src/jalview/gui/AnnotationColourChooser.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
   3  * Copyright (C) 2009 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 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     if (oldcs instanceof AnnotationColourGradient)
  97     {
  98       AnnotationColourGradient acg = (AnnotationColourGradient) oldcs;
  99       minColour.setBackground(acg.getMinColour());
 100       maxColour.setBackground(acg.getMaxColour());
 101     }
 102     else
 103     {
 104       minColour.setBackground(Color.orange);
 105       maxColour.setBackground(Color.red);
 106     }
 107
 108     adjusting = true;
 109     Vector list = new Vector();
 110     int index = 1;
 111     for (int i = 0; i < av.alignment.getAlignmentAnnotation().length; i++)
 112     {
 113       String label = av.alignment.getAlignmentAnnotation()[i].label;
 114       if (!list.contains(label))
 115         list.addElement(label);
 116       else
 117         list.addElement(label + "_" + (index++));
 118     }
 119
 120     annotations = new JComboBox(list);
 121
 122     threshold.addItem("No Threshold");
 123     threshold.addItem("Above Threshold");
 124     threshold.addItem("Below Threshold");
 125
 126     try
 127     {
 128       jbInit();
 129     } catch (Exception ex)
 130     {
 131     }
 132
 133     adjusting = false;
 134
 135     changeColour();
 136
 137   }
 138
 139   public AnnotationColourChooser()
 140   {
 141     try
 142     {
 143       jbInit();
 144     } catch (Exception ex)
 145     {
 146       ex.printStackTrace();
 147     }
 148   }
 149
 150   private void jbInit() throws Exception
 151   {
 152     minColour.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
 153     minColour.setBorder(BorderFactory.createEtchedBorder());
 154     minColour.setPreferredSize(new Dimension(40, 20));
 155     minColour.setToolTipText("Minimum Colour");
 156     minColour.addMouseListener(new MouseAdapter()
 157     {
 158       public void mousePressed(MouseEvent e)
 159       {
 160         if (minColour.isEnabled())
 161         {
 162           minColour_actionPerformed();
 163         }
 164       }
 165     });
 166     maxColour.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
 167     maxColour.setBorder(BorderFactory.createEtchedBorder());
 168     maxColour.setPreferredSize(new Dimension(40, 20));
 169     maxColour.setToolTipText("Maximum Colour");
 170     maxColour.addMouseListener(new MouseAdapter()
 171     {
 172       public void mousePressed(MouseEvent e)
 173       {
 174         if (maxColour.isEnabled())
 175         {
 176           maxColour_actionPerformed();
 177         }
 178       }
 179     });
 180     ok.setOpaque(false);
 181     ok.setText("OK");
 182     ok.addActionListener(new ActionListener()
 183     {
 184       public void actionPerformed(ActionEvent e)
 185       {
 186         ok_actionPerformed(e);
 187       }
 188     });
 189     cancel.setOpaque(false);
 190     cancel.setText("Cancel");
 191     cancel.addActionListener(new ActionListener()
 192     {
 193       public void actionPerformed(ActionEvent e)
 194       {
 195         cancel_actionPerformed(e);
 196       }
 197     });
 198     this.setLayout(borderLayout1);
 199     jPanel2.setLayout(flowLayout1);
 200     annotations.addActionListener(new ActionListener()
 201     {
 202       public void actionPerformed(ActionEvent e)
 203       {
 204         annotations_actionPerformed(e);
 205       }
 206     });
 207     jPanel1.setBackground(Color.white);
 208     jPanel2.setBackground(Color.white);
 209     threshold.addActionListener(new ActionListener()
 210     {
 211       public void actionPerformed(ActionEvent e)
 212       {
 213         threshold_actionPerformed(e);
 214       }
 215     });
 216     jPanel3.setLayout(flowLayout2);
 217     thresholdValue.addActionListener(new ActionListener()
 218     {
 219       public void actionPerformed(ActionEvent e)
 220       {
 221         thresholdValue_actionPerformed(e);
 222       }
 223     });
 224     slider.setPaintLabels(false);
 225     slider.setPaintTicks(true);
 226     slider.setBackground(Color.white);
 227     slider.setEnabled(false);
 228     slider.setOpaque(false);
 229     slider.setPreferredSize(new Dimension(100, 32));
 230     thresholdValue.setEnabled(false);
 231     thresholdValue.setColumns(7);
 232     jPanel3.setBackground(Color.white);
 233     currentColours.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
 234     currentColours.setOpaque(false);
 235     currentColours.setText("Use Original Colours");
 236     currentColours.addActionListener(new ActionListener()
 237     {
 238       public void actionPerformed(ActionEvent e)
 239       {
 240         currentColours_actionPerformed(e);
 241       }
 242     });
 243     thresholdIsMin.setBackground(Color.white);
 244     thresholdIsMin.setText("Threshold is Min/Max");
 245     thresholdIsMin.addActionListener(new ActionListener()
 246     {
 247       public void actionPerformed(ActionEvent actionEvent)
 248       {
 249         thresholdIsMin_actionPerformed(actionEvent);
 250       }
 251     });
 252     jPanel1.add(ok);
 253     jPanel1.add(cancel);
 254     jPanel2.add(annotations);
 255     jPanel2.add(currentColours);
 256     jPanel2.add(minColour);
 257     jPanel2.add(maxColour);
 258     this.add(jPanel3, java.awt.BorderLayout.CENTER);
 259     jPanel3.add(threshold);
 260     jPanel3.add(slider);
 261     jPanel3.add(thresholdValue);
 262     jPanel3.add(thresholdIsMin);
 263     this.add(jPanel1, java.awt.BorderLayout.SOUTH);
 264     this.add(jPanel2, java.awt.BorderLayout.NORTH);
 265   }
 266
 267   JComboBox annotations;
 268
 269   JPanel minColour = new JPanel();
 270
 271   JPanel maxColour = new JPanel();
 272
 273   JButton ok = new JButton();
 274
 275   JButton cancel = new JButton();
 276
 277   JPanel jPanel1 = new JPanel();
 278
 279   JPanel jPanel2 = new JPanel();
 280
 281   BorderLayout borderLayout1 = new BorderLayout();
 282
 283   JComboBox threshold = new JComboBox();
 284
 285   FlowLayout flowLayout1 = new FlowLayout();
 286
 287   JPanel jPanel3 = new JPanel();
 288
 289   FlowLayout flowLayout2 = new FlowLayout();
 290
 291   JSlider slider = new JSlider();
 292
 293   JTextField thresholdValue = new JTextField(20);
 294
 295   JCheckBox currentColours = new JCheckBox();
 296
 297   JCheckBox thresholdIsMin = new JCheckBox();
 298
 299   public void minColour_actionPerformed()
 300   {
 301     Color col = JColorChooser.showDialog(this,
 302             "Select Colour for Minimum Value", minColour.getBackground());
 303     if (col != null)
 304     {
 305       minColour.setBackground(col);
 306     }
 307     minColour.repaint();
 308     changeColour();
 309   }
 310
 311   public void maxColour_actionPerformed()
 312   {
 313     Color col = JColorChooser.showDialog(this,
 314             "Select Colour for Maximum Value", maxColour.getBackground());
 315     if (col != null)
 316     {
 317       maxColour.setBackground(col);
 318     }
 319     maxColour.repaint();
 320     changeColour();
 321   }
 322
 323   void changeColour()
 324   {
 325     // Check if combobox is still adjusting
 326     if (adjusting)
 327     {
 328       return;
 329     }
 330
 331     currentAnnotation = av.alignment.getAlignmentAnnotation()[annotations
 332             .getSelectedIndex()];
 333
 334     int aboveThreshold = -1;
 335     if (threshold.getSelectedItem().equals("Above Threshold"))
 336     {
 337       aboveThreshold = AnnotationColourGradient.ABOVE_THRESHOLD;
 338     }
 339     else if (threshold.getSelectedItem().equals("Below Threshold"))
 340     {
 341       aboveThreshold = AnnotationColourGradient.BELOW_THRESHOLD;
 342     }
 343
 344     slider.setEnabled(true);
 345     thresholdValue.setEnabled(true);
 346
 347     if (aboveThreshold == AnnotationColourGradient.NO_THRESHOLD)
 348     {
 349       slider.setEnabled(false);
 350       thresholdValue.setEnabled(false);
 351       thresholdValue.setText("");
 352     }
 353     else if (aboveThreshold != AnnotationColourGradient.NO_THRESHOLD
 354             && currentAnnotation.threshold == null)
 355     {
 356       currentAnnotation
 357               .setThreshold(new jalview.datamodel.GraphLine(
 358                       (currentAnnotation.graphMax - currentAnnotation.graphMin) / 2f,
 359                       "Threshold", Color.black));
 360     }
 361
 362     if (aboveThreshold != AnnotationColourGradient.NO_THRESHOLD)
 363     {
 364       adjusting = true;
 365       float range = currentAnnotation.graphMax * 1000
 366               - currentAnnotation.graphMin * 1000;
 367
 368       slider.setMinimum((int) (currentAnnotation.graphMin * 1000));
 369       slider.setMaximum((int) (currentAnnotation.graphMax * 1000));
 370       slider.setValue((int) (currentAnnotation.threshold.value * 1000));
 371       thresholdValue.setText(currentAnnotation.threshold.value + "");
 372       slider.setMajorTickSpacing((int) (range / 10f));
 373       slider.setEnabled(true);
 374       thresholdValue.setEnabled(true);
 375       adjusting = false;
 376     }
 377
 378     AnnotationColourGradient acg = null;
 379     if (currentColours.isSelected())
 380     {
 381       acg = new AnnotationColourGradient(currentAnnotation, av
 382               .getGlobalColourScheme(), aboveThreshold);
 383     }
 384     else
 385     {
 386       acg = new AnnotationColourGradient(currentAnnotation, minColour
 387               .getBackground(), maxColour.getBackground(), aboveThreshold);
 388     }
 389
 390     if (currentAnnotation.graphMin == 0f
 391             && currentAnnotation.graphMax == 0f)
 392     {
 393       acg.predefinedColours = true;
 394     }
 395
 396     acg.thresholdIsMinMax = thresholdIsMin.isSelected();
 397
 398     av.setGlobalColourScheme(acg);
 399
 400     if (av.alignment.getGroups() != null)
 401     {
 402       Vector allGroups = ap.av.alignment.getGroups();
 403       SequenceGroup sg;
 404       for (int g = 0; g < allGroups.size(); g++)
 405       {
 406         sg = (SequenceGroup) allGroups.get(g);
 407
 408         if (sg.cs == null)
 409         {
 410           continue;
 411         }
 412
 413         if (currentColours.isSelected())
 414         {
 415           sg.cs = new AnnotationColourGradient(currentAnnotation, sg.cs,
 416                   aboveThreshold);
 417         }
 418         else
 419         {
 420           sg.cs = new AnnotationColourGradient(currentAnnotation, minColour
 421                   .getBackground(), maxColour.getBackground(),
 422                   aboveThreshold);
 423         }
 424
 425       }
 426     }
 427
 428     ap.paintAlignment(false);
 429   }
 430
 431   public void ok_actionPerformed(ActionEvent e)
 432   {
 433     changeColour();
 434     try
 435     {
 436       frame.setClosed(true);
 437     } catch (Exception ex)
 438     {
 439     }
 440   }
 441
 442   public void cancel_actionPerformed(ActionEvent e)
 443   {
 444     reset();
 445     try
 446     {
 447       frame.setClosed(true);
 448     } catch (Exception ex)
 449     {
 450     }
 451   }
 452
 453   void reset()
 454   {
 455     av.setGlobalColourScheme(oldcs);
 456     if (av.alignment.getGroups() != null)
 457     {
 458       Vector allGroups = ap.av.alignment.getGroups();
 459       SequenceGroup sg;
 460       for (int g = 0; g < allGroups.size(); g++)
 461       {
 462         sg = (SequenceGroup) allGroups.get(g);
 463         sg.cs = (ColourSchemeI) oldgroupColours.get(sg);
 464       }
 465     }
 466   }
 467
 468   public void thresholdCheck_actionPerformed(ActionEvent e)
 469   {
 470     changeColour();
 471   }
 472
 473   public void annotations_actionPerformed(ActionEvent e)
 474   {
 475     changeColour();
 476   }
 477
 478   public void threshold_actionPerformed(ActionEvent e)
 479   {
 480     changeColour();
 481   }
 482
 483   public void thresholdValue_actionPerformed(ActionEvent e)
 484   {
 485     try
 486     {
 487       float f = Float.parseFloat(thresholdValue.getText());
 488       slider.setValue((int) (f * 1000));
 489     } catch (NumberFormatException ex)
 490     {
 491     }
 492   }
 493
 494   public void valueChanged()
 495   {
 496     if (currentColours.isSelected()
 497             && !(av.getGlobalColourScheme() instanceof AnnotationColourGradient))
 498     {
 499       changeColour();
 500     }
 501
 502     currentAnnotation.threshold.value = (float) slider.getValue() / 1000f;
 503     ap.paintAlignment(false);
 504   }
 505
 506   public void currentColours_actionPerformed(ActionEvent e)
 507   {
 508     if (currentColours.isSelected())
 509     {
 510       reset();
 511     }
 512
 513     maxColour.setEnabled(!currentColours.isSelected());
 514     minColour.setEnabled(!currentColours.isSelected());
 515
 516     changeColour();
 517   }
 518
 519   public void thresholdIsMin_actionPerformed(ActionEvent actionEvent)
 520   {
 521     changeColour();
 522   }
 523
 524 }