import java.awt.Color;
import java.awt.Graphics;
+import java.util.Iterator;
import jalview.api.AlignViewportI;
import jalview.datamodel.AlignmentAnnotation;
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;
+ x++;
+ continue;
}
+ // feature still in development - highlight or omit regions hidden in
+ // the alignment - currently marks them as red rows
+ boolean maskHiddenCols = false;
+ // TODO: pass visible column mask to the ContactGeometry object so it maps
+ // only visible contacts to geometry
// Bean holding mapping from contact list to pixels
final ContactGeometry cgeom = new ContactGeometry(contacts,
_aa.graphHeight);
// 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;
- boolean rowsel = false;
- if (!colsel && columnSelection != null)
+ boolean rowsel = false, containsHidden = false;
+ if (columnSelection != null)
{
if (_aa.sequenceRef == null)
{
// numbering
int s = _aa.sequenceRef.findIndex(ci.cStart);
int e = _aa.sequenceRef.findIndex(ci.cEnd);
+ if (maskHiddenCols && hasHiddenColumns)
+ {
+ // TODO: turn into function and create test !!
+ Iterator<int[]> viscont = hiddenColumns
+ .getVisContigsIterator(s, e, false);
+ containsHidden = !viscont.hasNext();
+ }
if (s > 0 && s < _aa.sequenceRef.getLength())
{
rowsel = columnSelection.intersects(s, e);
}
+
}
}
// TODO: show selected region
col = getSelectedColorForRange(min, max, contacts, ci.cStart,
ci.cEnd);
- g.setColor(col);
+ if (colsel && rowsel)
+ {
+ col = new Color(col.getBlue(), col.getGreen(), col.getRed());
+ }
+ else
+ {
+ col = new Color(col.getBlue(), col.getBlue(), col.getBlue());
+ }
}
else
{
col = getColorForRange(min, max, contacts, ci.cStart, ci.cEnd);
- g.setColor(col);
}
+ if (containsHidden)
+ {
+ col = Color.red;
+ }
+ g.setColor(col);
if (cgeom.pixels_step > 1)
{
g.fillRect(x * charWidth, ht, charWidth, 1 + cgeom.pixels_step);
}
// Shading parameters
- Color minColor = Color.white, maxColor = Color.green.darker().darker(),
- selMaxColor = Color.magenta.darker();
+ // 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)
{
ContactRange cr = cl.getRangeFor(i, j);
// average for moment - probably more interested in maxIntProj though
return jalview.util.ColorUtils.getGraduatedColour((float) cr.getMean(),
- 0, minColor, max, selMaxColor);
+ 0, selMinColor, max, selMaxColor);
}
}