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JAL-3567 report mapped location for virtual features in tooltip etc
[jalview.git] / src / jalview / gui / SeqPanel.java
diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java
index c648e53..f28217d 100644 (file)
--- a/src/jalview/gui/SeqPanel.java
+++ b/src/jalview/gui/SeqPanel.java
@@ -20,6 +20,24 @@
  */
 package jalview.gui;
 
+import java.awt.BorderLayout;
+import java.awt.Color;
+import java.awt.Font;
+import java.awt.FontMetrics;
+import java.awt.Point;
+import java.awt.event.MouseEvent;
+import java.awt.event.MouseListener;
+import java.awt.event.MouseMotionListener;
+import java.awt.event.MouseWheelEvent;
+import java.awt.event.MouseWheelListener;
+import java.util.ArrayList;
+import java.util.Collections;
+import java.util.List;
+
+import javax.swing.JPanel;
+import javax.swing.SwingUtilities;
+import javax.swing.ToolTipManager;
+
 import jalview.api.AlignViewportI;
 import jalview.bin.Cache;
 import jalview.commands.EditCommand;
@@ -53,24 +71,6 @@ import jalview.viewmodel.AlignmentViewport;
 import jalview.viewmodel.ViewportRanges;
 import jalview.viewmodel.seqfeatures.FeatureRendererModel;
 
-import java.awt.BorderLayout;
-import java.awt.Color;
-import java.awt.Font;
-import java.awt.FontMetrics;
-import java.awt.Point;
-import java.awt.event.MouseEvent;
-import java.awt.event.MouseListener;
-import java.awt.event.MouseMotionListener;
-import java.awt.event.MouseWheelEvent;
-import java.awt.event.MouseWheelListener;
-import java.util.ArrayList;
-import java.util.Collections;
-import java.util.List;
-
-import javax.swing.JPanel;
-import javax.swing.SwingUtilities;
-import javax.swing.ToolTipManager;
-
 /**
  * DOCUMENT ME!
  * 
@@ -207,8 +207,6 @@ public class SeqPanel extends JPanel
 
   StringBuffer keyboardNo2;
 
-  java.net.URL linkImageURL;
-
   private final SequenceAnnotationReport seqARep;
 
   StringBuilder tooltipText = new StringBuilder();
@@ -229,8 +227,7 @@ public class SeqPanel extends JPanel
    */
   public SeqPanel(AlignViewport viewport, AlignmentPanel alignPanel)
   {
-    linkImageURL = getClass().getResource("/images/link.gif");
-    seqARep = new SequenceAnnotationReport(linkImageURL.toString());
+    seqARep = new SequenceAnnotationReport(true);
     ToolTipManager.sharedInstance().registerComponent(this);
     ToolTipManager.sharedInstance().setInitialDelay(0);
     ToolTipManager.sharedInstance().setDismissDelay(10000);
@@ -913,7 +910,7 @@ public class SeqPanel extends JPanel
           for (SequenceFeature sf : mf.features)
           {
             String pv = mf.findProteinVariants(sf);
-            if (!infos.contains(pv))
+            if (pv.length() > 0 && !infos.contains(pv))
             {
               infos.add(pv);
             }
@@ -1042,12 +1039,14 @@ public class SeqPanel extends JPanel
      * add features that straddle the gap (pos may be the residue before or
      * after the gap)
      */
+    int unshownFeatures = 0;
     if (av.isShowSequenceFeatures())
     {
       List<SequenceFeature> features = ap.getFeatureRenderer()
               .findFeaturesAtColumn(sequence, column + 1);
-      seqARep.appendFeatures(tooltipText, pos, features,
-              this.ap.getSeqPanel().seqCanvas.fr);
+      unshownFeatures = seqARep.appendFeatures(tooltipText, pos,
+              features, this.ap.getSeqPanel().seqCanvas.fr,
+              MAX_TOOLTIP_LENGTH);
 
       /*
        * add features in CDS/protein complement at the corresponding
@@ -1065,23 +1064,31 @@ public class SeqPanel extends JPanel
                   pos);
           if (mf != null)
           {
-            seqARep.appendFeatures(tooltipText, pos, mf.features, fr2);
+            unshownFeatures = seqARep.appendFeatures(tooltipText,
+                    pos, mf, fr2, MAX_TOOLTIP_LENGTH);
           }
         }
       }
     }
-    if (tooltipText.length() == 6) // <html>
+    if (tooltipText.length() == 6) // "<html>"
     {
       setToolTipText(null);
       lastTooltip = null;
     }
     else
     {
-      if (tooltipText.length() > MAX_TOOLTIP_LENGTH) // constant
+      if (tooltipText.length() > MAX_TOOLTIP_LENGTH)
       {
         tooltipText.setLength(MAX_TOOLTIP_LENGTH);
         tooltipText.append("...");
       }
+      if (unshownFeatures > 0)
+      {
+        tooltipText.append("<br/>").append("... ").append("<i>")
+                .append(MessageManager.formatMessage(
+                        "label.features_not_shown", unshownFeatures))
+                .append("</i>");
+      }
       String textString = tooltipText.toString();
       if (lastTooltip == null || !lastTooltip.equals(textString))
       {
@@ -2049,7 +2056,7 @@ public class SeqPanel extends JPanel
       return;
     }
 
-    if (evt.getClickCount() > 1)
+    if (evt.getClickCount() > 1 && av.isShowSequenceFeatures())
     {
       sg = av.getSelectionGroup();
       if (sg != null && sg.getSize() == 1
@@ -2752,7 +2759,7 @@ public class SeqPanel extends JPanel
      * Map sequence selection
      */
     SequenceGroup sg = MappingUtils.mapSequenceGroup(seqsel, sourceAv, av);
-    av.setSelectionGroup(sg);
+    av.setSelectionGroup(sg != null && sg.getSize() > 0 ? sg : null);
     av.isSelectionGroupChanged(true);
 
     /*