated.setBackground(Color.white);
 328     seqAssociated.setFont(JvSwingUtils.getLabelFont());
 329     seqAssociated.setText("Per-sequence only");
 330     seqAssociated.addActionListener(new ActionListener()
 331     {
 332
 333       @Override
 334       public void actionPerformed(ActionEvent arg0)
 335       {
 336         seqAssociated_actionPerformed(arg0);
 337       }
 338     });
 339
 340     this.setLayout(borderLayout1);
 341     jPanel2.setLayout(new MigLayout("", "[left][center][right]", "[][][]"));
 342     jPanel1.setBackground(Color.white);
 343     jPanel2.setBackground(Color.white);
 344
 345     jPanel1.add(ok);
 346     jPanel1.add(cancel);
 347     jPanel2.add(annotations, "grow, wrap");
 348     jPanel2.add(seqAssociated);
 349     jPanel2.add(currentColours);
 350     JPanel colpanel = new JPanel(new FlowLayout());
 351     colpanel.setBackground(Color.white);
 352     colpanel.add(minColour);
 353     colpanel.add(maxColour);
 354     jPanel2.add(colpanel, "wrap");
 355     jPanel2.add(threshold);
 356     jPanel2.add(defColours, "skip 1, wrap");
 357     jPanel2.add(thresholdIsMin);
 358     jPanel2.add(slider, "grow");
 359     jPanel2.add(thresholdValue, "grow");
 360     this.add(jPanel1, java.awt.BorderLayout.SOUTH);
 361     this.add(jPanel2, java.awt.BorderLayout.CENTER);
 362     this.validate();
 363   }
 364
 365   protected void seqAssociated_actionPerformed(ActionEvent arg0)
 366   {
 367     adjusting = true;
 368     String cursel = (String) annotations.getSelectedItem();
 369     boolean isvalid = false, isseqs = seqAssociated.isSelected();
 370     this.annotations.removeAllItems();
 371     for (String anitem : getAnnotationItems(seqAssociated.isSelected()))
 372     {
 373       if (anitem.equals(cursel) || (isseqs && cursel.startsWith(anitem)))
 374       {
 375         isvalid = true;
 376         cursel = anitem;
 377       }
 378       this.annotations.addItem(anitem);
 379     }
 380     adjusting = false;
 381     if (isvalid)
 382     {
 383       this.annotations.setSelectedItem(cursel);
 384     }
 385     else
 386     {
 387       if (annotations.getItemCount() > 0)
 388       {
 389         annotations.setSelectedIndex(0);
 390       }
 391     }
 392   }
 393
 394   protected void resetColours_actionPerformed(ActionEvent arg0)
 395   {
 396     setDefaultMinMax();
 397     changeColour();
 398   }
 399
 400   JComboBox annotations;
 401
 402   int[] annmap;
 403
 404   JPanel minColour = new JPanel();
 405
 406   JPanel maxColour = new JPanel();
 407
 408   JButton defColours = new JButton();
 409
 410   JButton ok = new JButton();
 411
 412   JButton cancel = new JButton();
 413
 414   JPanel jPanel1 = new JPanel();
 415
 416   JPanel jPanel2 = new JPanel();
 417
 418   BorderLayout borderLayout1 = new BorderLayout();
 419
 420   JComboBox threshold = new JComboBox();
 421
 422   JSlider slider = new JSlider();
 423
 424   JTextField thresholdValue = new JTextField(20);
 425
 426   JCheckBox currentColours = new JCheckBox();
 427
 428   JCheckBox thresholdIsMin = new JCheckBox();
 429
 430   JCheckBox seqAssociated = new JCheckBox();
 431
 432   public void minColour_actionPerformed()
 433   {
 434     Color col = JColorChooser.showDialog(this,
 435             "Select Colour for Minimum Value", minColour.getBackground());
 436     if (col != null)
 437     {
 438       minColour.setBackground(col);
 439     }
 440     minColour.repaint();
 441     changeColour();
 442   }
 443
 444   public void maxColour_actionPerformed()
 445   {
 446     Color col = JColorChooser.showDialog(this,
 447             "Select Colour for Maximum Value", maxColour.getBackground());
 448     if (col != null)
 449     {
 450       maxColour.setBackground(col);
 451     }
 452     maxColour.repaint();
 453     changeColour();
 454   }
 455
 456   void changeColour()
 457   {
 458     // Check if combobox is still adjusting
 459     if (adjusting)
 460     {
 461       return;
 462     }
 463
 464     currentAnnotation = av.getAlignment().getAlignmentAnnotation()[annmap[annotations
 465             .getSelectedIndex()]];
 466
 467     int aboveThreshold = -1;
 468     if (threshold.getSelectedItem().equals("Above Threshold"))
 469     {
 470       aboveThreshold = AnnotationColourGradient.ABOVE_THRESHOLD;
 471     }
 472     else if (threshold.getSelectedItem().equals("Below Threshold"))
 473     {
 474       aboveThreshold = AnnotationColourGradient.BELOW_THRESHOLD;
 475     }
 476
 477     slider.setEnabled(true);
 478     thresholdValue.setEnabled(true);
 479     thresholdIsMin.setEnabled(true);
 480
 481     if (aboveThreshold == AnnotationColourGradient.NO_THRESHOLD)
 482     {
 483       slider.setEnabled(false);
 484       thresholdValue.setEnabled(false);
 485       thresholdValue.setText("");
 486       thresholdIsMin.setEnabled(false);
 487     }
 488     else if (aboveThreshold != AnnotationColourGradient.NO_THRESHOLD
 489             && currentAnnotation.threshold == null)
 490     {
 491       currentAnnotation
 492               .setThreshold(new jalview.datamodel.GraphLine(
 493                       (currentAnnotation.graphMax - currentAnnotation.graphMin) / 2f,
 494                       "Threshold", Color.black));
 495     }
 496
 497     if (aboveThreshold != AnnotationColourGradient.NO_THRESHOLD)
 498     {
 499       adjusting = true;
 500       float range = currentAnnotation.graphMax * 1000
 501               - currentAnnotation.graphMin * 1000;
 502
 503       slider.setMinimum((int) (currentAnnotation.graphMin * 1000));
 504       slider.setMaximum((int) (currentAnnotation.graphMax * 1000));
 505       slider.setValue((int) (currentAnnotation.threshold.value * 1000));
 506       thresholdValue.setText(currentAnnotation.threshold.value + "");
 507       slider.setMajorTickSpacing((int) (range / 10f));
 508       slider.setEnabled(true);
 509       thresholdValue.setEnabled(true);
 510       adjusting = false;
 511     }
 512
 513     AnnotationColourGradient acg = null;
 514     if (currentColours.isSelected())
 515     {
 516       acg = new AnnotationColourGradient(currentAnnotation,
 517               av.getGlobalColourScheme(), aboveThreshold);
 518     }
 519     else
 520     {
 521       acg = new AnnotationColourGradient(currentAnnotation,
 522               minColour.getBackground(), maxColour.getBackground(),
 523               aboveThreshold);
 524     }
 525     acg.setSeqAssociated(seqAssociated.isSelected());
 526
 527     if (currentAnnotation.graphMin == 0f
 528             && currentAnnotation.graphMax == 0f)
 529     {
 530       acg.predefinedColours = true;
 531     }
 532
 533     acg.thresholdIsMinMax = thresholdIsMin.isSelected();
 534
 535     av.setGlobalColourScheme(acg);
 536
 537     if (av.getAlignment().getGroups() != null)
 538     {
 539
 540       for (SequenceGroup sg : ap.av.getAlignment().getGroups())
 541       {
 542         if (sg.cs == null)
 543         {
 544           continue;
 545         }
 546
 547         if (currentColours.isSelected())
 548         {
 549           sg.cs = new AnnotationColourGradient(currentAnnotation, sg.cs,
 550                   aboveThreshold);
 551           ((AnnotationColourGradient) sg.cs).setSeqAssociated(seqAssociated
 552                   .isSelected());
 553
 554         }
 555         else
 556         {
 557           sg.cs = new AnnotationColourGradient(currentAnnotation,
 558                   minColour.getBackground(), maxColour.getBackground(),
 559                   aboveThreshold);
 560           ((AnnotationColourGradient) sg.cs).setSeqAssociated(seqAssociated
 561                   .isSelected());
 562         }
 563
 564       }
 565     }
 566     ap.alignmentChanged();
 567     // ensure all associated views (overviews, structures, etc) are notified of
 568     // updated colours.
 569     ap.paintAlignment(true);
 570   }
 571
 572   public void ok_actionPerformed(ActionEvent e)
 573   {
 574     changeColour();
 575     try
 576     {
 577       frame.setClosed(true);
 578     } catch (Exception ex)
 579     {
 580     }
 581   }
 582
 583   public void cancel_actionPerformed(ActionEvent e)
 584   {
 585     reset();
 586     // ensure all original colouring is propagated to listeners.
 587     ap.paintAlignment(true);
 588     try
 589     {
 590       frame.setClosed(true);
 591     } catch (Exception ex)
 592     {
 593     }
 594   }
 595
 596   void reset()
 597   {
 598     av.setGlobalColourScheme(oldcs);
 599     if (av.getAlignment().getGroups() != null)
 600     {
 601
 602       for (SequenceGroup sg : ap.av.getAlignment().getGroups())
 603       {
 604         sg.cs = (ColourSchemeI) oldgroupColours.get(sg);
 605       }
 606     }
 607   }
 608
 609   public void thresholdCheck_actionPerformed(ActionEvent e)
 610   {
 611     changeColour();
 612   }
 613
 614   public void annotations_actionPerformed(ActionEvent e)
 615   {
 616     changeColour();
 617   }
 618
 619   public void threshold_actionPerformed(ActionEvent e)
 620   {
 621     changeColour();
 622   }
 623
 624   public void thresholdValue_actionPerformed(ActionEvent e)
 625   {
 626     try
 627     {
 628       float f = Float.parseFloat(thresholdValue.getText());
 629       slider.setValue((int) (f * 1000));
 630     } catch (NumberFormatException ex)
 631     {
 632     }
 633   }
 634
 635   public void valueChanged()
 636   {
 637     if (currentColours.isSelected()
 638             && !(av.getGlobalColourScheme() instanceof AnnotationColourGradient))
 639     {
 640       changeColour();
 641     }
 642
 643     currentAnnotation.threshold.value = (float) slider.getValue() / 1000f;
 644     ap.paintAlignment(false);
 645   }
 646
 647   public void currentColours_actionPerformed(ActionEvent e)
 648   {
 649     if (currentColours.isSelected())
 650     {
 651       reset();
 652     }
 653
 654     maxColour.setEnabled(!currentColours.isSelected());
 655     minColour.setEnabled(!currentColours.isSelected());
 656
 657     changeColour();
 658   }
 659
 660   public void thresholdIsMin_actionPerformed(ActionEvent actionEvent)
 661   {
 662     changeColour();
 663   }
 664
 665 }