src/jalview/gui/AnnotationColourChooser.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
   3  * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
   4  *
   5  * This program is free software; you can redistribute it and/or
   6  * modify it under the terms of the GNU General Public License
   7  * as published by the Free Software Foundation; either version 2
   8  * of the License, or (at your option) any later version.
   9  *
  10  * This program is distributed in the hope that it will be useful,
  11  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  12  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  13  * GNU General Public License for more details.
  14  *
  15  * You should have received a copy of the GNU General Public License
  16  * along with this program; if not, write to the Free Software
  17  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  18  */
  19 package jalview.gui;
  20
  21 import java.util.*;
  22
  23 import java.awt.*;
  24 import java.awt.event.*;
  25 import javax.swing.*;
  26 import javax.swing.event.*;
  27
  28 import jalview.datamodel.*;
  29 import jalview.schemes.*;
  30 import java.awt.Dimension;
  31
  32 public class AnnotationColourChooser
  33     extends JPanel
  34 {
  35   JInternalFrame frame;
  36   AlignViewport av;
  37   AlignmentPanel ap;
  38   ColourSchemeI oldcs;
  39   Hashtable oldgroupColours;
  40   jalview.datamodel.AlignmentAnnotation currentAnnotation;
  41   boolean adjusting = false;
  42
  43   public AnnotationColourChooser(AlignViewport av, final AlignmentPanel ap)
  44   {
  45     oldcs = av.getGlobalColourScheme();
  46     if (av.alignment.getGroups() != null)
  47     {
  48       oldgroupColours = new Hashtable();
  49       Vector allGroups = ap.av.alignment.getGroups();
  50       SequenceGroup sg;
  51       for (int g = 0; g < allGroups.size(); g++)
  52       {
  53         sg = (SequenceGroup) allGroups.get(g);
  54         if (sg.cs != null)
  55         {
  56           oldgroupColours.put(sg, sg.cs);
  57         }
  58       }
  59     }
  60     this.av = av;
  61     this.ap = ap;
  62     frame = new JInternalFrame();
  63     frame.setContentPane(this);
  64     frame.setLayer(JLayeredPane.PALETTE_LAYER);
  65     Desktop.addInternalFrame(frame, "Colour by Annotation", 480, 145);
  66
  67
  68     slider.addChangeListener(new ChangeListener()
  69     {
  70       public void stateChanged(ChangeEvent evt)
  71       {
  72         if (!adjusting)
  73         {
  74           thresholdValue.setText( ( (float) slider.getValue() / 1000f) + "");
  75           valueChanged();
  76         }
  77       }
  78     });
  79     slider.addMouseListener(new MouseAdapter()
  80         {
  81           public void mouseReleased(MouseEvent evt)
  82           {
  83             ap.paintAlignment(true);
  84           }
  85         });
  86
  87     if (av.alignment.getAlignmentAnnotation() == null)
  88     {
  89       return;
  90     }
  91
  92     if (oldcs instanceof AnnotationColourGradient)
  93     {
  94       AnnotationColourGradient acg = (AnnotationColourGradient) oldcs;
  95       minColour.setBackground(acg.getMinColour());
  96       maxColour.setBackground(acg.getMaxColour());
  97     }
  98     else
  99     {
 100       minColour.setBackground(Color.orange);
 101       maxColour.setBackground(Color.red);
 102     }
 103
 104     adjusting = true;
 105     Vector list = new Vector();
 106     int index = 1;
 107     for (int i = 0; i < av.alignment.getAlignmentAnnotation().length; i++)
 108     {
 109       String label = av.alignment.getAlignmentAnnotation()[i].label;
 110       if (!list.contains(label))
 111         list.addElement(label);
 112       else
 113         list.addElement(label+"_"+(index++));
 114     }
 115
 116     annotations = new JComboBox(list);
 117
 118     threshold.addItem("No Threshold");
 119     threshold.addItem("Above Threshold");
 120     threshold.addItem("Below Threshold");
 121
 122     try
 123     {
 124       jbInit();
 125     }
 126     catch (Exception ex)
 127     {}
 128
 129     adjusting = false;
 130
 131     changeColour();
 132
 133   }
 134
 135   public AnnotationColourChooser()
 136   {
 137     try
 138     {
 139       jbInit();
 140     }
 141     catch (Exception ex)
 142     {
 143       ex.printStackTrace();
 144     }
 145   }
 146
 147   private void jbInit()
 148       throws Exception
 149   {
 150     minColour.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
 151     minColour.setBorder(BorderFactory.createEtchedBorder());
 152     minColour.setPreferredSize(new Dimension(40, 20));
 153     minColour.setToolTipText("Minimum Colour");
 154     minColour.addMouseListener(new MouseAdapter()
 155     {
 156       public void mousePressed(MouseEvent e)
 157       {
 158         if (minColour.isEnabled())
 159         {
 160           minColour_actionPerformed();
 161         }
 162       }
 163     });
 164     maxColour.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
 165     maxColour.setBorder(BorderFactory.createEtchedBorder());
 166     maxColour.setPreferredSize(new Dimension(40, 20));
 167     maxColour.setToolTipText("Maximum Colour");
 168     maxColour.addMouseListener(new MouseAdapter()
 169     {
 170       public void mousePressed(MouseEvent e)
 171       {
 172         if (maxColour.isEnabled())
 173         {
 174           maxColour_actionPerformed();
 175         }
 176       }
 177     });
 178     ok.setOpaque(false);
 179     ok.setText("OK");
 180     ok.addActionListener(new ActionListener()
 181     {
 182       public void actionPerformed(ActionEvent e)
 183       {
 184         ok_actionPerformed(e);
 185       }
 186     });
 187     cancel.setOpaque(false);
 188     cancel.setText("Cancel");
 189     cancel.addActionListener(new ActionListener()
 190     {
 191       public void actionPerformed(ActionEvent e)
 192       {
 193         cancel_actionPerformed(e);
 194       }
 195     });
 196     this.setLayout(borderLayout1);
 197     jPanel2.setLayout(flowLayout1);
 198     annotations.addActionListener(new ActionListener()
 199     {
 200       public void actionPerformed(ActionEvent e)
 201       {
 202         annotations_actionPerformed(e);
 203       }
 204     });
 205     jPanel1.setBackground(Color.white);
 206     jPanel2.setBackground(Color.white);
 207     threshold.addActionListener(new ActionListener()
 208     {
 209       public void actionPerformed(ActionEvent e)
 210       {
 211         threshold_actionPerformed(e);
 212       }
 213     });
 214     jPanel3.setLayout(flowLayout2);
 215     thresholdValue.addActionListener(new ActionListener()
 216     {
 217       public void actionPerformed(ActionEvent e)
 218       {
 219         thresholdValue_actionPerformed(e);
 220       }
 221     });
 222     slider.setPaintLabels(false);
 223     slider.setPaintTicks(true);
 224     slider.setBackground(Color.white);
 225     slider.setEnabled(false);
 226     slider.setOpaque(false);
 227     slider.setPreferredSize(new Dimension(100, 32));
 228     thresholdValue.setEnabled(false);
 229     thresholdValue.setColumns(7);
 230     jPanel3.setBackground(Color.white);
 231     currentColours.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
 232     currentColours.setOpaque(false);
 233     currentColours.setText("Use Original Colours");
 234     currentColours.addActionListener(new ActionListener()
 235     {
 236       public void actionPerformed(ActionEvent e)
 237       {
 238         currentColours_actionPerformed(e);
 239       }
 240     });
 241     thresholdIsMin.setBackground(Color.white);
 242     thresholdIsMin.setText("Threshold is Min/Max");
 243     thresholdIsMin.addActionListener(new ActionListener()
 244     {
 245       public void actionPerformed(ActionEvent actionEvent)
 246       {
 247         thresholdIsMin_actionPerformed(actionEvent);
 248       }
 249     });
 250     jPanel1.add(ok);
 251     jPanel1.add(cancel);
 252     jPanel2.add(annotations);
 253     jPanel2.add(currentColours);
 254     jPanel2.add(minColour);
 255     jPanel2.add(maxColour);
 256     this.add(jPanel3, java.awt.BorderLayout.CENTER);
 257     jPanel3.add(threshold);
 258     jPanel3.add(slider);
 259     jPanel3.add(thresholdValue);
 260     jPanel3.add(thresholdIsMin);
 261     this.add(jPanel1, java.awt.BorderLayout.SOUTH);
 262     this.add(jPanel2, java.awt.BorderLayout.NORTH);
 263   }
 264
 265   JComboBox annotations;
 266   JPanel minColour = new JPanel();
 267   JPanel maxColour = new JPanel();
 268   JButton ok = new JButton();
 269   JButton cancel = new JButton();
 270   JPanel jPanel1 = new JPanel();
 271   JPanel jPanel2 = new JPanel();
 272   BorderLayout borderLayout1 = new BorderLayout();
 273   JComboBox threshold = new JComboBox();
 274   FlowLayout flowLayout1 = new FlowLayout();
 275   JPanel jPanel3 = new JPanel();
 276   FlowLayout flowLayout2 = new FlowLayout();
 277   JSlider slider = new JSlider();
 278   JTextField thresholdValue = new JTextField(20);
 279   JCheckBox currentColours = new JCheckBox();
 280   JCheckBox thresholdIsMin = new JCheckBox();
 281
 282   public void minColour_actionPerformed()
 283   {
 284     Color col = JColorChooser.showDialog(this,
 285                                          "Select Colour for Minimum Value",
 286                                          minColour.getBackground());
 287     if (col != null)
 288     {
 289       minColour.setBackground(col);
 290     }
 291     minColour.repaint();
 292     changeColour();
 293   }
 294
 295   public void maxColour_actionPerformed()
 296   {
 297     Color col = JColorChooser.showDialog(this,
 298                                          "Select Colour for Maximum Value",
 299                                          maxColour.getBackground());
 300     if (col != null)
 301     {
 302       maxColour.setBackground(col);
 303     }
 304     maxColour.repaint();
 305     changeColour();
 306   }
 307
 308   void changeColour()
 309   {
 310     // Check if combobox is still adjusting
 311     if (adjusting)
 312     {
 313       return;
 314     }
 315
 316
 317     currentAnnotation = av.alignment.getAlignmentAnnotation()[annotations.getSelectedIndex()];
 318
 319     int aboveThreshold = -1;
 320     if (threshold.getSelectedItem().equals("Above Threshold"))
 321     {
 322       aboveThreshold = AnnotationColourGradient.ABOVE_THRESHOLD;
 323     }
 324     else if (threshold.getSelectedItem().equals("Below Threshold"))
 325     {
 326       aboveThreshold = AnnotationColourGradient.BELOW_THRESHOLD;
 327     }
 328
 329     slider.setEnabled(true);
 330     thresholdValue.setEnabled(true);
 331
 332     if (aboveThreshold == AnnotationColourGradient.NO_THRESHOLD)
 333     {
 334       slider.setEnabled(false);
 335       thresholdValue.setEnabled(false);
 336       thresholdValue.setText("");
 337     }
 338     else if (aboveThreshold != AnnotationColourGradient.NO_THRESHOLD &&
 339              currentAnnotation.threshold == null)
 340     {
 341       currentAnnotation.setThreshold(new jalview.datamodel.GraphLine
 342                                      ( (currentAnnotation.graphMax -
 343                                         currentAnnotation.graphMin) / 2f,
 344                                       "Threshold",
 345                                       Color.black));
 346     }
 347
 348     if (aboveThreshold != AnnotationColourGradient.NO_THRESHOLD)
 349     {
 350       adjusting = true;
 351       float range = currentAnnotation.graphMax * 1000 -
 352           currentAnnotation.graphMin * 1000;
 353
 354       slider.setMinimum( (int) (currentAnnotation.graphMin * 1000));
 355       slider.setMaximum( (int) (currentAnnotation.graphMax * 1000));
 356       slider.setValue( (int) (currentAnnotation.threshold.value * 1000));
 357       thresholdValue.setText(currentAnnotation.threshold.value + "");
 358       slider.setMajorTickSpacing( (int) (range / 10f));
 359       slider.setEnabled(true);
 360       thresholdValue.setEnabled(true);
 361       adjusting = false;
 362     }
 363
 364     AnnotationColourGradient acg = null;
 365     if (currentColours.isSelected())
 366     {
 367       acg = new AnnotationColourGradient(
 368           currentAnnotation,
 369           av.getGlobalColourScheme(), aboveThreshold);
 370     }
 371     else
 372     {
 373       acg =
 374           new AnnotationColourGradient(
 375               currentAnnotation,
 376               minColour.getBackground(),
 377               maxColour.getBackground(),
 378               aboveThreshold);
 379     }
 380
 381     if(currentAnnotation.graphMin==0f&& currentAnnotation.graphMax==0f)
 382     {
 383       acg.predefinedColours = true;
 384     }
 385
 386     acg.thresholdIsMinMax = thresholdIsMin.isSelected();
 387
 388     av.setGlobalColourScheme(acg);
 389
 390     if (av.alignment.getGroups() != null)
 391     {
 392       Vector allGroups = ap.av.alignment.getGroups();
 393       SequenceGroup sg;
 394       for (int g = 0; g < allGroups.size(); g++)
 395       {
 396         sg = (SequenceGroup) allGroups.get(g);
 397
 398         if (sg.cs == null)
 399         {
 400           continue;
 401         }
 402
 403         if (currentColours.isSelected())
 404         {
 405           sg.cs = new AnnotationColourGradient(
 406               currentAnnotation,
 407               sg.cs, aboveThreshold);
 408         }
 409         else
 410         {
 411           sg.cs = new AnnotationColourGradient(
 412               currentAnnotation,
 413               minColour.getBackground(),
 414               maxColour.getBackground(),
 415               aboveThreshold);
 416         }
 417
 418       }
 419     }
 420
 421     ap.paintAlignment(false);
 422   }
 423
 424   public void ok_actionPerformed(ActionEvent e)
 425   {
 426     changeColour();
 427     try
 428     {
 429       frame.setClosed(true);
 430     }
 431     catch (Exception ex)
 432     {}
 433   }
 434
 435   public void cancel_actionPerformed(ActionEvent e)
 436   {
 437     reset();
 438     try
 439     {
 440       frame.setClosed(true);
 441     }
 442     catch (Exception ex)
 443     {}
 444   }
 445
 446   void reset()
 447   {
 448     av.setGlobalColourScheme(oldcs);
 449     if (av.alignment.getGroups() != null)
 450     {
 451       Vector allGroups = ap.av.alignment.getGroups();
 452       SequenceGroup sg;
 453       for (int g = 0; g < allGroups.size(); g++)
 454       {
 455         sg = (SequenceGroup) allGroups.get(g);
 456         sg.cs = (ColourSchemeI) oldgroupColours.get(sg);
 457       }
 458     }
 459   }
 460
 461   public void thresholdCheck_actionPerformed(ActionEvent e)
 462   {
 463     changeColour();
 464   }
 465
 466   public void annotations_actionPerformed(ActionEvent e)
 467   {
 468     changeColour();
 469   }
 470
 471   public void threshold_actionPerformed(ActionEvent e)
 472   {
 473     changeColour();
 474   }
 475
 476   public void thresholdValue_actionPerformed(ActionEvent e)
 477   {
 478     try
 479     {
 480       float f = Float.parseFloat(thresholdValue.getText());
 481       slider.setValue( (int) (f * 1000));
 482     }
 483     catch (NumberFormatException ex)
 484     {}
 485   }
 486
 487   public void valueChanged()
 488   {
 489     if (currentColours.isSelected()
 490         && ! (av.getGlobalColourScheme() instanceof AnnotationColourGradient))
 491     {
 492       changeColour();
 493     }
 494
 495     currentAnnotation.threshold.value = (float) slider.getValue() / 1000f;
 496     ap.paintAlignment(false);
 497   }
 498
 499   public void currentColours_actionPerformed(ActionEvent e)
 500   {
 501     if (currentColours.isSelected())
 502     {
 503       reset();
 504     }
 505
 506     maxColour.setEnabled(!currentColours.isSelected());
 507     minColour.setEnabled(!currentColours.isSelected());
 508
 509     changeColour();
 510   }
 511
 512   public void thresholdIsMin_actionPerformed(ActionEvent actionEvent)
 513   {
 514     changeColour();
 515   }
 516
 517 }