{
column = hiddenColumns.visibleToAbsoluteColumn(column);
}
- // // TODO: highlight columns selected
- // boolean colsel = false;
- // if (columnSelection != null)
- // {
- // colsel = columnSelection.contains(column);
- // }
+ // TODO: highlight columns selected
+ boolean colsel = false;
+ if (columnSelection != null)
+ {
+ colsel = columnSelection.contains(column);
+ }
if (column > aaMax)
{
x++;
continue;
}
- if (_aa.sequenceRef != null)
- {
- // get the sequence position for the column
- column = _aa.sequenceRef.findPosition(column) - 1;
- }
ContactListI contacts = viewport.getContactList(_aa, column);
if (contacts == null)
{
- return;
- }
- int contact_height = contacts.getContactHeight();
- // fractional number of contacts covering each pixel
- double contacts_per_pixel = ((double) contact_height)
- / ((double) _aa.graphHeight);
-
- int pixels_step;
-
- if (contacts_per_pixel >= 1)
- {
- // many contacts rendered per pixel
- pixels_step = 1;
- }
- else
- {
- // pixel height for each contact
- pixels_step = (int) Math
- .ceil(((double) _aa.graphHeight) / (double) contact_height);
+ x++;
+ continue;
}
+ // Bean holding mapping from contact list to pixels
+ final ContactGeometry cgeom = new ContactGeometry(contacts,
+ _aa.graphHeight);
- int cstart = 0, cend;
-
- for (int ht = y2,
- eht = y2 - _aa.graphHeight; ht >= eht; ht -= pixels_step)
+ for (int ht = y2, eht = y2
+ - _aa.graphHeight; ht >= eht; ht -= cgeom.pixels_step)
{
- cstart = (int) Math.floor(((double) y2 - ht) * contacts_per_pixel);
- cend = (int) Math.min(contact_height,
- Math.ceil(cstart + contacts_per_pixel * pixels_step));
+ ContactGeometry.contactInterval ci = cgeom.mapFor(y2 - ht,
+ y2 - ht + cgeom.pixels_step);
+ // cstart = (int) Math.floor(((double) y2 - ht) * contacts_per_pixel);
+ // cend = (int) Math.min(contact_height,
+ // Math.ceil(cstart + contacts_per_pixel * pixels_step));
// TODO show maximum colour for range - sort of done
// also need a 'getMaxPosForRange(start,end)' to accurately render
- Color col = getColorForRange(min, max, contacts, cstart, cend);
-
+ Color col;
+ boolean rowsel = false;
+ if (columnSelection != null)
+ {
+ if (_aa.sequenceRef == null)
+ {
+ rowsel = columnSelection.intersects(ci.cStart, ci.cEnd);
+ }
+ else
+ {
+ // TODO check we have correctly mapped cstart to local sequence
+ // numbering
+ int s = _aa.sequenceRef.findIndex(ci.cStart);
+ int e = _aa.sequenceRef.findIndex(ci.cEnd);
+ if (s > 0 && s < _aa.sequenceRef.getLength())
+ {
+ rowsel = columnSelection.intersects(s, e);
+ }
+ }
+ }
// TODO: show selected region
- // if (colsel || columnSelection!=null &&
- // columnSelection.intersects(cstart,cend))
- // {
- // g.setColor(col.brighter());
- // }
- // else
+ if (colsel || rowsel)
{
+
+ col = getSelectedColorForRange(min, max, contacts, ci.cStart,
+ ci.cEnd);
+ if (colsel && rowsel)
+ {
+ col = new Color(col.getBlue(), col.getGreen(), col.getRed());
+ }
+ else
+ {
+ col = new Color(col.getBlue(), col.getBlue(), col.getBlue());
+ }
g.setColor(col);
}
- if (pixels_step > 1)
+ else
{
- g.fillRect(x * charWidth, ht, charWidth, 1 + pixels_step);
+ col = getColorForRange(min, max, contacts, ci.cStart, ci.cEnd);
+ g.setColor(col);
+ }
+ if (cgeom.pixels_step > 1)
+ {
+ g.fillRect(x * charWidth, ht, charWidth, 1 + cgeom.pixels_step);
}
else
{
}
// Shading parameters
- Color minColor = Color.white, maxColor = Color.magenta;
+ // currently hardwired for alphafold
+ Color maxColor = new Color(246, 252, 243),
+ minColor = new Color(0, 60, 26),
+ selMinColor = new Color(26, 0, 60),
+ selMaxColor = new Color(243, 246, 252);
Color shadeFor(float min, float max, float value)
{
return shadeFor(min, max, (float) cr.getMean());
}
+ public Color getSelectedColorForRange(float min, float max,
+ ContactListI cl, int i, int j)
+ {
+ ContactRange cr = cl.getRangeFor(i, j);
+ // average for moment - probably more interested in maxIntProj though
+ return jalview.util.ColorUtils.getGraduatedColour((float) cr.getMean(),
+ 0, selMinColor, max, selMaxColor);
+ }
+
}