JAL-3187 'on top' optional for complementary features

[jalview.git] / src / jalview / renderer / seqfeatures / FeatureRenderer.java

diff --git a/src/jalview/renderer/seqfeatures/FeatureRenderer.java b/src/jalview/renderer/seqfeatures/FeatureRenderer.java
index 4e81e69..78f4989 100644 (file)
--- a/src/jalview/renderer/seqfeatures/FeatureRenderer.java
+++ b/src/jalview/renderer/seqfeatures/FeatureRenderer.java
@@ -294,6 +294,16 @@ public class FeatureRenderer extends FeatureRendererModel
     Color drawnColour = null;
 
     /*
+     * draw 'complement' features below ours if configured to do so
+     */
+    if (av.isShowComplementFeatures()
+            && !av.isShowComplementFeaturesOnTop())
+    {
+      drawnColour = drawComplementFeatures(g, seq, start, end, y1,
+              colourOnly, visiblePositions, drawnColour);
+    }
+
+    /*
      * iterate over features in ordering of their rendering (last is on top)
      */
     for (int renderIndex = 0; renderIndex < renderOrder.length; renderIndex++)
@@ -399,27 +409,12 @@ public class FeatureRenderer extends FeatureRendererModel
     }
 
     /*
-     * if configured to do so, find and show complement's features
+     * draw 'complement' features above ours if configured to do so
      */
-    if (av.isShowComplementFeatures())
+    if (av.isShowComplementFeatures() && av.isShowComplementFeaturesOnTop())
     {
-      AlignViewportI comp = av.getCodingComplement();
-      FeatureRenderer fr2 = Desktop.getAlignFrameFor(comp)
-              .getFeatureRenderer();
-      for (int pos = visiblePositions.start; pos <= visiblePositions.end; pos++)
-      {
-        int column = seq.findIndex(pos);
-        List<SequenceFeature> features = fr2
-                .findComplementFeaturesAtResidue(seq, pos);
-        for (SequenceFeature sf : features)
-        {
-          FeatureColourI fc = fr2.getFeatureStyle(sf.getType());
-          Color featureColour = fr2.getColor(sf, fc);
-          renderFeature(g, seq, column - 1, column - 1, featureColour,
-                  start, end, y1, colourOnly);
-          drawnColour = featureColour;
-        }
-      }
+      drawnColour = drawComplementFeatures(g, seq, start, end, y1,
+              colourOnly, visiblePositions, drawnColour);
     }
 
     if (transparency != 1.0f && g != null)
@@ -435,6 +430,45 @@ public class FeatureRenderer extends FeatureRendererModel
   }
 
   /**
+   * Find any features on the CDS/protein complement of the sequence region and
+   * draw them, with visibility and colouring as configured in the complementary
+   * viewport
+   * 
+   * @param g
+   * @param seq
+   * @param start
+   * @param end
+   * @param y1
+   * @param colourOnly
+   * @param visiblePositions
+   * @param drawnColour
+   * @return
+   */
+  Color drawComplementFeatures(final Graphics g, final SequenceI seq,
+          int start, int end, int y1, boolean colourOnly,
+          Range visiblePositions, Color drawnColour)
+  {
+    AlignViewportI comp = av.getCodingComplement();
+    FeatureRenderer fr2 = Desktop.getAlignFrameFor(comp)
+            .getFeatureRenderer();
+    for (int pos = visiblePositions.start; pos <= visiblePositions.end; pos++)
+    {
+      int column = seq.findIndex(pos);
+      List<SequenceFeature> features = fr2
+              .findComplementFeaturesAtResidue(seq, pos);
+      for (SequenceFeature sf : features)
+      {
+        FeatureColourI fc = fr2.getFeatureStyle(sf.getType());
+        Color featureColour = fr2.getColor(sf, fc);
+        renderFeature(g, seq, column - 1, column - 1, featureColour,
+                start, end, y1, colourOnly);
+        drawnColour = featureColour;
+      }
+    }
+    return drawnColour;
+  }
+
+  /**
    * Called when alignment in associated view has new/modified features to
    * discover and display.
    * 
@@ -471,27 +505,12 @@ public class FeatureRenderer extends FeatureRendererModel
     /*
      * show complement features on top (if configured to show them)
      */
-    if (av.isShowComplementFeatures())
+    if (av.isShowComplementFeatures() && av.isShowComplementFeaturesOnTop())
     {
-      AlignViewportI complement = av.getCodingComplement();
-      AlignFrame af = Desktop.getAlignFrameFor(complement);
-      FeatureRendererModel fr2 = af.getFeatureRenderer();
-      List<SequenceFeature> features = fr2.findComplementFeaturesAtResidue(
-              seq, seq.findPosition(column - 1));
-
-      ReverseListIterator<SequenceFeature> it = new ReverseListIterator<>(
-              features);
-      while (it.hasNext())
+      Color col = findComplementFeatureColour(seq, column);
+      if (col != null)
       {
-        SequenceFeature sf = it.next();
-        if (!fr2.featureGroupNotShown(sf))
-        {
-          Color col = fr2.getColour(sf);
-          if (col != null)
-          {
-            return col;
-          }
-        }
+        return col;
       }
     }
 
@@ -524,8 +543,40 @@ public class FeatureRenderer extends FeatureRendererModel
     }
 
     /*
-     * no displayed feature found at position
+     * show complement features underneath (if configured to show them)
      */
+    Color col = null;
+    if (av.isShowComplementFeatures()
+            && !av.isShowComplementFeaturesOnTop())
+    {
+      col = findComplementFeatureColour(seq, column);
+    }
+
+    return col;
+  }
+
+  Color findComplementFeatureColour(SequenceI seq, int column)
+  {
+    AlignViewportI complement = av.getCodingComplement();
+    AlignFrame af = Desktop.getAlignFrameFor(complement);
+    FeatureRendererModel fr2 = af.getFeatureRenderer();
+    List<SequenceFeature> features = fr2.findComplementFeaturesAtResidue(
+            seq, seq.findPosition(column - 1));
+
+    ReverseListIterator<SequenceFeature> it = new ReverseListIterator<>(
+            features);
+    while (it.hasNext())
+    {
+      SequenceFeature sf = it.next();
+      if (!fr2.featureGroupNotShown(sf))
+      {
+        Color col = fr2.getColour(sf);
+        if (col != null)
+        {
+          return col;
+        }
+      }
+    }
     return null;
   }
 }