JAL-3490 match count independent of contiguous matches count

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

diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java
index cd1bc7b..dc2d3e9 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);
@@ -896,11 +893,12 @@ public class SeqPanel extends JPanel
     AlignFrame af = Desktop.getAlignFrameFor(complement);
     FeatureRendererModel fr2 = af.getFeatureRenderer();
 
-    int j = results.getSize();
+    List<SearchResultMatchI> matches = results.getResults();
+    int j = matches.size();
     List<String> infos = new ArrayList<>();
     for (int i = 0; i < j; i++)
     {
-      SearchResultMatchI match = results.getResults().get(i);
+      SearchResultMatchI match = matches.get(i);
       int pos = match.getStart();
       if (pos == match.getEnd())
       {
@@ -1043,12 +1041,14 @@ 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
@@ -1066,23 +1066,31 @@ public class SeqPanel extends JPanel
                   pos);
           if (mf != null)
           {
-            seqARep.appendFeatures(tooltipText, pos, mf, 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))
       {
@@ -1193,7 +1201,7 @@ public class SeqPanel extends JPanel
   {
     char sequenceChar = sequence.getCharAt(column);
     int pos = sequence.findPosition(column);
-    setStatusMessage(sequence, seqIndex, sequenceChar, pos);
+    setStatusMessage(sequence.getName(), seqIndex, sequenceChar, pos);
 
     return pos;
   }
@@ -1209,7 +1217,7 @@ public class SeqPanel extends JPanel
    * Sequence 6 ID: O.niloticus.3 Nucleotide: Uracil (2)
    * </pre>
    * 
-   * @param sequence
+   * @param seqName
    * @param seqIndex
    *          sequence position in the alignment (1..)
    * @param sequenceChar
@@ -1217,7 +1225,7 @@ public class SeqPanel extends JPanel
    * @param residuePos
    *          the sequence residue position (if not over a gap)
    */
-  protected void setStatusMessage(SequenceI sequence, int seqIndex,
+  protected void setStatusMessage(String seqName, int seqIndex,
           char sequenceChar, int residuePos)
   {
     StringBuilder text = new StringBuilder(32);
@@ -1227,7 +1235,7 @@ public class SeqPanel extends JPanel
      */
     String seqno = seqIndex == -1 ? "" : " " + (seqIndex + 1);
     text.append("Sequence").append(seqno).append(" ID: ")
-            .append(sequence.getName());
+            .append(seqName);
 
     String residue = null;
 
@@ -1272,7 +1280,8 @@ public class SeqPanel extends JPanel
     {
       return;
     }
-    SequenceI ds = al.getSequenceAt(sequenceIndex).getDatasetSequence();
+    SequenceI alignedSeq = al.getSequenceAt(sequenceIndex);
+    SequenceI ds = alignedSeq.getDatasetSequence();
     for (SearchResultMatchI m : results.getResults())
     {
       SequenceI seq = m.getSequence();
@@ -1284,8 +1293,8 @@ public class SeqPanel extends JPanel
       if (seq == ds)
       {
         int start = m.getStart();
-        setStatusMessage(seq, sequenceIndex, seq.getCharAt(start - 1),
-                start);
+        setStatusMessage(alignedSeq.getName(), sequenceIndex,
+                seq.getCharAt(start - 1), start);
         return;
       }
     }
@@ -2050,7 +2059,7 @@ 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
@@ -2753,7 +2762,7 @@ 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);
 
     /*