/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, 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.SequenceGroup;
+import jalview.datamodel.SequenceI;
+import jalview.datamodel.SequencePoint;
+import jalview.math.RotatableMatrix;
+import jalview.util.Format;
+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.Vector;
public class RotatableCanvas extends Panel 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;
boolean showLabels = false;
- public RotatableCanvas(AlignViewport av)
+ public RotatableCanvas(AlignmentViewport av)
{
this.av = av;
}
repaint();
}
+ @Override
public void setPoints(Vector points, int npoint)
{
this.points = points;
{
for (int j = 0; j < npoint; j++)
{
- SequencePoint sp = (SequencePoint) points.elementAt(j);
+ SequencePoint sp = points.elementAt(j);
if (sp.coord[i] >= max[i])
{
max[i] = sp.coord[i];
dim = height;
}
- return (float) (dim * scalefactor / (2 * maxwidth));
+ return dim * scalefactor / (2 * maxwidth);
}
public void findCentre()
// System.out.println("Centre z " + centre[2]);
}
+ @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
{
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))
+ .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);
}
}
}
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)
{
for (int i = 0; i < npoint; i++)
{
- SequencePoint sp = (SequencePoint) points.elementAt(i);
+ SequencePoint sp = points.elementAt(i);
Format.print(System.out, "%5d ", i);
for (int j = 0; j < 3; j++)
{
}
}
+ @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();
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());
repaint();
}
+ @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];
// 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.elementAt(i);
+ int tmp1 = (int) ((sp.coord[0] - centre[0]) * scale
+ + getSize().width / 2.0);
+ int tmp2 = (int) ((sp.coord[1] - centre[1]) * 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))
+ .contains(sequence))
{
- av.getSelectionGroup().addSequence(sp.sequence, true);
+ av.getSelectionGroup().addSequence(sequence, true);
}
}
}
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
{
git://source.jalview.org / jalview.git / blobdiff