2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
5 * This file is part of Jalview.
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
10 * of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License
18 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 * The Jalview Authors are detailed in the 'AUTHORS' file.
23 import jalview.analysis.Conservation;
24 import jalview.datamodel.SequenceGroup;
25 import jalview.jbgui.GSliderPanel;
26 import jalview.renderer.ResidueShaderI;
27 import jalview.util.MessageManager;
29 import java.awt.event.ActionEvent;
30 import java.awt.event.MouseAdapter;
31 import java.awt.event.MouseEvent;
32 import java.beans.PropertyVetoException;
33 import java.util.List;
35 import javax.swing.JInternalFrame;
36 import javax.swing.JLayeredPane;
37 import javax.swing.event.ChangeEvent;
38 import javax.swing.event.ChangeListener;
39 import javax.swing.event.InternalFrameAdapter;
40 import javax.swing.event.InternalFrameEvent;
48 public class SliderPanel extends GSliderPanel
50 private static final String BACKGROUND = "Background";
52 static JInternalFrame conservationSlider;
54 static JInternalFrame PIDSlider;
58 boolean forConservation = true;
63 * Returns the currently displayed slider panel (or null if none).
67 public static SliderPanel getSliderPanel()
69 if (conservationSlider != null && conservationSlider.isVisible())
71 return (SliderPanel) conservationSlider.getContentPane();
73 if (PIDSlider != null && PIDSlider.isVisible())
75 return (SliderPanel) PIDSlider.getContentPane();
81 * Creates a new SliderPanel object.
92 public SliderPanel(final AlignmentPanel ap, int value,
93 boolean forConserve, ResidueShaderI scheme)
97 forConservation = forConserve;
98 undoButton.setVisible(false);
99 applyButton.setVisible(false);
103 label.setText(MessageManager.getString(
104 "label.enter_value_increase_conservation_visibility"));
105 slider.setMinimum(0);
106 slider.setMaximum(100);
110 label.setText(MessageManager.getString(
111 "label.enter_percentage_identity_above_which_colour_residues"));
112 slider.setMinimum(0);
113 slider.setMaximum(100);
116 slider.addChangeListener(new ChangeListener()
119 public void stateChanged(ChangeEvent evt)
121 valueField.setText(slider.getValue() + "");
122 valueChanged(slider.getValue());
126 slider.addMouseListener(new MouseAdapter()
129 public void mouseReleased(MouseEvent evt)
131 ap.paintAlignment(true, true);
135 slider.setValue(value);
136 valueField.setText(value + "");
140 * Method to 'set focus' of the Conservation slider panel
143 * the panel to repaint on change of slider
145 * the colour scheme to update on change of slider
147 * a text description for the panel's title
151 public static int setConservationSlider(AlignmentPanel ap,
152 ResidueShaderI rs, String source)
154 SliderPanel sliderPanel = null;
156 if (conservationSlider == null)
158 sliderPanel = new SliderPanel(ap, rs.getConservationInc(), true, rs);
159 conservationSlider = new JInternalFrame();
160 conservationSlider.setContentPane(sliderPanel);
161 conservationSlider.setLayer(JLayeredPane.PALETTE_LAYER);
165 sliderPanel = (SliderPanel) conservationSlider.getContentPane();
166 sliderPanel.valueField
167 .setText(String.valueOf(rs.getConservationInc()));
170 sliderPanel.slider.setValue(rs.getConservationInc());
173 conservationSlider.setTitle(MessageManager.formatMessage(
174 "label.conservation_colour_increment", new String[]
175 { source == null ? BACKGROUND : source }));
177 List<SequenceGroup> groups = ap.av.getAlignment().getGroups();
178 if (groups != null && !groups.isEmpty())
180 sliderPanel.setAllGroupsCheckEnabled(true);
184 sliderPanel.setAllGroupsCheckEnabled(false);
187 return sliderPanel.getValue();
191 * Hides the PID slider panel if it is shown
193 public static void hidePIDSlider()
195 if (PIDSlider != null)
199 PIDSlider.setClosed(true);
201 } catch (PropertyVetoException ex)
208 * Hides the conservation slider panel if it is shown
210 public static void hideConservationSlider()
212 if (conservationSlider != null)
216 conservationSlider.setClosed(true);
217 conservationSlider = null;
218 } catch (PropertyVetoException ex)
227 public static void showConservationSlider()
231 if (!conservationSlider.isVisible())
233 Desktop.addInternalFrame(conservationSlider,
234 conservationSlider.getTitle(), 420, 90, false);
235 conservationSlider.addInternalFrameListener(new InternalFrameAdapter()
238 public void internalFrameClosed(InternalFrameEvent e)
240 conservationSlider = null;
243 conservationSlider.setLayer(JLayeredPane.PALETTE_LAYER);
248 * Method to 'set focus' of the PID slider panel
251 * the panel to repaint on change of slider
253 * the colour scheme to update on change of slider
255 * a text description for the panel's title
259 public static int setPIDSliderSource(AlignmentPanel ap, ResidueShaderI rs,
262 int threshold = rs.getThreshold();
264 SliderPanel sliderPanel = null;
266 if (PIDSlider == null)
268 sliderPanel = new SliderPanel(ap, threshold, false, rs);
269 PIDSlider = new JInternalFrame();
270 PIDSlider.setContentPane(sliderPanel);
271 PIDSlider.setLayer(JLayeredPane.PALETTE_LAYER);
275 sliderPanel = (SliderPanel) PIDSlider.getContentPane();
278 sliderPanel.valueField.setText(String.valueOf(rs.getThreshold()));
279 sliderPanel.slider.setValue(rs.getThreshold());
282 PIDSlider.setTitle(MessageManager.formatMessage(
283 "label.percentage_identity_threshold", new String[]
284 { source == null ? BACKGROUND : source }));
286 if (ap.av.getAlignment().getGroups() != null)
288 sliderPanel.setAllGroupsCheckEnabled(true);
292 sliderPanel.setAllGroupsCheckEnabled(false);
295 return sliderPanel.getValue();
303 public static JInternalFrame showPIDSlider()
305 hideConservationSlider();
307 if (!PIDSlider.isVisible())
309 Desktop.addInternalFrame(PIDSlider, PIDSlider.getTitle(), 420, 90,
311 PIDSlider.setLayer(JLayeredPane.PALETTE_LAYER);
312 PIDSlider.addInternalFrameListener(new InternalFrameAdapter()
315 public void internalFrameClosed(InternalFrameEvent e)
320 PIDSlider.setLayer(JLayeredPane.PALETTE_LAYER);
326 * Updates the colour scheme with the current (identity threshold or
327 * conservation) percentage value. Also updates all groups if 'apply to all
328 * groups' is selected.
332 public void valueChanged(int percent)
334 if (!forConservation)
336 ap.av.setThreshold(percent);
338 updateColourScheme(percent, cs, null);
340 if (allGroupsCheck.isSelected())
342 List<SequenceGroup> groups = ap.av.getAlignment().getGroups();
343 for (SequenceGroup sg : groups)
345 updateColourScheme(percent, sg.getGroupColourScheme(), sg);
349 ap.getSeqPanel().seqCanvas.repaint();
353 * Updates the colour scheme (if not null) with the current (identity
354 * threshold or conservation) percentage value
360 protected void updateColourScheme(int percent, ResidueShaderI scheme,
369 if (!scheme.conservationApplied() && sg != null)
372 * first time the colour scheme has had Conservation shading applied
373 * - compute conservation
375 Conservation c = new Conservation("Group", sg.getSequences(null),
376 sg.getStartRes(), sg.getEndRes());
378 c.verdict(false, ap.av.getConsPercGaps());
379 sg.cs.setConservation(c);
382 scheme.setConservationApplied(true);
383 scheme.setConservationInc(percent);
387 scheme.setThreshold(percent, ap.av.isIgnoreGapsConsensus());
397 public void setAllGroupsCheckEnabled(boolean b)
399 allGroupsCheck.setEnabled(b);
409 public void valueField_actionPerformed()
413 int i = Integer.parseInt(valueField.getText());
415 } catch (NumberFormatException ex)
417 valueField.setText(slider.getValue() + "");
427 public void setValue(int value)
429 slider.setValue(value);
435 * @return DOCUMENT ME!
437 public int getValue()
439 return Integer.parseInt(valueField.getText());
443 public void slider_mouseReleased(MouseEvent e)
445 if (ap.overviewPanel != null)
447 ap.overviewPanel.updateOverviewImage();
451 public static int getConservationValue()
453 return getValue(conservationSlider);
456 static int getValue(JInternalFrame slider)
458 return slider == null ? 0
459 : ((SliderPanel) slider.getContentPane()).getValue();
462 public static int getPIDValue()
464 return getValue(PIDSlider);
468 * Answers true if the SliderPanel is for Conservation, false if it is for PID
473 public boolean isForConservation()
475 return forConservation;
479 * Answers the title for the slider panel; this may include 'Background' if
480 * for the alignment, or the group id if for a group
484 public String getTitle()
487 if (isForConservation())
489 if (conservationSlider != null)
491 title = conservationSlider.getTitle();
494 else if (PIDSlider != null)
496 title = PIDSlider.getTitle();
502 protected void allGroupsCheck_actionPerformed(ActionEvent e)
504 if (allGroupsCheck.isSelected())
506 valueChanged(slider.getValue());