JAL-2754 Sequence.findFeatures(fromCol, toCol)

[jalview.git] / src / jalview / gui / SeqPanel.java

diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java
index 4b24dee..06568ca 100644 (file)
--- a/src/jalview/gui/SeqPanel.java
+++ b/src/jalview/gui/SeqPanel.java
@@ -62,7 +62,6 @@ import java.awt.event.MouseWheelListener;
 import java.util.ArrayList;
 import java.util.Collections;
 import java.util.List;
-import java.util.ListIterator;
 
 import javax.swing.JPanel;
 import javax.swing.SwingUtilities;
@@ -733,6 +732,7 @@ public class SeqPanel extends JPanel implements MouseListener,
     int seq = findSeq(evt);
     if (column < 0 || seq < 0 || seq >= av.getAlignment().getHeight())
     {
+      lastMouseSeq = -1;
       return;
     }
     if (column == lastMouseColumn && seq == lastMouseSeq)
@@ -794,11 +794,7 @@ public class SeqPanel extends JPanel implements MouseListener,
     if (av.isShowSequenceFeatures())
     {
       List<SequenceFeature> features = ap.getFeatureRenderer()
-              .findFeaturesAtRes(sequence.getDatasetSequence(), pos);
-      if (isGapped)
-      {
-        removeAdjacentFeatures(features, column + 1, sequence);
-      }
+              .findFeaturesAtColumn(sequence, column + 1);
       seqARep.appendFeatures(tooltipText, pos, features,
               this.ap.getSeqPanel().seqCanvas.fr.getMinMax());
     }
@@ -820,35 +816,6 @@ public class SeqPanel extends JPanel implements MouseListener,
     }
   }
 
-  /**
-   * Removes from the list of features any that start after, or end before, the
-   * given column position. This allows us to retain only those features
-   * adjacent to a gapped position that straddle the position. Contact features
-   * that 'straddle' the position are also removed, since they are not 'at' the
-   * position.
-   * 
-   * @param features
-   * @param column
-   *          alignment column (1..)
-   * @param sequence
-   */
-  protected void removeAdjacentFeatures(List<SequenceFeature> features,
-          final int column, SequenceI sequence)
-  {
-    // TODO should this be an AlignViewController method (and reused by applet)?
-    ListIterator<SequenceFeature> it = features.listIterator();
-    while (it.hasNext())
-    {
-      SequenceFeature sf = it.next();
-      if (sf.isContactFeature()
-              || sequence.findIndex(sf.getBegin()) > column
-              || sequence.findIndex(sf.getEnd()) < column)
-      {
-        it.remove();
-      }
-    }
-  }
-
   private Point lastp = null;
 
   /*
@@ -1587,19 +1554,13 @@ public class SeqPanel extends JPanel implements MouseListener,
       }
 
       int column = findColumn(evt);
-      boolean isGapped = Comparison.isGap(sequence.getCharAt(column));
 
       /*
        * find features at the position (if not gapped), or straddling
        * the position (if at a gap)
        */
       List<SequenceFeature> features = seqCanvas.getFeatureRenderer()
-              .findFeaturesAtRes(sequence.getDatasetSequence(),
-                      sequence.findPosition(column));
-      if (isGapped)
-      {
-        removeAdjacentFeatures(features, column, sequence);
-      }
+              .findFeaturesAtColumn(sequence, column + 1);
 
       if (!features.isEmpty())
       {
@@ -1776,12 +1737,11 @@ public class SeqPanel extends JPanel implements MouseListener,
    */
   void showPopupMenu(MouseEvent evt)
   {
-    final int res = findColumn(evt);
+    final int column = findColumn(evt);
     final int seq = findSeq(evt);
     SequenceI sequence = av.getAlignment().getSequenceAt(seq);
     List<SequenceFeature> allFeatures = ap.getFeatureRenderer()
-            .findFeaturesAtRes(sequence.getDatasetSequence(),
-                    sequence.findPosition(res));
+            .findFeaturesAtColumn(sequence, column + 1);
     List<String> links = new ArrayList<>();
     for (SequenceFeature sf : allFeatures)
     {