{
/**
* bean holding colours for shading
+ *
* @author jprocter
*
*/
*/
Color selMinColor, selMaxColor;
+ /**
+ *
+ * @param no_data - colour when no data available
+ * @param hidden - colour if this row is hidden
+ * @param maxColor - colour for maximum value of contact
+ * @param minColor - colour for minimum value of contact
+ * @param selMinColor - min colour if the contact has been selected
+ * @param selMaxColor - max colour if contact is selected
+ */
public Shading(Color no_data, Color hidden, Color maxColor,
Color minColor, Color selMinColor, Color selMaxColor)
{
/**
* build an EBI-AlphaFold style renderer of PAE matrices
+ *
* @return
*/
public static ContactMapRenderer newPAERenderer()
{
return new Shading(Color.pink, Color.red,
- new Color(246, 252, 243), new Color(0, 60, 26),
- new Color(26, 0, 60), new Color(243, 246, 252));
+ new Color(247, 252, 245), new Color(0, 68, 28),
+ new Color(28, 0, 68), new Color(245,247,252));
}
};
}
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);
+ if (cm==null)
+ {
+ return;
+ }
while (x < eRes - sRes)
{
column = sRes + x;
continue;
}
// ContactListI from viewport can map column -> group
- Color gpcol = (cm==null) ? Color.white: contacts.getColourForGroup(); // cm.getColourForGroup(cm.getGroupsFor(column));
-
+ 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;
- // TODO: optionally pass visible column mask to the ContactGeometry object so it maps
+ // TODO: optionally pass visible column mask to the ContactGeometry object
+ // so it maps
// only visible contacts to geometry
// Bean holding mapping from contact list to pixels
- // TODO: allow bracketing/limiting of range on contacts to render (like visible column mask but more flexible?)
-
+ // TODO: allow bracketing/limiting of range on contacts to render (like
+ // visible column mask but more flexible?)
+
// COntactListI provides mapping for column -> cm-groupmapping
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);
// cstart = (int) Math.floor(((double) y2 - ht) * contacts_per_pixel);
// cend = (int) Math.min(contact_height,
// Math.ceil(cstart + contacts_per_pixel * pixels_step));
Color col;
- boolean rowsel = false, containsHidden = false;
+ boolean rowsel = false;
+ boolean containsHidden = false;
if (columnSelection != null)
{
- rowsel = cgeom.intersects(ci, columnSelection, hiddenColumns, maskHiddenCols);
+ rowsel = cgeom.intersects(ci, columnSelection, hiddenColumns,
+ maskHiddenCols);
}
// TODO: show selected region
if (colsel || rowsel)
{
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.getRed()+gpcol.getRed()))/2f),
- (int)(((float)(col.getGreen()+gpcol.getGreen()))/2f),
- (int)(((float)(col.getBlue()+gpcol.getBlue()))/2f));
+ col = new Color(
+ (int) (((float) (col.getRed() + gpcol.getRed())) / 2f),
+ (int) (((float) (col.getGreen() + gpcol.getGreen()))
+ / 2f),
+ (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, 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++;
Color shadeFor(float min, float max, float value)
{
- return jalview.util.ColorUtils.getGraduatedColour(value, 0, shade.minColor,
- max, shade.maxColor);
+ return jalview.util.ColorUtils.getGraduatedColour(value, 0,
+ shade.minColor, max, shade.maxColor);
}
public Color getColorForRange(float min, float max, ContactListI cl,
{
ContactRange cr = cl.getRangeFor(i, j);
// average for moment - probably more interested in maxIntProj though
- return jalview.util.ColorUtils.getGraduatedColour((float) cr.getMean(),
+ return jalview.util.ColorUtils.getGraduatedColour((float) cr.getMin(),
0, shade.selMinColor, max, shade.selMaxColor);
}
git://source.jalview.org / jalview.git / blobdiff