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