X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Frenderer%2Fseqfeatures%2FFeatureRenderer.java;h=2186d4a34502e4dce4d8783e1d62c8b2a91ce1fe;hb=fa0d259c1527df04693dd3a44f2aa9ad09e6da8d;hp=38f281a0c04985fa0783d3c2ca402e760234164c;hpb=d0992d983a2462a92ce648d4becaa41c9d1a3ccc;p=jalview.git

diff --git a/src/jalview/renderer/seqfeatures/FeatureRenderer.java b/src/jalview/renderer/seqfeatures/FeatureRenderer.java
index 38f281a..2186d4a 100644
--- a/src/jalview/renderer/seqfeatures/FeatureRenderer.java
+++ b/src/jalview/renderer/seqfeatures/FeatureRenderer.java
@@ -20,9 +20,17 @@
  */
 package jalview.renderer.seqfeatures;
 
+import java.awt.AlphaComposite;
+import java.awt.Color;
+import java.awt.FontMetrics;
+import java.awt.Graphics;
+import java.awt.Graphics2D;
+import java.util.List;
+
 import jalview.api.AlignViewportI;
 import jalview.api.FeatureColourI;
-import jalview.datamodel.Range;
+import jalview.datamodel.ContiguousI;
+import jalview.datamodel.MappedFeatures;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
 import jalview.gui.AlignFrame;
@@ -31,13 +39,6 @@ import jalview.util.Comparison;
 import jalview.util.ReverseListIterator;
 import jalview.viewmodel.seqfeatures.FeatureRendererModel;
 
-import java.awt.AlphaComposite;
-import java.awt.Color;
-import java.awt.FontMetrics;
-import java.awt.Graphics;
-import java.awt.Graphics2D;
-import java.util.List;
-
 public class FeatureRenderer extends FeatureRendererModel
 {
   private static final AlphaComposite NO_TRANSPARENCY = AlphaComposite
@@ -111,6 +112,10 @@ public class FeatureRenderer extends FeatureRendererModel
         continue;
       }
 
+      /*
+       * JAL-3045 text is always drawn over features, even if
+       * 'Show Text' is unchecked in the format menu
+       */
       g.setColor(Color.white);
       int charOffset = (charWidth - fm.charWidth(s)) / 2;
       g.drawString(String.valueOf(s),
@@ -275,9 +280,9 @@ 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()
-            && !av.isShowComplementFeatures()))
+    ContiguousI visiblePositions = seq.findPositions(start + 1, end + 1);
+    if (visiblePositions == null || !seq.getFeatures().hasFeatures()
+            && !av.isShowComplementFeatures())
     {
       return null;
     }
@@ -294,6 +299,16 @@ 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++)
@@ -399,26 +414,12 @@ 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 = drawComplementFeatures(g, seq, start, end, y1,
+              colourOnly, visiblePositions, drawnColour);
     }
 
     if (transparency != 1.0f && g != null)
@@ -434,6 +435,52 @@ 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,
+          ContiguousI visiblePositions, Color drawnColour)
+  {
+    AlignViewportI comp = av.getCodingComplement();
+    FeatureRenderer fr2 = Desktop.getAlignFrameFor(comp)
+            .getFeatureRenderer();
+
+    final int visibleStart = visiblePositions.getBegin();
+    final int visibleEnd = visiblePositions.getEnd();
+
+    for (int pos = visibleStart; pos <= visibleEnd; pos++)
+    {
+      int column = seq.findIndex(pos);
+      MappedFeatures mf = fr2
+              .findComplementFeaturesAtResidue(seq, pos);
+      if (mf != null)
+      {
+        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.
    * 
@@ -470,27 +517,12 @@ 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;
       }
     }
 
@@ -523,8 +555,43 @@ 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));
+    if (mf == null)
+    {
+      return null;
+    }
+    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;
   }
 }