src/jalview/gui/AnnotationColourChooser.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
   3  * Copyright (C) 2010 J Procter, AM Waterhouse, 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.alignment.getGroups() != null)
  55     {
  56       oldgroupColours = new Hashtable();
  57       Vector allGroups = ap.av.alignment.getGroups();
  58       SequenceGroup sg;
  59       for (int g = 0; g < allGroups.size(); g++)
  60       {
  61         sg = (SequenceGroup) allGroups.get(g);
  62         if (sg.cs != null)
  63         {
  64           oldgroupColours.put(sg, sg.cs);
  65         }
  66       }
  67     }
  68     this.av = av;
  69     this.ap = ap;
  70     frame = new JInternalFrame();
  71     frame.setContentPane(this);
  72     frame.setLayer(JLayeredPane.PALETTE_LAYER);
  73     Desktop.addInternalFrame(frame, "Colour by Annotation", 520, 215);
  74
  75     slider.addChangeListener(new ChangeListener()
  76     {
  77       public void stateChanged(ChangeEvent evt)
  78       {
  79         if (!adjusting)
  80         {
  81           thresholdValue.setText(((float) slider.getValue() / 1000f) + "");
  82           valueChanged();
  83         }
  84       }
  85     });
  86     slider.addMouseListener(new MouseAdapter()
  87     {
  88       public void mouseReleased(MouseEvent evt)
  89       {
  90         ap.paintAlignment(true);
  91       }
  92     });
  93
  94     if (av.alignment.getAlignmentAnnotation() == null)
  95     {
  96       return;
  97     }
  98
  99     // Always get default shading from preferences.
 100     setDefaultMinMax();
 101
 102     if (oldcs instanceof AnnotationColourGradient)
 103     {
 104       AnnotationColourGradient acg = (AnnotationColourGradient) oldcs;
 105       currentColours.setSelected(acg.predefinedColours);
 106       if (!acg.predefinedColours)
 107       {
 108         minColour.setBackground(acg.getMinColour());
 109         maxColour.setBackground(acg.getMaxColour());
 110       }
 111     }
 112
 113     adjusting = true;
 114     Vector list = new Vector();
 115     int index = 1;
 116     for (int i = 0; i < av.alignment.getAlignmentAnnotation().length; i++)
 117     {
 118       String label = av.alignment.getAlignmentAnnotation()[i].label;
 119       if (!list.contains(label))
 120         list.addElement(label);
 121       else
 122         list.addElement(label + "_" + (index++));
 123     }
 124
 125     annotations = new JComboBox(list);
 126
 127     threshold.addItem("No Threshold");
 128     threshold.addItem("Above Threshold");
 129     threshold.addItem("Below Threshold");
 130
 131     if (oldcs instanceof AnnotationColourGradient)
 132     {
 133       AnnotationColourGradient acg = (AnnotationColourGradient) oldcs;
 134       annotations.setSelectedItem(acg.getAnnotation());
 135       switch (acg.getAboveThreshold()) {
 136       case AnnotationColourGradient.NO_THRESHOLD:
 137           threshold.setSelectedItem("No Threshold");
 138         break;
 139       case AnnotationColourGradient.ABOVE_THRESHOLD:
 140           threshold.setSelectedItem("Above Threshold");
 141         break;
 142       case AnnotationColourGradient.BELOW_THRESHOLD:
 143         threshold.setSelectedItem("Below Threshold");
 144         break;
 145         default:
 146           throw new Error("Implementation error: don't know about threshold setting for current AnnotationColourGradient.");
 147       }
 148       thresholdIsMin.setSelected(acg.thresholdIsMinMax);
 149       thresholdValue.setText(""+acg.getAnnotationThreshold());
 150     }
 151
 152     try
 153     {
 154       jbInit();
 155     } catch (Exception ex)
 156     {
 157     }
 158
 159     adjusting = false;
 160
 161     changeColour();
 162     validate();
 163
 164   }
 165
 166   private void setDefaultMinMax()
 167   {
 168     minColour.setBackground(Cache.getDefaultColour("ANNOTATIONCOLOUR_MIN", Color.orange));
 169     maxColour.setBackground(Cache.getDefaultColour("ANNOTATIONCOLOUR_MAX", Color.red));
 170   }
 171
 172   public AnnotationColourChooser()
 173   {
 174     try
 175     {
 176       jbInit();
 177     } catch (Exception ex)
 178     {
 179       ex.printStackTrace();
 180     }
 181   }
 182
 183   private void jbInit() throws Exception
 184   {
 185     minColour.setFont(JvSwingUtils.getLabelFont());
 186     minColour.setBorder(BorderFactory.createEtchedBorder());
 187     minColour.setPreferredSize(new Dimension(40, 20));
 188     minColour.setToolTipText("Minimum Colour");
 189     minColour.addMouseListener(new MouseAdapter()
 190     {
 191       public void mousePressed(MouseEvent e)
 192       {
 193         if (minColour.isEnabled())
 194         {
 195           minColour_actionPerformed();
 196         }
 197       }
 198     });
 199     maxColour.setFont(JvSwingUtils.getLabelFont());
 200     maxColour.setBorder(BorderFactory.createEtchedBorder());
 201     maxColour.setPreferredSize(new Dimension(40, 20));
 202     maxColour.setToolTipText("Maximum Colour");
 203     maxColour.addMouseListener(new MouseAdapter()
 204     {
 205       public void mousePressed(MouseEvent e)
 206       {
 207         if (maxColour.isEnabled())
 208         {
 209           maxColour_actionPerformed();
 210         }
 211       }
 212     });
 213     ok.setOpaque(false);
 214     ok.setText("OK");
 215     ok.addActionListener(new ActionListener()
 216     {
 217       public void actionPerformed(ActionEvent e)
 218       {
 219         ok_actionPerformed(e);
 220       }
 221     });
 222     cancel.setOpaque(false);
 223     cancel.setText("Cancel");
 224     cancel.addActionListener(new ActionListener()
 225     {
 226       public void actionPerformed(ActionEvent e)
 227       {
 228         cancel_actionPerformed(e);
 229       }
 230     });
 231     defColours.setOpaque(false);
 232     defColours.setText("Defaults");
 233     defColours.setToolTipText("Reset min and max colours to defaults from user preferences.");
 234     defColours.addActionListener(new ActionListener()
 235     {
 236
 237       @Override
 238       public void actionPerformed(ActionEvent arg0)
 239       {
 240         resetColours_actionPerformed(arg0);
 241       }
 242     });
 243
 244     annotations.addActionListener(new ActionListener()
 245     {
 246       public void actionPerformed(ActionEvent e)
 247       {
 248         annotations_actionPerformed(e);
 249       }
 250     });
 251     threshold.addActionListener(new ActionListener()
 252     {
 253       public void actionPerformed(ActionEvent e)
 254       {
 255         threshold_actionPerformed(e);
 256       }
 257     });
 258     thresholdValue.addActionListener(new ActionListener()
 259     {
 260       public void actionPerformed(ActionEvent e)
 261       {
 262         thresholdValue_actionPerformed(e);
 263       }
 264     });
 265     slider.setPaintLabels(false);
 266     slider.setPaintTicks(true);
 267     slider.setBackground(Color.white);
 268     slider.setEnabled(false);
 269     slider.setOpaque(false);
 270     slider.setPreferredSize(new Dimension(100, 32));
 271     thresholdValue.setEnabled(false);
 272     thresholdValue.setColumns(7);
 273     currentColours.setFont(JvSwingUtils.getLabelFont());
 274     currentColours.setOpaque(false);
 275     currentColours.setText("Use Original Colours");
 276     currentColours.addActionListener(new ActionListener()
 277     {
 278       public void actionPerformed(ActionEvent e)
 279       {
 280         currentColours_actionPerformed(e);
 281       }
 282     });
 283     thresholdIsMin.setBackground(Color.white);
 284     thresholdIsMin.setFont(JvSwingUtils.getLabelFont());
 285     thresholdIsMin.setText("Threshold is Min/Max");
 286     thresholdIsMin.addActionListener(new ActionListener()
 287     {
 288       public void actionPerformed(ActionEvent actionEvent)
 289       {
 290         thresholdIsMin_actionPerformed(actionEvent);
 291       }
 292     });
 293     this.setLayout(borderLayout1);
 294     jPanel2.setLayout(new MigLayout("","[left][center][right]","[][][]"));
 295     jPanel1.setBackground(Color.white);
 296     jPanel2.setBackground(Color.white);
 297
 298     jPanel1.add(ok);
 299     jPanel1.add(cancel);
 300     jPanel2.add(annotations);
 301     jPanel2.add(currentColours);
 302     JPanel colpanel = new JPanel(new FlowLayout());
 303     colpanel.setBackground(Color.white);
 304     colpanel.add(minColour);
 305     colpanel.add(maxColour);
 306     jPanel2.add(colpanel, "wrap");
 307
 308     jPanel2.add(threshold);
 309     jPanel2.add(defColours,"skip 1, wrap");
 310     jPanel2.add(thresholdIsMin);
 311     jPanel2.add(slider, "grow");
 312     jPanel2.add(thresholdValue, "grow");
 313     this.add(jPanel1, java.awt.BorderLayout.SOUTH);
 314     this.add(jPanel2, java.awt.BorderLayout.CENTER);
 315   }
 316
 317   protected void resetColours_actionPerformed(ActionEvent arg0)
 318   {
 319     setDefaultMinMax();
 320     changeColour();
 321   }
 322
 323   JComboBox annotations;
 324
 325   JPanel minColour = new JPanel();
 326
 327   JPanel maxColour = new JPanel();
 328   JButton defColours = new JButton();
 329   JButton ok = new JButton();
 330
 331   JButton cancel = new JButton();
 332
 333   JPanel jPanel1 = new JPanel();
 334   JPanel jPanel2 = new JPanel();
 335
 336   BorderLayout borderLayout1 = new BorderLayout();
 337
 338   JComboBox threshold = new JComboBox();
 339
 340
 341   JSlider slider = new JSlider();
 342
 343   JTextField thresholdValue = new JTextField(20);
 344
 345   JCheckBox currentColours = new JCheckBox();
 346
 347   JCheckBox thresholdIsMin = new JCheckBox();
 348
 349   public void minColour_actionPerformed()
 350   {
 351     Color col = JColorChooser.showDialog(this,
 352             "Select Colour for Minimum Value", minColour.getBackground());
 353     if (col != null)
 354     {
 355       minColour.setBackground(col);
 356     }
 357     minColour.repaint();
 358     changeColour();
 359   }
 360
 361   public void maxColour_actionPerformed()
 362   {
 363     Color col = JColorChooser.showDialog(this,
 364             "Select Colour for Maximum Value", maxColour.getBackground());
 365     if (col != null)
 366     {
 367       maxColour.setBackground(col);
 368     }
 369     maxColour.repaint();
 370     changeColour();
 371   }
 372
 373   void changeColour()
 374   {
 375     // Check if combobox is still adjusting
 376     if (adjusting)
 377     {
 378       return;
 379     }
 380
 381     currentAnnotation = av.alignment.getAlignmentAnnotation()[annotations
 382             .getSelectedIndex()];
 383
 384     int aboveThreshold = -1;
 385     if (threshold.getSelectedItem().equals("Above Threshold"))
 386     {
 387       aboveThreshold = AnnotationColourGradient.ABOVE_THRESHOLD;
 388     }
 389     else if (threshold.getSelectedItem().equals("Below Threshold"))
 390     {
 391       aboveThreshold = AnnotationColourGradient.BELOW_THRESHOLD;
 392     }
 393
 394     slider.setEnabled(true);
 395     thresholdValue.setEnabled(true);
 396     thresholdIsMin.setEnabled(true);
 397
 398     if (aboveThreshold == AnnotationColourGradient.NO_THRESHOLD)
 399     {
 400       slider.setEnabled(false);
 401       thresholdValue.setEnabled(false);
 402       thresholdValue.setText("");
 403       thresholdIsMin.setEnabled(false);
 404     }
 405     else if (aboveThreshold != AnnotationColourGradient.NO_THRESHOLD
 406             && currentAnnotation.threshold == null)
 407     {
 408       currentAnnotation
 409               .setThreshold(new jalview.datamodel.GraphLine(
 410                       (currentAnnotation.graphMax - currentAnnotation.graphMin) / 2f,
 411                       "Threshold", Color.black));
 412     }
 413
 414     if (aboveThreshold != AnnotationColourGradient.NO_THRESHOLD)
 415     {
 416       adjusting = true;
 417       float range = currentAnnotation.graphMax * 1000
 418               - currentAnnotation.graphMin * 1000;
 419
 420       slider.setMinimum((int) (currentAnnotation.graphMin * 1000));
 421       slider.setMaximum((int) (currentAnnotation.graphMax * 1000));
 422       slider.setValue((int) (currentAnnotation.threshold.value * 1000));
 423       thresholdValue.setText(currentAnnotation.threshold.value + "");
 424       slider.setMajorTickSpacing((int) (range / 10f));
 425       slider.setEnabled(true);
 426       thresholdValue.setEnabled(true);
 427       adjusting = false;
 428     }
 429
 430     AnnotationColourGradient acg = null;
 431     if (currentColours.isSelected())
 432     {
 433       acg = new AnnotationColourGradient(currentAnnotation,
 434               av.getGlobalColourScheme(), aboveThreshold);
 435     }
 436     else
 437     {
 438       acg = new AnnotationColourGradient(currentAnnotation,
 439               minColour.getBackground(), maxColour.getBackground(),
 440               aboveThreshold);
 441     }
 442
 443     if (currentAnnotation.graphMin == 0f
 444             && currentAnnotation.graphMax == 0f)
 445     {
 446       acg.predefinedColours = true;
 447     }
 448
 449     acg.thresholdIsMinMax = thresholdIsMin.isSelected();
 450
 451     av.setGlobalColourScheme(acg);
 452
 453     if (av.alignment.getGroups() != null)
 454     {
 455       Vector allGroups = ap.av.alignment.getGroups();
 456       SequenceGroup sg;
 457       for (int g = 0; g < allGroups.size(); g++)
 458       {
 459         sg = (SequenceGroup) allGroups.get(g);
 460
 461         if (sg.cs == null)
 462         {
 463           continue;
 464         }
 465
 466         if (currentColours.isSelected())
 467         {
 468           sg.cs = new AnnotationColourGradient(currentAnnotation, sg.cs,
 469                   aboveThreshold);
 470         }
 471         else
 472         {
 473           sg.cs = new AnnotationColourGradient(currentAnnotation,
 474                   minColour.getBackground(), maxColour.getBackground(),
 475                   aboveThreshold);
 476         }
 477
 478       }
 479     }
 480     // ensure all associated views (overviews, structures, etc) are notified of updated colours.
 481     ap.paintAlignment(true);
 482   }
 483
 484   public void ok_actionPerformed(ActionEvent e)
 485   {
 486     changeColour();
 487     try
 488     {
 489       frame.setClosed(true);
 490     } catch (Exception ex)
 491     {
 492     }
 493   }
 494
 495   public void cancel_actionPerformed(ActionEvent e)
 496   {
 497     reset();
 498     // ensure all original colouring is propagated to listeners.
 499     ap.paintAlignment(true);
 500     try
 501     {
 502       frame.setClosed(true);
 503     } catch (Exception ex)
 504     {
 505     }
 506   }
 507
 508   void reset()
 509   {
 510     av.setGlobalColourScheme(oldcs);
 511     if (av.alignment.getGroups() != null)
 512     {
 513       Vector allGroups = ap.av.alignment.getGroups();
 514       SequenceGroup sg;
 515       for (int g = 0; g < allGroups.size(); g++)
 516       {
 517         sg = (SequenceGroup) allGroups.get(g);
 518         sg.cs = (ColourSchemeI) oldgroupColours.get(sg);
 519       }
 520     }
 521   }
 522
 523   public void thresholdCheck_actionPerformed(ActionEvent e)
 524   {
 525     changeColour();
 526   }
 527
 528   public void annotations_actionPerformed(ActionEvent e)
 529   {
 530     changeColour();
 531   }
 532
 533   public void threshold_actionPerformed(ActionEvent e)
 534   {
 535     changeColour();
 536   }
 537
 538   public void thresholdValue_actionPerformed(ActionEvent e)
 539   {
 540     try
 541     {
 542       float f = Float.parseFloat(thresholdValue.getText());
 543       slider.setValue((int) (f * 1000));
 544     } catch (NumberFormatException ex)
 545     {
 546     }
 547   }
 548
 549   public void valueChanged()
 550   {
 551     if (currentColours.isSelected()
 552             && !(av.getGlobalColourScheme() instanceof AnnotationColourGradient))
 553     {
 554       changeColour();
 555     }
 556
 557     currentAnnotation.threshold.value = (float) slider.getValue() / 1000f;
 558     ap.paintAlignment(false);
 559   }
 560
 561   public void currentColours_actionPerformed(ActionEvent e)
 562   {
 563     if (currentColours.isSelected())
 564     {
 565       reset();
 566     }
 567
 568     maxColour.setEnabled(!currentColours.isSelected());
 569     minColour.setEnabled(!currentColours.isSelected());
 570
 571     changeColour();
 572   }
 573
 574   public void thresholdIsMin_actionPerformed(ActionEvent actionEvent)
 575   {
 576     changeColour();
 577   }
 578
 579 }