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.ColumnSelection;
24 import jalview.datamodel.SequenceGroup;
25 import jalview.datamodel.SequenceI;
26 import jalview.util.MessageManager;
28 import java.awt.Color;
29 import java.awt.FontMetrics;
30 import java.awt.Graphics;
31 import java.awt.Graphics2D;
32 import java.awt.RenderingHints;
33 import java.awt.event.ActionEvent;
34 import java.awt.event.ActionListener;
35 import java.awt.event.MouseEvent;
36 import java.awt.event.MouseListener;
37 import java.awt.event.MouseMotionListener;
38 import java.util.ArrayList;
39 import java.util.List;
41 import javax.swing.JMenuItem;
42 import javax.swing.JPanel;
43 import javax.swing.JPopupMenu;
44 import javax.swing.ToolTipManager;
52 public class ScalePanel extends JPanel implements MouseMotionListener,
55 protected int offy = 4;
60 protected AlignViewport av;
64 boolean stretchingGroup = false;
66 int min; // used by mouseDragged to see if user
68 int max; // used by mouseDragged to see if user
70 boolean mouseDragging = false;
72 // wants to delete columns
73 public ScalePanel(AlignViewport av, AlignmentPanel ap)
78 addMouseListener(this);
79 addMouseMotionListener(this);
89 public void mousePressed(MouseEvent evt)
91 int x = (evt.getX() / av.getCharWidth()) + av.getStartRes();
94 if (av.hasHiddenColumns())
96 x = av.getColumnSelection().adjustForHiddenColumns(x);
99 if (x >= av.getAlignment().getWidth())
101 res = av.getAlignment().getWidth() - 1;
111 if (evt.isPopupTrigger())
113 rightMouseButtonPressed(evt, res);
117 leftMouseButtonPressed(evt, res);
122 * Handles right mouse button press. If pressed in a selected column, opens
123 * context menu for 'Hide Columns'. If pressed on a hidden columns marker,
124 * opens context menu for 'Reveal / Reveal All'. Else does nothing.
129 protected void rightMouseButtonPressed(MouseEvent evt, final int res)
131 JPopupMenu pop = new JPopupMenu();
134 JMenuItem item = new JMenuItem(
135 MessageManager.getString("label.reveal"));
136 item.addActionListener(new ActionListener()
139 public void actionPerformed(ActionEvent e)
141 av.showColumn(reveal[0]);
143 ap.paintAlignment(true);
144 if (ap.overviewPanel != null)
146 ap.overviewPanel.updateOverviewImage();
153 if (av.getColumnSelection().hasHiddenColumns())
155 item = new JMenuItem(MessageManager.getString("action.reveal_all"));
156 item.addActionListener(new ActionListener()
159 public void actionPerformed(ActionEvent e)
161 av.showAllHiddenColumns();
163 ap.paintAlignment(true);
164 if (ap.overviewPanel != null)
166 ap.overviewPanel.updateOverviewImage();
173 pop.show(this, evt.getX(), evt.getY());
175 else if (av.getColumnSelection().contains(res))
177 JMenuItem item = new JMenuItem(
178 MessageManager.getString("label.hide_columns"));
179 item.addActionListener(new ActionListener()
182 public void actionPerformed(ActionEvent e)
184 av.hideColumns(res, res);
185 if (av.getSelectionGroup() != null
186 && av.getSelectionGroup().getSize() == av.getAlignment()
189 av.setSelectionGroup(null);
192 ap.paintAlignment(true);
193 if (ap.overviewPanel != null)
195 ap.overviewPanel.updateOverviewImage();
201 pop.show(this, evt.getX(), evt.getY());
206 * Handles left mouse button press
211 protected void leftMouseButtonPressed(MouseEvent evt, final int res)
213 if (!evt.isControlDown() && !evt.isShiftDown())
215 av.getColumnSelection().clear();
218 av.getColumnSelection().addElement(res);
219 SequenceGroup sg = new SequenceGroup();
220 // try to be as quick as possible
221 SequenceI[] iVec = av.getAlignment().getSequencesArray();
222 for (int i = 0; i < iVec.length; i++)
224 sg.addSequence(iVec[i], false);
231 if (evt.isShiftDown())
233 int min = Math.min(av.getColumnSelection().getMin(), res);
234 int max = Math.max(av.getColumnSelection().getMax(), res);
235 for (int i = min; i < max; i++)
237 av.getColumnSelection().addElement(i);
242 av.setSelectionGroup(sg);
243 ap.paintAlignment(false);
254 public void mouseReleased(MouseEvent evt)
256 mouseDragging = false;
258 int res = (evt.getX() / av.getCharWidth()) + av.getStartRes();
260 if (av.hasHiddenColumns())
262 res = av.getColumnSelection().adjustForHiddenColumns(res);
265 if (res >= av.getAlignment().getWidth())
267 res = av.getAlignment().getWidth() - 1;
270 if (!stretchingGroup)
272 ap.paintAlignment(false);
277 SequenceGroup sg = av.getSelectionGroup();
281 if (res > sg.getStartRes())
285 else if (res < sg.getStartRes())
290 stretchingGroup = false;
291 ap.paintAlignment(false);
302 public void mouseDragged(MouseEvent evt)
304 mouseDragging = true;
306 int res = (evt.getX() / av.getCharWidth()) + av.getStartRes();
312 if (av.hasHiddenColumns())
314 res = av.getColumnSelection().adjustForHiddenColumns(res);
317 if (res >= av.getAlignment().getWidth())
319 res = av.getAlignment().getWidth() - 1;
332 SequenceGroup sg = av.getSelectionGroup();
336 stretchingGroup = true;
338 if (!av.getColumnSelection().contains(res))
340 av.getColumnSelection().addElement(res);
343 if (res > sg.getStartRes())
347 if (res < sg.getStartRes())
353 for (int i = min; i <= max; i++)
355 col = i; // av.getColumnSelection().adjustForHiddenColumns(i);
357 if ((col < sg.getStartRes()) || (col > sg.getEndRes()))
359 av.getColumnSelection().removeElement(col);
363 av.getColumnSelection().addElement(col);
367 ap.paintAlignment(false);
372 public void mouseEntered(MouseEvent evt)
376 ap.getSeqPanel().scrollCanvas(null);
381 public void mouseExited(MouseEvent evt)
385 ap.getSeqPanel().scrollCanvas(evt);
390 public void mouseClicked(MouseEvent evt)
395 public void mouseMoved(MouseEvent evt)
397 if (!av.hasHiddenColumns())
402 int res = (evt.getX() / av.getCharWidth()) + av.getStartRes();
404 res = av.getColumnSelection().adjustForHiddenColumns(res);
407 if (av.getColumnSelection().getHiddenColumns() != null)
409 for (int[] region : av.getColumnSelection().getHiddenColumns())
411 if (res + 1 == region[0] || res - 1 == region[1])
414 ToolTipManager.sharedInstance().registerComponent(this);
415 this.setToolTipText(MessageManager
416 .getString("label.reveal_hidden_columns"));
421 this.setToolTipText(null);
437 public void paintComponent(Graphics g)
439 drawScale(g, av.getStartRes(), av.getEndRes(), getWidth(), getHeight());
442 // scalewidth will normally be screenwidth,
443 public void drawScale(Graphics g, int startx, int endx, int width,
446 Graphics2D gg = (Graphics2D) g;
447 gg.setFont(av.getFont());
451 gg.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
452 RenderingHints.VALUE_ANTIALIAS_ON);
455 // Fill in the background
456 gg.setColor(Color.white);
457 gg.fillRect(0, 0, width, height);
458 gg.setColor(Color.black);
460 // Fill the selected columns
461 ColumnSelection cs = av.getColumnSelection();
462 int avCharWidth = av.getCharWidth(), avCharHeight = av.getCharHeight();
467 gg.setColor(new Color(220, 0, 0));
469 for (int sel : cs.getSelected())
471 // TODO: JAL-2001 - provide a fast method to list visible selected in a
474 if (av.hasHiddenColumns())
476 if (cs.isVisible(sel))
478 sel = cs.findColumnPosition(sel);
486 if ((sel >= startx) && (sel <= endx))
488 gg.fillRect((sel - startx) * avCharWidth, 0, avCharWidth,
494 int widthx = 1 + endx - startx;
496 FontMetrics fm = gg.getFontMetrics(av.getFont());
497 int y = avCharHeight, yOf = fm.getDescent();
499 if (av.hasHiddenColumns())
501 // draw any hidden column markers
502 gg.setColor(Color.blue);
504 if (av.getShowHiddenMarkers()
505 && av.getColumnSelection().getHiddenColumns() != null)
507 for (int i = 0; i < av.getColumnSelection().getHiddenColumns()
510 res = av.getColumnSelection().findHiddenRegionPosition(i)
513 if (res < 0 || res > widthx)
518 gg.fillPolygon(new int[] {
519 -1 + res * avCharWidth - avCharHeight / 4,
520 -1 + res * avCharWidth + avCharHeight / 4,
521 -1 + res * avCharWidth }, new int[] { y, y, y + 2 * yOf }, 3);
526 // Draw the scale numbers
527 gg.setColor(Color.black);
529 List<Object[]> marks = calculateMarks(startx, endx);
531 for (Object[] mark : marks)
533 boolean major = Boolean.valueOf((Boolean) mark[0]);
534 int mpos = ((Integer) mark[1]).intValue(); // (i - startx - 1)
535 String mstring = (String) mark[2];
538 if (mpos * avCharWidth > maxX)
540 gg.drawString(mstring, mpos * avCharWidth, y);
541 maxX = (mpos + 2) * avCharWidth + fm.stringWidth(mstring);
546 gg.drawLine((mpos * avCharWidth) + (avCharWidth / 2), y + 2,
547 (mpos * avCharWidth) + (avCharWidth / 2), y + (yOf * 2));
551 gg.drawLine((mpos * avCharWidth) + (avCharWidth / 2), y + yOf,
552 (mpos * avCharWidth) + (avCharWidth / 2), y + (yOf * 2));
555 if (av.hasHiddenColumns())
557 if (reveal != null && reveal[0] > startx && reveal[0] < endx)
559 gg.drawString(MessageManager.getString("label.reveal_columns"),
560 reveal[0] * avCharWidth, 0);
567 * calculate positions markers on the alignment ruler
569 * @return List { Object { .. } } Boolean: true/false for major/minor mark,
570 * Integer: marker position in alignment column coords, String: null
571 * or a String to be rendered at the position.
573 public List<Object[]> calculateMarks(int startx, int endx)
575 new ArrayList<Object[]>();
577 int scalestartx = (startx / 10) * 10;
579 SequenceI refSeq = av.getAlignment().getSeqrep();
580 int refSp = 0, refEp = -1, refStart = 0, refEnd = -1, refStartI = 0, refEndI = -1;
583 // find bounds and set origin appopriately
584 // locate first visible position for this sequence
585 int[] refbounds = av.getColumnSelection()
586 .locateVisibleBoundsOfSequence(refSeq);
588 refSp = refbounds[0];
589 refEp = refbounds[1];
590 refStart = refbounds[2];
591 refEnd = refbounds[3];
592 refStartI = refbounds[4];
593 refEndI = refbounds[5];
594 scalestartx = refSp + ((scalestartx - refSp) / 10) * 10;
598 if (refSeq == null && scalestartx % 10 == 0)
602 List<Object[]> marks = new ArrayList<Object[]>();
604 int maxX = 0, refN, iadj;
605 // todo: add a 'reference origin column' to set column number relative to
606 for (int i = scalestartx; i < endx; i += 5)
608 Object[] amark = new Object[3];
609 if (((i - refSp) % 10) == 0)
613 iadj = av.getColumnSelection().adjustForHiddenColumns(i - 1) + 1;
614 string = String.valueOf(iadj);
618 iadj = av.getColumnSelection().adjustForHiddenColumns(i - 1);
619 refN = refSeq.findPosition(iadj);
620 // TODO show bounds if position is a gap
621 // - ie L--R -> "1L|2R" for
623 if (iadj < refStartI)
625 string = String.valueOf(iadj - refStartI);
627 else if (iadj > refEndI)
629 string = "+" + String.valueOf(iadj - refEndI);
633 string = String.valueOf(refN) + refSeq.getCharAt(iadj);
636 amark[0] = Boolean.TRUE;
637 amark[1] = Integer.valueOf(i - startx - 1);
643 amark[0] = Boolean.FALSE;
644 amark[1] = Integer.valueOf(i - startx - 1);