/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
- * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
- * This program 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 2
- * of the License, or (at your option) any later version.
+ * This file is part of Jalview.
*
- * This program 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.
+ * 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.
+ *
+ * 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 this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.gui;
-import java.util.*;
-
-import java.awt.*;
-import java.awt.event.*;
-import javax.swing.*;
-
-import jalview.datamodel.*;
-import jalview.math.*;
+import jalview.api.RotatableCanvasI;
+import jalview.bin.Cache;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+import jalview.datamodel.SequencePoint;
+import jalview.math.RotatableMatrix;
+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.Graphics2D;
+import java.awt.Image;
+import java.awt.RenderingHints;
+import java.awt.event.InputEvent;
+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.awt.event.MouseWheelEvent;
+import java.awt.event.MouseWheelListener;
+import java.util.Vector;
+
+import javax.swing.JPanel;
+import javax.swing.ToolTipManager;
/**
* DOCUMENT ME!
* @version $Revision$
*/
public class RotatableCanvas extends JPanel implements MouseListener,
- MouseMotionListener, KeyListener
+ MouseMotionListener, KeyListener, RotatableCanvasI
{
RotatableMatrix idmat = new RotatableMatrix(3, 3);
int npoint;
- Vector points;
+ Vector<SequencePoint> points;
float[][] orig;
float scalefactor = 1;
- AlignViewport av;
+ AlignmentViewport av;
AlignmentPanel ap;
boolean applyToAllViews = false;
- // Controller controller;
+ boolean first = true;
+
public RotatableCanvas(AlignmentPanel ap)
{
this.av = ap.av;
addMouseWheelListener(new MouseWheelListener()
{
+ @Override
public void mouseWheelMoved(MouseWheelEvent e)
{
- if (e.getWheelRotation() > 0)
+ double wheelRotation = e.getPreciseWheelRotation();
+ if (wheelRotation > 0)
{
+ /*
+ * zoom in
+ */
scale = (float) (scale * 1.1);
repaint();
}
-
- else
+ else if (wheelRotation < 0)
{
+ /*
+ * zoom out
+ */
scale = (float) (scale * 0.9);
repaint();
}
repaint();
}
- public void setPoints(Vector points, int npoint)
+ @Override
+ public void setPoints(Vector<SequencePoint> points, int npoint)
{
this.points = points;
this.npoint = npoint;
- ToolTipManager.sharedInstance().registerComponent(this);
- ToolTipManager.sharedInstance().setInitialDelay(0);
- ToolTipManager.sharedInstance().setDismissDelay(10000);
-
+ if (first)
+ {
+ ToolTipManager.sharedInstance().registerComponent(this);
+ ToolTipManager.sharedInstance().setInitialDelay(0);
+ ToolTipManager.sharedInstance().setDismissDelay(10000);
+ }
prefsize = getPreferredSize();
orig = new float[npoint][3];
for (int i = 0; i < npoint; i++)
{
- SequencePoint sp = (SequencePoint) points.elementAt(i);
+ SequencePoint sp = points.elementAt(i);
for (int j = 0; j < 3; j++)
{
findWidth();
scale = findScale();
+ if (first)
+ {
- addMouseListener(this);
-
- addMouseMotionListener(this);
+ addMouseListener(this);
+ addMouseMotionListener(this);
+ }
+ first = false;
}
public void initAxes()
{
for (int j = 0; j < npoint; j++)
{
- SequencePoint sp = (SequencePoint) points.elementAt(j);
+ SequencePoint sp = points.elementAt(j);
if (sp.coord[i] >= max[i])
{
public float findScale()
{
int dim;
- int width;
+ int w;
int height;
if (getWidth() != 0)
{
- width = getWidth();
+ w = getWidth();
height = getHeight();
}
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);
}
/**
*
* @return DOCUMENT ME!
*/
+ @Override
public Dimension getPreferredSize()
{
if (prefsize != null)
*
* @return DOCUMENT ME!
*/
+ @Override
public Dimension getMinimumSize()
{
return getPreferredSize();
* DOCUMENT ME!
*
* @param g
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
+ @Override
public void paintComponent(Graphics g1)
{
if (points == null)
{
g.setFont(new Font("Verdana", Font.PLAIN, 18));
- g.drawString("Calculating PCA....", 20, getHeight() / 2);
+ g.drawString(
+ MessageManager.getString("label.calculating_pca") + "....",
+ 20, getHeight() / 2);
}
else
{
drawBackground(ig, bgColour);
drawScene(ig);
- if (drawAxes == true)
+ if (drawAxes)
{
drawAxes(ig);
}
* DOCUMENT ME!
*
* @param g
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void drawAxes(Graphics g)
{
for (int i = 0; i < 3; i++)
{
- g.drawLine(getWidth() / 2, getHeight() / 2, (int) ((axes[i][0]
- * scale * max[0]) + (getWidth() / 2)), (int) ((axes[i][1]
- * scale * max[1]) + (getHeight() / 2)));
+ g.drawLine(getWidth() / 2, getHeight() / 2,
+ (int) ((axes[i][0] * scale * max[0]) + (getWidth() / 2)),
+ (int) ((axes[i][1] * scale * max[1]) + (getHeight() / 2)));
}
}
* DOCUMENT ME!
*
* @param g
- * DOCUMENT ME!
+ * DOCUMENT ME!
* @param col
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void drawBackground(Graphics g, Color col)
{
* DOCUMENT ME!
*
* @param g
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void drawScene(Graphics g1)
{
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)
+ SequencePoint sp = points.elementAt(i);
+ int x = (int) ((sp.coord[0] - centre[0]) * scale) + halfwidth;
+ int y = (int) ((sp.coord[1] - centre[1]) * scale)
+ halfheight;
float z = sp.coord[1] - centre[2];
- if (av.getSequenceColour(sp.sequence) == Color.black)
+ SequenceI sequence = sp.getSequence();
+ if (av.getSequenceColour(sequence) == Color.black)
{
g.setColor(Color.white);
}
else
{
- g.setColor(av.getSequenceColour(sp.sequence));
+ g.setColor(av.getSequenceColour(sequence));
}
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 (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);
}
}
* DOCUMENT ME!
*
* @param evt
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
+ @Override
public void keyTyped(KeyEvent evt)
{
}
* DOCUMENT ME!
*
* @param evt
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
+ @Override
public void keyReleased(KeyEvent evt)
{
}
* DOCUMENT ME!
*
* @param evt
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
+ @Override
public void keyPressed(KeyEvent evt)
{
if (evt.getKeyCode() == KeyEvent.VK_UP)
}
else if (evt.getKeyChar() == 's')
{
- System.err.println("DEBUG: Rectangle selection"); // log.debug
-
+ Cache.log.warn("DEBUG: Rectangle selection");
+ // todo not yet enabled as rectx2, recty2 are always -1
+ // need to set them in mouseDragged
if ((rectx2 != -1) && (recty2 != -1))
{
rectSelect(rectx1, recty1, rectx2, recty2);
repaint();
}
- /**
- * DOCUMENT ME!
- *
- * @param evt
- * DOCUMENT ME!
- */
+ @Override
public void mouseClicked(MouseEvent evt)
{
}
- /**
- * DOCUMENT ME!
- *
- * @param evt
- * DOCUMENT ME!
- */
+ @Override
public void mouseEntered(MouseEvent evt)
{
}
- /**
- * DOCUMENT ME!
- *
- * @param evt
- * DOCUMENT ME!
- */
+ @Override
public void mouseExited(MouseEvent evt)
{
}
- /**
- * DOCUMENT ME!
- *
- * @param evt
- * DOCUMENT ME!
- */
+ @Override
public void mouseReleased(MouseEvent evt)
{
}
/**
- * DOCUMENT ME!
- *
- * @param evt
- * DOCUMENT ME!
+ * If the mouse press is at (within 2 pixels of) a sequence point, toggles
+ * (adds or removes) the corresponding sequence as a member of the viewport
+ * selection group. This supports configuring a group in the alignment by
+ * clicking on points in the PCA display.
*/
+ @Override
public void mousePressed(MouseEvent evt)
{
int x = evt.getX();
rectx2 = -1;
recty2 = -1;
- SequenceI found = findPoint(x, y);
+ SequenceI found = findSequenceAtPoint(x, y);
if (found != null)
{
{
aps[a].av.setSelectionGroup(new SequenceGroup());
aps[a].av.getSelectionGroup().addOrRemove(found, true);
- aps[a].av.getSelectionGroup().setEndRes(
- aps[a].av.alignment.getWidth() - 1);
+ aps[a].av.getSelectionGroup()
+ .setEndRes(aps[a].av.getAlignment().getWidth() - 1);
}
}
PaintRefresher.Refresh(this, av.getSequenceSetId());
repaint();
}
- // private void fireSequenceSelectionEvent(Selection sel) {
- // controller.handleSequenceSelectionEvent(new
- // SequenceSelectionEvent(this,sel));
- // }
+ /**
+ * Sets the tooltip to the name of the sequence within 2 pixels of the mouse
+ * position, or clears the tooltip if none found
+ */
+ @Override
public void mouseMoved(MouseEvent evt)
{
- SequenceI found = findPoint(evt.getX(), evt.getY());
+ SequenceI found = findSequenceAtPoint(evt.getX(), evt.getY());
- if (found != null)
- {
- this.setToolTipText(found.getName());
- }
- else
- {
- this.setToolTipText(null);
- }
+ this.setToolTipText(found == null ? null : found.getName());
}
/**
* DOCUMENT ME!
*
* @param evt
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
+ @Override
public void mouseDragged(MouseEvent evt)
{
mx = evt.getX();
{
rotmat.setIdentity();
- rotmat.rotate((float) (my - omy), 'x');
- rotmat.rotate((float) (mx - omx), 'y');
+ rotmat.rotate(my - omy, 'x');
+ rotmat.rotate(mx - omx, 'y');
for (int i = 0; i < npoint; i++)
{
- SequencePoint sp = (SequencePoint) points.elementAt(i);
+ SequencePoint sp = points.elementAt(i);
sp.coord[0] -= centre[0];
sp.coord[1] -= centre[1];
sp.coord[2] -= centre[2];
}
/**
- * DOCUMENT ME!
+ * Adds any sequences whose displayed points are within the given rectangle to
+ * the viewport's current selection. Intended for key 's' after dragging to
+ * select a region of the PCA.
*
* @param x1
- * DOCUMENT ME!
* @param y1
- * DOCUMENT ME!
* @param x2
- * DOCUMENT ME!
* @param y2
- * DOCUMENT ME!
*/
public void rectSelect(int x1, int y1, int x2, int y2)
{
for (int i = 0; i < npoint; i++)
{
- SequencePoint sp = (SequencePoint) points.elementAt(i);
- int tmp1 = (int) (((sp.coord[0] - centre[0]) * scale) + ((float) getWidth() / 2.0));
- int tmp2 = (int) (((sp.coord[1] - centre[1]) * scale) + ((float) getHeight() / 2.0));
+ SequencePoint sp = points.elementAt(i);
+ int tmp1 = (int) (((sp.coord[0] - centre[0]) * scale)
+ + (getWidth() / 2.0));
+ int tmp2 = (int) (((sp.coord[1] - centre[1]) * scale)
+ + (getHeight() / 2.0));
if ((tmp1 > x1) && (tmp1 < x2) && (tmp2 > y1) && (tmp2 < y2))
{
if (av != null)
{
- if (!av.getSelectionGroup().getSequences(null).contains(
- sp.sequence))
+ SequenceI sequence = sp.getSequence();
+ if (!av.getSelectionGroup().getSequences(null)
+ .contains(sequence))
{
- av.getSelectionGroup().addSequence(sp.sequence, true);
+ av.getSelectionGroup().addSequence(sequence, true);
}
}
}
}
-
- // if (changedSel) {
- // fireSequenceSelectionEvent(av.getSelection());
- // }
}
/**
- * DOCUMENT ME!
+ * 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
- * DOCUMENT ME!
* @param y
- * DOCUMENT ME!
*
- * @return DOCUMENT ME!
+ * @return
*/
- public SequenceI findPoint(int x, int y)
+ public SequenceI findSequenceAtPoint(int x, int y)
{
int halfwidth = getWidth() / 2;
int halfheight = getHeight() / 2;
for (int i = 0; i < npoint; i++)
{
- SequencePoint sp = (SequencePoint) points.elementAt(i);
- int px = (int) ((float) (sp.coord[0] - centre[0]) * scale)
+ SequencePoint sp = points.elementAt(i);
+ int px = (int) ((sp.coord[0] - centre[0]) * scale)
+ halfwidth;
- int py = (int) ((float) (sp.coord[1] - centre[1]) * scale)
+ int py = (int) ((sp.coord[1] - centre[1]) * scale)
+ halfheight;
if ((Math.abs(px - x) < 3) && (Math.abs(py - y) < 3))
if (found != -1)
{
- return ((SequencePoint) points.elementAt(found)).sequence;
+ return points.elementAt(found).getSequence();
}
else
{
}
else
{
- return new AlignmentPanel[]
- { ap };
+ return new AlignmentPanel[] { ap };
}
}
+
+ /**
+ *
+ * @return x,y,z positions of point s (index into points) under current
+ * transform.
+ */
+ public double[] getPointPosition(int s)
+ {
+ double[] pts = new double[3];
+ float[] p = points.elementAt(s).coord;
+ pts[0] = p[0];
+ pts[1] = p[1];
+ pts[2] = p[2];
+ return pts;
+ }
+
}
git://source.jalview.org / jalview.git / blobdiff