src/jalview/gui/FeatureColourChooser.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 FeatureColourChooser extends JPanel
  33 {
  34   JInternalFrame frame;
  35
  36   FeatureRenderer fr;
  37
  38   FeatureSettings fs;
  39
  40   GraduatedColor cs;
  41   Object oldcs;
  42
  43   Hashtable oldgroupColours;
  44
  45   AlignmentPanel ap;
  46
  47
  48   boolean adjusting = false;
  49
  50   private float min;
  51
  52   private float max;
  53   String type = null;
  54   public FeatureColourChooser(FeatureSettings fsettings, String type)
  55   {
  56     this.fs = fsettings;
  57     this.type = type;
  58     fr = fsettings.fr;
  59     ap = fr.ap;
  60     frame = new JInternalFrame();
  61     frame.setContentPane(this);
  62     frame.setLayer(JLayeredPane.PALETTE_LAYER);
  63     Desktop.addInternalFrame(frame, "Graduated Feature Colour for "+type, 480, 145);
  64
  65     slider.addChangeListener(new ChangeListener()
  66     {
  67       public void stateChanged(ChangeEvent evt)
  68       {
  69         if (!adjusting)
  70         {
  71           thresholdValue.setText(((float) slider.getValue() / 1000f) + "");
  72           valueChanged();
  73         }
  74       }
  75     });
  76     slider.addMouseListener(new MouseAdapter()
  77     {
  78       public void mouseReleased(MouseEvent evt)
  79       {
  80         if (fr.ap!=null) { fr.ap.paintAlignment(true); };
  81       }
  82     });
  83
  84     float mm[] = ((float[][]) fr.minmax.get(type))[0];
  85     min = mm[0];
  86     max = mm[1];
  87     oldcs = fr.featureColours.get(type);
  88     if (oldcs instanceof GraduatedColor)
  89     {
  90       if (((GraduatedColor)oldcs).isAutoScale())
  91       {
  92         // update the scale
  93         cs = new GraduatedColor((GraduatedColor) oldcs, min, max);
  94       } else {
  95         cs = new GraduatedColor((GraduatedColor) oldcs);
  96       }
  97     } else {
  98       // promote original color to a graduated color
  99       Color bl = Color.black;
 100       if (oldcs instanceof Color)
 101       {
 102         bl = (Color) oldcs;
 103       }
 104       // original colour becomes the maximum colour
 105       cs = new GraduatedColor(Color.white,bl,mm[0],mm[1]);
 106       cs.setColourByLabel(false);
 107     }
 108     minColour.setBackground(cs.getMinColor());
 109     maxColour.setBackground(cs.getMaxColor());
 110     adjusting = true;
 111
 112     try
 113     {
 114       jbInit();
 115     } catch (Exception ex)
 116     {
 117     }
 118     // update the gui from threshold state
 119     thresholdIsMin.setSelected(!cs.isAutoScale());
 120     colourByLabel.setSelected(cs.isColourByLabel());
 121     if (cs.getThreshType()!=AnnotationColourGradient.NO_THRESHOLD)
 122     {
 123       // initialise threshold slider and selector
 124       threshold.setSelectedIndex(cs.getThreshType()==AnnotationColourGradient.ABOVE_THRESHOLD ? 1 : 2);
 125             slider.setEnabled(true);
 126       thresholdValue.setEnabled(true);
 127       threshline = new jalview.datamodel.GraphLine(
 128                         (max - min) / 2f,
 129                         "Threshold", Color.black);
 130
 131     }
 132
 133     adjusting = false;
 134
 135     changeColour();
 136
 137   }
 138
 139   public FeatureColourChooser()
 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     jPanel1.setBackground(Color.white);
 201     jPanel2.setBackground(Color.white);
 202     threshold.addActionListener(new ActionListener()
 203     {
 204       public void actionPerformed(ActionEvent e)
 205       {
 206         threshold_actionPerformed(e);
 207       }
 208     });
 209     threshold.addItem("No Threshold"); // index 0
 210     threshold.addItem("Above Threshold"); // index 1
 211     threshold.addItem("Below Threshold"); // index 2
 212     jPanel3.setLayout(flowLayout2);
 213     thresholdValue.addActionListener(new ActionListener()
 214     {
 215       public void actionPerformed(ActionEvent e)
 216       {
 217         thresholdValue_actionPerformed(e);
 218       }
 219     });
 220     slider.setPaintLabels(false);
 221     slider.setPaintTicks(true);
 222     slider.setBackground(Color.white);
 223     slider.setEnabled(false);
 224     slider.setOpaque(false);
 225     slider.setPreferredSize(new Dimension(100, 32));
 226     thresholdValue.setEnabled(false);
 227     thresholdValue.setColumns(7);
 228     jPanel3.setBackground(Color.white);
 229     currentColours.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
 230     currentColours.setOpaque(false);
 231     currentColours.setText("Use Original Colours");
 232     currentColours.addActionListener(new ActionListener()
 233     {
 234       public void actionPerformed(ActionEvent e)
 235       {
 236         currentColours_actionPerformed(e);
 237       }
 238     });
 239     thresholdIsMin.setBackground(Color.white);
 240     thresholdIsMin.setText("Threshold is Min/Max");
 241     thresholdIsMin.addActionListener(new ActionListener()
 242     {
 243       public void actionPerformed(ActionEvent actionEvent)
 244       {
 245         thresholdIsMin_actionPerformed(actionEvent);
 246       }
 247     });
 248     colourByLabel.setBackground(Color.white);
 249     colourByLabel.setText("Colour by Label");
 250     colourByLabel.addActionListener(new ActionListener()
 251     {
 252       public void actionPerformed(ActionEvent actionEvent)
 253       {
 254         colourByLabel_actionPerformed(actionEvent);
 255       }
 256     });
 257     jPanel1.add(ok);
 258     jPanel1.add(cancel);
 259     // jPanel2.add(currentColours);
 260     jPanel2.add(minColour);
 261     jPanel2.add(maxColour);
 262     this.add(jPanel3, java.awt.BorderLayout.CENTER);
 263     jPanel3.add(threshold);
 264     jPanel3.add(slider);
 265     jPanel3.add(thresholdValue);
 266     jPanel3.add(thresholdIsMin);
 267     jPanel3.add(colourByLabel);
 268     this.add(jPanel1, java.awt.BorderLayout.SOUTH);
 269     this.add(jPanel2, java.awt.BorderLayout.NORTH);
 270   }
 271
 272
 273   JPanel minColour = new JPanel();
 274
 275   JPanel maxColour = new JPanel();
 276
 277   JButton ok = new JButton();
 278
 279   JButton cancel = new JButton();
 280
 281   JPanel jPanel1 = new JPanel();
 282
 283   JPanel jPanel2 = new JPanel();
 284
 285   BorderLayout borderLayout1 = new BorderLayout();
 286
 287   JComboBox threshold = new JComboBox();
 288
 289   FlowLayout flowLayout1 = new FlowLayout();
 290
 291   JPanel jPanel3 = new JPanel();
 292
 293   FlowLayout flowLayout2 = new FlowLayout();
 294
 295   JSlider slider = new JSlider();
 296
 297   JTextField thresholdValue = new JTextField(20);
 298   // TODO refactor to tolower flag
 299   JCheckBox currentColours = new JCheckBox();
 300
 301   JCheckBox thresholdIsMin = new JCheckBox();
 302   JCheckBox colourByLabel = new JCheckBox();
 303
 304   private GraphLine threshline;
 305
 306   public void minColour_actionPerformed()
 307   {
 308     Color col = JColorChooser.showDialog(this,
 309             "Select Colour for Minimum Value", minColour.getBackground());
 310     if (col != null)
 311     {
 312       minColour.setBackground(col);
 313     }
 314     minColour.repaint();
 315     changeColour();
 316   }
 317
 318   public void maxColour_actionPerformed()
 319   {
 320     Color col = JColorChooser.showDialog(this,
 321             "Select Colour for Maximum Value", maxColour.getBackground());
 322     if (col != null)
 323     {
 324       maxColour.setBackground(col);
 325     }
 326     maxColour.repaint();
 327     changeColour();
 328   }
 329
 330   void changeColour()
 331   {
 332     // Check if combobox is still adjusting
 333     if (adjusting)
 334     {
 335       return;
 336     }
 337
 338
 339     int aboveThreshold = AnnotationColourGradient.NO_THRESHOLD;
 340     if (threshold.getSelectedItem().equals("Above Threshold"))
 341     {
 342       aboveThreshold = AnnotationColourGradient.ABOVE_THRESHOLD;
 343     }
 344     else if (threshold.getSelectedItem().equals("Below Threshold"))
 345     {
 346       aboveThreshold = AnnotationColourGradient.BELOW_THRESHOLD;
 347     }
 348
 349     slider.setEnabled(true);
 350     thresholdValue.setEnabled(true);
 351     GraduatedColor acg = new GraduatedColor(minColour.getBackground(), maxColour.getBackground(), min, max);
 352
 353     if (aboveThreshold == AnnotationColourGradient.NO_THRESHOLD)
 354     {
 355       slider.setEnabled(false);
 356       thresholdValue.setEnabled(false);
 357       thresholdValue.setText("");
 358     }
 359     else if (aboveThreshold != AnnotationColourGradient.NO_THRESHOLD
 360             && threshline == null)
 361     {
 362       // todo visual indication of feature threshold
 363       threshline = new jalview.datamodel.GraphLine(
 364                       (max - min) / 2f,
 365                       "Threshold", Color.black);
 366     }
 367
 368     if (aboveThreshold != AnnotationColourGradient.NO_THRESHOLD)
 369     {
 370       adjusting = true;
 371       acg.setThresh(threshline.value);
 372
 373       float range = max * 1000f
 374               - min * 1000f;
 375
 376       slider.setMinimum((int) (min * 1000));
 377       slider.setMaximum((int) (max * 1000));
 378       slider.setValue((int) (threshline.value * 1000));
 379       thresholdValue.setText(threshline.value + "");
 380       slider.setMajorTickSpacing((int) (range / 10f));
 381       slider.setEnabled(true);
 382       thresholdValue.setEnabled(true);
 383       adjusting = false;
 384     }
 385
 386     acg.setThreshType(aboveThreshold);
 387     if (thresholdIsMin.isSelected() && aboveThreshold != AnnotationColourGradient.NO_THRESHOLD)
 388     {
 389       acg.setAutoScaled(false);
 390       if (aboveThreshold==AnnotationColourGradient.ABOVE_THRESHOLD)
 391       {
 392         acg = new GraduatedColor(acg, threshline.value, max);
 393       } else {
 394         acg = new GraduatedColor(acg, min,threshline.value);
 395       }
 396     } else {
 397       acg.setAutoScaled(true);
 398     }
 399     acg.setColourByLabel(colourByLabel.isSelected());
 400     fr.featureColours.put(type,acg);
 401     cs = acg;
 402     ap.paintAlignment(false);
 403   }
 404
 405   public void ok_actionPerformed(ActionEvent e)
 406   {
 407     changeColour();
 408     try
 409     {
 410       frame.setClosed(true);
 411     } catch (Exception ex)
 412     {
 413     }
 414   }
 415
 416   public void cancel_actionPerformed(ActionEvent e)
 417   {
 418     reset();
 419     try
 420     {
 421       frame.setClosed(true);
 422     } catch (Exception ex)
 423     {
 424     }
 425   }
 426
 427   void reset()
 428   {
 429     fr.featureColours.put(type, oldcs);
 430   }
 431
 432   public void thresholdCheck_actionPerformed(ActionEvent e)
 433   {
 434     changeColour();
 435   }
 436
 437   public void annotations_actionPerformed(ActionEvent e)
 438   {
 439     changeColour();
 440   }
 441
 442   public void threshold_actionPerformed(ActionEvent e)
 443   {
 444     changeColour();
 445   }
 446
 447   public void thresholdValue_actionPerformed(ActionEvent e)
 448   {
 449     try
 450     {
 451       float f = Float.parseFloat(thresholdValue.getText());
 452       slider.setValue((int) (f * 1000));
 453       threshline.value = f;
 454     } catch (NumberFormatException ex)
 455     {
 456     }
 457   }
 458
 459   public void valueChanged()
 460   {
 461     threshline.value = (float) slider.getValue() / 1000f;
 462     cs.setThresh(threshline.value);
 463     changeColour();
 464     ap.paintAlignment(false);
 465   }
 466
 467   public void currentColours_actionPerformed(ActionEvent e)
 468   {
 469     if (currentColours.isSelected())
 470     {
 471       reset();
 472     }
 473
 474     maxColour.setEnabled(!currentColours.isSelected());
 475     minColour.setEnabled(!currentColours.isSelected());
 476
 477     changeColour();
 478   }
 479
 480   public void thresholdIsMin_actionPerformed(ActionEvent actionEvent)
 481   {
 482     changeColour();
 483   }
 484   public void colourByLabel_actionPerformed(ActionEvent actionEvent)
 485   {
 486     changeColour();
 487   }
 488
 489 }