*/
package jalview.renderer;
+import java.awt.Color;
+import java.awt.Graphics;
+
import jalview.api.AlignViewportI;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.Annotation;
import jalview.datamodel.ColumnSelection;
import jalview.datamodel.ContactListI;
+import jalview.datamodel.ContactRange;
+import jalview.datamodel.HiddenColumns;
import jalview.renderer.api.AnnotationRowRendererI;
-import java.awt.Color;
-import java.awt.Font;
-import java.awt.Graphics;
-
/**
* @author jprocter
*
*/
public class ContactMapRenderer implements AnnotationRowRendererI
{
- /*
- *
- * // TODO Auto-generated method stub
- void drawProfileDensity(Graphics g, AlignmentAnnotation _aa,
- Annotation[] aa_annotations, int sRes, int eRes, float min,
- float max, int y)
- {
- *
- *
- */
@Override
public void renderRow(Graphics g, int charWidth, int charHeight,
boolean hasHiddenColumns, AlignViewportI viewport,
- ColumnSelection columnSelection, AlignmentAnnotation _aa,
- Annotation[] aa_annotations, int sRes, int eRes, float min,
- float max, int y)
+ 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;
}
- Font ofont = g.getFont();
eRes = Math.min(eRes, aa_annotations.length);
int x = 0, y2 = y;
column = sRes + x;
if (hasHiddenColumns)
{
- column = columnSelection.adjustForHiddenColumns(column);
+ column = hiddenColumns.visibleToAbsoluteColumn(column);
+ }
+ // TODO: highlight columns selected
+ boolean colsel = false;
+ if (columnSelection != null)
+ {
+ colsel = columnSelection.contains(column);
}
if (column > aaMax)
x++;
continue;
}
- /*
- * {profile type, #values, total count, char1, pct1, char2, pct2...}
- */
ContactListI contacts = viewport.getContactList(_aa, column);
-
if (contacts == null)
{
- return;
+ x++;
+ continue;
}
+ // Bean holding mapping from contact list to pixels
+ final ContactGeometry cgeom = new ContactGeometry(contacts,
+ _aa.graphHeight);
-
- // cell height to render
- double scale = (_aa.graphHeight < contacts.getContactHeight()) ? 1
- : (((double) _aa.graphHeight) / (double) contacts
- .getContactHeight());
- // distance between contact map per cell
- int step = (int) ((contacts.getContactHeight()) * scale / _aa.graphHeight);
-
- // profl[1] is the number of values in the profile
- for (int stp = 0, ht = y2, eht = y2 - _aa.graphHeight; ht > eht; ht -= scale, stp++)
+ for (int ht = y2, eht = y2
+ - _aa.graphHeight; ht >= eht; ht -= cgeom.pixels_step)
{
- g.setColor(contacts
- .getColorForScore((int) (stp * step * ((double) _aa.graphHeight / (double) contacts
- .getContactHeight()))));
+ 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;
+ 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 || rowsel)
+ {
- if (scale > 1)
+ 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);
+ }
+ else
+ {
+ 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
{
- g.fillRect(x * charWidth, ht, charWidth, 1 + (int) scale);
- } else {
g.drawLine(x * charWidth, ht, (x + 1) * charWidth, ht);
}
}
}
}
+
+ // Shading parameters
+ // 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 jalview.util.ColorUtils.getGraduatedColour(value, 0, minColor,
+ max, maxColor);
+ }
+
+ public Color getColorForRange(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 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);
+ }
+
}
git://source.jalview.org / jalview.git / blobdiff