*/
package jalview.renderer;
+import java.awt.Color;
+import java.awt.Graphics;
+import java.util.Iterator;
+
import jalview.api.AlignViewportI;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.Annotation;
import jalview.datamodel.ColumnSelection;
import jalview.datamodel.ContactListI;
+import jalview.datamodel.ContactMatrixI;
import jalview.datamodel.ContactRange;
import jalview.datamodel.HiddenColumns;
import jalview.renderer.api.AnnotationRowRendererI;
-import java.awt.Color;
-import java.awt.Graphics;
-
/**
* @author jprocter
*
*/
-public class ContactMapRenderer implements AnnotationRowRendererI
+public abstract class ContactMapRenderer implements AnnotationRowRendererI
{
+ /**
+ * bean holding colours for shading
+ *
+ * @author jprocter
+ *
+ */
+ public class Shading
+ {
+ /**
+ * 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
+ */
+ Color maxColor, minColor;
+
+ /**
+ * linear shading scheme min/max for selected region
+ */
+ Color selMinColor, selMaxColor;
+
+ public Shading(Color no_data, Color hidden, Color maxColor,
+ Color minColor, Color selMinColor, Color selMaxColor)
+ {
+ super();
+ this.no_data = no_data;
+ this.hidden = hidden;
+ this.maxColor = maxColor;
+ this.minColor = minColor;
+ this.selMinColor = selMinColor;
+ this.selMaxColor = selMaxColor;
+ }
+
+ }
+
+ final Shading shade;
+
+ /**
+ * build an EBI-AlphaFold style renderer of PAE matrices
+ *
+ * @return
+ */
+ public static ContactMapRenderer newPAERenderer()
+ {
+ return new ContactMapRenderer()
+ {
+ @Override
+ public Shading getShade()
+ {
+ 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));
+ }
+ };
+ }
+
+ /**
+ *
+ * @return instance of Shading used to initialise the renderer
+ */
+ public abstract Shading getShade();
+
+ public ContactMapRenderer()
+ {
+ this.shade = getShade();
+ }
@Override
public void renderRow(Graphics g, int charWidth, int charHeight,
- boolean hasHiddenColumns, AlignViewportI viewport, HiddenColumns hiddenColumns,
- ColumnSelection columnSelection, AlignmentAnnotation _aa,
- Annotation[] aa_annotations, int sRes, int eRes, float min,
- float max, int y)
+ boolean hasHiddenColumns, AlignViewportI viewport,
+ HiddenColumns hiddenColumns, ColumnSelection columnSelection,
+ AlignmentAnnotation _aa, Annotation[] aa_annotations, int sRes,
+ int eRes, float min, float max, int y)
{
if (sRes > aa_annotations.length)
{
int x = 0, y2 = y;
- g.setColor(Color.pink);
+ g.setColor(shade.no_data);
g.drawLine(x, y2, (eRes - sRes) * charWidth, y2);
int column;
int aaMax = aa_annotations.length - 1;
+ ContactMatrixI cm = viewport.getContactMatrix(_aa);
while (x < eRes - sRes)
{
column = sRes + x;
{
column = hiddenColumns.visibleToAbsoluteColumn(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;
+ x++;
+ continue;
}
- int contact_height = contacts.getContactHeight();
- // fractional pixel height to render each contact cell
- double pixels_per_contact = ((double) _aa.graphHeight)
- / (double) contact_height;
- // fractional number of contacts covering each pixel
- double contacts_per_pixel = 1d/pixels_per_contact;
- // number of contacts to render at a time
- int step = (pixels_per_contact<1) ? (int) Math.floor(contacts_per_pixel) : (int) Math.ceil(pixels_per_contact);
-
- int pixels_step = (int) Math.ceil(step*pixels_per_contact);
- int cstart, cend = -1;
- for (int ht = y2, eht = y2 - _aa.graphHeight; ht >= eht; ht -= pixels_step)
+ Color gpcol = (cm == null) ? Color.white
+ : 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: 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);
+
+ for (int ht = y2, eht = y2
+ - _aa.graphHeight; ht >= eht; ht -= cgeom.pixels_step)
{
- cstart = cend + 1;
- cend = (int) Math.min(contact_height, cstart + step);
- // TODO show maximum colour for range - sort of done
- // also need a 'getMaxPosForRange(start,end)'
- g.setColor(getColorForRange(min, max, contacts, cstart, cend));
+ 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));
+
+ Color col;
+ boolean rowsel = false, containsHidden = 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 (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);
+ }
- if (pixels_step>1)
+ }
+ }
+ // TODO: show selected region
+ if (colsel || rowsel)
{
- g.fillRect(x * charWidth, ht, charWidth, 1 + (int) pixels_step);
+
+ 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());
+ }
+ }
+ else
+ {
+ col = getColorForRange(min, max, contacts, ci.cStart, ci.cEnd);
+ }
+ if (containsHidden)
+ {
+ col = shade.hidden;
+ }
+ if (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));
+ }
+ g.setColor(col);
+
+ if (cgeom.pixels_step > 1)
+ {
+ g.fillRect(x * charWidth, ht, charWidth, 1 + cgeom.pixels_step);
}
else
{
}
- Color minColor = Color.white, maxColor = Color.magenta;
-
-
Color shadeFor(float min, float max, float value)
{
- return jalview.util.ColorUtils.getGraduatedColour(value, 0, minColor,
- max, maxColor);
+ return jalview.util.ColorUtils.getGraduatedColour(value, 0,
+ shade.minColor, max, shade.maxColor);
}
public Color getColorForRange(float min, float max, ContactListI cl,
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, shade.selMinColor, max, shade.selMaxColor);
+ }
+
}
git://source.jalview.org / jalview.git / blobdiff