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Coverage Report

  1. Project Clover database Thu Aug 13 2020 12:04:21 BST
  2. Package jalview.gui

File AnnotationLabels.java

 

Coverage histogram

../../img/srcFileCovDistChart3.png
47% of files have more coverage

Code metrics

196
411
32
1
1,240
925
148
0.36
12.84
32
4.62

Classes

Class Line # Actions
AnnotationLabels 70 411 148
0.253521125.4%
 

Contributing tests

This file is covered by 109 tests. .

Source view

1    /*
2    * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3    * Copyright (C) $$Year-Rel$$ The Jalview Authors
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
10    * of the License, or (at your option) any later version.
11    *
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.
16    *
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.
20    */
21    package jalview.gui;
22   
23    import jalview.analysis.AlignSeq;
24    import jalview.analysis.AlignmentUtils;
25    import jalview.datamodel.Alignment;
26    import jalview.datamodel.AlignmentAnnotation;
27    import jalview.datamodel.Annotation;
28    import jalview.datamodel.HiddenColumns;
29    import jalview.datamodel.Sequence;
30    import jalview.datamodel.SequenceGroup;
31    import jalview.datamodel.SequenceI;
32    import jalview.io.FileFormat;
33    import jalview.io.FormatAdapter;
34    import jalview.util.Comparison;
35    import jalview.util.MessageManager;
36    import jalview.util.Platform;
37   
38    import java.awt.Color;
39    import java.awt.Cursor;
40    import java.awt.Dimension;
41    import java.awt.Font;
42    import java.awt.FontMetrics;
43    import java.awt.Graphics;
44    import java.awt.Graphics2D;
45    import java.awt.RenderingHints;
46    import java.awt.Toolkit;
47    import java.awt.datatransfer.StringSelection;
48    import java.awt.event.ActionEvent;
49    import java.awt.event.ActionListener;
50    import java.awt.event.MouseEvent;
51    import java.awt.event.MouseListener;
52    import java.awt.event.MouseMotionListener;
53    import java.awt.geom.AffineTransform;
54    import java.util.Arrays;
55    import java.util.Collections;
56    import java.util.Iterator;
57   
58    import javax.swing.JCheckBoxMenuItem;
59    import javax.swing.JMenuItem;
60    import javax.swing.JPanel;
61    import javax.swing.JPopupMenu;
62    import javax.swing.SwingUtilities;
63    import javax.swing.ToolTipManager;
64   
65    /**
66    * The panel that holds the labels for alignment annotations, providing
67    * tooltips, context menus, drag to reorder rows, and drag to adjust panel
68    * height
69    */
 
70    public class AnnotationLabels extends JPanel
71    implements MouseListener, MouseMotionListener, ActionListener
72    {
73    private static final String HTML_END_TAG = "</html>";
74   
75    private static final String HTML_START_TAG = "<html>";
76   
77    /**
78    * width in pixels within which height adjuster arrows are shown and active
79    */
80    private static final int HEIGHT_ADJUSTER_WIDTH = 50;
81   
82    /**
83    * height in pixels for allowing height adjuster to be active
84    */
85    private static int HEIGHT_ADJUSTER_HEIGHT = 10;
86   
87    private static final Font font = new Font("Arial", Font.PLAIN, 11);
88   
89    private static final String TOGGLE_LABELSCALE = MessageManager
90    .getString("label.scale_label_to_column");
91   
92    private static final String ADDNEW = MessageManager
93    .getString("label.add_new_row");
94   
95    private static final String EDITNAME = MessageManager
96    .getString("label.edit_label_description");
97   
98    private static final String HIDE = MessageManager
99    .getString("label.hide_row");
100   
101    private static final String DELETE = MessageManager
102    .getString("label.delete_row");
103   
104    private static final String SHOWALL = MessageManager
105    .getString("label.show_all_hidden_rows");
106   
107    private static final String OUTPUT_TEXT = MessageManager
108    .getString("label.export_annotation");
109   
110    private static final String COPYCONS_SEQ = MessageManager
111    .getString("label.copy_consensus_sequence");
112   
113    private final boolean debugRedraw = false;
114   
115    private AlignmentPanel ap;
116   
117    AlignViewport av;
118   
119    private MouseEvent dragEvent;
120   
121    private int oldY;
122   
123    private int selectedRow;
124   
125    private int scrollOffset = 0;
126   
127    private boolean hasHiddenRows;
128   
129    private boolean resizePanel = false;
130   
131    /**
132    * Creates a new AnnotationLabels object
133    *
134    * @param ap
135    */
 
136  267 toggle public AnnotationLabels(AlignmentPanel ap)
137    {
138   
139  267 this.ap = ap;
140  267 av = ap.av;
141  267 ToolTipManager.sharedInstance().registerComponent(this);
142   
143  267 addMouseListener(this);
144  267 addMouseMotionListener(this);
145  267 addMouseWheelListener(ap.getAnnotationPanel());
146    }
147   
 
148  122 toggle public AnnotationLabels(AlignViewport av)
149    {
150  122 this.av = av;
151    }
152   
153    /**
154    * DOCUMENT ME!
155    *
156    * @param y
157    * DOCUMENT ME!
158    */
 
159  448 toggle public void setScrollOffset(int y)
160    {
161  448 scrollOffset = y;
162  448 repaint();
163    }
164   
165    /**
166    * sets selectedRow to -2 if no annotation preset, -1 if no visible row is at
167    * y
168    *
169    * @param y
170    * coordinate position to search for a row
171    */
 
172  0 toggle void getSelectedRow(int y)
173    {
174  0 int height = 0;
175  0 AlignmentAnnotation[] aa = ap.av.getAlignment()
176    .getAlignmentAnnotation();
177  0 selectedRow = -2;
178  0 if (aa != null)
179    {
180  0 for (int i = 0; i < aa.length; i++)
181    {
182  0 selectedRow = -1;
183  0 if (!aa[i].visible)
184    {
185  0 continue;
186    }
187   
188  0 height += aa[i].height;
189   
190  0 if (y < height)
191    {
192  0 selectedRow = i;
193   
194  0 break;
195    }
196    }
197    }
198    }
199   
200    /**
201    * DOCUMENT ME!
202    *
203    * @param evt
204    * DOCUMENT ME!
205    */
 
206  0 toggle @Override
207    public void actionPerformed(ActionEvent evt)
208    {
209  0 AlignmentAnnotation[] aa = ap.av.getAlignment()
210    .getAlignmentAnnotation();
211   
212  0 String action = evt.getActionCommand();
213  0 if (ADDNEW.equals(action))
214    {
215    /*
216    * non-returning dialog
217    */
218  0 AlignmentAnnotation newAnnotation = new AlignmentAnnotation(null,
219    null, new Annotation[ap.av.getAlignment().getWidth()]);
220  0 editLabelDescription(newAnnotation, true);
221    }
222  0 else if (EDITNAME.equals(action))
223    {
224    /*
225    * non-returning dialog
226    */
227  0 editLabelDescription(aa[selectedRow], false);
228    }
229  0 else if (HIDE.equals(action))
230    {
231  0 aa[selectedRow].visible = false;
232    }
233  0 else if (DELETE.equals(action))
234    {
235  0 ap.av.getAlignment().deleteAnnotation(aa[selectedRow]);
236  0 ap.av.getCalcManager().removeWorkerForAnnotation(aa[selectedRow]);
237    }
238  0 else if (SHOWALL.equals(action))
239    {
240  0 for (int i = 0; i < aa.length; i++)
241    {
242  0 if (!aa[i].visible && aa[i].annotations != null)
243    {
244  0 aa[i].visible = true;
245    }
246    }
247    }
248  0 else if (OUTPUT_TEXT.equals(action))
249    {
250  0 new AnnotationExporter(ap).exportAnnotation(aa[selectedRow]);
251    }
252  0 else if (COPYCONS_SEQ.equals(action))
253    {
254  0 SequenceI cons = null;
255  0 if (aa[selectedRow].groupRef != null)
256    {
257  0 cons = aa[selectedRow].groupRef.getConsensusSeq();
258    }
259    else
260    {
261  0 cons = av.getConsensusSeq();
262    }
263  0 if (cons != null)
264    {
265  0 copy_annotseqtoclipboard(cons);
266    }
267    }
268  0 else if (TOGGLE_LABELSCALE.equals(action))
269    {
270  0 aa[selectedRow].scaleColLabel = !aa[selectedRow].scaleColLabel;
271    }
272   
273  0 ap.refresh(true);
274    }
275   
276    /**
277    * Shows a dialog where the annotation name and description may be edited. If
278    * parameter addNew is true, then on confirmation, a new AlignmentAnnotation
279    * is added, else an existing annotation is updated.
280    *
281    * @param annotation
282    * @param addNew
283    */
 
284  0 toggle void editLabelDescription(AlignmentAnnotation annotation, boolean addNew)
285    {
286  0 String name = MessageManager.getString("label.annotation_name");
287  0 String description = MessageManager
288    .getString("label.annotation_description");
289  0 String title = MessageManager
290    .getString("label.edit_annotation_name_description");
291  0 EditNameDialog dialog = new EditNameDialog(annotation.label,
292    annotation.description, name, description);
293   
294  0 dialog.showDialog(ap.alignFrame, title,
295    new Runnable()
296    {
 
297  0 toggle @Override
298    public void run()
299    {
300  0 annotation.label = dialog.getName();
301  0 String text = dialog.getDescription();
302  0 if (text != null && text.length() == 0)
303    {
304  0 text = null;
305    }
306  0 annotation.description = text;
307  0 if (addNew)
308    {
309  0 ap.av.getAlignment().addAnnotation(annotation);
310  0 ap.av.getAlignment().setAnnotationIndex(annotation, 0);
311    }
312  0 ap.refresh(true);
313    }
314    });
315    }
316   
 
317  0 toggle @Override
318    public void mousePressed(MouseEvent evt)
319    {
320  0 getSelectedRow(evt.getY() - getScrollOffset());
321  0 oldY = evt.getY();
322  0 if (evt.isPopupTrigger())
323    {
324  0 showPopupMenu(evt);
325    }
326    }
327   
328    /**
329    * Build and show the Pop-up menu at the right-click mouse position
330    *
331    * @param evt
332    */
 
333  0 toggle void showPopupMenu(MouseEvent evt)
334    {
335  0 evt.consume();
336  0 final AlignmentAnnotation[] aa = ap.av.getAlignment()
337    .getAlignmentAnnotation();
338   
339  0 JPopupMenu pop = new JPopupMenu(
340    MessageManager.getString("label.annotations"));
341  0 JMenuItem item = new JMenuItem(ADDNEW);
342  0 item.addActionListener(this);
343  0 pop.add(item);
344  0 if (selectedRow < 0)
345    {
346  0 if (hasHiddenRows)
347    { // let the user make everything visible again
348  0 item = new JMenuItem(SHOWALL);
349  0 item.addActionListener(this);
350  0 pop.add(item);
351    }
352  0 pop.show(this, evt.getX(), evt.getY());
353  0 return;
354    }
355  0 item = new JMenuItem(EDITNAME);
356  0 item.addActionListener(this);
357  0 pop.add(item);
358  0 item = new JMenuItem(HIDE);
359  0 item.addActionListener(this);
360  0 pop.add(item);
361    // JAL-1264 hide all sequence-specific annotations of this type
362  0 if (selectedRow < aa.length)
363    {
364  0 if (aa[selectedRow].sequenceRef != null)
365    {
366  0 final String label = aa[selectedRow].label;
367  0 JMenuItem hideType = new JMenuItem();
368  0 String text = MessageManager.getString("label.hide_all") + " "
369    + label;
370  0 hideType.setText(text);
371  0 hideType.addActionListener(new ActionListener()
372    {
 
373  0 toggle @Override
374    public void actionPerformed(ActionEvent e)
375    {
376  0 AlignmentUtils.showOrHideSequenceAnnotations(
377    ap.av.getAlignment(), Collections.singleton(label),
378    null, false, false);
379  0 ap.refresh(true);
380    }
381    });
382  0 pop.add(hideType);
383    }
384    }
385  0 item = new JMenuItem(DELETE);
386  0 item.addActionListener(this);
387  0 pop.add(item);
388  0 if (hasHiddenRows)
389    {
390  0 item = new JMenuItem(SHOWALL);
391  0 item.addActionListener(this);
392  0 pop.add(item);
393    }
394  0 item = new JMenuItem(OUTPUT_TEXT);
395  0 item.addActionListener(this);
396  0 pop.add(item);
397    // TODO: annotation object should be typed for autocalculated/derived
398    // property methods
399  0 if (selectedRow < aa.length)
400    {
401  0 final String label = aa[selectedRow].label;
402  0 if (!aa[selectedRow].autoCalculated)
403    {
404  0 if (aa[selectedRow].graph == AlignmentAnnotation.NO_GRAPH)
405    {
406    // display formatting settings for this row.
407  0 pop.addSeparator();
408    // av and sequencegroup need to implement same interface for
409  0 item = new JCheckBoxMenuItem(TOGGLE_LABELSCALE,
410    aa[selectedRow].scaleColLabel);
411  0 item.addActionListener(this);
412  0 pop.add(item);
413    }
414    }
415  0 else if (label.indexOf("Consensus") > -1)
416    {
417  0 addConsensusMenuOptions(ap, aa[selectedRow], pop);
418   
419  0 final JMenuItem consclipbrd = new JMenuItem(COPYCONS_SEQ);
420  0 consclipbrd.addActionListener(this);
421  0 pop.add(consclipbrd);
422    }
423    }
424  0 pop.show(this, evt.getX(), evt.getY());
425    }
426   
427    /**
428    * A helper method that adds menu options for calculation and visualisation of
429    * group and/or alignment consensus annotation to a popup menu. This is
430    * designed to be reusable for either unwrapped mode (popup menu is shown on
431    * component AnnotationLabels), or wrapped mode (popup menu is shown on
432    * IdPanel when the mouse is over an annotation label).
433    *
434    * @param ap
435    * @param ann
436    * @param pop
437    */
 
438  0 toggle static void addConsensusMenuOptions(AlignmentPanel ap,
439    AlignmentAnnotation ann,
440    JPopupMenu pop)
441    {
442  0 pop.addSeparator();
443   
444  0 final JCheckBoxMenuItem cbmi = new JCheckBoxMenuItem(
445    MessageManager.getString("label.ignore_gaps_consensus"),
446  0 (ann.groupRef != null) ? ann.groupRef.getIgnoreGapsConsensus()
447    : ap.av.isIgnoreGapsConsensus());
448  0 final AlignmentAnnotation aaa = ann;
449  0 cbmi.addActionListener(new ActionListener()
450    {
 
451  0 toggle @Override
452    public void actionPerformed(ActionEvent e)
453    {
454  0 if (aaa.groupRef != null)
455    {
456  0 aaa.groupRef.setIgnoreGapsConsensus(cbmi.getState());
457  0 ap.getAnnotationPanel()
458    .paint(ap.getAnnotationPanel().getGraphics());
459    }
460    else
461    {
462  0 ap.av.setIgnoreGapsConsensus(cbmi.getState(), ap);
463    }
464  0 ap.alignmentChanged();
465    }
466    });
467  0 pop.add(cbmi);
468   
469  0 if (aaa.groupRef != null)
470    {
471    /*
472    * group consensus options
473    */
474  0 final JCheckBoxMenuItem chist = new JCheckBoxMenuItem(
475    MessageManager.getString("label.show_group_histogram"),
476    ann.groupRef.isShowConsensusHistogram());
477  0 chist.addActionListener(new ActionListener()
478    {
 
479  0 toggle @Override
480    public void actionPerformed(ActionEvent e)
481    {
482  0 aaa.groupRef.setShowConsensusHistogram(chist.getState());
483  0 ap.repaint();
484    }
485    });
486  0 pop.add(chist);
487  0 final JCheckBoxMenuItem cprofl = new JCheckBoxMenuItem(
488    MessageManager.getString("label.show_group_logo"),
489    ann.groupRef.isShowSequenceLogo());
490  0 cprofl.addActionListener(new ActionListener()
491    {
 
492  0 toggle @Override
493    public void actionPerformed(ActionEvent e)
494    {
495  0 aaa.groupRef.setshowSequenceLogo(cprofl.getState());
496  0 ap.repaint();
497    }
498    });
499  0 pop.add(cprofl);
500  0 final JCheckBoxMenuItem cproflnorm = new JCheckBoxMenuItem(
501    MessageManager.getString("label.normalise_group_logo"),
502    ann.groupRef.isNormaliseSequenceLogo());
503  0 cproflnorm.addActionListener(new ActionListener()
504    {
 
505  0 toggle @Override
506    public void actionPerformed(ActionEvent e)
507    {
508  0 aaa.groupRef.setNormaliseSequenceLogo(cproflnorm.getState());
509    // automatically enable logo display if we're clicked
510  0 aaa.groupRef.setshowSequenceLogo(true);
511  0 ap.repaint();
512    }
513    });
514  0 pop.add(cproflnorm);
515    }
516    else
517    {
518    /*
519    * alignment consensus options
520    */
521  0 final JCheckBoxMenuItem chist = new JCheckBoxMenuItem(
522    MessageManager.getString("label.show_histogram"),
523    ap.av.isShowConsensusHistogram());
524  0 chist.addActionListener(new ActionListener()
525    {
 
526  0 toggle @Override
527    public void actionPerformed(ActionEvent e)
528    {
529  0 ap.av.setShowConsensusHistogram(chist.getState());
530  0 ap.alignFrame.setMenusForViewport();
531  0 ap.repaint();
532    }
533    });
534  0 pop.add(chist);
535  0 final JCheckBoxMenuItem cprof = new JCheckBoxMenuItem(
536    MessageManager.getString("label.show_logo"),
537    ap.av.isShowSequenceLogo());
538  0 cprof.addActionListener(new ActionListener()
539    {
 
540  0 toggle @Override
541    public void actionPerformed(ActionEvent e)
542    {
543  0 ap.av.setShowSequenceLogo(cprof.getState());
544  0 ap.alignFrame.setMenusForViewport();
545  0 ap.repaint();
546    }
547    });
548  0 pop.add(cprof);
549  0 final JCheckBoxMenuItem cprofnorm = new JCheckBoxMenuItem(
550    MessageManager.getString("label.normalise_logo"),
551    ap.av.isNormaliseSequenceLogo());
552  0 cprofnorm.addActionListener(new ActionListener()
553    {
 
554  0 toggle @Override
555    public void actionPerformed(ActionEvent e)
556    {
557  0 ap.av.setShowSequenceLogo(true);
558  0 ap.av.setNormaliseSequenceLogo(cprofnorm.getState());
559  0 ap.alignFrame.setMenusForViewport();
560  0 ap.repaint();
561    }
562    });
563  0 pop.add(cprofnorm);
564    }
565    }
566   
567    /**
568    * Reorders annotation rows after a drag of a label
569    *
570    * @param evt
571    */
 
572  0 toggle @Override
573    public void mouseReleased(MouseEvent evt)
574    {
575  0 if (evt.isPopupTrigger())
576    {
577  0 showPopupMenu(evt);
578  0 return;
579    }
580   
581  0 int start = selectedRow;
582  0 getSelectedRow(evt.getY() - getScrollOffset());
583  0 int end = selectedRow;
584   
585    /*
586    * if dragging to resize instead, start == end
587    */
588  0 if (start != end)
589    {
590    // Swap these annotations
591  0 AlignmentAnnotation startAA = ap.av.getAlignment()
592    .getAlignmentAnnotation()[start];
593  0 if (end == -1)
594    {
595  0 end = ap.av.getAlignment().getAlignmentAnnotation().length - 1;
596    }
597  0 AlignmentAnnotation endAA = ap.av.getAlignment()
598    .getAlignmentAnnotation()[end];
599   
600  0 ap.av.getAlignment().getAlignmentAnnotation()[end] = startAA;
601  0 ap.av.getAlignment().getAlignmentAnnotation()[start] = endAA;
602    }
603   
604  0 resizePanel = false;
605  0 dragEvent = null;
606  0 repaint();
607  0 ap.getAnnotationPanel().repaint();
608    }
609   
610    /**
611    * Removes the height adjuster image on leaving the panel, unless currently
612    * dragging it
613    */
 
614  0 toggle @Override
615    public void mouseExited(MouseEvent evt)
616    {
617  0 if (resizePanel && dragEvent == null)
618    {
619  0 resizePanel = false;
620  0 repaint();
621    }
622    }
623   
624    /**
625    * A mouse drag may be either an adjustment of the panel height (if flag
626    * resizePanel is set on), or a reordering of the annotation rows. The former
627    * is dealt with by this method, the latter in mouseReleased.
628    *
629    * @param evt
630    */
 
631  0 toggle @Override
632    public void mouseDragged(MouseEvent evt)
633    {
634  0 dragEvent = evt;
635   
636  0 if (resizePanel)
637    {
638  0 Dimension d = ap.annotationScroller.getPreferredSize();
639  0 int dif = evt.getY() - oldY;
640   
641  0 dif /= ap.av.getCharHeight();
642  0 dif *= ap.av.getCharHeight();
643   
644  0 if ((d.height - dif) > 20)
645    {
646  0 ap.annotationScroller
647    .setPreferredSize(new Dimension(d.width, d.height - dif));
648  0 d = ap.annotationSpaceFillerHolder.getPreferredSize();
649  0 ap.annotationSpaceFillerHolder
650    .setPreferredSize(new Dimension(d.width, d.height - dif));
651  0 ap.paintAlignment(true, false);
652    }
653   
654  0 ap.addNotify();
655    }
656    else
657    {
658  0 repaint();
659    }
660    }
661   
662    /**
663    * Updates the tooltip as the mouse moves over the labels
664    *
665    * @param evt
666    */
 
667  0 toggle @Override
668    public void mouseMoved(MouseEvent evt)
669    {
670  0 showOrHideAdjuster(evt);
671   
672  0 getSelectedRow(evt.getY() - getScrollOffset());
673   
674  0 if (selectedRow > -1 && ap.av.getAlignment()
675    .getAlignmentAnnotation().length > selectedRow)
676    {
677  0 AlignmentAnnotation[] anns = ap.av.getAlignment()
678    .getAlignmentAnnotation();
679  0 AlignmentAnnotation aa = anns[selectedRow];
680   
681  0 String desc = getTooltip(aa);
682  0 this.setToolTipText(desc);
683  0 String msg = getStatusMessage(aa, anns);
684  0 ap.alignFrame.setStatus(msg);
685    }
686    }
687   
688    /**
689    * Constructs suitable text to show in the status bar when over an annotation
690    * label, containing the associated sequence name (if any), and the annotation
691    * labels (or all labels for a graph group annotation)
692    *
693    * @param aa
694    * @param anns
695    * @return
696    */
 
697  6 toggle static String getStatusMessage(AlignmentAnnotation aa,
698    AlignmentAnnotation[] anns)
699    {
700  6 if (aa == null)
701    {
702  1 return null;
703    }
704   
705  5 StringBuilder msg = new StringBuilder(32);
706  5 if (aa.sequenceRef != null)
707    {
708  3 msg.append(aa.sequenceRef.getName()).append(" : ");
709    }
710   
711  5 if (aa.graphGroup == -1)
712    {
713  2 msg.append(aa.label);
714    }
715  3 else if (anns != null)
716    {
717  3 boolean first = true;
718  9 for (int i = anns.length - 1; i >= 0; i--)
719    {
720  6 if (anns[i].graphGroup == aa.graphGroup)
721    {
722  5 if (!first)
723    {
724  2 msg.append(", ");
725    }
726  5 msg.append(anns[i].label);
727  5 first = false;
728    }
729    }
730    }
731   
732  5 return msg.toString();
733    }
734   
735    /**
736    * Answers a tooltip, formatted as html, containing the annotation description
737    * (prefixed by associated sequence id if applicable), and the annotation
738    * (non-positional) score if it has one. Answers null if neither description
739    * nor score is found.
740    *
741    * @param aa
742    * @return
743    */
 
744  13 toggle static String getTooltip(AlignmentAnnotation aa)
745    {
746  13 if (aa == null)
747    {
748  1 return null;
749    }
750  12 StringBuilder tooltip = new StringBuilder();
751  12 if (aa.description != null && !aa.description.equals("New description"))
752    {
753    // TODO: we could refactor and merge this code with the code in
754    // jalview.gui.SeqPanel.mouseMoved(..) that formats sequence feature
755    // tooltips
756  10 String desc = aa.getDescription(true).trim();
757  10 if (!desc.toLowerCase().startsWith(HTML_START_TAG))
758    {
759  7 tooltip.append(HTML_START_TAG);
760  7 desc = desc.replace("<", "&lt;");
761    }
762  3 else if (desc.toLowerCase().endsWith(HTML_END_TAG))
763    {
764  3 desc = desc.substring(0, desc.length() - HTML_END_TAG.length());
765    }
766  10 tooltip.append(desc);
767    }
768    else
769    {
770    // begin the tooltip's html fragment
771  2 tooltip.append(HTML_START_TAG);
772    }
773  12 if (aa.hasScore())
774    {
775  5 if (tooltip.length() > HTML_START_TAG.length())
776    {
777  3 tooltip.append("<br/>");
778    }
779    // TODO: limit precision of score to avoid noise from imprecise
780    // doubles
781    // (64.7 becomes 64.7+/some tiny value).
782  5 tooltip.append(" Score: ").append(String.valueOf(aa.score));
783    }
784   
785  12 if (tooltip.length() > HTML_START_TAG.length())
786    {
787  10 return tooltip.append(HTML_END_TAG).toString();
788    }
789   
790    /*
791    * nothing in the tooltip (except "<html>")
792    */
793  2 return null;
794    }
795   
796    /**
797    * Shows the height adjuster image if the mouse moves into the top left
798    * region, or hides it if the mouse leaves the regio
799    *
800    * @param evt
801    */
 
802  0 toggle protected void showOrHideAdjuster(MouseEvent evt)
803    {
804  0 boolean was = resizePanel;
805  0 resizePanel = evt.getY() < HEIGHT_ADJUSTER_HEIGHT
806    && evt.getX() < HEIGHT_ADJUSTER_WIDTH;
807   
808  0 if (resizePanel != was)
809    {
810  0 setCursor(Cursor
811  0 .getPredefinedCursor(resizePanel ? Cursor.S_RESIZE_CURSOR
812    : Cursor.DEFAULT_CURSOR));
813  0 repaint();
814    }
815    }
816   
 
817  0 toggle @Override
818    public void mouseClicked(MouseEvent evt)
819    {
820  0 final AlignmentAnnotation[] aa = ap.av.getAlignment()
821    .getAlignmentAnnotation();
822  0 if (!evt.isPopupTrigger() && SwingUtilities.isLeftMouseButton(evt))
823    {
824  0 if (selectedRow > -1 && selectedRow < aa.length)
825    {
826  0 if (aa[selectedRow].groupRef != null)
827    {
828  0 if (evt.getClickCount() >= 2)
829    {
830    // todo: make the ap scroll to the selection - not necessary, first
831    // click highlights/scrolls, second selects
832  0 ap.getSeqPanel().ap.getIdPanel().highlightSearchResults(null);
833    // process modifiers
834  0 SequenceGroup sg = ap.av.getSelectionGroup();
835  0 if (sg == null || sg == aa[selectedRow].groupRef
836    || !(Platform.isControlDown(evt) || evt.isShiftDown()))
837    {
838  0 if (Platform.isControlDown(evt) || evt.isShiftDown())
839    {
840    // clone a new selection group from the associated group
841  0 ap.av.setSelectionGroup(
842    new SequenceGroup(aa[selectedRow].groupRef));
843    }
844    else
845    {
846    // set selection to the associated group so it can be edited
847  0 ap.av.setSelectionGroup(aa[selectedRow].groupRef);
848    }
849    }
850    else
851    {
852    // modify current selection with associated group
853  0 int remainToAdd = aa[selectedRow].groupRef.getSize();
854  0 for (SequenceI sgs : aa[selectedRow].groupRef.getSequences())
855    {
856  0 if (jalview.util.Platform.isControlDown(evt))
857    {
858  0 sg.addOrRemove(sgs, --remainToAdd == 0);
859    }
860    else
861    {
862    // notionally, we should also add intermediate sequences from
863    // last added sequence ?
864  0 sg.addSequence(sgs, --remainToAdd == 0);
865    }
866    }
867    }
868   
869  0 ap.paintAlignment(false, false);
870  0 PaintRefresher.Refresh(ap, ap.av.getSequenceSetId());
871  0 ap.av.sendSelection();
872    }
873    else
874    {
875  0 ap.getSeqPanel().ap.getIdPanel().highlightSearchResults(
876    aa[selectedRow].groupRef.getSequences(null));
877    }
878  0 return;
879    }
880  0 else if (aa[selectedRow].sequenceRef != null)
881    {
882  0 if (evt.getClickCount() == 1)
883    {
884  0 ap.getSeqPanel().ap.getIdPanel()
885    .highlightSearchResults(Arrays.asList(new SequenceI[]
886    { aa[selectedRow].sequenceRef }));
887    }
888  0 else if (evt.getClickCount() >= 2)
889    {
890  0 ap.getSeqPanel().ap.getIdPanel().highlightSearchResults(null);
891  0 SequenceGroup sg = ap.av.getSelectionGroup();
892  0 if (sg != null)
893    {
894    // we make a copy rather than edit the current selection if no
895    // modifiers pressed
896    // see Enhancement JAL-1557
897  0 if (!(Platform.isControlDown(evt) || evt.isShiftDown()))
898    {
899  0 sg = new SequenceGroup(sg);
900  0 sg.clear();
901  0 sg.addSequence(aa[selectedRow].sequenceRef, false);
902    }
903    else
904    {
905  0 if (Platform.isControlDown(evt))
906    {
907  0 sg.addOrRemove(aa[selectedRow].sequenceRef, true);
908    }
909    else
910    {
911    // notionally, we should also add intermediate sequences from
912    // last added sequence ?
913  0 sg.addSequence(aa[selectedRow].sequenceRef, true);
914    }
915    }
916    }
917    else
918    {
919  0 sg = new SequenceGroup();
920  0 sg.setStartRes(0);
921  0 sg.setEndRes(ap.av.getAlignment().getWidth() - 1);
922  0 sg.addSequence(aa[selectedRow].sequenceRef, false);
923    }
924  0 ap.av.setSelectionGroup(sg);
925  0 ap.paintAlignment(false, false);
926  0 PaintRefresher.Refresh(ap, ap.av.getSequenceSetId());
927  0 ap.av.sendSelection();
928    }
929   
930    }
931    }
932  0 return;
933    }
934    }
935   
936    /**
937    * do a single sequence copy to jalview and the system clipboard
938    *
939    * @param sq
940    * sequence to be copied to clipboard
941    */
 
942  0 toggle protected void copy_annotseqtoclipboard(SequenceI sq)
943    {
944  0 SequenceI[] seqs = new SequenceI[] { sq };
945  0 String[] omitHidden = null;
946  0 SequenceI[] dseqs = new SequenceI[] { sq.getDatasetSequence() };
947  0 if (dseqs[0] == null)
948    {
949  0 dseqs[0] = new Sequence(sq);
950  0 dseqs[0].setSequence(AlignSeq.extractGaps(Comparison.GapChars,
951    sq.getSequenceAsString()));
952   
953  0 sq.setDatasetSequence(dseqs[0]);
954    }
955  0 Alignment ds = new Alignment(dseqs);
956  0 if (av.hasHiddenColumns())
957    {
958  0 Iterator<int[]> it = av.getAlignment().getHiddenColumns()
959    .getVisContigsIterator(0, sq.getLength(), false);
960  0 omitHidden = new String[] { sq.getSequenceStringFromIterator(it) };
961    }
962   
963  0 int[] alignmentStartEnd = new int[] { 0, ds.getWidth() - 1 };
964  0 if (av.hasHiddenColumns())
965    {
966  0 alignmentStartEnd = av.getAlignment().getHiddenColumns()
967    .getVisibleStartAndEndIndex(av.getAlignment().getWidth());
968    }
969   
970  0 String output = new FormatAdapter().formatSequences(FileFormat.Fasta,
971    seqs, omitHidden, alignmentStartEnd);
972   
973  0 Toolkit.getDefaultToolkit().getSystemClipboard()
974    .setContents(new StringSelection(output), Desktop.instance);
975   
976  0 HiddenColumns hiddenColumns = null;
977   
978  0 if (av.hasHiddenColumns())
979    {
980  0 hiddenColumns = new HiddenColumns(
981    av.getAlignment().getHiddenColumns());
982    }
983   
984  0 Desktop.jalviewClipboard = new Object[] { seqs, ds, // what is the dataset
985    // of a consensus
986    // sequence ? need to
987    // flag
988    // sequence as special.
989    hiddenColumns };
990    }
991   
992    /**
993    * DOCUMENT ME!
994    *
995    * @param g1
996    * DOCUMENT ME!
997    */
 
998  478 toggle @Override
999    public void paintComponent(Graphics g)
1000    {
1001   
1002  478 int width = getWidth();
1003  478 if (width == 0)
1004    {
1005  0 width = ap.calculateIdWidth().width;
1006    }
1007   
1008  478 Graphics2D g2 = (Graphics2D) g;
1009  478 if (av.antiAlias)
1010    {
1011  0 g2.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
1012    RenderingHints.VALUE_ANTIALIAS_ON);
1013    }
1014   
1015  478 drawComponent(g2, true, width);
1016   
1017    }
1018   
1019    /**
1020    * Draw the full set of annotation Labels for the alignment at the given
1021    * cursor
1022    *
1023    * @param g
1024    * Graphics2D instance (needed for font scaling)
1025    * @param width
1026    * Width for scaling labels
1027    *
1028    */
 
1029  248 toggle public void drawComponent(Graphics g, int width)
1030    {
1031  248 drawComponent(g, false, width);
1032    }
1033   
1034    /**
1035    * Draw the full set of annotation Labels for the alignment at the given
1036    * cursor
1037    *
1038    * @param g
1039    * Graphics2D instance (needed for font scaling)
1040    * @param clip
1041    * - true indicates that only current visible area needs to be
1042    * rendered
1043    * @param width
1044    * Width for scaling labels
1045    */
 
1046  726 toggle public void drawComponent(Graphics g, boolean clip, int width)
1047    {
1048  726 if (av.getFont().getSize() < 10)
1049    {
1050  0 g.setFont(font);
1051    }
1052    else
1053    {
1054  726 g.setFont(av.getFont());
1055    }
1056   
1057  726 FontMetrics fm = g.getFontMetrics(g.getFont());
1058  726 g.setColor(Color.white);
1059  726 g.fillRect(0, 0, getWidth(), getHeight());
1060   
1061  726 g.translate(0, getScrollOffset());
1062  726 g.setColor(Color.black);
1063   
1064  726 AlignmentAnnotation[] aa = av.getAlignment().getAlignmentAnnotation();
1065  726 int fontHeight = g.getFont().getSize();
1066  726 int y = 0;
1067  726 int x = 0;
1068  726 int graphExtras = 0;
1069  726 int offset = 0;
1070  726 Font baseFont = g.getFont();
1071  726 FontMetrics baseMetrics = fm;
1072  726 int ofontH = fontHeight;
1073  726 int sOffset = 0;
1074  726 int visHeight = 0;
1075  726 int[] visr = (ap != null && ap.getAnnotationPanel() != null)
1076    ? ap.getAnnotationPanel().getVisibleVRange()
1077    : null;
1078  726 if (clip && visr != null)
1079    {
1080  478 sOffset = visr[0];
1081  478 visHeight = visr[1];
1082    }
1083  726 boolean visible = true, before = false, after = false;
1084  726 if (aa != null)
1085    {
1086  726 hasHiddenRows = false;
1087  726 int olY = 0;
1088  5126 for (int i = 0; i < aa.length; i++)
1089    {
1090  4400 visible = true;
1091  4400 if (!aa[i].visible)
1092    {
1093  420 hasHiddenRows = true;
1094  420 continue;
1095    }
1096  3980 olY = y;
1097  3980 y += aa[i].height;
1098  3980 if (clip)
1099    {
1100  2752 if (y < sOffset)
1101    {
1102  0 if (!before)
1103    {
1104  0 if (debugRedraw)
1105    {
1106  0 System.out.println("before vis: " + i);
1107    }
1108  0 before = true;
1109    }
1110    // don't draw what isn't visible
1111  0 continue;
1112    }
1113  2752 if (olY > visHeight)
1114    {
1115   
1116  126 if (!after)
1117    {
1118  118 if (debugRedraw)
1119    {
1120  0 System.out.println(
1121    "Scroll offset: " + sOffset + " after vis: " + i);
1122    }
1123  118 after = true;
1124    }
1125    // don't draw what isn't visible
1126  126 continue;
1127    }
1128    }
1129  3854 g.setColor(Color.black);
1130   
1131  3854 offset = -aa[i].height / 2;
1132   
1133  3854 if (aa[i].hasText)
1134    {
1135  3586 offset += fm.getHeight() / 2;
1136  3586 offset -= fm.getDescent();
1137    }
1138    else
1139    {
1140  268 offset += fm.getDescent();
1141    }
1142   
1143  3854 x = width - fm.stringWidth(aa[i].label) - 3;
1144   
1145  3854 if (aa[i].graphGroup > -1)
1146    {
1147  0 int groupSize = 0;
1148    // TODO: JAL-1291 revise rendering model so the graphGroup map is
1149    // computed efficiently for all visible labels
1150  0 for (int gg = 0; gg < aa.length; gg++)
1151    {
1152  0 if (aa[gg].graphGroup == aa[i].graphGroup)
1153    {
1154  0 groupSize++;
1155    }
1156    }
1157  0 if (groupSize * (fontHeight + 8) < aa[i].height)
1158    {
1159  0 graphExtras = (aa[i].height - (groupSize * (fontHeight + 8)))
1160    / 2;
1161    }
1162    else
1163    {
1164    // scale font to fit
1165  0 float h = aa[i].height / (float) groupSize, s;
1166  0 if (h < 9)
1167    {
1168  0 visible = false;
1169    }
1170    else
1171    {
1172  0 fontHeight = -8 + (int) h;
1173  0 s = ((float) fontHeight) / (float) ofontH;
1174  0 Font f = baseFont
1175    .deriveFont(AffineTransform.getScaleInstance(s, s));
1176  0 g.setFont(f);
1177  0 fm = g.getFontMetrics();
1178  0 graphExtras = (aa[i].height - (groupSize * (fontHeight + 8)))
1179    / 2;
1180    }
1181    }
1182  0 if (visible)
1183    {
1184  0 for (int gg = 0; gg < aa.length; gg++)
1185    {
1186  0 if (aa[gg].graphGroup == aa[i].graphGroup)
1187    {
1188  0 x = width - fm.stringWidth(aa[gg].label) - 3;
1189  0 g.drawString(aa[gg].label, x, y - graphExtras);
1190   
1191  0 if (aa[gg]._linecolour != null)
1192    {
1193   
1194  0 g.setColor(aa[gg]._linecolour);
1195  0 g.drawLine(x, y - graphExtras + 3,
1196    x + fm.stringWidth(aa[gg].label),
1197    y - graphExtras + 3);
1198    }
1199   
1200  0 g.setColor(Color.black);
1201  0 graphExtras += fontHeight + 8;
1202    }
1203    }
1204    }
1205  0 g.setFont(baseFont);
1206  0 fm = baseMetrics;
1207  0 fontHeight = ofontH;
1208    }
1209    else
1210    {
1211  3854 g.drawString(aa[i].label, x, y + offset);
1212    }
1213    }
1214    }
1215   
1216  726 if (!resizePanel && dragEvent != null && aa != null)
1217    {
1218  0 g.setColor(Color.lightGray);
1219  0 g.drawString(aa[selectedRow].label, dragEvent.getX(),
1220    dragEvent.getY() - getScrollOffset());
1221    }
1222   
1223  726 if (!av.getWrapAlignment() && ((aa == null) || (aa.length < 1)))
1224    {
1225  0 g.drawString(MessageManager.getString("label.right_click"), 2, 8);
1226  0 g.drawString(MessageManager.getString("label.to_add_annotation"), 2,
1227    18);
1228    }
1229    }
1230   
 
1231  1683 toggle public int getScrollOffset()
1232    {
1233  1683 return scrollOffset;
1234    }
1235   
 
1236  0 toggle @Override
1237    public void mouseEntered(MouseEvent e)
1238    {
1239    }
1240    }
  • Report generated by OpenClover v 4.4.1 on Thu Aug 13 2020 12:06:48 BST using coverage data from Thu Aug 13 2020 12:06:40 BST.
  • OpenClover is free and open-source software.