/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- *
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.appletgui;
-import java.util.*;
-
-import java.awt.*;
-import java.awt.event.*;
-
-import jalview.datamodel.*;
-import jalview.math.*;
-import jalview.util.*;
+import jalview.api.RotatableCanvasI;
+import jalview.datamodel.Point;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+import jalview.datamodel.SequencePoint;
+import jalview.math.RotatableMatrix;
+import jalview.math.RotatableMatrix.Axis;
+import jalview.util.MessageManager;
+import jalview.viewmodel.AlignmentViewport;
+
+import java.awt.Color;
+import java.awt.Dimension;
+import java.awt.Font;
+import java.awt.Graphics;
+import java.awt.Image;
+import java.awt.Panel;
+import java.awt.event.KeyEvent;
+import java.awt.event.KeyListener;
+import java.awt.event.MouseEvent;
+import java.awt.event.MouseListener;
+import java.awt.event.MouseMotionListener;
+import java.util.List;
public class RotatableCanvas extends Panel implements MouseListener,
- MouseMotionListener, KeyListener
+ MouseMotionListener, KeyListener, RotatableCanvasI
{
- RotatableMatrix idmat = new RotatableMatrix(3, 3);
-
- RotatableMatrix objmat = new RotatableMatrix(3, 3);
-
- RotatableMatrix rotmat = new RotatableMatrix(3, 3);
+ private static final int DIMS = 3;
String tooltip;
- int toolx, tooly;
+ int toolx;
+
+ int tooly;
// RubberbandRectangle rubberband;
boolean drawAxes = true;
- int omx = 0;
-
- int mx = 0;
+ int mouseX = 0;
- int omy = 0;
-
- int my = 0;
+ int mouseY = 0;
Image img;
Dimension prefsize;
- float centre[] = new float[3];
+ Point centre;
- float width[] = new float[3];
+ float[] width = new float[DIMS];
- float max[] = new float[3];
+ float[] max = new float[DIMS];
- float min[] = new float[3];
+ float[] min = new float[DIMS];
float maxwidth;
int npoint;
- Vector points;
+ List<SequencePoint> points;
- float[][] orig;
+ Point[] orig;
- float[][] axes;
+ Point[] axisEndPoints;
int startx;
float scalefactor = 1;
- AlignViewport av;
+ AlignmentViewport av;
boolean showLabels = false;
- public RotatableCanvas(AlignViewport av)
+ public RotatableCanvas(AlignmentViewport viewport)
{
- this.av = av;
+ this.av = viewport;
+ axisEndPoints = new Point[DIMS];
}
public void showLabels(boolean b)
repaint();
}
- public void setPoints(Vector points, int npoint)
+ @Override
+ public void setPoints(List<SequencePoint> points, int npoint)
{
this.points = points;
this.npoint = npoint;
PaintRefresher.Register(this, av.getSequenceSetId());
prefsize = getPreferredSize();
- orig = new float[npoint][3];
+ orig = new Point[npoint];
for (int i = 0; i < npoint; i++)
{
- SequencePoint sp = (SequencePoint) points.elementAt(i);
- for (int j = 0; j < 3; j++)
- {
- orig[i][j] = sp.coord[j];
- }
+ SequencePoint sp = points.get(i);
+ orig[i] = sp.coord;
}
- // Initialize the matrices to identity
- for (int i = 0; i < 3; i++)
- {
- for (int j = 0; j < 3; j++)
- {
- if (i != j)
- {
- idmat.addElement(i, j, 0);
- objmat.addElement(i, j, 0);
- rotmat.addElement(i, j, 0);
- }
- else
- {
- idmat.addElement(i, j, 0);
- objmat.addElement(i, j, 0);
- rotmat.addElement(i, j, 0);
- }
- }
- }
-
- axes = new float[3][3];
- initAxes();
+ resetAxes();
findCentre();
findWidth();
* super.removeNotify(); }
*/
- public void initAxes()
+ /**
+ * Resets axes to the initial state: x-axis to the right, y-axis up, z-axis to
+ * back (so obscured in a 2-D display)
+ */
+ public void resetAxes()
{
- for (int i = 0; i < 3; i++)
- {
- for (int j = 0; j < 3; j++)
- {
- if (i != j)
- {
- axes[i][j] = 0;
- }
- else
- {
- axes[i][j] = 1;
- }
- }
- }
+ axisEndPoints[0] = new Point(1f, 0f, 0f);
+ axisEndPoints[1] = new Point(0f, 1f, 0f);
+ axisEndPoints[2] = new Point(0f, 0f, 1f);
}
+ /**
+ * Computes and saves the maximum and minimum (x, y, z) positions of any
+ * sequence point, and also the min-max range (width) for each dimension, and
+ * the maximum width for all dimensions
+ */
public void findWidth()
{
max = new float[3];
min = new float[3];
- max[0] = (float) -1e30;
- max[1] = (float) -1e30;
- max[2] = (float) -1e30;
+ max[0] = Float.MIN_VALUE;
+ max[1] = Float.MIN_VALUE;
+ max[2] = Float.MIN_VALUE;
- min[0] = (float) 1e30;
- min[1] = (float) 1e30;
- min[2] = (float) 1e30;
+ min[0] = Float.MAX_VALUE;
+ min[1] = Float.MAX_VALUE;
+ min[2] = Float.MAX_VALUE;
- for (int i = 0; i < 3; i++)
+ for (SequencePoint sp : points)
{
- for (int j = 0; j < npoint; j++)
- {
- SequencePoint sp = (SequencePoint) points.elementAt(j);
- if (sp.coord[i] >= max[i])
- {
- max[i] = sp.coord[i];
- }
- if (sp.coord[i] <= min[i])
- {
- min[i] = sp.coord[i];
- }
- }
+ max[0] = Math.max(max[0], sp.coord.x);
+ max[1] = Math.max(max[1], sp.coord.y);
+ max[2] = Math.max(max[2], sp.coord.z);
+ min[0] = Math.min(min[0], sp.coord.x);
+ min[1] = Math.min(min[1], sp.coord.y);
+ min[2] = Math.min(min[2], sp.coord.z);
}
- // System.out.println("xmax " + max[0] + " min " + min[0]);
- // System.out.println("ymax " + max[1] + " min " + min[1]);
- // System.out.println("zmax " + max[2] + " min " + min[2]);
-
width[0] = Math.abs(max[0] - min[0]);
width[1] = Math.abs(max[1] - min[1]);
width[2] = Math.abs(max[2] - min[2]);
- maxwidth = width[0];
-
- if (width[1] > width[0])
- {
- maxwidth = width[1];
- }
- if (width[2] > width[1])
- {
- maxwidth = width[2];
- }
-
- // System.out.println("Maxwidth = " + maxwidth);
+ maxwidth = Math.max(width[0], Math.max(width[1], width[2]));
}
public float findScale()
{
- int dim, width, height;
+ int dim, w, height;
if (getSize().width != 0)
{
- width = getSize().width;
+ w = getSize().width;
height = getSize().height;
}
else
{
- width = prefsize.width;
+ w = prefsize.width;
height = prefsize.height;
}
- if (width < height)
+ if (w < height)
{
- dim = width;
+ dim = w;
}
else
{
dim = height;
}
- return (float) (dim * scalefactor / (2 * maxwidth));
+ return dim * scalefactor / (2 * maxwidth);
}
+ /**
+ * Computes and saves the position of the centre of the view
+ */
public void findCentre()
{
- // Find centre coordinate
findWidth();
- centre[0] = (max[0] + min[0]) / 2;
- centre[1] = (max[1] + min[1]) / 2;
- centre[2] = (max[2] + min[2]) / 2;
+ float x = (max[0] + min[0]) / 2;
+ float y = (max[1] + min[1]) / 2;
+ float z = (max[2] + min[2]) / 2;
- // System.out.println("Centre x " + centre[0]);
- // System.out.println("Centre y " + centre[1]);
- // System.out.println("Centre z " + centre[2]);
+ centre = new Point(x, y, z);
}
+ @Override
public Dimension getPreferredSize()
{
if (prefsize != null)
}
}
+ @Override
public Dimension getMinimumSize()
{
return getPreferredSize();
}
+ @Override
public void update(Graphics g)
{
paint(g);
}
+ @Override
public void paint(Graphics g)
{
if (points == null)
{
g.setFont(new Font("Verdana", Font.PLAIN, 18));
- g.drawString("Calculating PCA....", 20, getSize().height / 2);
+ g.drawString(
+ MessageManager.getString("label.calculating_pca") + "....",
+ 20, getSize().height / 2);
}
else
{
drawBackground(ig, Color.black);
drawScene(ig);
- if (drawAxes == true)
+ if (drawAxes)
{
drawAxes(ig);
}
for (int i = 0; i < 3; i++)
{
g.drawLine(getSize().width / 2, getSize().height / 2,
- (int) (axes[i][0] * scale * max[0] + getSize().width / 2),
- (int) (axes[i][1] * scale * max[1] + getSize().height / 2));
+ (int) (axisEndPoints[i].x * scale * max[0]
+ + getSize().width / 2),
+ (int) (axisEndPoints[i].y * scale * max[1]
+ + getSize().height / 2));
}
}
public void drawScene(Graphics g)
{
- // boolean darker = false;
-
- int halfwidth = getSize().width / 2;
- int halfheight = getSize().height / 2;
-
for (int i = 0; i < npoint; i++)
{
- SequencePoint sp = (SequencePoint) points.elementAt(i);
- int x = (int) ((float) (sp.coord[0] - centre[0]) * scale) + halfwidth;
- int y = (int) ((float) (sp.coord[1] - centre[1]) * scale)
- + halfheight;
- float z = sp.coord[1] - centre[2];
-
- if (av.getSequenceColour(sp.sequence) == Color.black)
- {
- g.setColor(Color.white);
- }
- else
- {
- g.setColor(av.getSequenceColour(sp.sequence));
- }
-
+ SequencePoint sp = points.get(i);
+ SequenceI sequence = sp.getSequence();
+ Color sequenceColour = av.getSequenceColour(sequence);
+ g.setColor(
+ sequenceColour == Color.black ? Color.white : sequenceColour);
if (av.getSelectionGroup() != null)
{
- if (av.getSelectionGroup().getSequences(null)
- .contains(((SequencePoint) points.elementAt(i)).sequence))
+ if (av.getSelectionGroup().getSequences(null).contains(sequence))
{
g.setColor(Color.gray);
}
}
- if (z < 0)
+
+ if (sp.coord.z < centre.z)
{
g.setColor(g.getColor().darker());
}
+ int halfwidth = getSize().width / 2;
+ int halfheight = getSize().height / 2;
+ int x = (int) ((sp.coord.x - centre.x) * scale) + halfwidth;
+ int y = (int) ((sp.coord.y - centre.y) * scale) + halfheight;
g.fillRect(x - 3, y - 3, 6, 6);
+
if (showLabels)
{
g.setColor(Color.red);
- g.drawString(
- ((SequencePoint) points.elementAt(i)).sequence.getName(),
- x - 3, y - 4);
+ g.drawString(sequence.getName(), x - 3, y - 4);
}
}
}
- public Dimension minimumsize()
- {
- return prefsize;
- }
-
- public Dimension preferredsize()
- {
- return prefsize;
- }
-
+ @Override
public void keyTyped(KeyEvent evt)
{
}
+ @Override
public void keyReleased(KeyEvent evt)
{
}
+ @Override
public void keyPressed(KeyEvent evt)
{
- if (evt.getKeyCode() == KeyEvent.VK_UP)
+ boolean shiftDown = evt.isShiftDown();
+ int keyCode = evt.getKeyCode();
+ if (keyCode == KeyEvent.VK_UP)
+ {
+ if (shiftDown)
+ {
+ rotate(0f, -1f);
+ }
+ else
+ {
+ zoom(1.1f);
+ }
+ }
+ else if (keyCode == KeyEvent.VK_DOWN)
+ {
+ if (shiftDown)
+ {
+ rotate(0f, 1f);
+ }
+ else
+ {
+ zoom(0.9f);
+ }
+ }
+ else if (shiftDown && keyCode == KeyEvent.VK_LEFT)
{
- scalefactor = (float) (scalefactor * 1.1);
- scale = findScale();
+ rotate(1f, 0f);
}
- else if (evt.getKeyCode() == KeyEvent.VK_DOWN)
+ else if (shiftDown && keyCode == KeyEvent.VK_RIGHT)
{
- scalefactor = (float) (scalefactor * 0.9);
- scale = findScale();
+ rotate(-1f, 0f);
}
else if (evt.getKeyChar() == 's')
{
repaint();
}
- public void printPoints()
- {
- for (int i = 0; i < npoint; i++)
- {
- SequencePoint sp = (SequencePoint) points.elementAt(i);
- Format.print(System.out, "%5d ", i);
- for (int j = 0; j < 3; j++)
- {
- Format.print(System.out, "%13.3f ", sp.coord[j]);
- }
- System.out.println();
- }
- }
-
+ @Override
public void mouseClicked(MouseEvent evt)
{
}
+ @Override
public void mouseEntered(MouseEvent evt)
{
}
+ @Override
public void mouseExited(MouseEvent evt)
{
}
+ @Override
public void mouseReleased(MouseEvent evt)
{
}
+ @Override
public void mousePressed(MouseEvent evt)
{
int x = evt.getX();
int y = evt.getY();
- mx = x;
- my = y;
-
- omx = mx;
- omy = my;
+ mouseX = x;
+ mouseY = y;
startx = x;
starty = y;
rectx2 = -1;
recty2 = -1;
- SequenceI found = findPoint(x, y);
+ SequenceI found = findSequenceAtPoint(x, y);
if (found != null)
{
- // TODO: applet PCA is not associatable with multi-panels - only parent view
+ // TODO: applet PCA is not associatable with multi-panels - only parent
+ // view
if (av.getSelectionGroup() != null)
{
av.getSelectionGroup().addOrRemove(found, true);
- av.getSelectionGroup().setEndRes(av.alignment.getWidth() - 1);
+ av.getSelectionGroup().setEndRes(av.getAlignment().getWidth() - 1);
}
else
{
av.setSelectionGroup(new SequenceGroup());
av.getSelectionGroup().addOrRemove(found, true);
- av.getSelectionGroup().setEndRes(av.alignment.getWidth() - 1);
+ av.getSelectionGroup().setEndRes(av.getAlignment().getWidth() - 1);
}
PaintRefresher.Refresh(this, av.getSequenceSetId());
repaint();
}
+ @Override
public void mouseMoved(MouseEvent evt)
{
- SequenceI found = findPoint(evt.getX(), evt.getY());
+ SequenceI found = findSequenceAtPoint(evt.getX(), evt.getY());
if (found == null)
{
tooltip = null;
repaint();
}
+ @Override
public void mouseDragged(MouseEvent evt)
{
- mx = evt.getX();
- my = evt.getY();
-
- rotmat.setIdentity();
-
- rotmat.rotate((float) (my - omy), 'x');
- rotmat.rotate((float) (mx - omx), 'y');
+ int xPos = evt.getX();
+ int yPos = evt.getY();
- for (int i = 0; i < npoint; i++)
+ if (xPos == mouseX && yPos == mouseY)
{
- SequencePoint sp = (SequencePoint) points.elementAt(i);
- sp.coord[0] -= centre[0];
- sp.coord[1] -= centre[1];
- sp.coord[2] -= centre[2];
-
- // Now apply the rotation matrix
- sp.coord = rotmat.vectorMultiply(sp.coord);
-
- // Now translate back again
- sp.coord[0] += centre[0];
- sp.coord[1] += centre[1];
- sp.coord[2] += centre[2];
+ return;
}
- for (int i = 0; i < 3; i++)
- {
- axes[i] = rotmat.vectorMultiply(axes[i]);
- }
- omx = mx;
- omy = my;
+ int xDelta = xPos - mouseX;
+ int yDelta = yPos - mouseY;
- paint(this.getGraphics());
+ rotate(xDelta, yDelta);
+ repaint();
}
public void rectSelect(int x1, int y1, int x2, int y2)
// boolean changedSel = false;
for (int i = 0; i < npoint; i++)
{
- SequencePoint sp = (SequencePoint) points.elementAt(i);
- int tmp1 = (int) ((sp.coord[0] - centre[0]) * scale + (float) getSize().width / 2.0);
- int tmp2 = (int) ((sp.coord[1] - centre[1]) * scale + (float) getSize().height / 2.0);
+ SequencePoint sp = points.get(i);
+ int tmp1 = (int) ((sp.coord.x - centre.x) * scale
+ + getSize().width / 2.0);
+ int tmp2 = (int) ((sp.coord.y - centre.y) * scale
+ + getSize().height / 2.0);
+ SequenceI sequence = sp.getSequence();
if (tmp1 > x1 && tmp1 < x2 && tmp2 > y1 && tmp2 < y2)
{
if (av != null)
{
- if (!av.getSelectionGroup().getSequences(null)
- .contains(sp.sequence))
+ if (!av.getSelectionGroup().getSequences(null).contains(sequence))
{
- av.getSelectionGroup().addSequence(sp.sequence, true);
+ av.getSelectionGroup().addSequence(sequence, true);
}
}
}
}
}
- public SequenceI findPoint(int x, int y)
+ /**
+ * Answers the first sequence found whose point on the display is within 2
+ * pixels of the given coordinates, or null if none is found
+ *
+ * @param x
+ * @param y
+ *
+ * @return
+ */
+ public SequenceI findSequenceAtPoint(int x, int y)
{
-
int halfwidth = getSize().width / 2;
int halfheight = getSize().height / 2;
for (int i = 0; i < npoint; i++)
{
- SequencePoint sp = (SequencePoint) points.elementAt(i);
- int px = (int) ((float) (sp.coord[0] - centre[0]) * scale)
- + halfwidth;
- int py = (int) ((float) (sp.coord[1] - centre[1]) * scale)
- + halfheight;
+ SequencePoint sp = points.get(i);
+ int px = (int) ((sp.coord.x - centre.x) * scale) + halfwidth;
+ int py = (int) ((sp.coord.y - centre.y) * scale) + halfheight;
if (Math.abs(px - x) < 3 && Math.abs(py - y) < 3)
{
found = i;
+ break;
}
}
+
if (found != -1)
{
- return ((SequencePoint) points.elementAt(found)).sequence;
+ return points.get(found).getSequence();
}
else
{
}
}
+ /**
+ * Resets the view to initial state (no rotation)
+ */
+ public void resetView()
+ {
+ img = null;
+ resetAxes();
+ }
+
+ @Override
+ public void zoom(float factor)
+ {
+ if (factor > 0f)
+ {
+ scalefactor *= factor;
+ }
+ scale = findScale();
+ }
+
+ @Override
+ public void rotate(float x, float y)
+ {
+ if (x == 0f && y == 0f)
+ {
+ return;
+ }
+
+ /*
+ * get the identity transformation...
+ */
+ RotatableMatrix rotmat = new RotatableMatrix();
+
+ /*
+ * rotate around the X axis for change in Y
+ * (mouse movement up/down); note we are equating a
+ * number of pixels with degrees of rotation here!
+ */
+ if (y != 0)
+ {
+ rotmat.rotate(y, Axis.X);
+ }
+
+ /*
+ * rotate around the Y axis for change in X
+ * (mouse movement left/right)
+ */
+ if (x != 0)
+ {
+ rotmat.rotate(x, Axis.Y);
+ }
+
+ /*
+ * apply the composite transformation to sequence points
+ */
+ for (int i = 0; i < npoint; i++)
+ {
+ SequencePoint sp = points.get(i);
+ sp.translate(-centre.x, -centre.y, -centre.z);
+
+ // Now apply the rotation matrix
+ sp.coord = rotmat.vectorMultiply(sp.coord);
+
+ // Now translate back again
+ sp.translate(centre.x, centre.y, centre.z);
+ }
+
+ /*
+ * rotate the x/y/z axis positions
+ */
+ for (int i = 0; i < DIMS; i++)
+ {
+ axisEndPoints[i] = rotmat.vectorMultiply(axisEndPoints[i]);
+ }
+ }
+
}
git://source.jalview.org / jalview.git / blobdiff