X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Frenderer%2Fseqfeatures%2FFeatureRenderer.java;h=13885b45370b005378ac348fdbf7edca256bc3a2;hb=bc18effe68ba80213a6d03ca7e6175adc6be71d6;hp=541288eaf1a2297fb61d07421a94e827159e1181;hpb=bba9e58f08fc55c0f789f8354d1444e5c5e1b0e6;p=jalview.git

diff --git a/src/jalview/renderer/seqfeatures/FeatureRenderer.java b/src/jalview/renderer/seqfeatures/FeatureRenderer.java
index 541288e..13885b4 100644
--- a/src/jalview/renderer/seqfeatures/FeatureRenderer.java
+++ b/src/jalview/renderer/seqfeatures/FeatureRenderer.java
@@ -22,7 +22,7 @@ package jalview.renderer.seqfeatures;
 
 import jalview.api.AlignViewportI;
 import jalview.api.FeatureColourI;
-import jalview.datamodel.Range;
+import jalview.datamodel.ContiguousI;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
 import jalview.util.Comparison;
@@ -101,8 +101,7 @@ 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)
       {
@@ -111,8 +110,8 @@ 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;
   }
@@ -200,8 +199,8 @@ 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;
   }
@@ -217,7 +216,8 @@ 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)))
     {
       /*
        * returning null allows the colour scheme to provide gap colour
@@ -272,7 +272,7 @@ 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);
+    ContiguousI visiblePositions = seq.findPositions(start + 1, end + 1);
     if (visiblePositions == null || !seq.getFeatures().hasFeatures())
     {
       return null;
@@ -304,19 +304,49 @@ 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);
-        int visibleStart = Math.max(sf.getBegin(),
-                visiblePositions.getBegin());
+        Color featureColour = getColor(sf, fc);
+        if (featureColour == null)
+        {
+          /*
+           * feature excluded by visibility settings, filters, or colour threshold
+           */
+          continue;
+        }
+
+        /*
+         * if feature starts/ends outside the visible range,
+         * restrict to visible positions (or if a contact feature,
+         * to a single position)
+         */
+        int visibleStart = sf.getBegin();
+        if (visibleStart < visiblePositions.getBegin())
+        {
+          visibleStart = sf.isContactFeature() ? sf.getEnd()
+                  : visiblePositions.getBegin();
+        }
+        int visibleEnd = sf.getEnd();
+        if (visibleEnd > visiblePositions.getEnd())
+        {
+          visibleEnd = sf.isContactFeature() ? sf.getBegin()
+                  : visiblePositions.getEnd();
+        }
+
         int featureStartCol = seq.findIndex(visibleStart);
-        int visibleEnd = Math.min(sf.getEnd(), visiblePositions.getEnd());
         int featureEndCol = sf.begin == sf.end ? featureStartCol : seq
                 .findIndex(visibleEnd);
 
-        if (sf.isContactFeature())
+        // Color featureColour = getColour(sequenceFeature);
+
+        boolean isContactFeature = sf.isContactFeature();
+
+        if (isContactFeature)
         {
           boolean drawn = renderFeature(g, seq, featureStartCol - 1,
                   featureStartCol - 1, featureColour, start, end, y1,
@@ -329,7 +359,7 @@ public class FeatureRenderer extends FeatureRendererModel
             drawnColour = featureColour;
           }
         }
-        else if (showFeature(sf))
+        else
         {
           /*
            * showing feature score by height of colour
@@ -391,7 +421,8 @@ 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
@@ -413,7 +444,8 @@ 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))
@@ -427,11 +459,15 @@ 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
      */