src/jalview/gui/FeatureColourChooser.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
   3  * Copyright (C) 2014 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 of the License, or (at your option) any later version.
  10  *
  11  * Jalview is distributed in the hope that it will be useful, but
  12  * WITHOUT ANY WARRANTY; without even the implied warranty
  13  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  14  * PURPOSE.  See the GNU General Public License for more details.
  15  *
  16  * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  17  * The Jalview Authors are detailed in the 'AUTHORS' file.
  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.border.LineBorder;
  27 import javax.swing.event.*;
  28
  29 import jalview.datamodel.*;
  30 import jalview.schemes.*;
  31 import jalview.util.MessageManager;
  32
  33 import java.awt.Dimension;
  34
  35 public class FeatureColourChooser extends JalviewDialog
  36 {
  37   // FeatureSettings fs;
  38   FeatureRenderer fr;
  39
  40   private GraduatedColor cs;
  41
  42   private Object oldcs;
  43
  44   /**
  45    *
  46    * @return the last colour setting selected by user - either oldcs (which may
  47    *         be a java.awt.Color) or the new GraduatedColor
  48    */
  49   public Object getLastColour()
  50   {
  51     if (cs == null)
  52     {
  53       return oldcs;
  54     }
  55     return cs;
  56   }
  57
  58   Hashtable oldgroupColours;
  59
  60   AlignmentPanel ap;
  61
  62   boolean adjusting = false;
  63
  64   private float min;
  65
  66   private float max;
  67
  68   String type = null;
  69
  70   public FeatureColourChooser(FeatureRenderer frender, String type)
  71   {
  72     this(frender, false, type);
  73   }
  74
  75   public FeatureColourChooser(FeatureRenderer frender, boolean block,
  76           String type)
  77   {
  78     this.fr = frender;
  79     this.type = type;
  80     ap = fr.ap;
  81     initDialogFrame(this, true, block, "Graduated Feature Colour for "
  82             + type, 480, 185);
  83     // frame.setLayer(JLayeredPane.PALETTE_LAYER);
  84     // Desktop.addInternalFrame(frame, "Graduated Feature Colour for "+type,
  85     // 480, 145);
  86
  87     slider.addChangeListener(new ChangeListener()
  88     {
  89       public void stateChanged(ChangeEvent evt)
  90       {
  91         if (!adjusting)
  92         {
  93           thresholdValue.setText(((float) slider.getValue() / 1000f) + "");
  94           valueChanged();
  95         }
  96       }
  97     });
  98     slider.addMouseListener(new MouseAdapter()
  99     {
 100       public void mouseReleased(MouseEvent evt)
 101       {
 102         if (ap != null)
 103         {
 104           ap.paintAlignment(true);
 105         }
 106         ;
 107       }
 108     });
 109
 110     float mm[] = ((float[][]) fr.minmax.get(type))[0];
 111     min = mm[0];
 112     max = mm[1];
 113     oldcs = fr.featureColours.get(type);
 114     if (oldcs instanceof GraduatedColor)
 115     {
 116       if (((GraduatedColor) oldcs).isAutoScale())
 117       {
 118         // update the scale
 119         cs = new GraduatedColor((GraduatedColor) oldcs, min, max);
 120       }
 121       else
 122       {
 123         cs = new GraduatedColor((GraduatedColor) oldcs);
 124       }
 125     }
 126     else
 127     {
 128       // promote original color to a graduated color
 129       Color bl = Color.black;
 130       if (oldcs instanceof Color)
 131       {
 132         bl = (Color) oldcs;
 133       }
 134       // original colour becomes the maximum colour
 135       cs = new GraduatedColor(Color.white, bl, mm[0], mm[1]);
 136       cs.setColourByLabel(false);
 137     }
 138     minColour.setBackground(oldminColour = cs.getMinColor());
 139     maxColour.setBackground(oldmaxColour = cs.getMaxColor());
 140     adjusting = true;
 141
 142     try
 143     {
 144       jbInit();
 145     } catch (Exception ex)
 146     {
 147     }
 148     // update the gui from threshold state
 149     thresholdIsMin.setSelected(!cs.isAutoScale());
 150     colourByLabel.setSelected(cs.isColourByLabel());
 151     if (cs.getThreshType() != AnnotationColourGradient.NO_THRESHOLD)
 152     {
 153       // initialise threshold slider and selector
 154       threshold
 155               .setSelectedIndex(cs.getThreshType() == AnnotationColourGradient.ABOVE_THRESHOLD ? 1
 156                       : 2);
 157       slider.setEnabled(true);
 158       thresholdValue.setEnabled(true);
 159       threshline = new jalview.datamodel.GraphLine((max - min) / 2f,
 160               "Threshold", Color.black);
 161
 162     }
 163
 164     adjusting = false;
 165
 166     changeColour();
 167     waitForInput();
 168   }
 169
 170   public FeatureColourChooser()
 171   {
 172     try
 173     {
 174       jbInit();
 175     } catch (Exception ex)
 176     {
 177       ex.printStackTrace();
 178     }
 179   }
 180
 181   private void jbInit() throws Exception
 182   {
 183
 184     minColour.setFont(JvSwingUtils.getLabelFont());
 185     minColour.setBorder(BorderFactory.createLineBorder(Color.black));
 186     minColour.setPreferredSize(new Dimension(40, 20));
 187     minColour.setToolTipText(MessageManager.getString("label.min_colour"));
 188     minColour.addMouseListener(new MouseAdapter()
 189     {
 190       public void mousePressed(MouseEvent e)
 191       {
 192         if (minColour.isEnabled())
 193         {
 194           minColour_actionPerformed();
 195         }
 196       }
 197     });
 198     maxColour.setFont(JvSwingUtils.getLabelFont());
 199     maxColour.setBorder(BorderFactory.createLineBorder(Color.black));
 200     maxColour.setPreferredSize(new Dimension(40, 20));
 201     maxColour.setToolTipText(MessageManager.getString("label.max_colour"));
 202     maxColour.addMouseListener(new MouseAdapter()
 203     {
 204       public void mousePressed(MouseEvent e)
 205       {
 206         if (maxColour.isEnabled())
 207         {
 208           maxColour_actionPerformed();
 209         }
 210       }
 211     });
 212     maxColour.setBorder(new LineBorder(Color.black));
 213     minText.setText(MessageManager.getString("label.min"));
 214     minText.setFont(JvSwingUtils.getLabelFont());
 215     maxText.setText(MessageManager.getString("label.max"));
 216     maxText.setFont(JvSwingUtils.getLabelFont());
 217     this.setLayout(borderLayout1);
 218     jPanel2.setLayout(flowLayout1);
 219     jPanel1.setBackground(Color.white);
 220     jPanel2.setBackground(Color.white);
 221     threshold.addActionListener(new ActionListener()
 222     {
 223       public void actionPerformed(ActionEvent e)
 224       {
 225         threshold_actionPerformed(e);
 226       }
 227     });
 228     threshold.setToolTipText(MessageManager.getString("label.threshold_feature_display_by_score"));
 229     threshold.addItem(MessageManager.getString("label.threshold_feature_no_thereshold")); // index 0
 230     threshold.addItem(MessageManager.getString("label.threshold_feature_above_thereshold")); // index 1
 231     threshold.addItem(MessageManager.getString("label.threshold_feature_below_thereshold")); // index 2
 232     jPanel3.setLayout(flowLayout2);
 233     thresholdValue.addActionListener(new ActionListener()
 234     {
 235       public void actionPerformed(ActionEvent e)
 236       {
 237         thresholdValue_actionPerformed(e);
 238       }
 239     });
 240     slider.setPaintLabels(false);
 241     slider.setPaintTicks(true);
 242     slider.setBackground(Color.white);
 243     slider.setEnabled(false);
 244     slider.setOpaque(false);
 245     slider.setPreferredSize(new Dimension(100, 32));
 246     slider.setToolTipText(MessageManager.getString("label.adjust_thereshold"));
 247     thresholdValue.setEnabled(false);
 248     thresholdValue.setColumns(7);
 249     jPanel3.setBackground(Color.white);
 250     thresholdIsMin.setBackground(Color.white);
 251     thresholdIsMin.setText(MessageManager.getString("label.threshold_minmax"));
 252     thresholdIsMin
 253             .setToolTipText(MessageManager.getString("label.toggle_absolute_relative_display_threshold"));
 254     thresholdIsMin.addActionListener(new ActionListener()
 255     {
 256       public void actionPerformed(ActionEvent actionEvent)
 257       {
 258         thresholdIsMin_actionPerformed(actionEvent);
 259       }
 260     });
 261     colourByLabel.setBackground(Color.white);
 262     colourByLabel.setText(MessageManager.getString("label.colour_by_label"));
 263     colourByLabel
 264             .setToolTipText(MessageManager.getString("label.display_features_same_type_different_label_using_different_colour"));
 265     colourByLabel.addActionListener(new ActionListener()
 266     {
 267       public void actionPerformed(ActionEvent actionEvent)
 268       {
 269         colourByLabel_actionPerformed(actionEvent);
 270       }
 271     });
 272     colourPanel.setBackground(Color.white);
 273     jPanel1.add(ok);
 274     jPanel1.add(cancel);
 275     jPanel2.add(colourByLabel, java.awt.BorderLayout.WEST);
 276     jPanel2.add(colourPanel, java.awt.BorderLayout.EAST);
 277     colourPanel.add(minText);
 278     colourPanel.add(minColour);
 279     colourPanel.add(maxText);
 280     colourPanel.add(maxColour);
 281     this.add(jPanel3, java.awt.BorderLayout.CENTER);
 282     jPanel3.add(threshold);
 283     jPanel3.add(slider);
 284     jPanel3.add(thresholdValue);
 285     jPanel3.add(thresholdIsMin);
 286     this.add(jPanel1, java.awt.BorderLayout.SOUTH);
 287     this.add(jPanel2, java.awt.BorderLayout.NORTH);
 288   }
 289
 290   JLabel minText = new JLabel();
 291
 292   JLabel maxText = new JLabel();
 293
 294   JPanel minColour = new JPanel();
 295
 296   JPanel maxColour = new JPanel();
 297
 298   JPanel colourPanel = new JPanel();
 299
 300   JPanel jPanel1 = new JPanel();
 301
 302   JPanel jPanel2 = new JPanel();
 303
 304   BorderLayout borderLayout1 = new BorderLayout();
 305
 306   JComboBox threshold = new JComboBox();
 307
 308   FlowLayout flowLayout1 = new FlowLayout();
 309
 310   JPanel jPanel3 = new JPanel();
 311
 312   FlowLayout flowLayout2 = new FlowLayout();
 313
 314   JSlider slider = new JSlider();
 315
 316   JTextField thresholdValue = new JTextField(20);
 317
 318   // TODO implement GUI for tolower flag
 319   // JCheckBox toLower = new JCheckBox();
 320
 321   JCheckBox thresholdIsMin = new JCheckBox();
 322
 323   JCheckBox colourByLabel = new JCheckBox();
 324
 325   private GraphLine threshline;
 326
 327   private Color oldmaxColour;
 328
 329   private Color oldminColour;
 330
 331   public void minColour_actionPerformed()
 332   {
 333     Color col = JColorChooser.showDialog(this,
 334             MessageManager.getString("label.select_colour_minimum_value"), minColour.getBackground());
 335     if (col != null)
 336     {
 337       minColour.setBackground(col);
 338       minColour.setForeground(col);
 339     }
 340     minColour.repaint();
 341     changeColour();
 342   }
 343
 344   public void maxColour_actionPerformed()
 345   {
 346     Color col = JColorChooser.showDialog(this,
 347             MessageManager.getString("label.select_colour_maximum_value"), maxColour.getBackground());
 348     if (col != null)
 349     {
 350       maxColour.setBackground(col);
 351       maxColour.setForeground(col);
 352     }
 353     maxColour.repaint();
 354     changeColour();
 355   }
 356
 357   void changeColour()
 358   {
 359     // Check if combobox is still adjusting
 360     if (adjusting)
 361     {
 362       return;
 363     }
 364
 365     int aboveThreshold = AnnotationColourGradient.NO_THRESHOLD;
 366     if (threshold.getSelectedIndex()==1)
 367     {
 368       aboveThreshold = AnnotationColourGradient.ABOVE_THRESHOLD;
 369     }
 370     else if (threshold.getSelectedIndex()==2)
 371     {
 372       aboveThreshold = AnnotationColourGradient.BELOW_THRESHOLD;
 373     }
 374
 375     slider.setEnabled(true);
 376     thresholdValue.setEnabled(true);
 377
 378     GraduatedColor acg;
 379     if (cs.isColourByLabel())
 380     {
 381       acg = new GraduatedColor(oldminColour, oldmaxColour, min, max);
 382     }
 383     else
 384     {
 385       acg = new GraduatedColor(oldminColour = minColour.getBackground(),
 386               oldmaxColour = maxColour.getBackground(), min, max);
 387
 388     }
 389
 390     if (aboveThreshold == AnnotationColourGradient.NO_THRESHOLD)
 391     {
 392       slider.setEnabled(false);
 393       thresholdValue.setEnabled(false);
 394       thresholdValue.setText("");
 395       thresholdIsMin.setEnabled(false);
 396     }
 397     else if (aboveThreshold != AnnotationColourGradient.NO_THRESHOLD
 398             && threshline == null)
 399     {
 400       // todo visual indication of feature threshold
 401       threshline = new jalview.datamodel.GraphLine((max - min) / 2f,
 402               "Threshold", Color.black);
 403     }
 404
 405     if (aboveThreshold != AnnotationColourGradient.NO_THRESHOLD)
 406     {
 407       adjusting = true;
 408       acg.setThresh(threshline.value);
 409
 410       float range = max * 1000f - min * 1000f;
 411
 412       slider.setMinimum((int) (min * 1000));
 413       slider.setMaximum((int) (max * 1000));
 414       slider.setValue((int) (threshline.value * 1000));
 415       thresholdValue.setText(threshline.value + "");
 416       slider.setMajorTickSpacing((int) (range / 10f));
 417       slider.setEnabled(true);
 418       thresholdValue.setEnabled(true);
 419       thresholdIsMin.setEnabled(!colourByLabel.isSelected());
 420       adjusting = false;
 421     }
 422
 423     acg.setThreshType(aboveThreshold);
 424     if (thresholdIsMin.isSelected()
 425             && aboveThreshold != AnnotationColourGradient.NO_THRESHOLD)
 426     {
 427       acg.setAutoScaled(false);
 428       if (aboveThreshold == AnnotationColourGradient.ABOVE_THRESHOLD)
 429       {
 430         acg = new GraduatedColor(acg, threshline.value, max);
 431       }
 432       else
 433       {
 434         acg = new GraduatedColor(acg, min, threshline.value);
 435       }
 436     }
 437     else
 438     {
 439       acg.setAutoScaled(true);
 440     }
 441     acg.setColourByLabel(colourByLabel.isSelected());
 442     if (acg.isColourByLabel())
 443     {
 444       maxColour.setEnabled(false);
 445       minColour.setEnabled(false);
 446       maxColour.setBackground(this.getBackground());
 447       maxColour.setForeground(this.getBackground());
 448       minColour.setBackground(this.getBackground());
 449       minColour.setForeground(this.getBackground());
 450
 451     }
 452     else
 453     {
 454       maxColour.setEnabled(true);
 455       minColour.setEnabled(true);
 456       maxColour.setBackground(oldmaxColour);
 457       minColour.setBackground(oldminColour);
 458       maxColour.setForeground(oldmaxColour);
 459       minColour.setForeground(oldminColour);
 460     }
 461     fr.featureColours.put(type, acg);
 462     cs = acg;
 463     ap.paintAlignment(false);
 464   }
 465
 466   protected void raiseClosed()
 467   {
 468     if (this.colourEditor != null)
 469     {
 470       colourEditor.actionPerformed(new ActionEvent(this, 0, "CLOSED"));
 471     }
 472   }
 473
 474   public void okPressed()
 475   {
 476     changeColour();
 477   }
 478
 479   public void cancelPressed()
 480   {
 481     reset();
 482   }
 483
 484   void reset()
 485   {
 486     fr.featureColours.put(type, oldcs);
 487     ap.paintAlignment(false);
 488     cs = null;
 489   }
 490
 491   public void thresholdCheck_actionPerformed(ActionEvent e)
 492   {
 493     changeColour();
 494   }
 495
 496   public void annotations_actionPerformed(ActionEvent e)
 497   {
 498     changeColour();
 499   }
 500
 501   public void threshold_actionPerformed(ActionEvent e)
 502   {
 503     changeColour();
 504   }
 505
 506   public void thresholdValue_actionPerformed(ActionEvent e)
 507   {
 508     try
 509     {
 510       float f = Float.parseFloat(thresholdValue.getText());
 511       slider.setValue((int) (f * 1000));
 512       threshline.value = f;
 513     } catch (NumberFormatException ex)
 514     {
 515     }
 516   }
 517
 518   public void valueChanged()
 519   {
 520     threshline.value = (float) slider.getValue() / 1000f;
 521     cs.setThresh(threshline.value);
 522     changeColour();
 523     ap.paintAlignment(false);
 524   }
 525
 526   public void thresholdIsMin_actionPerformed(ActionEvent actionEvent)
 527   {
 528     changeColour();
 529   }
 530
 531   public void colourByLabel_actionPerformed(ActionEvent actionEvent)
 532   {
 533     changeColour();
 534   }
 535
 536   ActionListener colourEditor = null;
 537
 538   public void addActionListener(ActionListener graduatedColorEditor)
 539   {
 540     if (colourEditor != null)
 541     {
 542       System.err
 543               .println("IMPLEMENTATION ISSUE: overwriting action listener for FeatureColourChooser");
 544     }
 545     colourEditor = graduatedColorEditor;
 546   }
 547
 548 }