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 27ceb27..dc2d3e9 100644 (file)
--- a/src/jalview/gui/SeqPanel.java
+++ b/src/jalview/gui/SeqPanel.java
@@ -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);
@@ -865,7 +862,8 @@ public class SeqPanel extends JPanel
     {
       setStatusMessage(results);
     }
-    return results.isEmpty() ? null : getHighlightInfo(results);
+    // JAL-3303 feature suppressed for now pending review
+    return null; // results.isEmpty() ? null : getHighlightInfo(results);
   }
 
   /**
@@ -895,11 +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())
       {
@@ -1047,9 +1046,9 @@ public class SeqPanel extends JPanel
     {
       List<SequenceFeature> features = ap.getFeatureRenderer()
               .findFeaturesAtColumn(sequence, column + 1);
-      unshownFeatures = seqARep.appendFeaturesLengthLimit(tooltipText, pos,
-              features,
-              this.ap.getSeqPanel().seqCanvas.fr, MAX_TOOLTIP_LENGTH);
+      unshownFeatures = seqARep.appendFeatures(tooltipText, pos,
+              features, this.ap.getSeqPanel().seqCanvas.fr,
+              MAX_TOOLTIP_LENGTH);
 
       /*
        * add features in CDS/protein complement at the corresponding
@@ -1067,9 +1066,8 @@ public class SeqPanel extends JPanel
                   pos);
           if (mf != null)
           {
-            unshownFeatures = seqARep.appendFeaturesLengthLimit(
-                    tooltipText, pos, mf, fr2,
-                    MAX_TOOLTIP_LENGTH);
+            unshownFeatures = seqARep.appendFeatures(tooltipText,
+                    pos, mf, fr2, MAX_TOOLTIP_LENGTH);
           }
         }
       }
@@ -1203,7 +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;
   }
@@ -1219,7 +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
@@ -1227,7 +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);
@@ -1237,7 +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;
 
@@ -1282,7 +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();
@@ -1294,8 +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;
       }
     }