JAL-3187 hacks to get peptide variant in to Jmol hover tooltip

[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 1f47da3..39d705b 100644 (file)
--- a/src/jalview/renderer/seqfeatures/FeatureRenderer.java
+++ b/src/jalview/renderer/seqfeatures/FeatureRenderer.java
@@ -22,10 +22,14 @@ package jalview.renderer.seqfeatures;
 
 import jalview.api.AlignViewportI;
 import jalview.api.FeatureColourI;
+import jalview.datamodel.MappedFeatures;
 import jalview.datamodel.Range;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
+import jalview.gui.AlignFrame;
+import jalview.gui.Desktop;
 import jalview.util.Comparison;
+import jalview.util.ReverseListIterator;
 import jalview.viewmodel.seqfeatures.FeatureRendererModel;
 
 import java.awt.AlphaComposite;
@@ -273,7 +277,8 @@ public class FeatureRenderer extends FeatureRendererModel
      * if columns are all gapped, or sequence has no features, nothing to do
      */
     Range visiblePositions = seq.findPositions(start+1, end+1);
-    if (visiblePositions == null || !seq.getFeatures().hasFeatures())
+    if (visiblePositions == null || (!seq.getFeatures().hasFeatures()
+            && !av.isShowComplementFeatures()))
     {
       return null;
     }
@@ -290,6 +295,16 @@ 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++)
@@ -304,14 +319,19 @@ public class FeatureRenderer extends FeatureRendererModel
       List<SequenceFeature> overlaps = seq.getFeatures().findFeatures(
               visiblePositions.getBegin(), visiblePositions.getEnd(), type);
 
-      filterFeaturesForDisplay(overlaps, fc);
+      if (fc.isSimpleColour())
+      {
+        filterFeaturesForDisplay(overlaps);
+      }
 
       for (SequenceFeature sf : overlaps)
       {
-        Color featureColour = fc.getColor(sf);
+        Color featureColour = getColor(sf, fc);
         if (featureColour == null)
         {
-          // score feature outwith threshold for colouring
+          /*
+           * feature excluded by filters, or colour threshold
+           */
           continue;
         }
 
@@ -389,6 +409,15 @@ public class FeatureRenderer extends FeatureRendererModel
       }
     }
 
+    /*
+     * draw 'complement' features above ours if configured to do so
+     */
+    if (av.isShowComplementFeatures() && av.isShowComplementFeaturesOnTop())
+    {
+      drawnColour = drawComplementFeatures(g, seq, start, end, y1,
+              colourOnly, visiblePositions, drawnColour);
+    }
+
     if (transparency != 1.0f && g != null)
     {
       /*
@@ -402,6 +431,45 @@ 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);
+      MappedFeatures mf = fr2
+              .findComplementFeaturesAtResidue(seq, pos);
+      for (SequenceFeature sf : mf.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.
    * 
@@ -436,6 +504,18 @@ public class FeatureRenderer extends FeatureRendererModel
     updateFeatures();
 
     /*
+     * show complement features on top (if configured to show them)
+     */
+    if (av.isShowComplementFeatures() && av.isShowComplementFeaturesOnTop())
+    {
+      Color col = findComplementFeatureColour(seq, column);
+      if (col != null)
+      {
+        return col;
+      }
+    }
+
+    /*
      * inspect features in reverse renderOrder (the last in the array is 
      * displayed on top) until we find one that is rendered at the position
      */
@@ -464,8 +544,40 @@ 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();
+    MappedFeatures mf = fr2.findComplementFeaturesAtResidue(
+            seq, seq.findPosition(column - 1));
+
+    ReverseListIterator<SequenceFeature> it = new ReverseListIterator<>(
+            mf.features);
+    while (it.hasNext())
+    {
+      SequenceFeature sf = it.next();
+      if (!fr2.featureGroupNotShown(sf))
+      {
+        Color col = fr2.getColour(sf);
+        if (col != null)
+        {
+          return col;
+        }
+      }
+    }
     return null;
   }
 }