--- /dev/null
+/*
+ * 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 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.ContactMatrixI;
+import jalview.datamodel.ContactRange;
+import jalview.datamodel.HiddenColumns;
+import jalview.renderer.api.AnnotationRowRendererI;
+
+/**
+ * @author jprocter
+ *
+ */
+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,
+ 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)
+ {
+ return;
+ }
+ eRes = Math.min(eRes, aa_annotations.length);
+
+ 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;
+ if (hasHiddenColumns)
+ {
+ column = hiddenColumns.visibleToAbsoluteColumn(column);
+ }
+ // TODO: highlight columns selected
+ boolean colsel = false;
+ if (columnSelection != null)
+ {
+ colsel = columnSelection.contains(column);
+ }
+
+ if (column > aaMax)
+ {
+ break;
+ }
+
+ if (aa_annotations[column] == null)
+ {
+ x++;
+ continue;
+ }
+ ContactListI contacts = viewport.getContactList(_aa, column);
+ if (contacts == null)
+ {
+ 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 = 0, botY = topY
+ - _aa.height; ht < _aa.graphHeight; 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;
+ boolean containsHidden = false;
+ if (columnSelection != null)
+ {
+ rowsel = cgeom.intersects(ci, columnSelection, hiddenColumns,
+ maskHiddenCols);
+ }
+ // TODO: show selected region
+ if (colsel || rowsel)
+ {
+
+ 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 (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, botY + ht, charWidth,
+ cgeom.pixels_step);
+ }
+ else
+ {
+ 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);
+ }
+
+ 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.getMin(),
+ 0, shade.selMinColor, max, shade.selMaxColor);
+ }
+
+}
git://source.jalview.org / jalview.git / blobdiff