employ test and secondary structure character for determining base pairing direction...

diff --git a/src/jalview/renderer/AnnotationRenderer.java b/src/jalview/renderer/AnnotationRenderer.java
index 5348aaa..d5b2f49 100644 (file)
--- a/src/jalview/renderer/AnnotationRenderer.java
+++ b/src/jalview/renderer/AnnotationRenderer.java
@@ -27,6 +27,7 @@ import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.Annotation;
 import jalview.datamodel.ColumnSelection;
 import jalview.schemes.ColourSchemeI;
+import jalview.schemes.ResidueProperties;
 
 import java.awt.BasicStroke;
 import java.awt.Color;
@@ -77,17 +78,17 @@ public class AnnotationRenderer
     int x2 = (x * charWidth);
     Regex closeparen = new Regex("(\\))");
 
-    String dc = (column == 0 || row_annotations[column - 1] == null) ? ""
-            : row_annotations[column - 1].displayCharacter;
+    char dc = (column == 0 || row_annotations[column - 1] == null) ? ' '
+            : row_annotations[column - 1].secondaryStructure;
 
     boolean diffupstream = sCol == 0 || row_annotations[sCol - 1] == null
-            || !dc.equals(row_annotations[sCol - 1].displayCharacter);
+            || dc != row_annotations[sCol - 1].secondaryStructure;
     boolean diffdownstream = !validRes || !validEnd
             || row_annotations[column] == null
-            || !dc.equals(row_annotations[column].displayCharacter);
+            || dc != row_annotations[column].secondaryStructure;
     // System.out.println("Column "+column+" diff up: "+diffupstream+" down:"+diffdownstream);
     // If a closing base pair half of the stem, display a backward arrow
-    if (column > 0 && closeparen.search(dc))
+    if (column > 0 && ResidueProperties.isCloseParenRNA(dc))
     {
 
       if (diffupstream)
@@ -574,11 +575,15 @@ public class AnnotationRenderer
                 }
               }
             }
-            if (!row.isValidStruc())
+            if (row.getInvalidStrucPos() > x)
             {
               g.setColor(Color.orange);
-              g.fillRect((int) row.getInvalidStrucPos() * charWidth, y,
-                      charWidth, charHeight);
+              g.fillRect(x * charWidth, y, charWidth, charHeight);
+            }
+            else if (row.getInvalidStrucPos() == x)
+            {
+              g.setColor(Color.orange.darker());
+              g.fillRect(x * charWidth, y, charWidth, charHeight);
             }
             if (validCharWidth
                     && validRes