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.
21 package jalview.appletgui;
23 import jalview.datamodel.SequenceGroup;
24 import jalview.schemes.CollectionColourSchemeI;
25 import jalview.util.MessageManager;
27 import java.awt.BorderLayout;
28 import java.awt.Button;
29 import java.awt.Checkbox;
30 import java.awt.Color;
31 import java.awt.FlowLayout;
32 import java.awt.Frame;
33 import java.awt.Label;
34 import java.awt.Panel;
35 import java.awt.Scrollbar;
36 import java.awt.TextField;
37 import java.awt.event.ActionEvent;
38 import java.awt.event.ActionListener;
39 import java.awt.event.AdjustmentEvent;
40 import java.awt.event.AdjustmentListener;
41 import java.awt.event.MouseEvent;
42 import java.awt.event.MouseListener;
43 import java.awt.event.WindowAdapter;
44 import java.awt.event.WindowEvent;
45 import java.util.Iterator;
47 public class SliderPanel extends Panel implements ActionListener,
48 AdjustmentListener, MouseListener
52 boolean forConservation = true;
54 CollectionColourSchemeI cs;
56 static Frame conservationSlider;
58 static Frame PIDSlider;
60 public static int setConservationSlider(AlignmentPanel ap,
61 CollectionColourSchemeI collectionColourSchemeI, String source)
63 SliderPanel sp = null;
65 if (conservationSlider == null)
67 sp = new SliderPanel(ap,
68 collectionColourSchemeI.getConservationInc(), true,
69 collectionColourSchemeI);
70 conservationSlider = new Frame();
71 conservationSlider.add(sp);
75 sp = (SliderPanel) conservationSlider.getComponent(0);
76 sp.cs = collectionColourSchemeI;
80 .setTitle(MessageManager.formatMessage(
81 "label.conservation_colour_increment",
82 new String[] { source }));
83 if (ap.av.getAlignment().getGroups() != null)
85 sp.setAllGroupsCheckEnabled(true);
89 sp.setAllGroupsCheckEnabled(false);
95 public static void showConservationSlider()
99 PIDSlider.setVisible(false);
101 } catch (Exception ex)
105 if (!conservationSlider.isVisible())
107 jalview.bin.JalviewLite.addFrame(conservationSlider,
108 conservationSlider.getTitle(), 420, 100);
109 conservationSlider.addWindowListener(new WindowAdapter()
112 public void windowClosing(WindowEvent e)
114 conservationSlider = null;
122 public static int setPIDSliderSource(AlignmentPanel ap,
123 CollectionColourSchemeI collectionColourSchemeI, String source)
125 SliderPanel pid = null;
126 if (PIDSlider == null)
128 pid = new SliderPanel(ap, 50, false, collectionColourSchemeI);
129 PIDSlider = new Frame();
134 pid = (SliderPanel) PIDSlider.getComponent(0);
135 pid.cs = collectionColourSchemeI;
138 .setTitle(MessageManager.formatMessage(
139 "label.percentage_identity_threshold",
140 new String[] { source }));
142 if (ap.av.getAlignment().getGroups() != null)
144 pid.setAllGroupsCheckEnabled(true);
148 pid.setAllGroupsCheckEnabled(false);
151 return pid.getValue();
155 public static void showPIDSlider()
159 conservationSlider.setVisible(false);
160 conservationSlider = null;
161 } catch (Exception ex)
165 if (!PIDSlider.isVisible())
167 jalview.bin.JalviewLite.addFrame(PIDSlider, PIDSlider.getTitle(),
169 PIDSlider.addWindowListener(new WindowAdapter()
172 public void windowClosing(WindowEvent e)
181 public SliderPanel(AlignmentPanel ap, int value, boolean forConserve,
182 CollectionColourSchemeI collectionColourSchemeI)
187 } catch (Exception e)
192 this.cs = collectionColourSchemeI;
193 forConservation = forConserve;
194 undoButton.setVisible(false);
195 applyButton.setVisible(false);
198 label.setText(MessageManager
199 .getString("label.modify_conservation_visibility"));
200 slider.setMinimum(0);
201 slider.setMaximum(50 + slider.getVisibleAmount());
202 slider.setUnitIncrement(1);
206 label.setText(MessageManager
207 .getString("label.colour_residues_above_occurence"));
208 slider.setMinimum(0);
209 slider.setMaximum(100 + slider.getVisibleAmount());
210 slider.setBlockIncrement(1);
213 slider.addAdjustmentListener(this);
214 slider.addMouseListener(this);
216 slider.setValue(value);
217 valueField.setText(value + "");
220 public void valueChanged(int i)
227 CollectionColourSchemeI toChange = cs;
228 Iterator<SequenceGroup> allGroups = null;
230 if (allGroupsCheck.getState())
232 allGroups = ap.av.getAlignment().getGroups().listIterator();
235 while (toChange != null)
239 toChange.setConservationInc(i);
243 toChange.setThreshold(i, ap.av.isIgnoreGapsConsensus());
245 if (allGroups != null && allGroups.hasNext())
247 while ((toChange = allGroups.next().cs) == null
248 && allGroups.hasNext())
259 ap.seqPanel.seqCanvas.repaint();
263 public void setAllGroupsCheckEnabled(boolean b)
265 allGroupsCheck.setEnabled(b);
269 public void actionPerformed(ActionEvent evt)
271 if (evt.getSource() == applyButton)
273 applyButton_actionPerformed();
275 else if (evt.getSource() == undoButton)
277 undoButton_actionPerformed();
279 else if (evt.getSource() == valueField)
281 valueField_actionPerformed();
286 public void adjustmentValueChanged(AdjustmentEvent evt)
288 valueField.setText(slider.getValue() + "");
289 valueChanged(slider.getValue());
292 public void valueField_actionPerformed()
296 int i = Integer.parseInt(valueField.getText());
298 } catch (Exception ex)
300 valueField.setText(slider.getValue() + "");
304 public void setValue(int value)
306 slider.setValue(value);
309 public int getValue()
311 return Integer.parseInt(valueField.getText());
314 // this is used for conservation colours, PID colours and redundancy threshold
315 protected Scrollbar slider = new Scrollbar();
317 protected TextField valueField = new TextField();
319 protected Label label = new Label();
321 Panel jPanel1 = new Panel();
323 Panel jPanel2 = new Panel();
325 protected Button applyButton = new Button();
327 protected Button undoButton = new Button();
329 FlowLayout flowLayout1 = new FlowLayout();
331 protected Checkbox allGroupsCheck = new Checkbox();
333 BorderLayout borderLayout1 = new BorderLayout();
335 BorderLayout borderLayout2 = new BorderLayout();
337 FlowLayout flowLayout2 = new FlowLayout();
339 private void jbInit() throws Exception
341 this.setLayout(borderLayout2);
343 // slider.setMajorTickSpacing(10);
344 // slider.setMinorTickSpacing(1);
345 // slider.setPaintTicks(true);
346 slider.setBackground(Color.white);
347 slider.setFont(new java.awt.Font("Verdana", 0, 11));
348 slider.setOrientation(0);
349 valueField.setFont(new java.awt.Font("Verdana", 0, 11));
350 valueField.setText(" ");
351 valueField.addActionListener(this);
352 valueField.setColumns(3);
353 label.setFont(new java.awt.Font("Verdana", 0, 11));
354 label.setText(MessageManager.getString("label.set_this_label_text"));
355 jPanel1.setLayout(borderLayout1);
356 jPanel2.setLayout(flowLayout1);
357 applyButton.setFont(new java.awt.Font("Verdana", 0, 11));
358 applyButton.setLabel(MessageManager.getString("action.apply"));
359 applyButton.addActionListener(this);
360 undoButton.setEnabled(false);
361 undoButton.setFont(new java.awt.Font("Verdana", 0, 11));
362 undoButton.setLabel(MessageManager.getString("action.undo"));
363 undoButton.addActionListener(this);
364 allGroupsCheck.setEnabled(false);
365 allGroupsCheck.setFont(new java.awt.Font("Verdana", 0, 11));
366 allGroupsCheck.setLabel(MessageManager
367 .getString("action.apply_threshold_all_groups"));
368 allGroupsCheck.setName(MessageManager
369 .getString("action.apply_all_groups"));
370 this.setBackground(Color.white);
371 this.setForeground(Color.black);
372 jPanel2.add(label, null);
373 jPanel2.add(applyButton, null);
374 jPanel2.add(undoButton, null);
375 jPanel2.add(allGroupsCheck);
376 jPanel1.add(valueField, java.awt.BorderLayout.EAST);
377 jPanel1.add(slider, java.awt.BorderLayout.CENTER);
378 this.add(jPanel1, java.awt.BorderLayout.SOUTH);
379 this.add(jPanel2, java.awt.BorderLayout.CENTER);
382 protected void applyButton_actionPerformed()
386 protected void undoButton_actionPerformed()
391 public void mousePressed(MouseEvent evt)
396 public void mouseReleased(MouseEvent evt)
398 ap.paintAlignment(true);
402 public void mouseClicked(MouseEvent evt)
407 public void mouseEntered(MouseEvent evt)
412 public void mouseExited(MouseEvent evt)