* shown when no data available from map
*/
Color no_data;
-
/**
* shown for region not currently visible - should normally not see this
*/
Color hidden;
-
/**
* linear shading scheme min/max
*/
HiddenColumns hiddenColumns, ColumnSelection columnSelection,
AlignmentAnnotation _aa, Annotation[] aa_annotations, int sRes,
int eRes, float min, float max, int y)
- {
+ {
if (sRes > aa_annotations.length)
{
return;
}
eRes = Math.min(eRes, aa_annotations.length);
- int x = 0, y2 = y;
-
- g.setColor(shade.no_data);
-
- g.drawLine(x, y2, (eRes - sRes) * charWidth, y2);
+ int x = 0, topY = y;
+ // uncomment below to render whole area of matrix as pink
+ // g.setColor(shade.no_data);
+ // g.fillRect(x, topY-_aa.height, (eRes - sRes) * charWidth, _aa.graphHeight);
+
+ boolean showGroups = _aa.isShowGroupsForContactMatrix();
int column;
int aaMax = aa_annotations.length - 1;
ContactMatrixI cm = viewport.getContactMatrix(_aa);
// ContactListI from viewport can map column -> group
Color gpcol = (cm == null) ? Color.white
: contacts.getColourForGroup(); // cm.getColourForGroup(cm.getGroupsFor(column));
-
// feature still in development - highlight or omit regions hidden in
// the alignment - currently marks them as red rows
boolean maskHiddenCols = false;
final ContactGeometry cgeom = new ContactGeometry(contacts,
_aa.graphHeight);
- for (int ht = y2, eht = y2
- - _aa.graphHeight; ht >= eht; ht -= cgeom.pixels_step)
+ for (int ht = 0, botY = topY
+ - _aa.height; ht < _aa.graphHeight; ht += cgeom.pixels_step)
{
-
- ContactGeometry.contactInterval ci = cgeom.mapFor(y2 - ht,
- y2 - ht + cgeom.pixels_step);
+ ContactGeometry.contactInterval ci = cgeom.mapFor(ht,
+ 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));
{
col = shade.hidden;
}
- if (gpcol != null && gpcol != Color.white)
+ if (showGroups && gpcol != null && gpcol != Color.white)
{
// todo - could overlay group as a transparent rectangle ?
col = new Color(
(int) (((float) (col.getBlue() + gpcol.getBlue())) / 2f));
}
g.setColor(col);
-
if (cgeom.pixels_step > 1)
{
- g.fillRect(x * charWidth, ht, charWidth, 1 + cgeom.pixels_step);
+ g.fillRect(x * charWidth, botY+ht, charWidth, 1 + cgeom.pixels_step);
}
else
{
- g.drawLine(x * charWidth, ht, (x + 1) * charWidth, ht);
+ g.drawLine(x * charWidth, botY+ht, (x + 1) * charWidth, botY+ht);
}
}
x++;