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     Vector list = new Vector();
 112     int index = 1;
 113     for (int i = 0; i < av.getAlignment().getAlignmentAnnotation().length; i++)
 114     {
 115       String label = av.getAlignment().getAlignmentAnnotation()[i].label;
 116       if (!list.contains(label))
 117         list.addElement(label);
 118       else
 119         list.addElement(label + "_" + (index++));
 120     }
 121
 122     annotations = new JComboBox(list);
 123
 124     threshold.addItem("No Threshold");
 125     threshold.addItem("Above Threshold");
 126     threshold.addItem("Below Threshold");
 127
 128     if (oldcs instanceof AnnotationColourGradient)
 129     {
 130       AnnotationColourGradient acg = (AnnotationColourGradient) oldcs;
 131       annotations.setSelectedItem(acg.getAnnotation());
 132       switch (acg.getAboveThreshold()) {
 133       case AnnotationColourGradient.NO_THRESHOLD:
 134           threshold.setSelectedItem("No Threshold");
 135         break;
 136       case AnnotationColourGradient.ABOVE_THRESHOLD:
 137           threshold.setSelectedItem("Above Threshold");
 138         break;
 139       case AnnotationColourGradient.BELOW_THRESHOLD:
 140         threshold.setSelectedItem("Below Threshold");
 141         break;
 142         default:
 143           throw new Error("Implementation error: don't know about threshold setting for current AnnotationColourGradient.");
 144       }
 145       thresholdIsMin.setSelected(acg.thresholdIsMinMax);
 146       thresholdValue.setText(""+acg.getAnnotationThreshold());
 147     }
 148
 149     try
 150     {
 151       jbInit();
 152     } catch (Exception ex)
 153     {
 154     }
 155
 156     adjusting = false;
 157
 158     changeColour();
 159     frame.invalidate();
 160     frame.pack();
 161
 162   }
 163
 164   private void setDefaultMinMax()
 165   {
 166     minColour.setBackground(Cache.getDefaultColour("ANNOTATIONCOLOUR_MIN", Color.orange));
 167     maxColour.setBackground(Cache.getDefaultColour("ANNOTATIONCOLOUR_MAX", Color.red));
 168   }
 169
 170   public AnnotationColourChooser()
 171   {
 172     try
 173     {
 174       jbInit();
 175     } catch (Exception ex)
 176     {
 177       ex.printStackTrace();
 178     }
 179   }
 180
 181   private void jbInit() throws Exception
 182   {
 183     minColour.setFont(JvSwingUtils.getLabelFont());
 184     minColour.setBorder(BorderFactory.createEtchedBorder());
 185     minColour.setPreferredSize(new Dimension(40, 20));
 186     minColour.setToolTipText("Minimum Colour");
 187     minColour.addMouseListener(new MouseAdapter()
 188     {
 189       public void mousePressed(MouseEvent e)
 190       {
 191         if (minColour.isEnabled())
 192         {
 193           minColour_actionPerformed();
 194         }
 195       }
 196     });
 197     maxColour.setFont(JvSwingUtils.getLabelFont());
 198     maxColour.setBorder(BorderFactory.createEtchedBorder());
 199     maxColour.setPreferredSize(new Dimension(40, 20));
 200     maxColour.setToolTipText("Maximum Colour");
 201     maxColour.addMouseListener(new MouseAdapter()
 202     {
 203       public void mousePressed(MouseEvent e)
 204       {
 205         if (maxColour.isEnabled())
 206         {
 207           maxColour_actionPerformed();
 208         }
 209       }
 210     });
 211     ok.setOpaque(false);
 212     ok.setText("OK");
 213     ok.addActionListener(new ActionListener()
 214     {
 215       public void actionPerformed(ActionEvent e)
 216       {
 217         ok_actionPerformed(e);
 218       }
 219     });
 220     cancel.setOpaque(false);
 221     cancel.setText("Cancel");
 222     cancel.addActionListener(new ActionListener()
 223     {
 224       public void actionPerformed(ActionEvent e)
 225       {
 226         cancel_actionPerformed(e);
 227       }
 228     });
 229     defColours.setOpaque(false);
 230     defColours.setText("Defaults");
 231     defColours.setToolTipText("Reset min and max colours to defaults from user preferences.");
 232     defColours.addActionListener(new ActionListener()
 233     {
 234
 235       @Override
 236       public void actionPerformed(ActionEvent arg0)
 237       {
 238         resetColours_actionPerformed(arg0);
 239       }
 240     });
 241
 242     annotations.addActionListener(new ActionListener()
 243     {
 244       public void actionPerformed(ActionEvent e)
 245       {
 246         annotations_actionPerformed(e);
 247       }
 248     });
 249     threshold.addActionListener(new ActionListener()
 250     {
 251       public void actionPerformed(ActionEvent e)
 252       {
 253         threshold_actionPerformed(e);
 254       }
 255     });
 256     thresholdValue.addActionListener(new ActionListener()
 257     {
 258       public void actionPerformed(ActionEvent e)
 259       {
 260         thresholdValue_actionPerformed(e);
 261       }
 262     });
 263     slider.setPaintLabels(false);
 264     slider.setPaintTicks(true);
 265     slider.setBackground(Color.white);
 266     slider.setEnabled(false);
 267     slider.setOpaque(false);
 268     slider.setPreferredSize(new Dimension(100, 32));
 269     thresholdValue.setEnabled(false);
 270     thresholdValue.setColumns(7);
 271     currentColours.setFont(JvSwingUtils.getLabelFont());
 272     currentColours.setOpaque(false);
 273     currentColours.setText("Use Original Colours");
 274     currentColours.addActionListener(new ActionListener()
 275     {
 276       public void actionPerformed(ActionEvent e)
 277       {
 278         currentColours_actionPerformed(e);
 279       }
 280     });
 281     thresholdIsMin.setBackground(Color.white);
 282     thresholdIsMin.setFont(JvSwingUtils.getLabelFont());
 283     thresholdIsMin.setText("Threshold is Min/Max");
 284     thresholdIsMin.addActionListener(new ActionListener()
 285     {
 286       public void actionPerformed(ActionEvent actionEvent)
 287       {
 288         thresholdIsMin_actionPerformed(actionEvent);
 289       }
 290     });
 291     seqAssociated.setBackground(Color.white);
 292     seqAssociated.setFont(JvSwingUtils.getLabelFont());
 293     seqAssociated.setText("Per-sequence only");
 294     seqAssociated.addActionListener(new ActionListener()
 295     {
 296
 297       @Override
 298       public void actionPerformed(ActionEvent arg0)
 299       {
 300         seqAssociated_actionPerformed(arg0);
 301       }
 302     });
 303
 304     this.setLayout(borderLayout1);
 305     jPanel2.setLayout(new MigLayout("","[left][center][right]","[][][]"));
 306     jPanel1.setBackground(Color.white);
 307     jPanel2.setBackground(Color.white);
 308
 309     jPanel1.add(ok);
 310     jPanel1.add(cancel);
 311     jPanel2.add(annotations);
 312     jPanel2.add(currentColours);
 313     JPanel colpanel = new JPanel(new FlowLayout());
 314     colpanel.setBackground(Color.white);
 315     colpanel.add(minColour);
 316     colpanel.add(maxColour);
 317     jPanel2.add(colpanel, "wrap");
 318     jPanel2.add(seqAssociated, "wrap");
 319     jPanel2.add(threshold);
 320     jPanel2.add(defColours,"skip 1, wrap");
 321     jPanel2.add(thresholdIsMin);
 322     jPanel2.add(slider, "grow");
 323     jPanel2.add(thresholdValue, "grow");
 324     this.add(jPanel1, java.awt.BorderLayout.SOUTH);
 325     this.add(jPanel2, java.awt.BorderLayout.CENTER);
 326     this.validate();
 327   }
 328
 329   protected void seqAssociated_actionPerformed(ActionEvent arg0)
 330   {
 331     changeColour();
 332   }
 333
 334   protected void resetColours_actionPerformed(ActionEvent arg0)
 335   {
 336     setDefaultMinMax();
 337     changeColour();
 338   }
 339
 340   JComboBox annotations;
 341
 342   JPanel minColour = new JPanel();
 343
 344   JPanel maxColour = new JPanel();
 345   JButton defColours = new JButton();
 346   JButton ok = new JButton();
 347
 348   JButton cancel = new JButton();
 349
 350   JPanel jPanel1 = new JPanel();
 351   JPanel jPanel2 = new JPanel();
 352
 353   BorderLayout borderLayout1 = new BorderLayout();
 354
 355   JComboBox threshold = new JComboBox();
 356
 357
 358   JSlider slider = new JSlider();
 359
 360   JTextField thresholdValue = new JTextField(20);
 361
 362   JCheckBox currentColours = new JCheckBox();
 363
 364   JCheckBox thresholdIsMin = new JCheckBox();
 365
 366   JCheckBox seqAssociated = new JCheckBox();
 367
 368   public void minColour_actionPerformed()
 369   {
 370     Color col = JColorChooser.showDialog(this,
 371             "Select Colour for Minimum Value", minColour.getBackground());
 372     if (col != null)
 373     {
 374       minColour.setBackground(col);
 375     }
 376     minColour.repaint();
 377     changeColour();
 378   }
 379
 380   public void maxColour_actionPerformed()
 381   {
 382     Color col = JColorChooser.showDialog(this,
 383             "Select Colour for Maximum Value", maxColour.getBackground());
 384     if (col != null)
 385     {
 386       maxColour.setBackground(col);
 387     }
 388     maxColour.repaint();
 389     changeColour();
 390   }
 391
 392   void changeColour()
 393   {
 394     // Check if combobox is still adjusting
 395     if (adjusting)
 396     {
 397       return;
 398     }
 399
 400     currentAnnotation = av.getAlignment().getAlignmentAnnotation()[annotations
 401             .getSelectedIndex()];
 402
 403     int aboveThreshold = -1;
 404     if (threshold.getSelectedItem().equals("Above Threshold"))
 405     {
 406       aboveThreshold = AnnotationColourGradient.ABOVE_THRESHOLD;
 407     }
 408     else if (threshold.getSelectedItem().equals("Below Threshold"))
 409     {
 410       aboveThreshold = AnnotationColourGradient.BELOW_THRESHOLD;
 411     }
 412
 413     slider.setEnabled(true);
 414     thresholdValue.setEnabled(true);
 415     thresholdIsMin.setEnabled(true);
 416
 417     if (aboveThreshold == AnnotationColourGradient.NO_THRESHOLD)
 418     {
 419       slider.setEnabled(false);
 420       thresholdValue.setEnabled(false);
 421       thresholdValue.setText("");
 422       thresholdIsMin.setEnabled(false);
 423     }
 424     else if (aboveThreshold != AnnotationColourGradient.NO_THRESHOLD
 425             && currentAnnotation.threshold == null)
 426     {
 427       currentAnnotation
 428               .setThreshold(new jalview.datamodel.GraphLine(
 429                       (currentAnnotation.graphMax - currentAnnotation.graphMin) / 2f,
 430                       "Threshold", Color.black));
 431     }
 432
 433     if (aboveThreshold != AnnotationColourGradient.NO_THRESHOLD)
 434     {
 435       adjusting = true;
 436       float range = currentAnnotation.graphMax * 1000
 437               - currentAnnotation.graphMin * 1000;
 438
 439       slider.setMinimum((int) (currentAnnotation.graphMin * 1000));
 440       slider.setMaximum((int) (currentAnnotation.graphMax * 1000));
 441       slider.setValue((int) (currentAnnotation.threshold.value * 1000));
 442       thresholdValue.setText(currentAnnotation.threshold.value + "");
 443       slider.setMajorTickSpacing((int) (range / 10f));
 444       slider.setEnabled(true);
 445       thresholdValue.setEnabled(true);
 446       adjusting = false;
 447     }
 448
 449     AnnotationColourGradient acg = null;
 450     if (currentColours.isSelected())
 451     {
 452       acg = new AnnotationColourGradient(currentAnnotation,
 453               av.getGlobalColourScheme(), aboveThreshold);
 454     }
 455     else
 456     {
 457       acg = new AnnotationColourGradient(currentAnnotation,
 458               minColour.getBackground(), maxColour.getBackground(),
 459               aboveThreshold);
 460     }
 461     acg.setSeqAssociated(seqAssociated.isSelected());
 462
 463     if (currentAnnotation.graphMin == 0f
 464             && currentAnnotation.graphMax == 0f)
 465     {
 466       acg.predefinedColours = true;
 467     }
 468
 469     acg.thresholdIsMinMax = thresholdIsMin.isSelected();
 470
 471     av.setGlobalColourScheme(acg);
 472
 473     if (av.getAlignment().getGroups() != null)
 474     {
 475
 476       for (SequenceGroup sg:ap.av.getAlignment().getGroups())
 477       {
 478         if (sg.cs == null)
 479         {
 480           continue;
 481         }
 482
 483         if (currentColours.isSelected())
 484         {
 485           sg.cs = new AnnotationColourGradient(currentAnnotation, sg.cs,
 486                   aboveThreshold);
 487           ((AnnotationColourGradient)sg.cs).setSeqAssociated(seqAssociated.isSelected());
 488
 489         }
 490         else
 491         {
 492           sg.cs = new AnnotationColourGradient(currentAnnotation,
 493                   minColour.getBackground(), maxColour.getBackground(),
 494                   aboveThreshold);
 495           ((AnnotationColourGradient)sg.cs).setSeqAssociated(seqAssociated.isSelected());
 496         }
 497
 498       }
 499     }
 500     ap.alignmentChanged();
 501     // ensure all associated views (overviews, structures, etc) are notified of updated colours.
 502     ap.paintAlignment(true);
 503   }
 504
 505   public void ok_actionPerformed(ActionEvent e)
 506   {
 507     changeColour();
 508     try
 509     {
 510       frame.setClosed(true);
 511     } catch (Exception ex)
 512     {
 513     }
 514   }
 515
 516   public void cancel_actionPerformed(ActionEvent e)
 517   {
 518     reset();
 519     // ensure all original colouring is propagated to listeners.
 520     ap.paintAlignment(true);
 521     try
 522     {
 523       frame.setClosed(true);
 524     } catch (Exception ex)
 525     {
 526     }
 527   }
 528
 529   void reset()
 530   {
 531     av.setGlobalColourScheme(oldcs);
 532     if (av.getAlignment().getGroups() != null)
 533     {
 534
 535       for (SequenceGroup sg:ap.av.getAlignment().getGroups())
 536       {
 537         sg.cs = (ColourSchemeI) oldgroupColours.get(sg);
 538       }
 539     }
 540   }
 541
 542   public void thresholdCheck_actionPerformed(ActionEvent e)
 543   {
 544     changeColour();
 545   }
 546
 547   public void annotations_actionPerformed(ActionEvent e)
 548   {
 549     changeColour();
 550   }
 551
 552   public void threshold_actionPerformed(ActionEvent e)
 553   {
 554     changeColour();
 555   }
 556
 557   public void thresholdValue_actionPerformed(ActionEvent e)
 558   {
 559     try
 560     {
 561       float f = Float.parseFloat(thresholdValue.getText());
 562       slider.setValue((int) (f * 1000));
 563     } catch (NumberFormatException ex)
 564     {
 565     }
 566   }
 567
 568   public void valueChanged()
 569   {
 570     if (currentColours.isSelected()
 571             && !(av.getGlobalColourScheme() instanceof AnnotationColourGradient))
 572     {
 573       changeColour();
 574     }
 575
 576     currentAnnotation.threshold.value = (float) slider.getValue() / 1000f;
 577     ap.paintAlignment(false);
 578   }
 579
 580   public void currentColours_actionPerformed(ActionEvent e)
 581   {
 582     if (currentColours.isSelected())
 583     {
 584       reset();
 585     }
 586
 587     maxColour.setEnabled(!currentColours.isSelected());
 588     minColour.setEnabled(!currentColours.isSelected());
 589
 590     changeColour();
 591   }
 592
 593   public void thresholdIsMin_actionPerformed(ActionEvent actionEvent)
 594   {
 595     changeColour();
 596   }
 597
 598 }