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.api.RotatableCanvasI;
24 import jalview.datamodel.Point;
25 import jalview.datamodel.SequenceGroup;
26 import jalview.datamodel.SequenceI;
27 import jalview.datamodel.SequencePoint;
28 import jalview.math.RotatableMatrix;
29 import jalview.math.RotatableMatrix.Axis;
30 import jalview.util.ColorUtils;
31 import jalview.util.MessageManager;
32 import jalview.viewmodel.AlignmentViewport;
34 import java.awt.Color;
35 import java.awt.Dimension;
37 import java.awt.Graphics;
38 import java.awt.Graphics2D;
39 import java.awt.Image;
40 import java.awt.RenderingHints;
41 import java.awt.event.InputEvent;
42 import java.awt.event.KeyEvent;
43 import java.awt.event.KeyListener;
44 import java.awt.event.MouseEvent;
45 import java.awt.event.MouseListener;
46 import java.awt.event.MouseMotionListener;
47 import java.awt.event.MouseWheelEvent;
48 import java.awt.event.MouseWheelListener;
49 import java.util.Arrays;
50 import java.util.Iterator;
51 import java.util.List;
53 import javax.swing.JPanel;
54 import javax.swing.ToolTipManager;
57 * Models a Panel on which a set of points, and optionally x/y/z axes, can be
58 * drawn, and rotated or zoomed with the mouse
60 public class RotatableCanvas extends JPanel implements MouseListener,
61 MouseMotionListener, KeyListener, RotatableCanvasI,
64 private static final float ZOOM_OUT = 0.9f;
66 private static final float ZOOM_IN = 1.1f;
69 * pixels distance within which tooltip shows sequence name
71 private static final int NEARBY = 3;
73 private static final List<String> AXES = Arrays.asList("x", "y", "z");
75 private static final Color AXIS_COLOUR = Color.yellow;
77 private static final int DIMS = 3;
79 boolean drawAxes = true;
92 * the min-max [x, y, z] values of sequence points when the points
93 * were set on the object, or when the view is reset;
94 * x and y ranges are not recomputed as points are rotated, as this
95 * would make scaling (zoom) unstable, but z ranges are (for correct
96 * graduated colour brightness based on z-coordinate)
103 * a scale factor used in drawing; when equal to 1, the points span
104 * half the available width or height (whichever is less); increase this
105 * factor to zoom in, decrease it to zoom out
112 * sequences and their (x, y, z) PCA dimension values
114 List<SequencePoint> sequencePoints;
117 * x, y, z axis end points (PCA dimension values)
119 Point[] axisEndPoints;
121 // fields for 'select rectangle' (JAL-1124)
127 AlignmentViewport av;
135 boolean applyToAllViews;
142 public RotatableCanvas(AlignmentPanel panel)
146 axisEndPoints = new Point[DIMS];
148 applyToAllViews = false;
149 bgColour = Color.BLACK;
152 ToolTipManager.sharedInstance().registerComponent(this);
154 addMouseListener(this);
155 addMouseMotionListener(this);
156 addMouseWheelListener(this);
160 * Refreshes the display with labels shown (or not)
164 public void showLabels(boolean show)
171 public void setPoints(List<SequencePoint> points, int np)
173 this.sequencePoints = points;
175 prefSize = getPreferredSize();
183 * Resets axes to the initial state: x-axis to the right, y-axis up, z-axis to
184 * back (so obscured in a 2-D display)
186 protected void resetAxes()
188 axisEndPoints[0] = new Point(1f, 0f, 0f);
189 axisEndPoints[1] = new Point(0f, 1f, 0f);
190 axisEndPoints[2] = new Point(0f, 0f, 1f);
194 * Computes and saves the min-max ranges of x/y/z positions of the sequence
197 protected void findWidths()
199 float[] max = new float[DIMS];
200 float[] min = new float[DIMS];
202 max[0] = -Float.MAX_VALUE;
203 max[1] = -Float.MAX_VALUE;
204 max[2] = -Float.MAX_VALUE;
206 min[0] = Float.MAX_VALUE;
207 min[1] = Float.MAX_VALUE;
208 min[2] = Float.MAX_VALUE;
210 for (SequencePoint sp : sequencePoints)
212 max[0] = Math.max(max[0], sp.coord.x);
213 max[1] = Math.max(max[1], sp.coord.y);
214 max[2] = Math.max(max[2], sp.coord.z);
215 min[0] = Math.min(min[0], sp.coord.x);
216 min[1] = Math.min(min[1], sp.coord.y);
217 min[2] = Math.min(min[2], sp.coord.z);
225 * Answers the preferred size if it has been set, else 400 x 400
230 public Dimension getPreferredSize()
232 if (prefSize != null)
238 return new Dimension(400, 400);
243 * Answers the preferred size
246 * @see RotatableCanvas#getPreferredSize()
249 public Dimension getMinimumSize()
251 return getPreferredSize();
260 public void paintComponent(Graphics g1)
263 Graphics2D g = (Graphics2D) g1;
265 g.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
266 RenderingHints.VALUE_ANTIALIAS_ON);
267 if (sequencePoints == null)
269 g.setFont(new Font("Verdana", Font.PLAIN, 18));
271 MessageManager.getString("label.calculating_pca") + "....",
272 20, getHeight() / 2);
277 * create the image at the beginning or after a resize
279 boolean resized = prefSize.width != getWidth()
280 || prefSize.height != getHeight();
281 if (img == null || resized)
283 prefSize.width = getWidth();
284 prefSize.height = getHeight();
286 img = createImage(getWidth(), getHeight());
287 ig = img.getGraphics();
290 drawBackground(ig, bgColour);
298 g.drawImage(img, 0, 0, this);
303 * Resets the rotation and choice of axes to the initial state (without change
306 public void resetView()
315 * Draws lines for the x, y, z axes
319 public void drawAxes(Graphics g)
321 g.setColor(AXIS_COLOUR);
323 int midX = getWidth() / 2;
324 int midY = getHeight() / 2;
325 float maxWidth = Math.max(Math.abs(seqMax[0] - seqMin[0]),
326 Math.abs(seqMax[1] - seqMin[1]));
327 int pix = Math.min(getWidth(), getHeight());
328 float scaleBy = pix * scaleFactor / (2f * maxWidth);
330 for (int i = 0; i < DIMS; i++)
332 g.drawLine(midX, midY,
333 midX + (int) (axisEndPoints[i].x * scaleBy * seqMax[0]),
334 midY + (int) (axisEndPoints[i].y * scaleBy * seqMax[1]));
339 * Fills the background with the specified colour
344 public void drawBackground(Graphics g, Color col)
347 g.fillRect(0, 0, prefSize.width, prefSize.height);
351 * Draws points (6x6 squares) for the sequences of the PCA, and labels
352 * (sequence names) if configured to do so. The sequence points colours are
353 * taken from the sequence ids in the alignment (converting black to white).
354 * Sequences 'at the back' (z-coordinate is negative) are shaded slightly
355 * darker to help give a 3-D sensation.
359 public void drawScene(Graphics g1)
361 Graphics2D g = (Graphics2D) g1;
363 g.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
364 RenderingHints.VALUE_ANTIALIAS_ON);
365 int pix = Math.min(getWidth(), getHeight());
366 float xWidth = Math.abs(seqMax[0] - seqMin[0]);
367 float yWidth = Math.abs(seqMax[1] - seqMin[1]);
368 float maxWidth = Math.max(xWidth, yWidth);
369 float scaleBy = pix * scaleFactor / (2f * maxWidth);
371 float[] centre = getCentre();
373 for (int i = 0; i < npoint; i++)
376 * sequence point colour as sequence id, but
377 * gray if sequence is currently selected
379 SequencePoint sp = sequencePoints.get(i);
380 Color sequenceColour = getSequencePointColour(sp);
381 g.setColor(sequenceColour);
383 int halfwidth = getWidth() / 2;
384 int halfheight = getHeight() / 2;
385 int x = (int) ((sp.coord.x - centre[0]) * scaleBy) + halfwidth;
386 int y = (int) ((sp.coord.y - centre[1]) * scaleBy) + halfheight;
387 g.fillRect(x - 3, y - 3, 6, 6);
391 g.setColor(Color.red);
392 g.drawString(sp.getSequence().getName(), x - 3, y - 4);
397 g.setColor(AXIS_COLOUR);
398 int midX = getWidth() / 2;
399 int midY = getHeight() / 2;
400 Iterator<String> axes = AXES.iterator();
401 for (Point p : axisEndPoints)
403 int x = midX + (int) (p.x * scaleBy * seqMax[0]);
404 int y = midY + (int) (p.y * scaleBy * seqMax[1]);
405 g.drawString(axes.next(), x - 3, y - 4);
408 // //Now the rectangle
409 // if (rectx2 != -1 && recty2 != -1) {
410 // g.setColor(Color.white);
412 // g.drawRect(rectx1,recty1,rectx2-rectx1,recty2-recty1);
417 * Determines the colour to use when drawing a sequence point. The colour is
418 * taken from the sequence id, with black converted to white, and then
419 * graduated from darker (at the back) to brighter (at the front) based on the
420 * z-axis coordinate of the point.
425 protected Color getSequencePointColour(SequencePoint sp)
427 SequenceI sequence = sp.getSequence();
428 Color sequenceColour = av.getSequenceColour(sequence);
429 if (sequenceColour == Color.black)
431 sequenceColour = Color.white;
433 if (av.getSelectionGroup() != null)
435 if (av.getSelectionGroup().getSequences(null).contains(sequence))
437 sequenceColour = Color.gray;
442 * graduate brighter for point in front of centre, darker if behind centre
444 float zCentre = (seqMin[2] + seqMax[2]) / 2f;
445 if (sp.coord.z > zCentre)
447 sequenceColour = ColorUtils.getGraduatedColour(sp.coord.z, 0,
448 sequenceColour, seqMax[2], sequenceColour.brighter());
450 else if (sp.coord.z < zCentre)
452 sequenceColour = ColorUtils.getGraduatedColour(sp.coord.z, seqMin[2],
453 sequenceColour.darker(), 0, sequenceColour);
456 return sequenceColour;
460 public void keyTyped(KeyEvent evt)
465 public void keyReleased(KeyEvent evt)
470 * Responds to up or down arrow key by zooming in or out, respectively
475 public void keyPressed(KeyEvent evt)
477 int keyCode = evt.getKeyCode();
478 boolean shiftDown = evt.isShiftDown();
480 if (keyCode == KeyEvent.VK_UP)
491 else if (keyCode == KeyEvent.VK_DOWN)
502 else if (shiftDown && keyCode == KeyEvent.VK_LEFT)
506 else if (shiftDown && keyCode == KeyEvent.VK_RIGHT)
510 else if (evt.getKeyChar() == 's')
512 // Cache.log.warn("DEBUG: Rectangle selection");
513 // todo not yet enabled as rectx2, recty2 are always -1
514 // need to set them in mouseDragged; JAL-1124
515 // if ((rectx2 != -1) && (recty2 != -1))
517 // rectSelect(rectx1, recty1, rectx2, recty2);
525 public void zoom(float factor)
529 scaleFactor *= factor;
534 public void mouseClicked(MouseEvent evt)
539 public void mouseEntered(MouseEvent evt)
544 public void mouseExited(MouseEvent evt)
549 public void mouseReleased(MouseEvent evt)
554 * If the mouse press is at (within 2 pixels of) a sequence point, toggles
555 * (adds or removes) the corresponding sequence as a member of the viewport
556 * selection group. This supports configuring a group in the alignment by
557 * clicking on points in the PCA display.
560 public void mousePressed(MouseEvent evt)
573 SequenceI found = findSequenceAtPoint(x, y);
577 AlignmentPanel[] aps = getAssociatedPanels();
579 for (int a = 0; a < aps.length; a++)
581 if (aps[a].av.getSelectionGroup() != null)
583 aps[a].av.getSelectionGroup().addOrRemove(found, true);
587 aps[a].av.setSelectionGroup(new SequenceGroup());
588 aps[a].av.getSelectionGroup().addOrRemove(found, true);
589 aps[a].av.getSelectionGroup()
590 .setEndRes(aps[a].av.getAlignment().getWidth() - 1);
593 PaintRefresher.Refresh(this, av.getSequenceSetId());
594 // canonical selection is sent to other listeners
602 * Sets the tooltip to the name of the sequence within 2 pixels of the mouse
603 * position, or clears the tooltip if none found
606 public void mouseMoved(MouseEvent evt)
608 SequenceI found = findSequenceAtPoint(evt.getX(), evt.getY());
610 this.setToolTipText(found == null ? null : found.getName());
614 * Action handler for a mouse drag. Rotates the display around the X axis (for
615 * up/down mouse movement) and/or the Y axis (for left/right mouse movement).
620 public void mouseDragged(MouseEvent evt)
622 int xPos = evt.getX();
623 int yPos = evt.getY();
625 if (xPos == mouseX && yPos == mouseY)
630 int xDelta = xPos - mouseX;
631 int yDelta = yPos - mouseY;
633 // Check if this is a rectangle drawing drag
634 if ((evt.getModifiers() & InputEvent.BUTTON2_MASK) != 0)
636 // rectx2 = evt.getX();
637 // recty2 = evt.getY();
641 rotate(xDelta, yDelta);
653 public void rotate(float x, float y)
655 if (x == 0f && y == 0f)
661 * get the identity transformation...
663 RotatableMatrix rotmat = new RotatableMatrix();
666 * rotate around the X axis for change in Y
667 * (mouse movement up/down); note we are equating a
668 * number of pixels with degrees of rotation here!
672 rotmat.rotate(y, Axis.X);
676 * rotate around the Y axis for change in X
677 * (mouse movement left/right)
681 rotmat.rotate(x, Axis.Y);
685 * apply the composite transformation to sequence points;
686 * update z min-max range (affects colour graduation), but not
687 * x or y min-max (as this would affect axis scaling)
689 float[] centre = getCentre();
690 float zMin = Float.MAX_VALUE;
691 float zMax = -Float.MAX_VALUE;
693 for (int i = 0; i < npoint; i++)
695 SequencePoint sp = sequencePoints.get(i);
696 sp.translate(-centre[0], -centre[1], -centre[2]);
698 // Now apply the rotation matrix
699 sp.coord = rotmat.vectorMultiply(sp.coord);
701 // Now translate back again
702 sp.translate(centre[0], centre[1], centre[2]);
704 zMin = Math.min(zMin, sp.coord.z);
705 zMax = Math.max(zMax, sp.coord.z);
712 * rotate the x/y/z axis positions
714 for (int i = 0; i < DIMS; i++)
716 axisEndPoints[i] = rotmat.vectorMultiply(axisEndPoints[i]);
721 * Answers the x/y/z coordinates that are midway between the maximum and
722 * minimum sequence point values
726 private float[] getCentre()
728 float xCentre = (seqMin[0] + seqMax[0]) / 2f;
729 float yCentre = (seqMin[1] + seqMax[1]) / 2f;
730 float zCentre = (seqMin[2] + seqMax[2]) / 2f;
732 return new float[] { xCentre, yCentre, zCentre };
736 * Adds any sequences whose displayed points are within the given rectangle to
737 * the viewport's current selection. Intended for key 's' after dragging to
738 * select a region of the PCA.
745 protected void rectSelect(int x1, int y1, int x2, int y2)
747 float[] centre = getCentre();
749 for (int i = 0; i < npoint; i++)
751 SequencePoint sp = sequencePoints.get(i);
752 int tmp1 = (int) (((sp.coord.x - centre[0]) * scaleFactor)
753 + (getWidth() / 2.0));
754 int tmp2 = (int) (((sp.coord.y - centre[1]) * scaleFactor)
755 + (getHeight() / 2.0));
757 if ((tmp1 > x1) && (tmp1 < x2) && (tmp2 > y1) && (tmp2 < y2))
761 SequenceI sequence = sp.getSequence();
762 if (!av.getSelectionGroup().getSequences(null)
765 av.getSelectionGroup().addSequence(sequence, true);
773 * Answers the first sequence found whose point on the display is within 2
774 * pixels of the given coordinates, or null if none is found
781 protected SequenceI findSequenceAtPoint(int x, int y)
783 int halfwidth = getWidth() / 2;
784 int halfheight = getHeight() / 2;
787 int pix = Math.min(getWidth(), getHeight());
788 float xWidth = Math.abs(seqMax[0] - seqMin[0]);
789 float yWidth = Math.abs(seqMax[1] - seqMin[1]);
790 float maxWidth = Math.max(xWidth, yWidth);
791 float scaleBy = pix * scaleFactor / (2f * maxWidth);
793 float[] centre = getCentre();
795 for (int i = 0; i < npoint; i++)
797 SequencePoint sp = sequencePoints.get(i);
798 int px = (int) ((sp.coord.x - centre[0]) * scaleBy)
800 int py = (int) ((sp.coord.y - centre[1]) * scaleBy)
803 if ((Math.abs(px - x) < NEARBY) && (Math.abs(py - y) < NEARBY))
812 return sequencePoints.get(found).getSequence();
821 * Answers the panel the PCA is associated with (all panels for this alignment
822 * if 'associate with all panels' is selected).
826 AlignmentPanel[] getAssociatedPanels()
830 return PaintRefresher.getAssociatedPanels(av.getSequenceSetId());
834 return new AlignmentPanel[] { ap };
838 public Color getBackgroundColour()
844 * Zooms in or out in response to mouse wheel movement
847 public void mouseWheelMoved(MouseWheelEvent e)
849 double wheelRotation = e.getPreciseWheelRotation();
850 if (wheelRotation > 0)
855 else if (wheelRotation < 0)
863 * Answers the sequence point minimum [x, y, z] values. Note these are derived
864 * when sequence points are set, but x and y values are not updated on
865 * rotation (because this would result in changes to scaling).
869 public float[] getSeqMin()
875 * Answers the sequence point maximum [x, y, z] values. Note these are derived
876 * when sequence points are set, but x and y values are not updated on
877 * rotation (because this would result in changes to scaling).
881 public float[] getSeqMax()
887 * Sets the minimum and maximum [x, y, z] positions for sequence points. For
888 * use when restoring a saved PCA from state data.
893 public void setSeqMinMax(float[] min, float[] max)