-/**
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
*
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.renderer;
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;
* @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;
+
+ /**
+ *
+ * @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)
+ {
+ 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(247, 252, 245), new Color(0, 68, 28),
+ new Color(28, 0, 68), new Color(245, 247, 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,
}
eRes = Math.min(eRes, aa_annotations.length);
- int x = 0, y2 = y;
+ int x = 0, topY = y;
- g.setColor(Color.pink);
-
- g.drawLine(x, y2, (eRes - sRes) * charWidth, y2);
+ // 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;
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;
}
+ // 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;
+ // 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?)
+
+ // 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));
- // 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 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 (s > 0 && s < _aa.sequenceRef.getLength())
- {
- rowsel = columnSelection.intersects(s, e);
- }
- }
+ rowsel = cgeom.intersects(ci, columnSelection, hiddenColumns,
+ maskHiddenCols);
}
// TODO: show selected region
if (colsel || rowsel)
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 = shade.hidden;
+ }
+ if (showGroups && gpcol != null && gpcol != Color.white)
+ {
+ // todo - could overlay group as a transparent rectangle ?
+ col = new Color((int) ((col.getRed() + gpcol.getRed()) / 2f),
+ (int) ((col.getGreen() + gpcol.getGreen()) / 2f),
+ (int) ((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++;
}
- // Shading parameters
- Color minColor = Color.white, maxColor = Color.green.darker().darker(),
- selMaxColor = Color.magenta.darker();
-
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,
{
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);
+ return jalview.util.ColorUtils.getGraduatedColour((float) cr.getMin(),
+ 0, shade.selMinColor, max, shade.selMaxColor);
}
}
git://source.jalview.org / jalview.git / blobdiff