Merge branch 'develop' into feature/JAL-1713_overviewInProject

[jalview.git] / src / jalview / renderer / ContactMapRenderer.java

diff --git a/src/jalview/renderer/ContactMapRenderer.java b/src/jalview/renderer/ContactMapRenderer.java
new file mode 100644 (file)
index 0000000..ca7b0c8
--- /dev/null
+++ b/src/jalview/renderer/ContactMapRenderer.java
@@ -0,0 +1,191 @@
+/**
+ * 
+ */
+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.ContactRange;
+import jalview.datamodel.HiddenColumns;
+import jalview.renderer.api.AnnotationRowRendererI;
+
+/**
+ * @author jprocter
+ *
+ */
+public class ContactMapRenderer implements AnnotationRowRendererI
+{
+
+  @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, y2 = y;
+
+    g.setColor(Color.pink);
+
+    g.drawLine(x, y2, (eRes - sRes) * charWidth, y2);
+
+    int column;
+    int aaMax = aa_annotations.length - 1;
+    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;
+      }
+      // 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)
+      {
+        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);
+            }
+
+          }
+        }
+        // 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 = Color.red;
+        }
+        g.setColor(col);
+        if (cgeom.pixels_step > 1)
+        {
+          g.fillRect(x * charWidth, ht, charWidth, 1 + cgeom.pixels_step);
+        }
+        else
+        {
+          g.drawLine(x * charWidth, ht, (x + 1) * charWidth, ht);
+        }
+      }
+      x++;
+    }
+
+  }
+
+  // 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);
+  }
+
+}