src/jalview/gui/AnnotationColourChooser.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
   3  * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
   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  */
  18 package jalview.gui;
  19
  20 import java.util.*;
  21
  22 import java.awt.*;
  23 import java.awt.event.*;
  24 import javax.swing.*;
  25 import javax.swing.event.*;
  26
  27 import jalview.datamodel.*;
  28 import jalview.schemes.*;
  29 import java.awt.Dimension;
  30
  31 public class AnnotationColourChooser extends JPanel
  32 {
  33   JInternalFrame frame;
  34
  35   AlignViewport av;
  36
  37   AlignmentPanel ap;
  38
  39   ColourSchemeI oldcs;
  40
  41   Hashtable oldgroupColours;
  42
  43   jalview.datamodel.AlignmentAnnotation currentAnnotation;
  44
  45   boolean adjusting = false;
  46
  47   public AnnotationColourChooser(AlignViewport av, final AlignmentPanel ap)
  48   {
  49     oldcs = av.getGlobalColourScheme();
  50     if (av.alignment.getGroups() != null)
  51     {
  52       oldgroupColours = new Hashtable();
  53       Vector allGroups = ap.av.alignment.getGroups();
  54       SequenceGroup sg;
  55       for (int g = 0; g < allGroups.size(); g++)
  56       {
  57         sg = (SequenceGroup) allGroups.get(g);
  58         if (sg.cs != null)
  59         {
  60           oldgroupColours.put(sg, sg.cs);
  61         }
  62       }
  63     }
  64     this.av = av;
  65     this.ap = ap;
  66     frame = new JInternalFrame();
  67     frame.setContentPane(this);
  68     frame.setLayer(JLayeredPane.PALETTE_LAYER);
  69     Desktop.addInternalFrame(frame, "Colour by Annotation", 480, 145);
  70
  71     slider.addChangeListener(new ChangeListener()
  72     {
  73       public void stateChanged(ChangeEvent evt)
  74       {
  75         if (!adjusting)
  76         {
  77           thresholdValue.setText(((float) slider.getValue() / 1000f) + "");
  78           valueChanged();
  79         }
  80       }
  81     });
  82     slider.addMouseListener(new MouseAdapter()
  83     {
  84       public void mouseReleased(MouseEvent evt)
  85       {
  86         ap.paintAlignment(true);
  87       }
  88     });
  89
  90     if (av.alignment.getAlignmentAnnotation() == null)
  91     {
  92       return;
  93     }
  94
  95     if (oldcs instanceof AnnotationColourGradient)
  96     {
  97       AnnotationColourGradient acg = (AnnotationColourGradient) oldcs;
  98       minColour.setBackground(acg.getMinColour());
  99       maxColour.setBackground(acg.getMaxColour());
 100     }
 101     else
 102     {
 103       minColour.setBackground(Color.orange);
 104       maxColour.setBackground(Color.red);
 105     }
 106
 107     adjusting = true;
 108     Vector list = new Vector();
 109     int index = 1;
 110     for (int i = 0; i < av.alignment.getAlignmentAnnotation().length; i++)
 111     {
 112       String label = av.alignment.getAlignmentAnnotation()[i].label;
 113       if (!list.contains(label))
 114         list.addElement(label);
 115       else
 116         list.addElement(label + "_" + (index++));
 117     }
 118
 119     annotations = new JComboBox(list);
 120
 121     threshold.addItem("No Threshold");
 122     threshold.addItem("Above Threshold");
 123     threshold.addItem("Below Threshold");
 124
 125     try
 126     {
 127       jbInit();
 128     } catch (Exception ex)
 129     {
 130     }
 131
 132     adjusting = false;
 133
 134     changeColour();
 135
 136   }
 137
 138   public AnnotationColourChooser()
 139   {
 140     try
 141     {
 142       jbInit();
 143     } catch (Exception ex)
 144     {
 145       ex.printStackTrace();
 146     }
 147   }
 148
 149   private void jbInit() throws Exception
 150   {
 151     minColour.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
 152     minColour.setBorder(BorderFactory.createEtchedBorder());
 153     minColour.setPreferredSize(new Dimension(40, 20));
 154     minColour.setToolTipText("Minimum Colour");
 155     minColour.addMouseListener(new MouseAdapter()
 156     {
 157       public void mousePressed(MouseEvent e)
 158       {
 159         if (minColour.isEnabled())
 160         {
 161           minColour_actionPerformed();
 162         }
 163       }
 164     });
 165     maxColour.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
 166     maxColour.setBorder(BorderFactory.createEtchedBorder());
 167     maxColour.setPreferredSize(new Dimension(40, 20));
 168     maxColour.setToolTipText("Maximum Colour");
 169     maxColour.addMouseListener(new MouseAdapter()
 170     {
 171       public void mousePressed(MouseEvent e)
 172       {
 173         if (maxColour.isEnabled())
 174         {
 175           maxColour_actionPerformed();
 176         }
 177       }
 178     });
 179     ok.setOpaque(false);
 180     ok.setText("OK");
 181     ok.addActionListener(new ActionListener()
 182     {
 183       public void actionPerformed(ActionEvent e)
 184       {
 185         ok_actionPerformed(e);
 186       }
 187     });
 188     cancel.setOpaque(false);
 189     cancel.setText("Cancel");
 190     cancel.addActionListener(new ActionListener()
 191     {
 192       public void actionPerformed(ActionEvent e)
 193       {
 194         cancel_actionPerformed(e);
 195       }
 196     });
 197     this.setLayout(borderLayout1);
 198     jPanel2.setLayout(flowLayout1);
 199     annotations.addActionListener(new ActionListener()
 200     {
 201       public void actionPerformed(ActionEvent e)
 202       {
 203         annotations_actionPerformed(e);
 204       }
 205     });
 206     jPanel1.setBackground(Color.white);
 207     jPanel2.setBackground(Color.white);
 208     threshold.addActionListener(new ActionListener()
 209     {
 210       public void actionPerformed(ActionEvent e)
 211       {
 212         threshold_actionPerformed(e);
 213       }
 214     });
 215     jPanel3.setLayout(flowLayout2);
 216     thresholdValue.addActionListener(new ActionListener()
 217     {
 218       public void actionPerformed(ActionEvent e)
 219       {
 220         thresholdValue_actionPerformed(e);
 221       }
 222     });
 223     slider.setPaintLabels(false);
 224     slider.setPaintTicks(true);
 225     slider.setBackground(Color.white);
 226     slider.setEnabled(false);
 227     slider.setOpaque(false);
 228     slider.setPreferredSize(new Dimension(100, 32));
 229     thresholdValue.setEnabled(false);
 230     thresholdValue.setColumns(7);
 231     jPanel3.setBackground(Color.white);
 232     currentColours.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
 233     currentColours.setOpaque(false);
 234     currentColours.setText("Use Original Colours");
 235     currentColours.addActionListener(new ActionListener()
 236     {
 237       public void actionPerformed(ActionEvent e)
 238       {
 239         currentColours_actionPerformed(e);
 240       }
 241     });
 242     thresholdIsMin.setBackground(Color.white);
 243     thresholdIsMin.setText("Threshold is Min/Max");
 244     thresholdIsMin.addActionListener(new ActionListener()
 245     {
 246       public void actionPerformed(ActionEvent actionEvent)
 247       {
 248         thresholdIsMin_actionPerformed(actionEvent);
 249       }
 250     });
 251     jPanel1.add(ok);
 252     jPanel1.add(cancel);
 253     jPanel2.add(annotations);
 254     jPanel2.add(currentColours);
 255     jPanel2.add(minColour);
 256     jPanel2.add(maxColour);
 257     this.add(jPanel3, java.awt.BorderLayout.CENTER);
 258     jPanel3.add(threshold);
 259     jPanel3.add(slider);
 260     jPanel3.add(thresholdValue);
 261     jPanel3.add(thresholdIsMin);
 262     this.add(jPanel1, java.awt.BorderLayout.SOUTH);
 263     this.add(jPanel2, java.awt.BorderLayout.NORTH);
 264   }
 265
 266   JComboBox annotations;
 267
 268   JPanel minColour = new JPanel();
 269
 270   JPanel maxColour = new JPanel();
 271
 272   JButton ok = new JButton();
 273
 274   JButton cancel = new JButton();
 275
 276   JPanel jPanel1 = new JPanel();
 277
 278   JPanel jPanel2 = new JPanel();
 279
 280   BorderLayout borderLayout1 = new BorderLayout();
 281
 282   JComboBox threshold = new JComboBox();
 283
 284   FlowLayout flowLayout1 = new FlowLayout();
 285
 286   JPanel jPanel3 = new JPanel();
 287
 288   FlowLayout flowLayout2 = new FlowLayout();
 289
 290   JSlider slider = new JSlider();
 291
 292   JTextField thresholdValue = new JTextField(20);
 293
 294   JCheckBox currentColours = new JCheckBox();
 295
 296   JCheckBox thresholdIsMin = new JCheckBox();
 297
 298   public void minColour_actionPerformed()
 299   {
 300     Color col = JColorChooser.showDialog(this,
 301             "Select Colour for Minimum Value", minColour.getBackground());
 302     if (col != null)
 303     {
 304       minColour.setBackground(col);
 305     }
 306     minColour.repaint();
 307     changeColour();
 308   }
 309
 310   public void maxColour_actionPerformed()
 311   {
 312     Color col = JColorChooser.showDialog(this,
 313             "Select Colour for Maximum Value", maxColour.getBackground());
 314     if (col != null)
 315     {
 316       maxColour.setBackground(col);
 317     }
 318     maxColour.repaint();
 319     changeColour();
 320   }
 321
 322   void changeColour()
 323   {
 324     // Check if combobox is still adjusting
 325     if (adjusting)
 326     {
 327       return;
 328     }
 329
 330     currentAnnotation = av.alignment.getAlignmentAnnotation()[annotations
 331             .getSelectedIndex()];
 332
 333     int aboveThreshold = -1;
 334     if (threshold.getSelectedItem().equals("Above Threshold"))
 335     {
 336       aboveThreshold = AnnotationColourGradient.ABOVE_THRESHOLD;
 337     }
 338     else if (threshold.getSelectedItem().equals("Below Threshold"))
 339     {
 340       aboveThreshold = AnnotationColourGradient.BELOW_THRESHOLD;
 341     }
 342
 343     slider.setEnabled(true);
 344     thresholdValue.setEnabled(true);
 345
 346     if (aboveThreshold == AnnotationColourGradient.NO_THRESHOLD)
 347     {
 348       slider.setEnabled(false);
 349       thresholdValue.setEnabled(false);
 350       thresholdValue.setText("");
 351     }
 352     else if (aboveThreshold != AnnotationColourGradient.NO_THRESHOLD
 353             && currentAnnotation.threshold == null)
 354     {
 355       currentAnnotation
 356               .setThreshold(new jalview.datamodel.GraphLine(
 357                       (currentAnnotation.graphMax - currentAnnotation.graphMin) / 2f,
 358                       "Threshold", Color.black));
 359     }
 360
 361     if (aboveThreshold != AnnotationColourGradient.NO_THRESHOLD)
 362     {
 363       adjusting = true;
 364       float range = currentAnnotation.graphMax * 1000
 365               - currentAnnotation.graphMin * 1000;
 366
 367       slider.setMinimum((int) (currentAnnotation.graphMin * 1000));
 368       slider.setMaximum((int) (currentAnnotation.graphMax * 1000));
 369       slider.setValue((int) (currentAnnotation.threshold.value * 1000));
 370       thresholdValue.setText(currentAnnotation.threshold.value + "");
 371       slider.setMajorTickSpacing((int) (range / 10f));
 372       slider.setEnabled(true);
 373       thresholdValue.setEnabled(true);
 374       adjusting = false;
 375     }
 376
 377     AnnotationColourGradient acg = null;
 378     if (currentColours.isSelected())
 379     {
 380       acg = new AnnotationColourGradient(currentAnnotation, av
 381               .getGlobalColourScheme(), aboveThreshold);
 382     }
 383     else
 384     {
 385       acg = new AnnotationColourGradient(currentAnnotation, minColour
 386               .getBackground(), maxColour.getBackground(), aboveThreshold);
 387     }
 388
 389     if (currentAnnotation.graphMin == 0f
 390             && currentAnnotation.graphMax == 0f)
 391     {
 392       acg.predefinedColours = true;
 393     }
 394
 395     acg.thresholdIsMinMax = thresholdIsMin.isSelected();
 396
 397     av.setGlobalColourScheme(acg);
 398
 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
 407         if (sg.cs == null)
 408         {
 409           continue;
 410         }
 411
 412         if (currentColours.isSelected())
 413         {
 414           sg.cs = new AnnotationColourGradient(currentAnnotation, sg.cs,
 415                   aboveThreshold);
 416         }
 417         else
 418         {
 419           sg.cs = new AnnotationColourGradient(currentAnnotation, minColour
 420                   .getBackground(), maxColour.getBackground(),
 421                   aboveThreshold);
 422         }
 423
 424       }
 425     }
 426
 427     ap.paintAlignment(false);
 428   }
 429
 430   public void ok_actionPerformed(ActionEvent e)
 431   {
 432     changeColour();
 433     try
 434     {
 435       frame.setClosed(true);
 436     } catch (Exception ex)
 437     {
 438     }
 439   }
 440
 441   public void cancel_actionPerformed(ActionEvent e)
 442   {
 443     reset();
 444     try
 445     {
 446       frame.setClosed(true);
 447     } catch (Exception ex)
 448     {
 449     }
 450   }
 451
 452   void reset()
 453   {
 454     av.setGlobalColourScheme(oldcs);
 455     if (av.alignment.getGroups() != null)
 456     {
 457       Vector allGroups = ap.av.alignment.getGroups();
 458       SequenceGroup sg;
 459       for (int g = 0; g < allGroups.size(); g++)
 460       {
 461         sg = (SequenceGroup) allGroups.get(g);
 462         sg.cs = (ColourSchemeI) oldgroupColours.get(sg);
 463       }
 464     }
 465   }
 466
 467   public void thresholdCheck_actionPerformed(ActionEvent e)
 468   {
 469     changeColour();
 470   }
 471
 472   public void annotations_actionPerformed(ActionEvent e)
 473   {
 474     changeColour();
 475   }
 476
 477   public void threshold_actionPerformed(ActionEvent e)
 478   {
 479     changeColour();
 480   }
 481
 482   public void thresholdValue_actionPerformed(ActionEvent e)
 483   {
 484     try
 485     {
 486       float f = Float.parseFloat(thresholdValue.getText());
 487       slider.setValue((int) (f * 1000));
 488     } catch (NumberFormatException ex)
 489     {
 490     }
 491   }
 492
 493   public void valueChanged()
 494   {
 495     if (currentColours.isSelected()
 496             && !(av.getGlobalColourScheme() instanceof AnnotationColourGradient))
 497     {
 498       changeColour();
 499     }
 500
 501     currentAnnotation.threshold.value = (float) slider.getValue() / 1000f;
 502     ap.paintAlignment(false);
 503   }
 504
 505   public void currentColours_actionPerformed(ActionEvent e)
 506   {
 507     if (currentColours.isSelected())
 508     {
 509       reset();
 510     }
 511
 512     maxColour.setEnabled(!currentColours.isSelected());
 513     minColour.setEnabled(!currentColours.isSelected());
 514
 515     changeColour();
 516   }
 517
 518   public void thresholdIsMin_actionPerformed(ActionEvent actionEvent)
 519   {
 520     changeColour();
 521   }
 522
 523 }