From 47a6e772d30202cfb73fe296fea6c8474bc2b8bb Mon Sep 17 00:00:00 2001
From: Jim Procter <j.procter@dundee.ac.uk>
Date: Mon, 17 Oct 2022 17:56:51 +0100
Subject: [PATCH] JAL-2349 JAL-3855 column selection highlighting

---
 src/jalview/datamodel/ColumnSelection.java   |   22 ++++++++--
 src/jalview/renderer/ContactMapRenderer.java |   60 +++++++++++++++++++-------
 2 files changed, 64 insertions(+), 18 deletions(-)

diff --git a/src/jalview/datamodel/ColumnSelection.java b/src/jalview/datamodel/ColumnSelection.java
index 6f14e21..140a366 100644
--- a/src/jalview/datamodel/ColumnSelection.java
+++ b/src/jalview/datamodel/ColumnSelection.java
@@ -20,15 +20,15 @@
  */
 package jalview.datamodel;
 
-import jalview.viewmodel.annotationfilter.AnnotationFilterParameter;
-import jalview.viewmodel.annotationfilter.AnnotationFilterParameter.SearchableAnnotationField;
-
 import java.util.ArrayList;
 import java.util.BitSet;
 import java.util.Collections;
 import java.util.List;
 import java.util.regex.PatternSyntaxException;
 
+import jalview.viewmodel.annotationfilter.AnnotationFilterParameter;
+import jalview.viewmodel.annotationfilter.AnnotationFilterParameter.SearchableAnnotationField;
+
 /**
  * Data class holding the selected columns and hidden column ranges for a view.
  * Ranges are base 1.
@@ -354,6 +354,22 @@ public class ColumnSelection
   }
 
   /**
+   * 
+   */
+  public boolean intersects(int from, int to)
+  {
+    // TODO: do this in a more efficient bitwise way
+    for (int f = from; f <= to; f++)
+    {
+      if (selection.isSelected(f))
+      {
+        return true;
+      }
+    }
+    return false;
+  }
+
+  /**
    * Answers true if no columns are selected, else false
    */
   public boolean isEmpty()
diff --git a/src/jalview/renderer/ContactMapRenderer.java b/src/jalview/renderer/ContactMapRenderer.java
index 11c51e9..f5c4c31 100644
--- a/src/jalview/renderer/ContactMapRenderer.java
+++ b/src/jalview/renderer/ContactMapRenderer.java
@@ -50,12 +50,12 @@ public class ContactMapRenderer implements AnnotationRowRendererI
       {
         column = hiddenColumns.visibleToAbsoluteColumn(column);
       }
-      // // TODO: highlight columns selected
-      // boolean colsel = false;
-      // if (columnSelection != null)
-      // {
-      // colsel = columnSelection.contains(column);
-      // }
+      // TODO: highlight columns selected
+      boolean colsel = false;
+      if (columnSelection != null)
+      {
+        colsel = columnSelection.contains(column);
+      }
 
       if (column > aaMax)
       {
@@ -107,16 +107,36 @@ public class ContactMapRenderer implements AnnotationRowRendererI
 
         // TODO show maximum colour for range - sort of done
         // also need a 'getMaxPosForRange(start,end)' to accurately render
-        Color col = getColorForRange(min, max, contacts, cstart, cend);
-
+        Color col;
+        boolean rowsel = false;
+        if (!colsel && columnSelection != null)
+        {
+          if (_aa.sequenceRef == null)
+          {
+            rowsel = columnSelection.intersects(cstart, cend);
+          }
+          else
+          {
+            // TODO check we have correctly mapped cstart to local sequence
+            // numbering
+            int s = _aa.sequenceRef.findIndex(cstart);
+            int e = _aa.sequenceRef.findIndex(cend);
+            if (s > 0 && s < _aa.sequenceRef.getLength())
+            {
+              rowsel = columnSelection.intersects(s, e);
+            }
+          }
+        }
         // TODO: show selected region
-        // if (colsel || columnSelection!=null &&
-        // columnSelection.intersects(cstart,cend))
-        // {
-        // g.setColor(col.brighter());
-        // }
-        // else
+        if (colsel || rowsel)
         {
+
+          col = getSelectedColorForRange(min, max, contacts, cstart, cend);
+          g.setColor(col);
+        }
+        else
+        {
+          col = getColorForRange(min, max, contacts, cstart, cend);
           g.setColor(col);
         }
         if (pixels_step > 1)
@@ -134,7 +154,8 @@ public class ContactMapRenderer implements AnnotationRowRendererI
   }
 
   // Shading parameters
-  Color minColor = Color.white, maxColor = Color.magenta;
+  Color minColor = Color.white, maxColor = Color.green.darker().darker(),
+          selMaxColor = Color.magenta.darker();
 
   Color shadeFor(float min, float max, float value)
   {
@@ -150,4 +171,13 @@ public class ContactMapRenderer implements AnnotationRowRendererI
     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, minColor, max, selMaxColor);
+  }
+
 }
-- 
1.7.10.2