JAL-3140 NCList now via IntervalStore library

[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 5e071f9..9db55d3 100644 (file)
--- a/src/jalview/renderer/seqfeatures/FeatureRenderer.java
+++ b/src/jalview/renderer/seqfeatures/FeatureRenderer.java
@@ -21,6 +21,7 @@
 package jalview.renderer.seqfeatures;
 
 import jalview.api.AlignViewportI;
+import jalview.api.FeatureColourI;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
 import jalview.util.Comparison;
@@ -33,6 +34,8 @@ import java.awt.Graphics;
 import java.awt.Graphics2D;
 import java.util.List;
 
+import intervalstore.api.IntervalI;
+
 public class FeatureRenderer extends FeatureRendererModel
 {
   private static final AlphaComposite NO_TRANSPARENCY = AlphaComposite
@@ -99,8 +102,7 @@ public class FeatureRenderer extends FeatureRendererModel
 
       g.setColor(featureColour);
 
-      g.fillRect((i - start) * charWidth, y1, charWidth,
-              charHeight);
+      g.fillRect((i - start) * charWidth, y1, charWidth, charHeight);
 
       if (colourOnly || !validCharWidth)
       {
@@ -109,8 +111,8 @@ public class FeatureRenderer extends FeatureRendererModel
 
       g.setColor(Color.white);
       int charOffset = (charWidth - fm.charWidth(s)) / 2;
-      g.drawString(String.valueOf(s), charOffset
-              + (charWidth * (i - start)), pady);
+      g.drawString(String.valueOf(s),
+              charOffset + (charWidth * (i - start)), pady);
     }
     return true;
   }
@@ -198,8 +200,8 @@ public class FeatureRenderer extends FeatureRendererModel
 
       g.setColor(Color.black);
       int charOffset = (charWidth - fm.charWidth(s)) / 2;
-      g.drawString(String.valueOf(s), charOffset
-              + (charWidth * (i - start)), pady);
+      g.drawString(String.valueOf(s),
+              charOffset + (charWidth * (i - start)), pady);
     }
     return true;
   }
@@ -215,9 +217,14 @@ public class FeatureRenderer extends FeatureRendererModel
       return null;
     }
 
-    if (Comparison.isGap(seq.getCharAt(column)))
+    // column is 'base 1' but getCharAt is an array index (ie from 0)
+    if (Comparison.isGap(seq.getCharAt(column - 1)))
     {
-      return Color.white;
+      /*
+       * returning null allows the colour scheme to provide gap colour
+       * - normally white, but can be customised
+       */
+      return null;
     }
 
     Color renderedColour = null;
@@ -263,7 +270,11 @@ public class FeatureRenderer extends FeatureRendererModel
           final SequenceI seq, int start, int end, int y1,
           boolean colourOnly)
   {
-    if (!seq.getFeatures().hasFeatures())
+    /*
+     * if columns are all gapped, or sequence has no features, nothing to do
+     */
+    IntervalI visiblePositions = seq.findPositions(start + 1, end + 1);
+    if (visiblePositions == null || !seq.getFeatures().hasFeatures())
     {
       return null;
     }
@@ -290,25 +301,52 @@ public class FeatureRenderer extends FeatureRendererModel
         continue;
       }
 
-      List<SequenceFeature> overlaps = seq.findFeatures(start + 1, end + 1,
-              type);
+      FeatureColourI fc = getFeatureStyle(type);
+      List<SequenceFeature> overlaps = seq.getFeatures().findFeatures(
+              visiblePositions.getBegin(), visiblePositions.getEnd(), type);
+
+      if (fc.isSimpleColour())
+      {
+        filterFeaturesForDisplay(overlaps);
+      }
+
       for (SequenceFeature sf : overlaps)
       {
+        Color featureColour = getColor(sf, fc);
+        if (featureColour == null)
+        {
+          /*
+           * feature excluded by visibility settings, filters, or colour threshold
+           */
+          continue;
+        }
+
         /*
-         * a feature type may be flagged as shown but the group 
-         * an instance of it belongs to may be hidden
+         * if feature starts/ends outside the visible range,
+         * restrict to visible positions (or if a contact feature,
+         * to a single position)
          */
-        if (featureGroupNotShown(sf))
+        int visibleStart = sf.getBegin();
+        if (visibleStart < visiblePositions.getBegin())
         {
-          continue;
+          visibleStart = sf.isContactFeature() ? sf.getEnd()
+                  : visiblePositions.getBegin();
+        }
+        int visibleEnd = sf.getEnd();
+        if (visibleEnd > visiblePositions.getEnd())
+        {
+          visibleEnd = sf.isContactFeature() ? sf.getBegin()
+                  : visiblePositions.getEnd();
         }
 
-        Color featureColour = getColour(sf);
+        int featureStartCol = seq.findIndex(visibleStart);
+        int featureEndCol = sf.begin == sf.end ? featureStartCol : seq
+                .findIndex(visibleEnd);
+
+        // Color featureColour = getColour(sequenceFeature);
+
         boolean isContactFeature = sf.isContactFeature();
 
-        int featureStartCol = seq.findIndex(sf.begin);
-        int featureEndCol = sf.begin == sf.end ? featureStartCol : seq
-                .findIndex(sf.end);
         if (isContactFeature)
         {
           boolean drawn = renderFeature(g, seq, featureStartCol - 1,
@@ -322,7 +360,7 @@ public class FeatureRenderer extends FeatureRendererModel
             drawnColour = featureColour;
           }
         }
-        else if (showFeature(sf))
+        else
         {
           /*
            * showing feature score by height of colour
@@ -384,7 +422,8 @@ public class FeatureRenderer extends FeatureRendererModel
    * Returns the sequence feature colour rendered at the given column position,
    * or null if none found. The feature of highest render order (i.e. on top) is
    * found, subject to both feature type and feature group being visible, and
-   * its colour returned.
+   * its colour returned. This method is suitable when no feature transparency
+   * applied (only the topmost visible feature colour is rendered).
    * <p>
    * Note this method does not check for a gap in the column so would return the
    * colour for features enclosing a gapped column. Check for gap before calling
@@ -406,7 +445,8 @@ public class FeatureRenderer extends FeatureRendererModel
      * inspect features in reverse renderOrder (the last in the array is 
      * displayed on top) until we find one that is rendered at the position
      */
-    for (int renderIndex = renderOrder.length - 1; renderIndex >= 0; renderIndex--)
+    for (int renderIndex = renderOrder.length
+            - 1; renderIndex >= 0; renderIndex--)
     {
       String type = renderOrder[renderIndex];
       if (!showFeatureOfType(type))
@@ -420,11 +460,15 @@ public class FeatureRenderer extends FeatureRendererModel
       {
         if (!featureGroupNotShown(sequenceFeature))
         {
-          return getColour(sequenceFeature);
+          Color col = getColour(sequenceFeature);
+          if (col != null)
+          {
+            return col;
+          }
         }
       }
     }
-  
+
     /*
      * no displayed feature found at position
      */