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 import javax.swing.*;
  25 import javax.swing.event.*;
  26
  27 import jalview.bin.Cache;
  28 import jalview.datamodel.*;
  29 import jalview.schemes.*;
  30 import java.awt.Dimension;
  31
  32 public class AnnotationColourChooser extends JPanel
  33 {
  34   JInternalFrame frame;
  35
  36   AlignViewport av;
  37
  38   AlignmentPanel ap;
  39
  40   ColourSchemeI oldcs;
  41
  42   Hashtable oldgroupColours;
  43
  44   jalview.datamodel.AlignmentAnnotation currentAnnotation;
  45
  46   boolean adjusting = false;
  47
  48   public AnnotationColourChooser(AlignViewport av, final AlignmentPanel ap)
  49   {
  50     oldcs = av.getGlobalColourScheme();
  51     if (av.alignment.getGroups() != null)
  52     {
  53       oldgroupColours = new Hashtable();
  54       Vector allGroups = ap.av.alignment.getGroups();
  55       SequenceGroup sg;
  56       for (int g = 0; g < allGroups.size(); g++)
  57       {
  58         sg = (SequenceGroup) allGroups.get(g);
  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", 480, 145);
  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.alignment.getAlignmentAnnotation() == null)
  92     {
  93       return;
  94     }
  95
  96     // Always get default shading from preferences.
  97     minColour.setBackground(Cache.getDefaultColour("ANNOTATIONCOLOUR_MIN", Color.orange));
  98     maxColour.setBackground(Cache.getDefaultColour("ANNOTATIONCOLOUR_MAX", Color.red));
  99
 100     if (oldcs instanceof AnnotationColourGradient)
 101     {
 102       AnnotationColourGradient acg = (AnnotationColourGradient) oldcs;
 103       currentColours.setSelected(acg.predefinedColours);
 104       if (!acg.predefinedColours)
 105       {
 106         minColour.setBackground(acg.getMinColour());
 107         maxColour.setBackground(acg.getMaxColour());
 108       }
 109     }
 110
 111     adjusting = true;
 112     Vector list = new Vector();
 113     int index = 1;
 114     for (int i = 0; i < av.alignment.getAlignmentAnnotation().length; i++)
 115     {
 116       String label = av.alignment.getAlignmentAnnotation()[i].label;
 117       if (!list.contains(label))
 118         list.addElement(label);
 119       else
 120         list.addElement(label + "_" + (index++));
 121     }
 122
 123     annotations = new JComboBox(list);
 124
 125     threshold.addItem("No Threshold");
 126     threshold.addItem("Above Threshold");
 127     threshold.addItem("Below Threshold");
 128
 129     if (oldcs instanceof AnnotationColourGradient)
 130     {
 131       AnnotationColourGradient acg = (AnnotationColourGradient) oldcs;
 132       annotations.setSelectedItem(acg.getAnnotation());
 133       switch (acg.getAboveThreshold()) {
 134       case AnnotationColourGradient.NO_THRESHOLD:
 135           threshold.setSelectedItem("No Threshold");
 136         break;
 137       case AnnotationColourGradient.ABOVE_THRESHOLD:
 138           threshold.setSelectedItem("Above Threshold");
 139         break;
 140       case AnnotationColourGradient.BELOW_THRESHOLD:
 141         threshold.setSelectedItem("Below Threshold");
 142         break;
 143         default:
 144           throw new Error("Implementation error: don't know about threshold setting for current AnnotationColourGradient.");
 145       }
 146       thresholdIsMin.setSelected(acg.thresholdIsMinMax);
 147       thresholdValue.setText(""+acg.getAnnotationThreshold());
 148     }
 149
 150     try
 151     {
 152       jbInit();
 153     } catch (Exception ex)
 154     {
 155     }
 156
 157     adjusting = false;
 158
 159     changeColour();
 160     validate();
 161
 162   }
 163
 164   public AnnotationColourChooser()
 165   {
 166     try
 167     {
 168       jbInit();
 169     } catch (Exception ex)
 170     {
 171       ex.printStackTrace();
 172     }
 173   }
 174
 175   private void jbInit() throws Exception
 176   {
 177     minColour.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
 178     minColour.setBorder(BorderFactory.createEtchedBorder());
 179     minColour.setPreferredSize(new Dimension(40, 20));
 180     minColour.setToolTipText("Minimum Colour");
 181     minColour.addMouseListener(new MouseAdapter()
 182     {
 183       public void mousePressed(MouseEvent e)
 184       {
 185         if (minColour.isEnabled())
 186         {
 187           minColour_actionPerformed();
 188         }
 189       }
 190     });
 191     maxColour.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
 192     maxColour.setBorder(BorderFactory.createEtchedBorder());
 193     maxColour.setPreferredSize(new Dimension(40, 20));
 194     maxColour.setToolTipText("Maximum Colour");
 195     maxColour.addMouseListener(new MouseAdapter()
 196     {
 197       public void mousePressed(MouseEvent e)
 198       {
 199         if (maxColour.isEnabled())
 200         {
 201           maxColour_actionPerformed();
 202         }
 203       }
 204     });
 205     ok.setOpaque(false);
 206     ok.setText("OK");
 207     ok.addActionListener(new ActionListener()
 208     {
 209       public void actionPerformed(ActionEvent e)
 210       {
 211         ok_actionPerformed(e);
 212       }
 213     });
 214     cancel.setOpaque(false);
 215     cancel.setText("Cancel");
 216     cancel.addActionListener(new ActionListener()
 217     {
 218       public void actionPerformed(ActionEvent e)
 219       {
 220         cancel_actionPerformed(e);
 221       }
 222     });
 223     this.setLayout(borderLayout1);
 224     jPanel2.setLayout(flowLayout1);
 225     annotations.addActionListener(new ActionListener()
 226     {
 227       public void actionPerformed(ActionEvent e)
 228       {
 229         annotations_actionPerformed(e);
 230       }
 231     });
 232     jPanel1.setBackground(Color.white);
 233     jPanel2.setBackground(Color.white);
 234     threshold.addActionListener(new ActionListener()
 235     {
 236       public void actionPerformed(ActionEvent e)
 237       {
 238         threshold_actionPerformed(e);
 239       }
 240     });
 241     jPanel3.setLayout(flowLayout2);
 242     thresholdValue.addActionListener(new ActionListener()
 243     {
 244       public void actionPerformed(ActionEvent e)
 245       {
 246         thresholdValue_actionPerformed(e);
 247       }
 248     });
 249     slider.setPaintLabels(false);
 250     slider.setPaintTicks(true);
 251     slider.setBackground(Color.white);
 252     slider.setEnabled(false);
 253     slider.setOpaque(false);
 254     slider.setPreferredSize(new Dimension(100, 32));
 255     thresholdValue.setEnabled(false);
 256     thresholdValue.setColumns(7);
 257     jPanel3.setBackground(Color.white);
 258     currentColours.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
 259     currentColours.setOpaque(false);
 260     currentColours.setText("Use Original Colours");
 261     currentColours.addActionListener(new ActionListener()
 262     {
 263       public void actionPerformed(ActionEvent e)
 264       {
 265         currentColours_actionPerformed(e);
 266       }
 267     });
 268     thresholdIsMin.setBackground(Color.white);
 269     thresholdIsMin.setText("Threshold is Min/Max");
 270     thresholdIsMin.addActionListener(new ActionListener()
 271     {
 272       public void actionPerformed(ActionEvent actionEvent)
 273       {
 274         thresholdIsMin_actionPerformed(actionEvent);
 275       }
 276     });
 277     jPanel1.add(ok);
 278     jPanel1.add(cancel);
 279     jPanel2.add(annotations);
 280     jPanel2.add(currentColours);
 281     jPanel2.add(minColour);
 282     jPanel2.add(maxColour);
 283     this.add(jPanel3, java.awt.BorderLayout.CENTER);
 284     jPanel3.add(threshold);
 285     jPanel3.add(slider);
 286     jPanel3.add(thresholdValue);
 287     jPanel3.add(thresholdIsMin);
 288     this.add(jPanel1, java.awt.BorderLayout.SOUTH);
 289     this.add(jPanel2, java.awt.BorderLayout.NORTH);
 290   }
 291
 292   JComboBox annotations;
 293
 294   JPanel minColour = new JPanel();
 295
 296   JPanel maxColour = new JPanel();
 297
 298   JButton ok = new JButton();
 299
 300   JButton cancel = new JButton();
 301
 302   JPanel jPanel1 = new JPanel();
 303
 304   JPanel jPanel2 = new JPanel();
 305
 306   BorderLayout borderLayout1 = new BorderLayout();
 307
 308   JComboBox threshold = new JComboBox();
 309
 310   FlowLayout flowLayout1 = new FlowLayout();
 311
 312   JPanel jPanel3 = new JPanel();
 313
 314   FlowLayout flowLayout2 = new FlowLayout();
 315
 316   JSlider slider = new JSlider();
 317
 318   JTextField thresholdValue = new JTextField(20);
 319
 320   JCheckBox currentColours = new JCheckBox();
 321
 322   JCheckBox thresholdIsMin = new JCheckBox();
 323
 324   public void minColour_actionPerformed()
 325   {
 326     Color col = JColorChooser.showDialog(this,
 327             "Select Colour for Minimum Value", minColour.getBackground());
 328     if (col != null)
 329     {
 330       minColour.setBackground(col);
 331     }
 332     minColour.repaint();
 333     changeColour();
 334   }
 335
 336   public void maxColour_actionPerformed()
 337   {
 338     Color col = JColorChooser.showDialog(this,
 339             "Select Colour for Maximum Value", maxColour.getBackground());
 340     if (col != null)
 341     {
 342       maxColour.setBackground(col);
 343     }
 344     maxColour.repaint();
 345     changeColour();
 346   }
 347
 348   void changeColour()
 349   {
 350     // Check if combobox is still adjusting
 351     if (adjusting)
 352     {
 353       return;
 354     }
 355
 356     currentAnnotation = av.alignment.getAlignmentAnnotation()[annotations
 357             .getSelectedIndex()];
 358
 359     int aboveThreshold = -1;
 360     if (threshold.getSelectedItem().equals("Above Threshold"))
 361     {
 362       aboveThreshold = AnnotationColourGradient.ABOVE_THRESHOLD;
 363     }
 364     else if (threshold.getSelectedItem().equals("Below Threshold"))
 365     {
 366       aboveThreshold = AnnotationColourGradient.BELOW_THRESHOLD;
 367     }
 368
 369     slider.setEnabled(true);
 370     thresholdValue.setEnabled(true);
 371
 372     if (aboveThreshold == AnnotationColourGradient.NO_THRESHOLD)
 373     {
 374       slider.setEnabled(false);
 375       thresholdValue.setEnabled(false);
 376       thresholdValue.setText("");
 377     }
 378     else if (aboveThreshold != AnnotationColourGradient.NO_THRESHOLD
 379             && currentAnnotation.threshold == null)
 380     {
 381       currentAnnotation
 382               .setThreshold(new jalview.datamodel.GraphLine(
 383                       (currentAnnotation.graphMax - currentAnnotation.graphMin) / 2f,
 384                       "Threshold", Color.black));
 385     }
 386
 387     if (aboveThreshold != AnnotationColourGradient.NO_THRESHOLD)
 388     {
 389       adjusting = true;
 390       float range = currentAnnotation.graphMax * 1000
 391               - currentAnnotation.graphMin * 1000;
 392
 393       slider.setMinimum((int) (currentAnnotation.graphMin * 1000));
 394       slider.setMaximum((int) (currentAnnotation.graphMax * 1000));
 395       slider.setValue((int) (currentAnnotation.threshold.value * 1000));
 396       thresholdValue.setText(currentAnnotation.threshold.value + "");
 397       slider.setMajorTickSpacing((int) (range / 10f));
 398       slider.setEnabled(true);
 399       thresholdValue.setEnabled(true);
 400       adjusting = false;
 401     }
 402
 403     AnnotationColourGradient acg = null;
 404     if (currentColours.isSelected())
 405     {
 406       acg = new AnnotationColourGradient(currentAnnotation,
 407               av.getGlobalColourScheme(), aboveThreshold);
 408     }
 409     else
 410     {
 411       acg = new AnnotationColourGradient(currentAnnotation,
 412               minColour.getBackground(), maxColour.getBackground(),
 413               aboveThreshold);
 414     }
 415
 416     if (currentAnnotation.graphMin == 0f
 417             && currentAnnotation.graphMax == 0f)
 418     {
 419       acg.predefinedColours = true;
 420     }
 421
 422     acg.thresholdIsMinMax = thresholdIsMin.isSelected();
 423
 424     av.setGlobalColourScheme(acg);
 425
 426     if (av.alignment.getGroups() != null)
 427     {
 428       Vector allGroups = ap.av.alignment.getGroups();
 429       SequenceGroup sg;
 430       for (int g = 0; g < allGroups.size(); g++)
 431       {
 432         sg = (SequenceGroup) allGroups.get(g);
 433
 434         if (sg.cs == null)
 435         {
 436           continue;
 437         }
 438
 439         if (currentColours.isSelected())
 440         {
 441           sg.cs = new AnnotationColourGradient(currentAnnotation, sg.cs,
 442                   aboveThreshold);
 443         }
 444         else
 445         {
 446           sg.cs = new AnnotationColourGradient(currentAnnotation,
 447                   minColour.getBackground(), maxColour.getBackground(),
 448                   aboveThreshold);
 449         }
 450
 451       }
 452     }
 453     // ensure all associated views (overviews, structures, etc) are notified of updated colours.
 454     ap.paintAlignment(true);
 455   }
 456
 457   public void ok_actionPerformed(ActionEvent e)
 458   {
 459     changeColour();
 460     try
 461     {
 462       frame.setClosed(true);
 463     } catch (Exception ex)
 464     {
 465     }
 466   }
 467
 468   public void cancel_actionPerformed(ActionEvent e)
 469   {
 470     reset();
 471     try
 472     {
 473       frame.setClosed(true);
 474     } catch (Exception ex)
 475     {
 476     }
 477   }
 478
 479   void reset()
 480   {
 481     av.setGlobalColourScheme(oldcs);
 482     if (av.alignment.getGroups() != null)
 483     {
 484       Vector allGroups = ap.av.alignment.getGroups();
 485       SequenceGroup sg;
 486       for (int g = 0; g < allGroups.size(); g++)
 487       {
 488         sg = (SequenceGroup) allGroups.get(g);
 489         sg.cs = (ColourSchemeI) oldgroupColours.get(sg);
 490       }
 491     }
 492   }
 493
 494   public void thresholdCheck_actionPerformed(ActionEvent e)
 495   {
 496     changeColour();
 497   }
 498
 499   public void annotations_actionPerformed(ActionEvent e)
 500   {
 501     changeColour();
 502   }
 503
 504   public void threshold_actionPerformed(ActionEvent e)
 505   {
 506     changeColour();
 507   }
 508
 509   public void thresholdValue_actionPerformed(ActionEvent e)
 510   {
 511     try
 512     {
 513       float f = Float.parseFloat(thresholdValue.getText());
 514       slider.setValue((int) (f * 1000));
 515     } catch (NumberFormatException ex)
 516     {
 517     }
 518   }
 519
 520   public void valueChanged()
 521   {
 522     if (currentColours.isSelected()
 523             && !(av.getGlobalColourScheme() instanceof AnnotationColourGradient))
 524     {
 525       changeColour();
 526     }
 527
 528     currentAnnotation.threshold.value = (float) slider.getValue() / 1000f;
 529     ap.paintAlignment(false);
 530   }
 531
 532   public void currentColours_actionPerformed(ActionEvent e)
 533   {
 534     if (currentColours.isSelected())
 535     {
 536       reset();
 537     }
 538
 539     maxColour.setEnabled(!currentColours.isSelected());
 540     minColour.setEnabled(!currentColours.isSelected());
 541
 542     changeColour();
 543   }
 544
 545   public void thresholdIsMin_actionPerformed(ActionEvent actionEvent)
 546   {
 547     changeColour();
 548   }
 549
 550 }