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Merge branch 'develop' into JAL-1483_featureBasedTreeCalc
[jalview.git] / src / jalview / gui / SeqPanel.java
diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java
index 03821d7..4836915 100644 (file)
--- a/src/jalview/gui/SeqPanel.java
+++ b/src/jalview/gui/SeqPanel.java
@@ -225,42 +225,6 @@ 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;
-  }
-
   void endEditing()
   {
     if (editCommand != null && editCommand.getSize() > 0)
@@ -520,29 +484,34 @@ public class SeqPanel extends JPanel implements MouseListener,
 
   int getKeyboardNo1()
   {
-    try {
-    if (keyboardNo1 != null) 
+    try
     {
-      int value = Integer.parseInt(keyboardNo1.toString());
-      keyboardNo1 = null;
-      return value;
-    }
+      if (keyboardNo1 != null)
+      {
+        int value = Integer.parseInt(keyboardNo1.toString());
+        keyboardNo1 = null;
+        return value;
+      }
     } catch (Exception x)
-    {}
+    {
+    }
     keyboardNo1 = null;
     return 1;
   }
 
   int getKeyboardNo2()
   {
-    try {
-    if (keyboardNo2!=null){
-      int value = Integer.parseInt(keyboardNo2.toString());
-      keyboardNo2 = null;
-      return value;
-    }
+    try
+    {
+      if (keyboardNo2 != null)
+      {
+        int value = Integer.parseInt(keyboardNo2.toString());
+        keyboardNo2 = null;
+        return value;
+      }
     } catch (Exception x)
-    {}
+    {
+    }
     keyboardNo2 = null;
     return 1;
   }
@@ -721,14 +690,14 @@ 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.seqPanel.seqCanvas.fr.getMinMax());
     }
     if (tooltipText.length() == 6) // <html></html>
     {
@@ -944,7 +913,7 @@ public class SeqPanel extends JPanel implements MouseListener,
       message.append("Edit group:");
       if (editCommand == null)
       {
-        editCommand = new EditCommand("Edit Group");
+        editCommand = new EditCommand(MessageManager.getString("action.edit_group"));
       }
     }
     else
@@ -957,7 +926,7 @@ public class SeqPanel extends JPanel implements MouseListener,
       }
       if (editCommand == null)
       {
-        editCommand = new EditCommand("Edit " + label);
+        editCommand = new EditCommand(MessageManager.formatMessage("label.edit_params", new String[]{label}));
       }
     }
 
@@ -1365,21 +1334,21 @@ 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);
       }
@@ -1432,9 +1401,10 @@ public class SeqPanel extends JPanel implements MouseListener,
 
     if (av.wrapAlignment && seq > av.getAlignment().getHeight())
     {
-      JOptionPane.showInternalMessageDialog(Desktop.desktop,
-              MessageManager.getString("label.cannot_edit_annotations_in_wrapped_view"),
-              MessageManager.getString("label.wrapped_view_no_edit"), JOptionPane.WARNING_MESSAGE);
+      JOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager
+              .getString("label.cannot_edit_annotations_in_wrapped_view"),
+              MessageManager.getString("label.wrapped_view_no_edit"),
+              JOptionPane.WARNING_MESSAGE);
       return;
     }
 
@@ -1493,16 +1463,16 @@ 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));
           }
         }
       }