src/jalview/gui/AnnotationColourChooser.java

   1 /*
   2 * Jalview - A Sequence Alignment Editor and Viewer
   3 * Copyright (C) 2006 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 javax.swing.*;
  22 import java.awt.event.*;
  23 import java.awt.*;
  24
  25 import jalview.schemes.*;
  26 import javax.swing.event.*;
  27 import java.util.*;
  28 import jalview.datamodel.SequenceGroup;
  29
  30 public class AnnotationColourChooser
  31     extends JPanel
  32 {
  33   JInternalFrame frame;
  34   AlignViewport av;
  35   AlignmentPanel ap;
  36   ColourSchemeI oldcs;
  37   Hashtable oldgroupColours;
  38   jalview.datamodel.AlignmentAnnotation currentAnnotation;
  39   boolean adjusting = false;
  40
  41   public AnnotationColourChooser(AlignViewport av, AlignmentPanel ap)
  42   {
  43     oldcs = av.getGlobalColourScheme();
  44     if (av.alignment.getGroups() != null)
  45     {
  46       oldgroupColours = new Hashtable();
  47       Vector allGroups = ap.av.alignment.getGroups();
  48       SequenceGroup sg;
  49       for (int g = 0; g < allGroups.size(); g++)
  50       {
  51         sg = (SequenceGroup) allGroups.get(g);
  52         if(sg.cs!=null)
  53           oldgroupColours.put(sg, sg.cs);
  54       }
  55     }
  56     this.av = av;
  57     this.ap = ap;
  58     frame = new JInternalFrame();
  59     frame.setContentPane(this);
  60     frame.setLayer(JLayeredPane.PALETTE_LAYER);
  61     Desktop.addInternalFrame(frame, "Colour by Annotation", 480, 145);
  62
  63     try
  64     {
  65       jbInit();
  66     }
  67     catch (Exception ex)
  68     {}
  69
  70     slider.addChangeListener(new ChangeListener()
  71     {
  72       public void stateChanged(ChangeEvent evt)
  73       {
  74         if(!adjusting)
  75         {
  76           thresholdValue.setText( ( (float) slider.getValue() / 1000f) + "");
  77           valueChanged();
  78         }
  79       }
  80     });
  81
  82     if (av.alignment.getAlignmentAnnotation() == null)
  83       return;
  84
  85     if (oldcs instanceof AnnotationColourGradient)
  86     {
  87       AnnotationColourGradient acg = (AnnotationColourGradient) oldcs;
  88       minColour.setBackground(acg.getMinColour());
  89       maxColour.setBackground(acg.getMaxColour());
  90     }
  91     else
  92     {
  93       minColour.setBackground(Color.orange);
  94       maxColour.setBackground(Color.red);
  95     }
  96
  97     adjusting = true;
  98     for (int i = 0; i < av.alignment.getAlignmentAnnotation().length; i++)
  99     {
 100       if (av.alignment.getAlignmentAnnotation()[i].graph > 0)
 101         annotations.addItem(av.alignment.getAlignmentAnnotation()[i].label);
 102     }
 103
 104     threshold.addItem("No Threshold");
 105     threshold.addItem("Above Threshold");
 106     threshold.addItem("Below Threshold");
 107
 108     adjusting = false;
 109
 110     changeColour();
 111
 112   }
 113
 114   public AnnotationColourChooser()
 115   {
 116     try
 117     {
 118       jbInit();
 119     }
 120     catch (Exception ex)
 121     {
 122       ex.printStackTrace();
 123     }
 124   }
 125
 126   private void jbInit()
 127       throws Exception
 128   {
 129     minColour.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
 130     minColour.setToolTipText("");
 131     minColour.setMargin(new Insets(2, 2, 2, 2));
 132     minColour.setText("Min Colour");
 133     minColour.addActionListener(new ActionListener()
 134     {
 135       public void actionPerformed(ActionEvent e)
 136       {
 137         minColour_actionPerformed(e);
 138       }
 139     });
 140     maxColour.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
 141     maxColour.setMargin(new Insets(2, 2, 2, 2));
 142     maxColour.setText("Max Colour");
 143     maxColour.addActionListener(new ActionListener()
 144     {
 145       public void actionPerformed(ActionEvent e)
 146       {
 147         maxColour_actionPerformed(e);
 148       }
 149     });
 150     ok.setOpaque(false);
 151     ok.setText("OK");
 152     ok.addActionListener(new ActionListener()
 153     {
 154       public void actionPerformed(ActionEvent e)
 155       {
 156         ok_actionPerformed(e);
 157       }
 158     });
 159     cancel.setOpaque(false);
 160     cancel.setText("Cancel");
 161     cancel.addActionListener(new ActionListener()
 162     {
 163       public void actionPerformed(ActionEvent e)
 164       {
 165         cancel_actionPerformed(e);
 166       }
 167     });
 168     this.setLayout(borderLayout1);
 169     jPanel2.setLayout(flowLayout1);
 170     annotations.addActionListener(new ActionListener()
 171     {
 172       public void actionPerformed(ActionEvent e)
 173       {
 174         annotations_actionPerformed(e);
 175       }
 176     });
 177     jPanel1.setBackground(Color.white);
 178     jPanel2.setBackground(Color.white);
 179     threshold.addActionListener(new ActionListener()
 180     {
 181       public void actionPerformed(ActionEvent e)
 182       {
 183         threshold_actionPerformed(e);
 184       }
 185     });
 186     jPanel3.setLayout(flowLayout2);
 187     thresholdValue.addActionListener(new ActionListener()
 188     {
 189       public void actionPerformed(ActionEvent e)
 190       {
 191         thresholdValue_actionPerformed(e);
 192       }
 193     });
 194     slider.setPaintLabels(false);
 195     slider.setPaintTicks(true);
 196     slider.setBackground(Color.white);
 197     slider.setEnabled(false);
 198     slider.setOpaque(false);
 199     slider.setPreferredSize(new Dimension(150, 32));
 200     thresholdValue.setEnabled(false);
 201     thresholdValue.setColumns(10);
 202     jPanel3.setBackground(Color.white);
 203     currentColours.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
 204     currentColours.setOpaque(false);
 205     currentColours.setText("Use Original Colours");
 206     currentColours.addActionListener(new ActionListener()
 207     {
 208       public void actionPerformed(ActionEvent e)
 209       {
 210         currentColours_actionPerformed(e);
 211       }
 212     });
 213     jPanel1.add(ok);
 214     jPanel1.add(cancel);
 215     jPanel2.add(annotations);
 216     jPanel2.add(currentColours);
 217     jPanel2.add(minColour);
 218     jPanel2.add(maxColour);
 219     this.add(jPanel3, java.awt.BorderLayout.CENTER);
 220     jPanel3.add(threshold);
 221     jPanel3.add(slider);
 222     jPanel3.add(thresholdValue);
 223     this.add(jPanel1, java.awt.BorderLayout.SOUTH);
 224     this.add(jPanel2, java.awt.BorderLayout.NORTH);
 225   }
 226
 227   JComboBox annotations = new JComboBox();
 228   JButton minColour = new JButton();
 229   JButton maxColour = new JButton();
 230   JButton ok = new JButton();
 231   JButton cancel = new JButton();
 232   JPanel jPanel1 = new JPanel();
 233   JPanel jPanel2 = new JPanel();
 234   BorderLayout borderLayout1 = new BorderLayout();
 235   JComboBox threshold = new JComboBox();
 236   FlowLayout flowLayout1 = new FlowLayout();
 237   JPanel jPanel3 = new JPanel();
 238   FlowLayout flowLayout2 = new FlowLayout();
 239   JSlider slider = new JSlider();
 240   JTextField thresholdValue = new JTextField(20);
 241   JCheckBox currentColours = new JCheckBox();
 242
 243   public void minColour_actionPerformed(ActionEvent e)
 244   {
 245     Color col = JColorChooser.showDialog(this,
 246                                          "Select Colour for Minimum Value",
 247                                          minColour.getBackground());
 248     if (col != null)
 249       minColour.setBackground(col);
 250     minColour.repaint();
 251     changeColour();
 252   }
 253
 254   public void maxColour_actionPerformed(ActionEvent e)
 255   {
 256     Color col = JColorChooser.showDialog(this,
 257                                          "Select Colour for Maximum Value",
 258                                          maxColour.getBackground());
 259     if (col != null)
 260       maxColour.setBackground(col);
 261     maxColour.repaint();
 262     changeColour();
 263   }
 264
 265   void changeColour()
 266   {
 267     // Check if combobox is still adjusting
 268     if (adjusting)
 269       return;
 270
 271     // We removed the non-graph annotations when filling the combobox
 272     // so allow for them again here
 273     int nograph = 0, graph = -1;
 274     for (int i = 0; i < av.alignment.getAlignmentAnnotation().length; i++)
 275     {
 276       if (av.alignment.getAlignmentAnnotation()[i].graph == 0)
 277         nograph++;
 278       else
 279         graph++;
 280
 281       if (graph == annotations.getSelectedIndex())
 282         break;
 283     }
 284
 285     currentAnnotation = av.alignment.getAlignmentAnnotation()[graph + nograph];
 286
 287     int aboveThreshold = -1;
 288     if (threshold.getSelectedItem().equals("Above Threshold"))
 289       aboveThreshold = AnnotationColourGradient.ABOVE_THRESHOLD;
 290     else if (threshold.getSelectedItem().equals("Below Threshold"))
 291       aboveThreshold = AnnotationColourGradient.BELOW_THRESHOLD;
 292
 293     slider.setEnabled(true);
 294     thresholdValue.setEnabled(true);
 295
 296     if (aboveThreshold == AnnotationColourGradient.NO_THRESHOLD)
 297     {
 298       slider.setEnabled(false);
 299       thresholdValue.setEnabled(false);
 300       thresholdValue.setText("");
 301     }
 302     else if (aboveThreshold != AnnotationColourGradient.NO_THRESHOLD &&
 303              currentAnnotation.threshold == null)
 304     {
 305       currentAnnotation.setThreshold(new jalview.datamodel.GraphLine
 306                                      ( (currentAnnotation.graphMax -
 307                                         currentAnnotation.graphMin) / 2f,
 308                                       "Threshold",
 309                                       Color.black));
 310     }
 311
 312     if(aboveThreshold != AnnotationColourGradient.NO_THRESHOLD)
 313     {
 314       adjusting = true;
 315       float range = currentAnnotation.graphMax * 1000 -
 316           currentAnnotation.graphMin * 1000;
 317
 318       slider.setMinimum( (int) (currentAnnotation.graphMin * 1000));
 319       slider.setMaximum( (int) (currentAnnotation.graphMax * 1000));
 320       slider.setValue( (int) (currentAnnotation.threshold.value * 1000));
 321       thresholdValue.setText(currentAnnotation.threshold.value + "");
 322       slider.setMajorTickSpacing( (int) (range / 10f));
 323       slider.setEnabled(true);
 324       thresholdValue.setEnabled(true);
 325       adjusting = false;
 326     }
 327
 328     AnnotationColourGradient acg = null;
 329     if (currentColours.isSelected())
 330       acg = new AnnotationColourGradient(
 331           currentAnnotation,
 332           av.getGlobalColourScheme(), aboveThreshold);
 333     else
 334       acg =
 335           new AnnotationColourGradient(
 336               currentAnnotation,
 337               minColour.getBackground(),
 338               maxColour.getBackground(),
 339               aboveThreshold);
 340
 341     av.setGlobalColourScheme(acg);
 342
 343     if (av.alignment.getGroups() != null)
 344     {
 345       Vector allGroups = ap.av.alignment.getGroups();
 346       SequenceGroup sg;
 347       for (int g = 0; g < allGroups.size(); g++)
 348       {
 349         sg = (SequenceGroup) allGroups.get(g);
 350
 351         if (sg.cs == null)
 352         {
 353           continue;
 354         }
 355
 356         if (currentColours.isSelected())
 357           sg.cs = new AnnotationColourGradient(
 358               currentAnnotation,
 359               sg.cs, aboveThreshold);
 360         else
 361           sg.cs = new AnnotationColourGradient(
 362               currentAnnotation,
 363               minColour.getBackground(),
 364               maxColour.getBackground(),
 365               aboveThreshold);
 366
 367       }
 368     }
 369
 370     ap.repaint();
 371   }
 372
 373   public void ok_actionPerformed(ActionEvent e)
 374   {
 375     changeColour();
 376     try
 377     {
 378       frame.setClosed(true);
 379     }
 380     catch (Exception ex)
 381     {}
 382   }
 383
 384   public void cancel_actionPerformed(ActionEvent e)
 385   {
 386     reset();
 387     try
 388     {
 389       frame.setClosed(true);
 390     }
 391     catch (Exception ex)
 392     {}
 393   }
 394
 395
 396   void reset()
 397   {
 398     av.setGlobalColourScheme(oldcs);
 399     if (av.alignment.getGroups() != null)
 400     {
 401       Vector allGroups = ap.av.alignment.getGroups();
 402       SequenceGroup sg;
 403       for (int g = 0; g < allGroups.size(); g++)
 404       {
 405         sg = (SequenceGroup) allGroups.get(g);
 406         sg.cs = (ColourSchemeI)oldgroupColours.get(sg);
 407       }
 408     }
 409   }
 410
 411   public void thresholdCheck_actionPerformed(ActionEvent e)
 412   {
 413     changeColour();
 414   }
 415
 416   public void annotations_actionPerformed(ActionEvent e)
 417   {
 418     changeColour();
 419   }
 420
 421   public void threshold_actionPerformed(ActionEvent e)
 422   {
 423     changeColour();
 424   }
 425
 426   public void thresholdValue_actionPerformed(ActionEvent e)
 427   {
 428     try
 429     {
 430       float f = Float.parseFloat(thresholdValue.getText());
 431       slider.setValue( (int) (f * 1000));
 432     }
 433     catch (NumberFormatException ex)
 434     {}
 435   }
 436
 437   public void valueChanged()
 438   {
 439     if (currentColours.isSelected()
 440         && !(av.getGlobalColourScheme() instanceof AnnotationColourGradient))
 441     {
 442       changeColour();
 443     }
 444
 445     currentAnnotation.threshold.value = (float)slider.getValue()/1000f;
 446     ap.repaint();
 447   }
 448
 449   public void currentColours_actionPerformed(ActionEvent e)
 450   {
 451     if(currentColours.isSelected())
 452     {
 453       reset();
 454     }
 455
 456     maxColour.setEnabled(!currentColours.isSelected());
 457     minColour.setEnabled(!currentColours.isSelected());
 458
 459     changeColour();
 460   }
 461
 462 }