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);
133 * update the text field from the threshold slider. preserves state of
134 * 'adjusting' so safe to call in init.
136 protected void setThresholdValueText()
138 boolean oldadj = adjusting;
140 if (percentThreshold.isSelected())
142 thresholdValue.setText("" + (slider.getValue() - slider.getMinimum())
143 * 100f / (slider.getMaximum() - slider.getMinimum()));
147 thresholdValue.setText((slider.getValue() / 1000f) + "");
151 protected void addSliderMouseListeners()
154 slider.addMouseListener(new MouseAdapter()
157 public void mousePressed(MouseEvent e)
159 sliderDragging = true;
160 super.mousePressed(e);
164 public void mouseDragged(MouseEvent e)
166 sliderDragging = true;
167 super.mouseDragged(e);
171 public void mouseReleased(MouseEvent evt)
175 sliderDragging = false;
178 ap.paintAlignment(true);
184 * Builds and returns a list of menu items (display text) for choice of
185 * annotation. Also builds maps between annotations, their positions in the
186 * list, and their display labels in the list.
188 * @param isSeqAssociated
191 public Vector<String> getAnnotationItems(boolean isSeqAssociated)
193 annotationLabels = new HashMap<AlignmentAnnotation, String>();
195 Vector<String> list = new Vector<String>();
197 int[] anmap = new int[av.getAlignment().getAlignmentAnnotation().length];
198 seqAssociated.setEnabled(false);
199 for (int i = 0; i < av.getAlignment().getAlignmentAnnotation().length; i++)
201 AlignmentAnnotation annotation = av.getAlignment()
202 .getAlignmentAnnotation()[i];
203 if (annotation.sequenceRef == null)
212 seqAssociated.setEnabled(true);
214 String label = annotation.label;
215 // add associated sequence ID if available
216 if (!isSeqAssociated && annotation.sequenceRef != null)
218 label = label + "_" + annotation.sequenceRef.getName();
221 if (!list.contains(label))
223 anmap[list.size()] = i;
225 annotationLabels.put(annotation, label);
229 if (!isSeqAssociated)
231 anmap[list.size()] = i;
232 label = label + "_" + (index++);
234 annotationLabels.put(annotation, label);
238 this.annmap = new int[list.size()];
239 System.arraycopy(anmap, 0, this.annmap, 0, this.annmap.length);
243 protected int getSelectedThresholdItem(int indexValue)
245 int selectedThresholdItem = -1;
248 selectedThresholdItem = AnnotationColourGradient.ABOVE_THRESHOLD;
250 else if (indexValue == 2)
252 selectedThresholdItem = AnnotationColourGradient.BELOW_THRESHOLD;
254 return selectedThresholdItem;
257 public void ok_actionPerformed()
261 frame.setClosed(true);
262 } catch (Exception ex)
267 public void cancel_actionPerformed()
270 ap.paintAlignment(true);
273 frame.setClosed(true);
274 } catch (Exception ex)
279 protected void thresholdCheck_actionPerformed()
284 protected void selectedAnnotationChanged()
289 protected void threshold_actionPerformed()
294 protected void thresholdValue_actionPerformed()
298 float f = Float.parseFloat(thresholdValue.getText());
299 if (percentThreshold.isSelected())
301 slider.setValue(slider.getMinimum()
302 + ((int) ((f / 100f) * (slider.getMaximum() - slider
307 slider.setValue((int) (f * 1000));
310 } catch (NumberFormatException ex)
315 protected void percentageValue_actionPerformed()
317 setThresholdValueText();
320 protected void thresholdIsMin_actionPerformed()
325 protected void populateThresholdComboBox(JComboBox<String> thresh)
327 thresh.addItem(MessageManager
328 .getString("label.threshold_feature_no_threshold"));
329 thresh.addItem(MessageManager
330 .getString("label.threshold_feature_above_threshold"));
331 thresh.addItem(MessageManager
332 .getString("label.threshold_feature_below_threshold"));
336 * Rebuilds the drop-down list of annotations to choose from when the 'per
337 * sequence only' checkbox is checked or unchecked.
341 protected void seqAssociated_actionPerformed(JComboBox<String> anns)
344 String cursel = (String) anns.getSelectedItem();
345 boolean isvalid = false;
346 boolean isseqs = seqAssociated.isSelected();
347 anns.removeAllItems();
348 for (String anitem : getAnnotationItems(seqAssociated.isSelected()))
350 if (anitem.equals(cursel) || (isseqs && cursel.startsWith(anitem)))
355 anns.addItem(anitem);
359 anns.setSelectedItem(cursel);
363 if (anns.getItemCount() > 0)
365 anns.setSelectedIndex(0);
373 protected void propagateSeqAssociatedThreshold(boolean allAnnotation,
374 AlignmentAnnotation annotation)
376 if (annotation.sequenceRef == null || annotation.threshold == null)
381 float thr = annotation.threshold.value;
382 for (int i = 0; i < av.getAlignment().getAlignmentAnnotation().length; i++)
384 AlignmentAnnotation aa = av.getAlignment().getAlignmentAnnotation()[i];
385 if (aa.label.equals(annotation.label)
386 && (annotation.getCalcId() == null ? aa.getCalcId() == null
387 : annotation.getCalcId().equals(aa.getCalcId())))
389 if (aa.threshold == null)
391 aa.threshold = new GraphLine(annotation.threshold);
395 aa.threshold.value = thr;
401 public AlignmentAnnotation getCurrentAnnotation()
403 return currentAnnotation;
406 protected void setCurrentAnnotation(AlignmentAnnotation annotation)
408 this.currentAnnotation = annotation;
411 protected abstract void valueChanged(boolean updateAllAnnotation);
413 protected abstract void updateView();
415 protected abstract void reset();
417 protected String getAnnotationMenuLabel(AlignmentAnnotation ann)
419 return annotationLabels.get(ann);
422 protected void jbInit()
425 ok.setText(MessageManager.getString("action.ok"));
426 ok.addActionListener(new ActionListener()
429 public void actionPerformed(ActionEvent e)
431 ok_actionPerformed();
435 cancel.setOpaque(false);
436 cancel.setText(MessageManager.getString("action.cancel"));
437 cancel.addActionListener(new ActionListener()
440 public void actionPerformed(ActionEvent e)
442 cancel_actionPerformed();
446 annotations.addItemListener(new ItemListener()
449 public void itemStateChanged(ItemEvent e)
451 selectedAnnotationChanged();
454 annotations.setToolTipText(MessageManager
455 .getString("info.select_annotation_row"));
457 threshold.addActionListener(new ActionListener()
460 public void actionPerformed(ActionEvent e)
462 threshold_actionPerformed();
466 thresholdValue.setEnabled(false);
467 thresholdValue.setColumns(7);
468 thresholdValue.addActionListener(new ActionListener()
471 public void actionPerformed(ActionEvent e)
473 thresholdValue_actionPerformed();
477 percentThreshold.setText(MessageManager.getString("label.as_percentage"));
478 percentThreshold.addActionListener(new ActionListener()
481 public void actionPerformed(ActionEvent e)
485 percentageValue_actionPerformed();
489 slider.setPaintLabels(false);
490 slider.setPaintTicks(true);
491 slider.setBackground(Color.white);
492 slider.setEnabled(false);
493 slider.setOpaque(false);
494 slider.setPreferredSize(new Dimension(100, 32));
497 public JComboBox<String> getThreshold()
502 public void setThreshold(JComboBox<String> thresh)
504 this.threshold = thresh;
507 public JComboBox<String> getAnnotations()
512 public void setAnnotations(JComboBox<String> anns)
514 this.annotations = anns;