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Coverage Report

  1. Project Clover database Mon Sep 2 2024 17:57:51 BST
  2. Package jalview.gui

File ScalePanel.java

 

Coverage histogram

../../img/srcFileCovDistChart8.png
21% of files have more coverage

Code metrics

68
170
18
1
581
389
57
0.34
9.44
18
3.17

Classes

Class Line # Actions
ScalePanel 57 170 57
0.710937571.1%
 

Contributing tests

This file is covered by 188 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 java.awt.Color;
24    import java.awt.FontMetrics;
25    import java.awt.Graphics;
26    import java.awt.Graphics2D;
27    import java.awt.Point;
28    import java.awt.RenderingHints;
29    import java.awt.event.ActionEvent;
30    import java.awt.event.ActionListener;
31    import java.awt.event.MouseEvent;
32    import java.awt.event.MouseListener;
33    import java.awt.event.MouseMotionListener;
34    import java.beans.PropertyChangeEvent;
35    import java.util.Iterator;
36    import java.util.List;
37   
38    import javax.swing.JMenuItem;
39    import javax.swing.JPanel;
40    import javax.swing.JPopupMenu;
41    import javax.swing.ToolTipManager;
42   
43    import jalview.datamodel.ColumnSelection;
44    import jalview.datamodel.HiddenColumns;
45    import jalview.datamodel.SequenceGroup;
46    import jalview.renderer.ScaleRenderer;
47    import jalview.renderer.ScaleRenderer.ScaleMark;
48    import jalview.util.MessageManager;
49    import jalview.util.Platform;
50    import jalview.viewmodel.ViewportListenerI;
51    import jalview.viewmodel.ViewportRanges;
52   
53    /**
54    * The panel containing the sequence ruler (when not in wrapped mode), and
55    * supports a range of mouse operations to select, hide or reveal columns.
56    */
 
57    public class ScalePanel extends JPanel
58    implements MouseMotionListener, MouseListener, ViewportListenerI
59    {
60    protected int offy = 4;
61   
62    public int width;
63   
64    protected AlignViewport av;
65   
66    AlignmentPanel ap;
67   
68    boolean stretchingGroup = false;
69   
70    /*
71    * min, max hold the extent of a mouse drag action
72    */
73    int min;
74   
75    int max;
76   
77    boolean mouseDragging = false;
78   
79    /*
80    * holds a hidden column range when the mouse is over an adjacent column
81    */
82    int[] reveal;
83   
84    /**
85    * Constructor
86    *
87    * @param av
88    * @param ap
89    */
 
90  478 toggle public ScalePanel(AlignViewport av, AlignmentPanel ap)
91    {
92  478 this.av = av;
93  478 this.ap = ap;
94   
95  478 addMouseListener(this);
96  478 addMouseMotionListener(this);
97   
98  478 av.getRanges().addPropertyChangeListener(this);
99    }
100   
101    /**
102    * DOCUMENT ME!
103    *
104    * @param evt
105    * DOCUMENT ME!
106    */
 
107  3 toggle @Override
108    public void mousePressed(MouseEvent evt)
109    {
110  3 int res = ap.getSeqPanel().findAlignmentColumn(evt);
111   
112  3 min = res;
113  3 max = res;
114   
115  3 if (evt.isPopupTrigger()) // Mac: mousePressed
116    {
117  0 rightMouseButtonPressed(evt, res);
118  0 return;
119    }
120  3 if (Platform.isWinRightButton(evt))
121    {
122    /*
123    * defer right-mouse click handling to mouse up on Windows
124    * (where isPopupTrigger() will answer true)
125    * but accept Cmd-click on Mac which passes isRightMouseButton
126    */
127  0 return;
128    }
129  3 leftMouseButtonPressed(evt, res);
130    }
131   
132    /**
133    * Handles right mouse button press. If pressed in a selected column, opens
134    * context menu for 'Hide Columns'. If pressed on a hidden columns marker,
135    * opens context menu for 'Reveal / Reveal All'. Else does nothing.
136    *
137    * @param evt
138    * @param res
139    */
 
140  0 toggle protected void rightMouseButtonPressed(MouseEvent evt, final int res)
141    {
142  0 JPopupMenu pop = buildPopupMenu(res);
143  0 if (pop.getSubElements().length > 0)
144    {
145  0 pop.show(this, evt.getX(), evt.getY());
146    }
147    }
148   
149    /**
150    * Builds a popup menu with 'Hide' or 'Reveal' options, or both, or neither
151    *
152    * @param res
153    * column number (0..)
154    * @return
155    */
 
156  9 toggle protected JPopupMenu buildPopupMenu(final int res)
157    {
158  9 JPopupMenu pop = new JPopupMenu();
159   
160    /*
161    * logic here depends on 'reveal', set in mouseMoved;
162    * grab the hidden range in case mouseMoved nulls it later
163    */
164  9 final int[] hiddenRange = reveal;
165  9 if (hiddenRange != null)
166    {
167  6 JMenuItem item = new JMenuItem(
168    MessageManager.getString("label.reveal"));
169  6 item.addActionListener(new ActionListener()
170    {
 
171  0 toggle @Override
172    public void actionPerformed(ActionEvent e)
173    {
174  0 av.showColumn(hiddenRange[0]);
175  0 reveal = null;
176  0 ap.updateLayout();
177  0 ap.paintAlignment(true, true);
178  0 av.sendSelection();
179    }
180    });
181  6 pop.add(item);
182   
183  6 if (av.getAlignment().getHiddenColumns()
184    .hasMultiHiddenColumnRegions())
185    {
186  2 item = new JMenuItem(MessageManager.getString("action.reveal_all"));
187  2 item.addActionListener(new ActionListener()
188    {
 
189  0 toggle @Override
190    public void actionPerformed(ActionEvent e)
191    {
192  0 av.showAllHiddenColumns();
193  0 reveal = null;
194  0 ap.updateLayout();
195  0 ap.paintAlignment(true, true);
196  0 av.sendSelection();
197    }
198    });
199  2 pop.add(item);
200    }
201    }
202   
203  9 if (av.getColumnSelection().contains(res))
204    {
205  4 JMenuItem item = new JMenuItem(
206    MessageManager.getString("label.hide_columns"));
207  4 item.addActionListener(new ActionListener()
208    {
 
209  0 toggle @Override
210    public void actionPerformed(ActionEvent e)
211    {
212  0 av.hideColumns(res, res);
213  0 if (av.getSelectionGroup() != null && av.getSelectionGroup()
214    .getSize() == av.getAlignment().getHeight())
215    {
216  0 av.setSelectionGroup(null);
217    }
218   
219  0 ap.updateLayout();
220  0 ap.paintAlignment(true, true);
221  0 av.sendSelection();
222    }
223    });
224  4 pop.add(item);
225    }
226  9 return pop;
227    }
228   
229    /**
230    * Handles left mouse button press
231    *
232    * @param evt
233    * @param res
234    */
 
235  3 toggle protected void leftMouseButtonPressed(MouseEvent evt, final int res)
236    {
237    /*
238    * Ctrl-click/Cmd-click adds to the selection
239    * Shift-click extends the selection
240    */
241    // TODO Problem: right-click on Windows not reported until mouseReleased?!?
242  3 if (!Platform.isControlDown(evt) && !evt.isShiftDown())
243    {
244  3 av.getColumnSelection().clear();
245    }
246   
247  3 av.getColumnSelection().addElement(res);
248  3 SequenceGroup sg = new SequenceGroup(av.getAlignment().getSequences());
249  3 sg.setStartRes(res);
250  3 sg.setEndRes(res);
251   
252  3 if (evt.isShiftDown())
253    {
254  0 int min = Math.min(av.getColumnSelection().getMin(), res);
255  0 int max = Math.max(av.getColumnSelection().getMax(), res);
256  0 for (int i = min; i < max; i++)
257    {
258  0 av.getColumnSelection().addElement(i);
259    }
260  0 sg.setStartRes(min);
261  0 sg.setEndRes(max);
262    }
263  3 av.setSelectionGroup(sg);
264  3 ap.paintAlignment(false, false);
265  3 PaintRefresher.Refresh(this, av.getSequenceSetId());
266  3 av.sendSelection();
267    }
268   
269    /**
270    * Action on mouseUp is to set the limit of the current selection group (if
271    * there is one) and broadcast the selection
272    *
273    * @param evt
274    */
 
275  3 toggle @Override
276    public void mouseReleased(MouseEvent evt)
277    {
278  3 boolean wasDragging = mouseDragging;
279  3 mouseDragging = false;
280  3 ap.getSeqPanel().stopScrolling();
281   
282  3 int res = ap.getSeqPanel().findAlignmentColumn(evt);
283   
284  3 if (!stretchingGroup)
285    {
286  0 if (evt.isPopupTrigger()) // Windows: mouseReleased
287    {
288  0 rightMouseButtonPressed(evt, res);
289    }
290    else
291    {
292  0 ap.paintAlignment(false, false);
293    }
294  0 return;
295    }
296   
297  3 SequenceGroup sg = av.getSelectionGroup();
298   
299  3 if (sg != null)
300    {
301  3 if (res > sg.getStartRes())
302    {
303  2 sg.setEndRes(res);
304    }
305  1 else if (res < sg.getStartRes())
306    {
307  0 sg.setStartRes(res);
308    }
309  3 if (wasDragging)
310    {
311  3 min = Math.min(res, min);
312  3 max = Math.max(res, max);
313  3 av.getColumnSelection().stretchGroup(res, sg, min, max);
314    }
315    }
316  3 stretchingGroup = false;
317  3 ap.paintAlignment(false, false);
318  3 av.isSelectionGroupChanged(true);
319  3 av.isColSelChanged(true);
320  3 PaintRefresher.Refresh(ap, av.getSequenceSetId());
321  3 av.sendSelection();
322    }
323   
324    /**
325    * Action on dragging the mouse in the scale panel is to expand or shrink the
326    * selection group range (including any hidden columns that it spans). Note
327    * that the selection is only broadcast at the start of the drag (on
328    * mousePressed) and at the end (on mouseReleased), to avoid overload
329    * redrawing of other views.
330    *
331    * @param evt
332    */
 
333  3 toggle @Override
334    public void mouseDragged(MouseEvent evt)
335    {
336  3 mouseDragging = true;
337  3 int res = ap.getSeqPanel().findAlignmentColumn(evt);
338   
339  3 ColumnSelection cs = av.getColumnSelection();
340   
341  3 min = Math.min(res, min);
342  3 max = Math.max(res, max);
343   
344  3 SequenceGroup sg = av.getSelectionGroup();
345  3 if (sg != null)
346    {
347  3 stretchingGroup = true;
348  3 cs.stretchGroup(res, sg, min, max);
349  3 ap.paintAlignment(false, false);
350  3 PaintRefresher.Refresh(ap, av.getSequenceSetId());
351    }
352    }
353   
 
354  1 toggle @Override
355    public void mouseEntered(MouseEvent evt)
356    {
357  1 if (mouseDragging)
358    {
359  0 mouseDragging = false;
360  0 ap.getSeqPanel().stopScrolling();
361    }
362    }
363   
364    /**
365    * Action on leaving the panel bounds with mouse drag in progress is to start
366    * scrolling the alignment in the direction of the mouse. To restrict
367    * scrolling to left-right (not up-down), the y-value of the mouse position is
368    * replaced with zero.
369    */
 
370  0 toggle @Override
371    public void mouseExited(MouseEvent evt)
372    {
373  0 if (mouseDragging)
374    {
375  0 ap.getSeqPanel().startScrolling(new Point(evt.getX(), 0));
376    }
377    }
378   
 
379  0 toggle @Override
380    public void mouseClicked(MouseEvent evt)
381    {
382    }
383   
384    /**
385    * Creates a tooltip when the mouse is over a hidden columns marker
386    */
 
387  8 toggle @Override
388    public void mouseMoved(MouseEvent evt)
389    {
390  8 this.setToolTipText(null);
391  8 reveal = null;
392  8 final int res = ap.getSeqPanel().findAlignmentColumn(evt);
393   
394  8 highlightAllStructPos(res);
395  8 if (!av.hasHiddenColumns())
396    {
397  0 return;
398    }
399  8 reveal = av.getAlignment().getHiddenColumns()
400    .getRegionWithEdgeAtRes(av.getAlignment().getHiddenColumns()
401    .absoluteToVisibleColumn(res));
402  8 if (reveal == null)
403    {
404  3 return;
405    }
406  5 ToolTipManager.sharedInstance().registerComponent(this);
407  5 this.setToolTipText(
408    MessageManager.getString("label.reveal_hidden_columns"));
409  5 repaint();
410    }
411   
 
412  8 toggle public void highlightAllStructPos(int col)
413    {
414  8 ap.getStructureSelectionManager().highlightPositionsOnMany(
415    ap.av.getAlignment().getSequencesArray(), new int[]
416    { col, col }, ap);
417   
418    }
419   
420    /**
421    * DOCUMENT ME!
422    *
423    * @param g
424    * DOCUMENT ME!
425    */
 
426  2439 toggle @Override
427    public void paintComponent(Graphics g)
428    {
429    // super.paintComponent(g); // BH 2019
430   
431    /*
432    * shouldn't get called in wrapped mode as the scale above is
433    * drawn instead by SeqCanvas.drawNorthScale
434    */
435  2439 if (!av.getWrapAlignment())
436    {
437  2152 drawScale(g, av.getRanges().getStartRes(), av.getRanges().getEndRes(),
438    getWidth(), getHeight());
439    }
440    }
441   
442    // scalewidth will normally be screenwidth,
 
443  2190 toggle public void drawScale(Graphics g, int startx, int endx, int width,
444    int height)
445    {
446  2190 Graphics2D gg = (Graphics2D) g;
447  2190 gg.setFont(av.getFont());
448   
449  2190 if (av.antiAlias)
450    {
451  771 gg.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
452    RenderingHints.VALUE_ANTIALIAS_ON);
453    }
454   
455    // Fill in the background
456  2190 gg.setColor(Color.white);
457  2190 gg.fillRect(0, 0, width, height);
458  2190 gg.setColor(Color.black);
459   
460    // Fill the selected columns
461  2190 ColumnSelection cs = av.getColumnSelection();
462  2190 HiddenColumns hidden = av.getAlignment().getHiddenColumns();
463  2190 int avCharWidth = av.getCharWidth();
464  2190 int avCharHeight = av.getCharHeight();
465   
466  2190 if (cs != null)
467    {
468  2190 gg.setColor(new Color(220, 0, 0));
469   
470  2190 for (int sel : cs.getSelected())
471    {
472    // TODO: JAL-2001 - provide a fast method to list visible selected in a
473    // given range
474   
475  56 if (av.hasHiddenColumns())
476    {
477  0 if (hidden.isVisible(sel))
478    {
479  0 sel = hidden.absoluteToVisibleColumn(sel);
480    }
481    else
482    {
483  0 continue;
484    }
485    }
486   
487  56 if ((sel >= startx) && (sel <= endx))
488    {
489  56 gg.fillRect((sel - startx) * avCharWidth, 0, avCharWidth,
490    getHeight());
491    }
492    }
493    }
494   
495  2190 int widthx = 1 + endx - startx;
496   
497  2190 FontMetrics fm = gg.getFontMetrics(av.getFont());
498  2190 int y = avCharHeight;
499  2190 int yOf = fm.getDescent();
500  2190 y -= yOf;
501  2190 if (av.hasHiddenColumns())
502    {
503    // draw any hidden column markers
504  210 gg.setColor(Color.blue);
505  210 int res;
506   
507  210 if (av.getShowHiddenMarkers())
508    {
509  210 Iterator<Integer> it = hidden.getStartRegionIterator(startx,
510    startx + widthx + 1);
511  408 while (it.hasNext())
512    {
513  198 res = it.next() - startx;
514   
515  198 gg.fillPolygon(
516    new int[]
517    { -1 + res * avCharWidth - avCharHeight / 4,
518    -1 + res * avCharWidth + avCharHeight / 4,
519    -1 + res * avCharWidth },
520    new int[]
521    { y, y, y + 2 * yOf }, 3);
522    }
523    }
524    }
525    // Draw the scale numbers
526  2190 gg.setColor(Color.black);
527   
528  2190 int maxX = 0;
529  2190 List<ScaleMark> marks = new ScaleRenderer().calculateMarks(av, startx,
530    endx);
531   
532  2190 for (ScaleMark mark : marks)
533    {
534  20365 boolean major = mark.major;
535  20365 int mpos = mark.column; // (i - startx - 1)
536  20365 String mstring = mark.text;
537  20365 if (mstring != null)
538    {
539  9726 if (mpos * avCharWidth > maxX)
540    {
541  9500 gg.drawString(mstring, mpos * avCharWidth, y);
542  9500 maxX = (mpos + 2) * avCharWidth + fm.stringWidth(mstring);
543    }
544    }
545  20365 if (major)
546    {
547  9726 gg.drawLine((mpos * avCharWidth) + (avCharWidth / 2), y + 2,
548    (mpos * avCharWidth) + (avCharWidth / 2), y + (yOf * 2));
549    }
550    else
551    {
552  10639 gg.drawLine((mpos * avCharWidth) + (avCharWidth / 2), y + yOf,
553    (mpos * avCharWidth) + (avCharWidth / 2), y + (yOf * 2));
554    }
555    }
556    }
557   
 
558  635 toggle @Override
559    public void propertyChange(PropertyChangeEvent evt)
560    {
561    // Respond to viewport change events (e.g. alignment panel was scrolled)
562    // Both scrolling and resizing change viewport ranges: scrolling changes
563    // both start and end points, but resize only changes end values.
564    // Here we only want to fastpaint on a scroll, with resize using a normal
565    // paint, so scroll events are identified as changes to the horizontal or
566    // vertical start value.
567  635 if (evt.getPropertyName().equals(ViewportRanges.STARTRES)
568    || evt.getPropertyName().equals(ViewportRanges.STARTRESANDSEQ)
569    || evt.getPropertyName().equals(ViewportRanges.MOVE_VIEWPORT))
570    {
571    // scroll event, repaint panel
572   
573    // Call repaint on alignment panel so that repaints from other alignment
574    // panel components can be aggregated. Otherwise performance of the
575    // overview
576    // window and others may be adversely affected.
577  36 av.getAlignPanel().repaint();
578    }
579    }
580   
581    }