unused/appletgui/AnnotationColourChooser.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
   3  * Copyright (C) $$Year-Rel$$ The Jalview Authors
   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
  10  * of the License, or (at your option) any later version.
  11  *
  12  * Jalview is distributed in the hope that it will be useful, but
  13  * WITHOUT ANY WARRANTY; without even the implied warranty
  14  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  15  * PURPOSE.  See the GNU General Public License for more details.
  16  *
  17  * You should have received a copy of the GNU General Public License
  18  * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  19  * The Jalview Authors are detailed in the 'AUTHORS' file.
  20  */
  21 package jalview.appletgui;
  22
  23 import jalview.bin.JalviewLite;
  24 import jalview.datamodel.AlignmentAnnotation;
  25 import jalview.datamodel.GraphLine;
  26 import jalview.datamodel.SequenceGroup;
  27 import jalview.schemes.AnnotationColourGradient;
  28 import jalview.schemes.ColourSchemeI;
  29 import jalview.util.MessageManager;
  30
  31 import java.awt.BorderLayout;
  32 import java.awt.Color;
  33 import java.awt.Dimension;
  34 import java.awt.FlowLayout;
  35 import java.awt.Font;
  36 import java.awt.event.ActionEvent;
  37 import java.awt.event.ActionListener;
  38 import java.awt.event.AdjustmentEvent;
  39 import java.awt.event.AdjustmentListener;
  40 import java.awt.event.ItemEvent;
  41 import java.awt.event.ItemListener;
  42 import java.awt.event.MouseEvent;
  43 import java.awt.event.MouseListener;
  44 import java.util.Hashtable;
  45 import java.util.Vector;
  46
  47 import javax.swing.JButton;
  48 import javax.swing.JCheckBox;
  49 import javax.swing.JComboBox;
  50 import javax.swing.JFrame;
  51 import javax.swing.JPanel;
  52 import javax.swing.JScrollBar;
  53 import javax.swing.JTextField;
  54
  55 public class AnnotationColourChooser extends JPanel implements
  56         ActionListener, AdjustmentListener, ItemListener, MouseListener
  57 {
  58   JFrame frame;
  59
  60   AlignViewport av;
  61
  62   AlignmentPanel ap;
  63
  64   ColourSchemeI oldcs;
  65
  66   Hashtable oldgroupColours;
  67
  68   AlignmentAnnotation currentAnnotation;
  69
  70   boolean adjusting = false;
  71
  72   public AnnotationColourChooser(AlignViewport av, AlignmentPanel ap)
  73   {
  74     try
  75     {
  76       jbInit();
  77     } catch (Exception ex)
  78     {
  79     }
  80
  81     oldcs = av.getGlobalColourScheme();
  82     if (av.getAlignment().getGroups() != null)
  83     {
  84       oldgroupColours = new Hashtable();
  85       for (SequenceGroup sg : ap.av.getAlignment().getGroups())
  86       {
  87         if (sg.cs != null)
  88         {
  89           oldgroupColours.put(sg, sg.cs);
  90         }
  91         else
  92         {
  93           oldgroupColours.put(sg, "null");
  94         }
  95       }
  96     }
  97     this.av = av;
  98     this.ap = ap;
  99
 100     slider.addAdjustmentListener(this);
 101     slider.addMouseListener(this);
 102
 103     if (av.getAlignment().getAlignmentAnnotation() == null)
 104     {
 105       return;
 106     }
 107
 108     setDefaultMinMax();
 109
 110     adjusting = true;
 111     if (oldcs instanceof AnnotationColourGradient)
 112     {
 113       AnnotationColourGradient acg = (AnnotationColourGradient) oldcs;
 114       currentColours.setSelected(acg.isPredefinedColours()
 115               || acg.getBaseColour() != null);
 116       if (!acg.isPredefinedColours() && acg.getBaseColour() == null)
 117       {
 118         minColour.setBackground(acg.getMinColour());
 119         maxColour.setBackground(acg.getMaxColour());
 120       }
 121       // seqAssociated.setState(acg.isSeqAssociated());
 122     }
 123
 124     Vector list = new Vector();
 125     int index = 1;
 126     for (int i = 0; i < av.getAlignment().getAlignmentAnnotation().length; i++)
 127     {
 128       String label = av.getAlignment().getAlignmentAnnotation()[i].label;
 129       if (!list.contains(label))
 130       {
 131         list.addElement(label);
 132       }
 133       else
 134       {
 135         list.addElement(label + "_" + (index++));
 136       }
 137     }
 138
 139     for (int i = 0; i < list.size(); i++)
 140     {
 141       annotations.addItem(list.elementAt(i).toString());
 142     }
 143
 144     threshold.addItem(MessageManager
 145             .getString("label.threshold_feature_no_thereshold"));
 146     threshold.addItem(MessageManager
 147             .getString("label.threshold_feature_above_thereshold"));
 148     threshold.addItem(MessageManager
 149             .getString("label.threshold_feature_below_thereshold"));
 150
 151     if (oldcs instanceof AnnotationColourGradient)
 152     {
 153       AnnotationColourGradient acg = (AnnotationColourGradient) oldcs;
 154       annotations.select(acg.getAnnotation());
 155       switch (acg.getAboveThreshold())
 156       {
 157       case AnnotationColourGradient.NO_THRESHOLD:
 158         threshold.select(0);
 159         break;
 160       case AnnotationColourGradient.ABOVE_THRESHOLD:
 161         threshold.select(1);
 162         break;
 163       case AnnotationColourGradient.BELOW_THRESHOLD:
 164         threshold.select(1);
 165         break;
 166       default:
 167         throw new Error(
 168                 MessageManager
 169                         .getString("error.implementation_error_dont_know_thereshold_annotationcolourgradient"));
 170       }
 171       thresholdIsMin.setSelected(acg.thresholdIsMinMax);
 172       thresholdValue.setText("" + acg.getAnnotationThreshold());
 173     }
 174
 175     adjusting = false;
 176
 177     changeColour();
 178
 179     frame = new JFrame();
 180     frame.add(this);
 181     JalviewLite.addFrame(frame,
 182             MessageManager.getString("label.colour_by_annotation"), 560,
 183             175);
 184     validate();
 185   }
 186
 187   private void setDefaultMinMax()
 188   {
 189     minColour.setBackground(av.applet.getDefaultColourParameter(
 190             "ANNOTATIONCOLOUR_MIN", Color.orange));
 191     maxColour.setBackground(av.applet.getDefaultColourParameter(
 192             "ANNOTATIONCOLOUR_MAX", Color.red));
 193
 194   }
 195
 196   public AnnotationColourChooser()
 197   {
 198     try
 199     {
 200       jbInit();
 201     } catch (Exception ex)
 202     {
 203       ex.printStackTrace();
 204     }
 205   }
 206
 207   private void jbInit() throws Exception
 208   {
 209     minColour.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
 210     minColour.setLabel(MessageManager.getString("label.min_colour"));
 211     minColour.addActionListener(this);
 212
 213     maxColour.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
 214     maxColour.setLabel(MessageManager.getString("label.max_colour"));
 215     maxColour.addActionListener(this);
 216
 217     thresholdIsMin.addItemListener(this);
 218     ok.setLabel(MessageManager.getString("action.ok"));
 219     ok.addActionListener(this);
 220
 221     cancel.setLabel(MessageManager.getString("action.cancel"));
 222     cancel.addActionListener(this);
 223
 224     defColours.setLabel(MessageManager.getString("action.set_defaults"));
 225     defColours.addActionListener(this);
 226
 227     annotations.addItemListener(this);
 228
 229     thresholdValue.addActionListener(this);
 230     slider.setBackground(Color.white);
 231     slider.setPreferredSize(new Dimension(193, 21));
 232     slider.setEnabled(false);
 233     thresholdValue.setPreferredSize(new Dimension(79, 22));
 234     thresholdValue.setEnabled(false);
 235     thresholdValue.setColumns(5);
 236     currentColours.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
 237     currentColours.setLabel(MessageManager
 238             .getString("label.use_original_colours"));
 239     currentColours.addItemListener(this);
 240
 241     thresholdIsMin.setBackground(Color.white);
 242     thresholdIsMin.setLabel(MessageManager
 243             .getString("label.threshold_minmax"));
 244
 245     this.setLayout(borderLayout1);
 246
 247     jPanel1.setBackground(Color.white);
 248
 249     jPanel2.setLayout(new FlowLayout());
 250     jPanel2.setBackground(Color.white);
 251     threshold.addItemListener(this);
 252     jPanel3.setLayout(new FlowLayout());
 253     jPanel3.setBackground(Color.white);
 254     JPanel jPanel4 = new JPanel();
 255     jPanel4.setLayout(new BorderLayout());
 256     jPanel4.setBackground(Color.white);
 257
 258     jPanel1.add(ok);
 259     jPanel1.add(cancel);
 260
 261     jPanel2.add(annotations);
 262     jPanel2.add(currentColours);
 263     jPanel2.add(minColour);
 264     jPanel2.add(maxColour);
 265
 266     jPanel4.add(thresholdIsMin, BorderLayout.WEST);
 267     jPanel4.add(slider, BorderLayout.CENTER);
 268     jPanel4.add(thresholdValue, BorderLayout.EAST);
 269
 270     JPanel jPanel34 = new JPanel();
 271     jPanel34.setLayout(new BorderLayout());
 272     jPanel34.setBackground(Color.white);
 273     jPanel34.add(jPanel2, BorderLayout.NORTH);
 274     jPanel34.add(threshold, BorderLayout.WEST);
 275     jPanel3.add(defColours);
 276     jPanel34.add(jPanel3, BorderLayout.EAST);
 277     jPanel34.add(jPanel4, BorderLayout.SOUTH);
 278
 279     this.add(jPanel34, java.awt.BorderLayout.CENTER);
 280     this.add(jPanel1, java.awt.BorderLayout.SOUTH);
 281
 282   }
 283
 284   Choice annotations = new Choice();
 285
 286   JButton minColour = new JButton();
 287
 288   JButton maxColour = new JButton();
 289
 290   JButton ok = new JButton();
 291
 292   JButton cancel = new JButton();
 293
 294   JButton defColours = new JButton();
 295
 296   JPanel jPanel1 = new JPanel();
 297
 298   JPanel jPanel2 = new JPanel();
 299
 300   Choice threshold = new Choice();
 301
 302   FlowLayout flowLayout1 = new FlowLayout();
 303
 304   JPanel jPanel3 = new JPanel();
 305
 306   JScrollBar slider = new JScrollBar(JScrollBar.HORIZONTAL);
 307
 308   JTextField thresholdValue = new JTextField(20);
 309
 310   JCheckBox currentColours = new JCheckBox();
 311
 312   BorderLayout borderLayout1 = new BorderLayout();
 313
 314   JCheckBox thresholdIsMin = new JCheckBox();
 315
 316   public void actionPerformed(ActionEvent evt)
 317   {
 318     if (evt.getSource() == thresholdValue)
 319     {
 320       try
 321       {
 322         float f = new Float(thresholdValue.getText()).floatValue();
 323         slider.setValue((int) (f * 1000));
 324         adjustmentValueChanged(null);
 325       } catch (NumberFormatException ex)
 326       {
 327       }
 328     }
 329     else if (evt.getSource() == minColour)
 330     {
 331       minColour_actionPerformed(null);
 332     }
 333     else if (evt.getSource() == maxColour)
 334     {
 335       maxColour_actionPerformed(null);
 336     }
 337     else if (evt.getSource() == defColours)
 338     {
 339       defColour_actionPerformed();
 340     }
 341     else if (evt.getSource() == ok)
 342     {
 343       changeColour();
 344       frame.setVisible(false);
 345     }
 346     else if (evt.getSource() == cancel)
 347     {
 348       reset();
 349       ap.paintAlignment(true);
 350       frame.setVisible(false);
 351     }
 352
 353     else
 354     {
 355       changeColour();
 356     }
 357   }
 358
 359   public void itemStateChanged(ItemEvent evt)
 360   {
 361     if (evt.getSource() == currentColours)
 362     {
 363       if (currentColours.isSelected())
 364       {
 365         reset();
 366       }
 367
 368       maxColour.setEnabled(!currentColours.isSelected());
 369       minColour.setEnabled(!currentColours.isSelected());
 370
 371     }
 372
 373     changeColour();
 374   }
 375
 376   public void adjustmentValueChanged(AdjustmentEvent evt)
 377   {
 378     if (!adjusting)
 379     {
 380       thresholdValue.setText((slider.getValue() / 1000f) + "");
 381       if (currentColours.isSelected()
 382               && !(av.getGlobalColourScheme() instanceof AnnotationColourGradient))
 383       {
 384         changeColour();
 385       }
 386
 387       currentAnnotation.threshold.value = slider.getValue() / 1000f;
 388       ap.paintAlignment(false);
 389     }
 390   }
 391
 392   public void minColour_actionPerformed(Color newCol)
 393   {
 394     if (newCol != null)
 395     {
 396       minColour.setBackground(newCol);
 397       minColour.repaint();
 398       changeColour();
 399     }
 400     else
 401     {
 402       new UserDefinedColours(this, "Min Colour", minColour.getBackground());
 403     }
 404
 405   }
 406
 407   public void maxColour_actionPerformed(Color newCol)
 408   {
 409     if (newCol != null)
 410     {
 411       maxColour.setBackground(newCol);
 412       maxColour.repaint();
 413       changeColour();
 414     }
 415     else
 416     {
 417       new UserDefinedColours(this, "Max Colour", maxColour.getBackground());
 418     }
 419   }
 420
 421   public void defColour_actionPerformed()
 422   {
 423     setDefaultMinMax();
 424     minColour.repaint();
 425     maxColour.repaint();
 426     changeColour();
 427   }
 428
 429   void changeColour()
 430   {
 431     // Check if combobox is still adjusting
 432     if (adjusting)
 433     {
 434       return;
 435     }
 436
 437     currentAnnotation = av.getAlignment().getAlignmentAnnotation()[annotations
 438             .getSelectedIndex()];
 439
 440     int aboveThreshold = -1;
 441     if (threshold.getSelectedIndex() == 1)
 442     {
 443       aboveThreshold = AnnotationColourGradient.ABOVE_THRESHOLD;
 444     }
 445     else if (threshold.getSelectedIndex() == 2)
 446     {
 447       aboveThreshold = AnnotationColourGradient.BELOW_THRESHOLD;
 448     }
 449
 450     slider.setEnabled(true);
 451     thresholdValue.setEnabled(true);
 452     thresholdIsMin.setEnabled(true);
 453
 454     if (aboveThreshold == AnnotationColourGradient.NO_THRESHOLD)
 455     {
 456       slider.setEnabled(false);
 457       thresholdValue.setEnabled(false);
 458       thresholdIsMin.setEnabled(false);
 459       thresholdValue.setText("");
 460     }
 461     else if (aboveThreshold != AnnotationColourGradient.NO_THRESHOLD
 462             && currentAnnotation.threshold == null)
 463     {
 464       currentAnnotation
 465               .setThreshold(new GraphLine(
 466                       (currentAnnotation.graphMax - currentAnnotation.graphMin) / 2f,
 467                       "Threshold", Color.black));
 468     }
 469
 470     if (aboveThreshold != AnnotationColourGradient.NO_THRESHOLD)
 471     {
 472       adjusting = true;
 473
 474       slider.setMinimum((int) (currentAnnotation.graphMin * 1000));
 475       slider.setMaximum((int) (currentAnnotation.graphMax * 1000));
 476       slider.setValue((int) (currentAnnotation.threshold.value * 1000));
 477       thresholdValue.setText(currentAnnotation.threshold.value + "");
 478       slider.setEnabled(true);
 479       thresholdValue.setEnabled(true);
 480       adjusting = false;
 481     }
 482
 483     AnnotationColourGradient acg = null;
 484     if (currentColours.isSelected())
 485     {
 486       acg = new AnnotationColourGradient(currentAnnotation,
 487               av.getGlobalColourScheme(), aboveThreshold);
 488     }
 489     else
 490     {
 491       acg = new AnnotationColourGradient(currentAnnotation,
 492               minColour.getBackground(), maxColour.getBackground(),
 493               aboveThreshold);
 494     }
 495
 496     if (currentAnnotation.graphMin == 0f
 497             && currentAnnotation.graphMax == 0f)
 498     {
 499       acg.setPredefinedColours(true);
 500     }
 501
 502     acg.thresholdIsMinMax = thresholdIsMin.isSelected();
 503
 504     av.setGlobalColourScheme(acg);
 505
 506     // TODO: per group colour propagation not always desired
 507     if (av.getAlignment().getGroups() != null)
 508     {
 509       for (SequenceGroup sg : ap.av.getAlignment().getGroups())
 510       {
 511
 512         if (sg.cs == null)
 513         {
 514           continue;
 515         }
 516
 517         if (currentColours.isSelected())
 518         {
 519           sg.cs = new AnnotationColourGradient(currentAnnotation, sg.cs,
 520                   aboveThreshold);
 521         }
 522         else
 523         {
 524           sg.cs = new AnnotationColourGradient(currentAnnotation,
 525                   minColour.getBackground(), maxColour.getBackground(),
 526                   aboveThreshold);
 527         }
 528
 529       }
 530     }
 531
 532     // update colours in linked windows
 533     ap.alignmentChanged();
 534     ap.paintAlignment(true);
 535   }
 536
 537   void reset()
 538   {
 539     av.setGlobalColourScheme(oldcs);
 540     if (av.getAlignment().getGroups() != null)
 541     {
 542       for (SequenceGroup sg : ap.av.getAlignment().getGroups())
 543       {
 544         Object cs = oldgroupColours.get(sg);
 545         if (cs instanceof ColourSchemeI)
 546         {
 547           sg.cs = (ColourSchemeI) cs;
 548         }
 549         else
 550         {
 551           // probably the "null" string we set it to if it was null originally.
 552           sg.cs = null;
 553         }
 554       }
 555     }
 556     ap.paintAlignment(true);
 557
 558   }
 559
 560   public void mouseClicked(MouseEvent evt)
 561   {
 562   }
 563
 564   public void mousePressed(MouseEvent evt)
 565   {
 566   }
 567
 568   public void mouseReleased(MouseEvent evt)
 569   {
 570     ap.paintAlignment(true);
 571   }
 572
 573   public void mouseEntered(MouseEvent evt)
 574   {
 575   }
 576
 577   public void mouseExited(MouseEvent evt)
 578   {
 579   }
 580
 581 }