int npoint;
- Vector points;
+ Vector<SequencePoint> points;
float[][] orig;
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)
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();
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);
+ SequencePoint sp = points.elementAt(i);
int tmp1 = (int) ((sp.coord[0] - centre[0]) * scale
- + (float) getSize().width / 2.0);
+ + getSize().width / 2.0);
int tmp2 = (int) ((sp.coord[1] - centre[1]) * scale
- + (float) getSize().height / 2.0);
+ + 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
{