JAL-2526 Sequence.findPositions to get residue positions for column

[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 72ac2c8..5dce2b8 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.datamodel.Range;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
 import jalview.util.Comparison;
@@ -31,6 +32,7 @@ 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
 {
@@ -214,13 +216,6 @@ public class FeatureRenderer extends FeatureRendererModel
       return null;
     }
 
-    SequenceFeature[] sequenceFeatures = seq.getSequenceFeatures();
-
-    if (sequenceFeatures == null || sequenceFeatures.length == 0)
-    {
-      return null;
-    }
-
     if (Comparison.isGap(seq.getCharAt(column)))
     {
       return Color.white;
@@ -269,8 +264,7 @@ public class FeatureRenderer extends FeatureRendererModel
           final SequenceI seq, int start, int end, int y1,
           boolean colourOnly)
   {
-    SequenceFeature[] sequenceFeatures = seq.getSequenceFeatures();
-    if (sequenceFeatures == null || sequenceFeatures.length == 0)
+    if (!seq.getFeatures().hasFeatures())
     {
       return null;
     }
@@ -284,10 +278,15 @@ public class FeatureRenderer extends FeatureRendererModel
               transparency));
     }
 
-    int startPos = seq.findPosition(start);
-    int endPos = seq.findPosition(end);
+    /*
+     * get range of sequence positions within column range
+     */
+    Range seqRange = seq.findPositions(start, end);
+    if (seqRange == null)
+    {
+      return null;
+    }
 
-    int sfSize = sequenceFeatures.length;
     Color drawnColour = null;
 
     /*
@@ -301,16 +300,10 @@ public class FeatureRenderer extends FeatureRendererModel
         continue;
       }
 
-      // loop through all features in sequence to find
-      // current feature to render
-      for (int sfindex = 0; sfindex < sfSize; sfindex++)
+      List<SequenceFeature> overlaps = seq.findFeatures(seqRange.start,
+              seqRange.end, type);
+      for (SequenceFeature sequenceFeature : overlaps)
       {
-        final SequenceFeature sequenceFeature = sequenceFeatures[sfindex];
-        if (!sequenceFeature.type.equals(type))
-        {
-          continue;
-        }
-
         /*
          * a feature type may be flagged as shown but the group 
          * an instance of it belongs to may be hidden
@@ -320,28 +313,21 @@ public class FeatureRenderer extends FeatureRendererModel
           continue;
         }
 
-        /*
-         * check feature overlaps the target range
-         * TODO: efficient retrieval of features overlapping a range
-         */
-        if (sequenceFeature.getBegin() > endPos
-                || sequenceFeature.getEnd() < startPos)
-        {
-          continue;
-        }
-
         Color featureColour = getColour(sequenceFeature);
         boolean isContactFeature = sequenceFeature.isContactFeature();
 
+        // todo overload findIndex using Location data
+        int featureStartCol = seq.findIndex(sequenceFeature.begin);
+        int featureEndCol = seq.findIndex(sequenceFeature.end);
         if (isContactFeature)
         {
           boolean drawn = renderFeature(g, seq,
-                  seq.findIndex(sequenceFeature.begin) - 1,
-                  seq.findIndex(sequenceFeature.begin) - 1, featureColour,
+                  featureStartCol - 1,
+                  featureStartCol - 1, featureColour,
                   start, end, y1, colourOnly);
           drawn |= renderFeature(g, seq,
-                  seq.findIndex(sequenceFeature.end) - 1,
-                  seq.findIndex(sequenceFeature.end) - 1, featureColour,
+                  featureEndCol - 1,
+                  featureEndCol - 1, featureColour,
                   start, end, y1, colourOnly);
           if (drawn)
           {
@@ -350,6 +336,10 @@ public class FeatureRenderer extends FeatureRendererModel
         }
         else if (showFeature(sequenceFeature))
         {
+          /*
+           * showing feature score by height of colour
+           * is not implemented as a selectable option 
+           *
           if (av.isShowSequenceFeaturesHeight()
                   && !Float.isNaN(sequenceFeature.score))
           {
@@ -365,15 +355,16 @@ public class FeatureRenderer extends FeatureRendererModel
           }
           else
           {
+          */
             boolean drawn = renderFeature(g, seq,
-                    seq.findIndex(sequenceFeature.begin) - 1,
-                    seq.findIndex(sequenceFeature.end) - 1, featureColour,
+                    featureStartCol - 1,
+                    featureEndCol - 1, featureColour,
                     start, end, y1, colourOnly);
             if (drawn)
             {
               drawnColour = featureColour;
             }
-          }
+          /*}*/
         }
       }
     }
@@ -391,24 +382,6 @@ public class FeatureRenderer extends FeatureRendererModel
   }
 
   /**
-   * Answers true if the feature belongs to a feature group which is not
-   * currently displayed, else false
-   * 
-   * @param sequenceFeature
-   * @return
-   */
-  protected boolean featureGroupNotShown(
-          final SequenceFeature sequenceFeature)
-  {
-    return featureGroups != null
-            && sequenceFeature.featureGroup != null
-            && sequenceFeature.featureGroup.length() != 0
-            && featureGroups.containsKey(sequenceFeature.featureGroup)
-            && !featureGroups.get(sequenceFeature.featureGroup)
-                    .booleanValue();
-  }
-
-  /**
    * Called when alignment in associated view has new/modified features to
    * discover and display.
    * 
@@ -431,12 +404,6 @@ public class FeatureRenderer extends FeatureRendererModel
    */
   Color findFeatureColour(SequenceI seq, int pos)
   {
-    SequenceFeature[] sequenceFeatures = seq.getSequenceFeatures();
-    if (sequenceFeatures == null || sequenceFeatures.length == 0)
-    {
-      return null;
-    }
-  
     /*
      * check for new feature added while processing
      */
@@ -454,31 +421,10 @@ public class FeatureRenderer extends FeatureRendererModel
         continue;
       }
 
-      for (int sfindex = 0; sfindex < sequenceFeatures.length; sfindex++)
+      List<SequenceFeature> overlaps = seq.findFeatures(pos, pos, type);
+      for (SequenceFeature sequenceFeature : overlaps)
       {
-        SequenceFeature sequenceFeature = sequenceFeatures[sfindex];
-        if (!sequenceFeature.type.equals(type))
-        {
-          continue;
-        }
-
-        if (featureGroupNotShown(sequenceFeature))
-        {
-          continue;
-        }
-
-        /*
-         * check the column position is within the feature range
-         * (or is one of the two contact positions for a contact feature)
-         */
-        boolean featureIsAtPosition = sequenceFeature.begin <= pos
-                && sequenceFeature.end >= pos;
-        if (sequenceFeature.isContactFeature())
-        {
-          featureIsAtPosition = sequenceFeature.begin == pos
-                  || sequenceFeature.end == pos;
-        }
-        if (featureIsAtPosition)
+        if (!featureGroupNotShown(sequenceFeature))
         {
           return getColour(sequenceFeature);
         }