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.
21 package jalview.appletgui;
23 import jalview.api.RotatableCanvasI;
24 import jalview.datamodel.SequenceGroup;
25 import jalview.datamodel.SequenceI;
26 import jalview.datamodel.SequencePoint;
27 import jalview.math.RotatableMatrix;
28 import jalview.util.Format;
29 import jalview.util.MessageManager;
30 import jalview.viewmodel.AlignmentViewport;
32 import java.awt.Color;
33 import java.awt.Dimension;
35 import java.awt.Graphics;
36 import java.awt.Image;
37 import java.awt.Panel;
38 import java.awt.event.KeyEvent;
39 import java.awt.event.KeyListener;
40 import java.awt.event.MouseEvent;
41 import java.awt.event.MouseListener;
42 import java.awt.event.MouseMotionListener;
43 import java.util.Vector;
45 public class RotatableCanvas extends Panel implements MouseListener,
46 MouseMotionListener, KeyListener, RotatableCanvasI
48 RotatableMatrix idmat = new RotatableMatrix(3, 3);
50 RotatableMatrix objmat = new RotatableMatrix(3, 3);
52 RotatableMatrix rotmat = new RotatableMatrix(3, 3);
58 // RubberbandRectangle rubberband;
60 boolean drawAxes = true;
76 float centre[] = new float[3];
78 float width[] = new float[3];
80 float max[] = new float[3];
82 float min[] = new float[3];
90 Vector<SequencePoint> points;
112 float scalefactor = 1;
114 AlignmentViewport av;
116 boolean showLabels = false;
118 public RotatableCanvas(AlignmentViewport av)
123 public void showLabels(boolean b)
130 public void setPoints(Vector points, int npoint)
132 this.points = points;
133 this.npoint = npoint;
134 PaintRefresher.Register(this, av.getSequenceSetId());
136 prefsize = getPreferredSize();
137 orig = new float[npoint][3];
139 for (int i = 0; i < npoint; i++)
141 SequencePoint sp = (SequencePoint) points.elementAt(i);
142 for (int j = 0; j < 3; j++)
144 orig[i][j] = sp.coord[j];
147 // Initialize the matrices to identity
149 for (int i = 0; i < 3; i++)
151 for (int j = 0; j < 3; j++)
155 idmat.addElement(i, j, 0);
156 objmat.addElement(i, j, 0);
157 rotmat.addElement(i, j, 0);
161 idmat.addElement(i, j, 0);
162 objmat.addElement(i, j, 0);
163 rotmat.addElement(i, j, 0);
168 axes = new float[3][3];
176 // System.out.println("Scale factor = " + scale);
178 addMouseListener(this);
179 addKeyListener(this);
180 // if (getParent() != null) {
181 // getParent().addKeyListener(this);
183 addMouseMotionListener(this);
186 // rubberband = new RubberbandRectangle(this);
187 // rubberband.setActive(true);
188 // rubberband.addListener(this);
192 * public boolean handleSequenceSelectionEvent(SequenceSelectionEvent evt) {
193 * redrawneeded = true; repaint(); return true; }
195 * public void removeNotify() { controller.removeListener(this);
196 * super.removeNotify(); }
199 public void initAxes()
201 for (int i = 0; i < 3; i++)
203 for (int j = 0; j < 3; j++)
217 public void findWidth()
222 max[0] = (float) -1e30;
223 max[1] = (float) -1e30;
224 max[2] = (float) -1e30;
226 min[0] = (float) 1e30;
227 min[1] = (float) 1e30;
228 min[2] = (float) 1e30;
230 for (int i = 0; i < 3; i++)
232 for (int j = 0; j < npoint; j++)
234 SequencePoint sp = points.elementAt(j);
235 if (sp.coord[i] >= max[i])
237 max[i] = sp.coord[i];
239 if (sp.coord[i] <= min[i])
241 min[i] = sp.coord[i];
246 // System.out.println("xmax " + max[0] + " min " + min[0]);
247 // System.out.println("ymax " + max[1] + " min " + min[1]);
248 // System.out.println("zmax " + max[2] + " min " + min[2]);
250 width[0] = Math.abs(max[0] - min[0]);
251 width[1] = Math.abs(max[1] - min[1]);
252 width[2] = Math.abs(max[2] - min[2]);
256 if (width[1] > width[0])
260 if (width[2] > width[1])
265 // System.out.println("Maxwidth = " + maxwidth);
268 public float findScale()
270 int dim, width, height;
271 if (getSize().width != 0)
273 width = getSize().width;
274 height = getSize().height;
278 width = prefsize.width;
279 height = prefsize.height;
291 return dim * scalefactor / (2 * maxwidth);
294 public void findCentre()
296 // Find centre coordinate
299 centre[0] = (max[0] + min[0]) / 2;
300 centre[1] = (max[1] + min[1]) / 2;
301 centre[2] = (max[2] + min[2]) / 2;
303 // System.out.println("Centre x " + centre[0]);
304 // System.out.println("Centre y " + centre[1]);
305 // System.out.println("Centre z " + centre[2]);
309 public Dimension getPreferredSize()
311 if (prefsize != null)
317 return new Dimension(400, 400);
322 public Dimension getMinimumSize()
324 return getPreferredSize();
328 public void update(Graphics g)
334 public void paint(Graphics g)
338 g.setFont(new Font("Verdana", Font.PLAIN, 18));
340 MessageManager.getString("label.calculating_pca") + "....",
341 20, getSize().height / 2);
346 // Only create the image at the beginning -
347 if ((img == null) || (prefsize.width != getSize().width)
348 || (prefsize.height != getSize().height))
350 prefsize.width = getSize().width;
351 prefsize.height = getSize().height;
355 // System.out.println("New scale = " + scale);
356 img = createImage(getSize().width, getSize().height);
357 ig = img.getGraphics();
361 drawBackground(ig, Color.black);
363 if (drawAxes == true)
370 ig.setColor(Color.red);
371 ig.drawString(tooltip, toolx, tooly);
374 g.drawImage(img, 0, 0, this);
378 public void drawAxes(Graphics g)
381 g.setColor(Color.yellow);
382 for (int i = 0; i < 3; i++)
384 g.drawLine(getSize().width / 2, getSize().height / 2,
385 (int) (axes[i][0] * scale * max[0] + getSize().width / 2),
386 (int) (axes[i][1] * scale * max[1] + getSize().height / 2));
390 public void drawBackground(Graphics g, Color col)
393 g.fillRect(0, 0, prefsize.width, prefsize.height);
396 public void drawScene(Graphics g)
398 // boolean darker = false;
400 int halfwidth = getSize().width / 2;
401 int halfheight = getSize().height / 2;
403 for (int i = 0; i < npoint; i++)
405 SequencePoint sp = points.elementAt(i);
406 int x = (int) ((sp.coord[0] - centre[0]) * scale) + halfwidth;
407 int y = (int) ((sp.coord[1] - centre[1]) * scale)
409 float z = sp.coord[1] - centre[2];
411 SequenceI sequence = sp.getSequence();
412 if (av.getSequenceColour(sequence) == Color.black)
414 g.setColor(Color.white);
418 g.setColor(av.getSequenceColour(sequence));
421 if (av.getSelectionGroup() != null)
423 if (av.getSelectionGroup().getSequences(null)
426 g.setColor(Color.gray);
431 g.setColor(g.getColor().darker());
434 g.fillRect(x - 3, y - 3, 6, 6);
437 g.setColor(Color.red);
438 g.drawString(sequence.getName(), x - 3, y - 4);
443 public Dimension minimumsize()
448 public Dimension preferredsize()
454 public void keyTyped(KeyEvent evt)
459 public void keyReleased(KeyEvent evt)
464 public void keyPressed(KeyEvent evt)
466 if (evt.getKeyCode() == KeyEvent.VK_UP)
468 scalefactor = (float) (scalefactor * 1.1);
471 else if (evt.getKeyCode() == KeyEvent.VK_DOWN)
473 scalefactor = (float) (scalefactor * 0.9);
476 else if (evt.getKeyChar() == 's')
478 System.err.println("DEBUG: Rectangle selection"); // log.debug
479 if (rectx2 != -1 && recty2 != -1)
481 rectSelect(rectx1, recty1, rectx2, recty2);
488 public void printPoints()
490 for (int i = 0; i < npoint; i++)
492 SequencePoint sp = points.elementAt(i);
493 Format.print(System.out, "%5d ", i);
494 for (int j = 0; j < 3; j++)
496 Format.print(System.out, "%13.3f ", sp.coord[j]);
498 System.out.println();
503 public void mouseClicked(MouseEvent evt)
508 public void mouseEntered(MouseEvent evt)
513 public void mouseExited(MouseEvent evt)
518 public void mouseReleased(MouseEvent evt)
523 public void mousePressed(MouseEvent evt)
543 SequenceI found = findPoint(x, y);
547 // TODO: applet PCA is not associatable with multi-panels - only parent
549 if (av.getSelectionGroup() != null)
551 av.getSelectionGroup().addOrRemove(found, true);
552 av.getSelectionGroup().setEndRes(av.getAlignment().getWidth() - 1);
556 av.setSelectionGroup(new SequenceGroup());
557 av.getSelectionGroup().addOrRemove(found, true);
558 av.getSelectionGroup().setEndRes(av.getAlignment().getWidth() - 1);
561 PaintRefresher.Refresh(this, av.getSequenceSetId());
568 public void mouseMoved(MouseEvent evt)
570 SequenceI found = findPoint(evt.getX(), evt.getY());
577 tooltip = found.getName();
585 public void mouseDragged(MouseEvent evt)
590 rotmat.setIdentity();
592 rotmat.rotate(my - omy, 'x');
593 rotmat.rotate(mx - omx, 'y');
595 for (int i = 0; i < npoint; i++)
597 SequencePoint sp = points.elementAt(i);
598 sp.coord[0] -= centre[0];
599 sp.coord[1] -= centre[1];
600 sp.coord[2] -= centre[2];
602 // Now apply the rotation matrix
603 sp.coord = rotmat.vectorMultiply(sp.coord);
605 // Now translate back again
606 sp.coord[0] += centre[0];
607 sp.coord[1] += centre[1];
608 sp.coord[2] += centre[2];
611 for (int i = 0; i < 3; i++)
613 axes[i] = rotmat.vectorMultiply(axes[i]);
618 paint(this.getGraphics());
621 public void rectSelect(int x1, int y1, int x2, int y2)
623 // boolean changedSel = false;
624 for (int i = 0; i < npoint; i++)
626 SequencePoint sp = points.elementAt(i);
627 int tmp1 = (int) ((sp.coord[0] - centre[0]) * scale
628 + getSize().width / 2.0);
629 int tmp2 = (int) ((sp.coord[1] - centre[1]) * scale
630 + getSize().height / 2.0);
632 SequenceI sequence = sp.getSequence();
633 if (tmp1 > x1 && tmp1 < x2 && tmp2 > y1 && tmp2 < y2)
637 if (!av.getSelectionGroup().getSequences(null)
640 av.getSelectionGroup().addSequence(sequence, true);
647 public SequenceI findPoint(int x, int y)
650 int halfwidth = getSize().width / 2;
651 int halfheight = getSize().height / 2;
655 for (int i = 0; i < npoint; i++)
658 SequencePoint sp = points.elementAt(i);
659 int px = (int) ((sp.coord[0] - centre[0]) * scale)
661 int py = (int) ((sp.coord[1] - centre[1]) * scale)
664 if (Math.abs(px - x) < 3 && Math.abs(py - y) < 3)
671 return points.elementAt(found).getSequence();