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