JAL-892 tidy Varna panel names; JAL-1789 simplified mouseover

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

diff --git a/src/jalview/gui/AppVarna.java b/src/jalview/gui/AppVarna.java
index 9316b05..beb4980 100644 (file)
--- a/src/jalview/gui/AppVarna.java
+++ b/src/jalview/gui/AppVarna.java
@@ -22,6 +22,7 @@ package jalview.gui;
 
 import java.awt.BorderLayout;
 import java.awt.Color;
+import java.lang.reflect.InvocationTargetException;
 import java.util.Collection;
 import java.util.Hashtable;
 import java.util.LinkedHashMap;
@@ -167,8 +168,6 @@ public class AppVarna extends JInternalFrame implements SelectionListener,
   /**
    * Constructor
    * 
-   * @param sname
-   *          a descriptive name
    * @param seq
    *          the RNA sequence
    * @param aa
@@ -176,41 +175,18 @@ public class AppVarna extends JInternalFrame implements SelectionListener,
    * @param ap
    *          the AlignmentPanel creating this object
    */
-  public AppVarna(String sname, SequenceI seq, AlignmentAnnotation aa,
-          AlignmentPanel ap)
+  public AppVarna(SequenceI seq, AlignmentAnnotation aa, AlignmentPanel ap)
   {
     this(ap);
 
-    String name = sname + " trimmed to " + seq.getName();
-    String fullName = MessageManager.formatMessage("label.varna_params",
+    String sname = aa.sequenceRef == null ? "secondary structure (alignment)"
+            : seq.getName() + " structure";
+    String theTitle = sname
+            + (aa.sequenceRef == null ? " trimmed to " + seq.getName() : "");
+    theTitle = MessageManager.formatMessage("label.varna_params",
             new String[]
-            { name });
-    setTitle(fullName);
-
-    /*
-     * if (!aa.isValidStruc()) { throw new
-     * IllegalArgumentException("Invalid RNA structure annotation"); } final
-     * String struc = aa.getRNAStruc();
-     * 
-     * String strucseq = seq.getSequenceAsString();
-     * 
-     * String gappedTitle = sname + " (with gaps)"; String rnaTitle =
-     * gappedTitle; RNA gapped = new RNA(rnaTitle); try {
-     * gapped.setRNA(strucseq, replaceOddGaps(struc)); } catch
-     * (ExceptionUnmatchedClosingParentheses e2) { e2.printStackTrace(); } catch
-     * (ExceptionFileFormatOrSyntax e3) { e3.printStackTrace(); }
-     * models.put(gapped, new RnaModel(rnaTitle, aa, seq, gapped, true, null));
-     * 
-     * String trimmedTitle = "trimmed " + sname; rnaTitle = trimmedTitle; RNA
-     * trimmed = trimRNA(gapped, rnaTitle); models.put(trimmed, new
-     * RnaModel(rnaTitle, aa, seq, trimmed, false, null));
-     */
-    // vab = new AppVarnaBinding(Arrays.asList(new RNA[]
-    // { trimmed, gapped }));
-    // vab = new AppVarnaBinding();
-    // // String seqName = seq.getName();
-    // // String name = sname + " trimmed to " + seqName;
-    // initVarna(name);
+            { theTitle });
+    setTitle(theTitle);
 
     String gappedTitle = sname + " (with gaps)";
     RnaModel gappedModel = new RnaModel(gappedTitle, aa, seq, null, true,
@@ -409,25 +385,35 @@ public class AppVarna extends JInternalFrame implements SelectionListener,
    * selected RNA in the VARNA window is highlighted at the specific position.
    * To be able to remove it before the next highlight it is saved in
    * _lastHighlight
+   * 
+   * @param sequence
+   * @param index
+   *          the aligned sequence position (base 0)
+   * @param position
+   *          the dataset sequence position (base 1)
    */
   @Override
-  public void mouseOverSequence(SequenceI sequence, int index)
+  public void mouseOverSequence(SequenceI sequence, final int index,
+          final int position)
   {
     RNA rna = vab.getSelectedRNA();
     if (rna == null)
     {
       return;
     }
-    if (models.get(rna).seq == sequence)
-    {
-      ShiftList shift = offsets.get(rna);
-      if (shift != null)
-      {
-        // System.err.print("Orig pos:"+index);
-        index = shift.shift(index);
-        // System.err.println("\nFinal pos:"+index);
-      }
-      mouseOverHighlighter.highlightRegion(rna, index, index);
+    RnaModel rnaModel = models.get(rna);
+    if (rnaModel.seq == sequence)
+    {
+      int highlightPos = rnaModel.gapped ? index : position - 1;
+      // int highlightPos = index;
+      // ShiftList shift = offsets.get(rna);
+      // if (shift != null)
+      // {
+      // System.err.print("Orig pos:" + index);
+      // highlightPos = shift.shift(index);
+      // System.err.println("\nFinal pos:" + index);
+      // }
+      mouseOverHighlighter.highlightRegion(rna, highlightPos, highlightPos);
       vab.updateSelectedRNA(rna);
     }
   }
@@ -630,7 +616,6 @@ public class AppVarna extends JInternalFrame implements SelectionListener,
         {
           registerOffset(rna, buildOffset(model.seq));
         }
-        // TODO and add mapping (offsets)
         models.put(rna, newModel);
         // capture rna selection state when saved
         selectionHighlighter = new VarnaHighlighter(rna);
@@ -680,6 +665,7 @@ public class AppVarna extends JInternalFrame implements SelectionListener,
   protected ShiftList buildOffset(SequenceI seq)
   {
     // TODO refactor to avoid duplication with trimRNA()
+    // TODO JAL-1789 bugs in use of ShiftList here
     ShiftList offset = new ShiftList();
     int ofstart = -1;
     int sleng = seq.getLength();
@@ -715,10 +701,10 @@ public class AppVarna extends JInternalFrame implements SelectionListener,
   /**
    * Set the selected index in the model selection list
    * 
-   * @param selectedRna
+   * @param selectedR
    */
-  public void setSelectedIndex(int selectedRna)
+  public void setInitialSelection(final int selectedIndex)
   {
-    vab.setSelectedIndex(selectedRna);
+    vab.setSelectedIndex(selectedIndex);
   }
 }