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Merge remote-tracking branch 'origin/develop' into
[jalview.git] / src / jalview / gui / SeqPanel.java
diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java
index 891aa0d..f52f926 100644 (file)
--- a/src/jalview/gui/SeqPanel.java
+++ b/src/jalview/gui/SeqPanel.java
@@ -249,44 +249,6 @@ public class SeqPanel extends JPanel implements MouseListener,
     return seq;
   }
 
-  SequenceFeature[] findFeaturesAtRes(SequenceI sequence, int res)
-  {
-    Vector tmp = new Vector();
-    SequenceFeature[] features = sequence.getSequenceFeatures();
-    if (features != null)
-    {
-      for (int i = 0; i < features.length; i++)
-      {
-        if (av.featuresDisplayed == null
-                || !av.featuresDisplayed.containsKey(features[i].getType()))
-        {
-          continue;
-        }
-
-        if (features[i].featureGroup != null
-                && seqCanvas.fr.featureGroups != null
-                && seqCanvas.fr.featureGroups
-                        .containsKey(features[i].featureGroup)
-                && !((Boolean) seqCanvas.fr.featureGroups
-                        .get(features[i].featureGroup)).booleanValue())
-        {
-          continue;
-        }
-
-        if ((features[i].getBegin() <= res)
-                && (features[i].getEnd() >= res))
-        {
-          tmp.addElement(features[i]);
-        }
-      }
-    }
-
-    features = new SequenceFeature[tmp.size()];
-    tmp.copyInto(features);
-
-    return features;
-  }
-
   /**
    * When all of a sequence of edits are complete, put the resulting edit list
    * on the history stack (undo list), and reset flags for editing in progress.
@@ -666,6 +628,7 @@ public class SeqPanel extends JPanel implements MouseListener,
 
   String lastMessage;
 
+  @Override
   public void mouseOverSequence(SequenceI sequence, int index, int pos)
   {
     String tmp = sequence.hashCode() + " " + index + " " + pos;
@@ -696,6 +659,7 @@ public class SeqPanel extends JPanel implements MouseListener,
   {
     return this.ap == null ? null : this.ap.av;
   }
+  @Override
   public void updateColours(SequenceI seq, int index)
   {
     System.out.println("update the seqPanel colours");
@@ -763,14 +727,14 @@ public class SeqPanel extends JPanel implements MouseListener,
     }
 
     // use aa to see if the mouse pointer is on a
-    if (av.showSequenceFeatures)
+    if (av.isShowSequenceFeatures())
     {
       int rpos;
-      SequenceFeature[] features = findFeaturesAtRes(
+      List<SequenceFeature> features = ap.getFeatureRenderer().findFeaturesAtRes(
               sequence.getDatasetSequence(),
               rpos = sequence.findPosition(res));
       seqARep.appendFeatures(tooltipText, rpos, features,
-              this.ap.seqPanel.seqCanvas.fr.minmax);
+              this.ap.getSeqPanel().seqCanvas.fr.getMinMax());
     }
     if (tooltipText.length() == 6) // <html></html>
     {
@@ -1424,21 +1388,21 @@ public class SeqPanel extends JPanel implements MouseListener,
         av.setSelectionGroup(null);
       }
 
-      SequenceFeature[] features = findFeaturesAtRes(
+      List<SequenceFeature> features = seqCanvas.getFeatureRenderer().findFeaturesAtRes(
               sequence.getDatasetSequence(),
               sequence.findPosition(findRes(evt)));
 
-      if (features != null && features.length > 0)
+      if (features != null && features.size()> 0)
       {
         SearchResults highlight = new SearchResults();
-        highlight.addResult(sequence, features[0].getBegin(),
-                features[0].getEnd());
+        highlight.addResult(sequence, features.get(0).getBegin(),
+                features.get(0).getEnd());
         seqCanvas.highlightSearchResults(highlight);
       }
-      if (features != null && features.length > 0)
+      if (features != null && features.size()> 0)
       {
         seqCanvas.getFeatureRenderer().amendFeatures(new SequenceI[]
-        { sequence }, features, false, ap);
+        { sequence }, features.toArray(new SequenceFeature[features.size()]), false, ap);
 
         seqCanvas.highlightSearchResults(null);
       }
@@ -1553,16 +1517,16 @@ public class SeqPanel extends JPanel implements MouseListener,
 
     if (javax.swing.SwingUtilities.isRightMouseButton(evt))
     {
-      SequenceFeature[] allFeatures = findFeaturesAtRes(
+      List<SequenceFeature> allFeatures = ap.getFeatureRenderer().findFeaturesAtRes(
               sequence.getDatasetSequence(), sequence.findPosition(res));
       Vector links = new Vector();
-      for (int i = 0; i < allFeatures.length; i++)
+      for (SequenceFeature sf:allFeatures)
       {
-        if (allFeatures[i].links != null)
+        if (sf.links != null)
         {
-          for (int j = 0; j < allFeatures[i].links.size(); j++)
+          for (int j = 0; j < sf.links.size(); j++)
           {
-            links.addElement(allFeatures[i].links.elementAt(j));
+            links.addElement(sf.links.elementAt(j));
           }
         }
       }