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.datamodel.AlignmentAnnotation;
24 import jalview.datamodel.GraphLine;
25 import jalview.schemes.AnnotationColourGradient;
26 import jalview.util.MessageManager;
28 import java.awt.Color;
29 import java.awt.Dimension;
30 import java.awt.event.ActionEvent;
31 import java.awt.event.ActionListener;
32 import java.awt.event.FocusAdapter;
33 import java.awt.event.FocusEvent;
34 import java.awt.event.ItemEvent;
35 import java.awt.event.ItemListener;
36 import java.awt.event.MouseAdapter;
37 import java.awt.event.MouseEvent;
38 import java.util.HashMap;
40 import java.util.Vector;
42 import javax.swing.JButton;
43 import javax.swing.JCheckBox;
44 import javax.swing.JComboBox;
45 import javax.swing.JInternalFrame;
46 import javax.swing.JPanel;
47 import javax.swing.JSlider;
48 import javax.swing.JTextField;
49 import javax.swing.event.ChangeEvent;
50 import javax.swing.event.ChangeListener;
52 @SuppressWarnings("serial")
53 public abstract class AnnotationRowFilter extends JPanel
55 protected AlignViewport av;
57 protected AlignmentPanel ap;
59 protected int[] annmap;
61 protected boolean adjusting = false;
63 protected JCheckBox seqAssociated = new JCheckBox();
65 protected JCheckBox percentThreshold = new JCheckBox();
67 protected JSlider slider = new JSlider();
69 protected JTextField thresholdValue = new JTextField(20);
71 protected JInternalFrame frame;
73 protected JButton ok = new JButton();
75 protected JButton cancel = new JButton();
78 * enabled if the user is dragging the slider - try to keep updates to a
81 protected boolean sliderDragging = false;
83 protected JComboBox<String> threshold = new JComboBox<String>();
85 protected JComboBox<String> annotations;
88 * map from annotation to its menu item display label
89 * - so we know which item to pre-select on restore
91 private Map<AlignmentAnnotation, String> annotationLabels;
93 private AlignmentAnnotation currentAnnotation;
101 public AnnotationRowFilter(AlignViewport viewport, final AlignmentPanel alignPanel)
104 this.ap = alignPanel;
105 thresholdValue.addFocusListener(new FocusAdapter()
108 public void focusLost(FocusEvent e)
110 thresholdValue_actionPerformed();
115 protected void addSliderChangeListener()
118 slider.addChangeListener(new ChangeListener()
121 public void stateChanged(ChangeEvent evt)
125 setThresholdValueText();
126 valueChanged(!sliderDragging);
132 protected void setThresholdValueText()
135 if (percentThreshold.isSelected())
137 thresholdValue.setText("" + (slider.getValue() - slider.getMinimum())
138 * 100f / (slider.getMaximum() - slider.getMinimum()));
142 thresholdValue.setText((slider.getValue() / 1000f) + "");
146 protected void addSliderMouseListeners()
149 slider.addMouseListener(new MouseAdapter()
152 public void mousePressed(MouseEvent e)
154 sliderDragging = true;
155 super.mousePressed(e);
159 public void mouseDragged(MouseEvent e)
161 sliderDragging = true;
162 super.mouseDragged(e);
166 public void mouseReleased(MouseEvent evt)
170 sliderDragging = false;
173 ap.paintAlignment(true);
179 * Builds and returns a list of menu items (display text) for choice of
180 * annotation. Also builds maps between annotations, their positions in the
181 * list, and their display labels in the list.
183 * @param isSeqAssociated
186 public Vector<String> getAnnotationItems(boolean isSeqAssociated)
188 annotationLabels = new HashMap<AlignmentAnnotation, String>();
190 Vector<String> list = new Vector<String>();
192 int[] anmap = new int[av.getAlignment().getAlignmentAnnotation().length];
193 seqAssociated.setEnabled(false);
194 for (int i = 0; i < av.getAlignment().getAlignmentAnnotation().length; i++)
196 AlignmentAnnotation annotation = av.getAlignment()
197 .getAlignmentAnnotation()[i];
198 if (annotation.sequenceRef == null)
207 seqAssociated.setEnabled(true);
209 String label = annotation.label;
210 // add associated sequence ID if available
211 if (!isSeqAssociated && annotation.sequenceRef != null)
213 label = label + "_" + annotation.sequenceRef.getName();
216 if (!list.contains(label))
218 anmap[list.size()] = i;
220 annotationLabels.put(annotation, label);
224 if (!isSeqAssociated)
226 anmap[list.size()] = i;
227 label = label + "_" + (index++);
229 annotationLabels.put(annotation, label);
233 this.annmap = new int[list.size()];
234 System.arraycopy(anmap, 0, this.annmap, 0, this.annmap.length);
238 protected int getSelectedThresholdItem(int indexValue)
240 int selectedThresholdItem = -1;
243 selectedThresholdItem = AnnotationColourGradient.ABOVE_THRESHOLD;
245 else if (indexValue == 2)
247 selectedThresholdItem = AnnotationColourGradient.BELOW_THRESHOLD;
249 return selectedThresholdItem;
252 public void ok_actionPerformed()
256 frame.setClosed(true);
257 } catch (Exception ex)
262 public void cancel_actionPerformed()
265 ap.paintAlignment(true);
268 frame.setClosed(true);
269 } catch (Exception ex)
274 protected void thresholdCheck_actionPerformed()
279 protected void selectedAnnotationChanged()
284 protected void threshold_actionPerformed()
289 protected void thresholdValue_actionPerformed()
293 float f = Float.parseFloat(thresholdValue.getText());
294 if (percentThreshold.isEnabled())
296 slider.setValue(slider.getMinimum()
297 + ((int) ((f / 100f) * (slider.getMaximum() - slider
302 slider.setValue((int) (f * 1000));
305 } catch (NumberFormatException ex)
310 protected void percentageValue_actionPerformed()
312 setThresholdValueText();
315 protected void thresholdIsMin_actionPerformed()
320 protected void populateThresholdComboBox(JComboBox<String> thresh)
322 thresh.addItem(MessageManager
323 .getString("label.threshold_feature_no_threshold"));
324 thresh.addItem(MessageManager
325 .getString("label.threshold_feature_above_threshold"));
326 thresh.addItem(MessageManager
327 .getString("label.threshold_feature_below_threshold"));
331 * Rebuilds the drop-down list of annotations to choose from when the 'per
332 * sequence only' checkbox is checked or unchecked.
336 protected void seqAssociated_actionPerformed(JComboBox<String> anns)
339 String cursel = (String) anns.getSelectedItem();
340 boolean isvalid = false;
341 boolean isseqs = seqAssociated.isSelected();
342 anns.removeAllItems();
343 for (String anitem : getAnnotationItems(seqAssociated.isSelected()))
345 if (anitem.equals(cursel) || (isseqs && cursel.startsWith(anitem)))
350 anns.addItem(anitem);
354 anns.setSelectedItem(cursel);
358 if (anns.getItemCount() > 0)
360 anns.setSelectedIndex(0);
368 protected void propagateSeqAssociatedThreshold(boolean allAnnotation,
369 AlignmentAnnotation annotation)
371 if (annotation.sequenceRef == null || annotation.threshold == null)
376 float thr = annotation.threshold.value;
377 for (int i = 0; i < av.getAlignment().getAlignmentAnnotation().length; i++)
379 AlignmentAnnotation aa = av.getAlignment().getAlignmentAnnotation()[i];
380 if (aa.label.equals(annotation.label)
381 && (annotation.getCalcId() == null ? aa.getCalcId() == null
382 : annotation.getCalcId().equals(aa.getCalcId())))
384 if (aa.threshold == null)
386 aa.threshold = new GraphLine(annotation.threshold);
390 aa.threshold.value = thr;
396 public AlignmentAnnotation getCurrentAnnotation()
398 return currentAnnotation;
401 protected void setCurrentAnnotation(AlignmentAnnotation annotation)
403 this.currentAnnotation = annotation;
406 protected abstract void valueChanged(boolean updateAllAnnotation);
408 protected abstract void updateView();
410 protected abstract void reset();
412 protected String getAnnotationMenuLabel(AlignmentAnnotation ann)
414 return annotationLabels.get(ann);
417 protected void jbInit()
420 ok.setText(MessageManager.getString("action.ok"));
421 ok.addActionListener(new ActionListener()
424 public void actionPerformed(ActionEvent e)
426 ok_actionPerformed();
430 cancel.setOpaque(false);
431 cancel.setText(MessageManager.getString("action.cancel"));
432 cancel.addActionListener(new ActionListener()
435 public void actionPerformed(ActionEvent e)
437 cancel_actionPerformed();
441 annotations.addItemListener(new ItemListener()
444 public void itemStateChanged(ItemEvent e)
446 selectedAnnotationChanged();
449 annotations.setToolTipText(MessageManager
450 .getString("info.select_annotation_row"));
452 threshold.addActionListener(new ActionListener()
455 public void actionPerformed(ActionEvent e)
457 threshold_actionPerformed();
461 thresholdValue.setEnabled(false);
462 thresholdValue.setColumns(7);
463 thresholdValue.addActionListener(new ActionListener()
466 public void actionPerformed(ActionEvent e)
468 thresholdValue_actionPerformed();
472 percentThreshold.setText(MessageManager.getString("label.as_percentage"));
473 percentThreshold.addActionListener(new ActionListener()
476 public void actionPerformed(ActionEvent e)
480 percentageValue_actionPerformed();
484 slider.setPaintLabels(false);
485 slider.setPaintTicks(true);
486 slider.setBackground(Color.white);
487 slider.setEnabled(false);
488 slider.setOpaque(false);
489 slider.setPreferredSize(new Dimension(100, 32));
492 public JComboBox<String> getThreshold()
497 public void setThreshold(JComboBox<String> thresh)
499 this.threshold = thresh;
502 public JComboBox<String> getAnnotations()
507 public void setAnnotations(JComboBox<String> anns)
509 this.annotations = anns;