X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Frenderer%2FAnnotationRenderer.java;h=b5dac0d50f95fb5daf98ac5379724f0bea3d6697;hb=3fdc889794e3566af57628f0b6a308eb23886f96;hp=24fbb2645c0225e7fe90853e06983f10c7061cc3;hpb=427b5193ff4e96cf2a28cf72c1857a1ab5250201;p=jalview.git

diff --git a/src/jalview/renderer/AnnotationRenderer.java b/src/jalview/renderer/AnnotationRenderer.java
index 24fbb26..b5dac0d 100644
--- a/src/jalview/renderer/AnnotationRenderer.java
+++ b/src/jalview/renderer/AnnotationRenderer.java
@@ -175,7 +175,6 @@ public class AnnotationRenderer
           int x, int y, int iconOffset, int startRes, int column,
           boolean validRes, boolean validEnd)
   {
-    g.setColor(STEM_COLOUR);
     int sCol = (lastSSX / charWidth)
             + hiddenColumns.visibleToAbsoluteColumn(startRes);
     int x1 = lastSSX;
@@ -185,11 +184,19 @@ public class AnnotationRenderer
             : row_annotations[column - 1].secondaryStructure;
 
     boolean diffupstream = sCol == 0 || row_annotations[sCol - 1] == null
-            || dc != row_annotations[sCol - 1].secondaryStructure;
+            || dc != row_annotations[sCol - 1].secondaryStructure
+            || !validEnd;
     boolean diffdownstream = !validRes || !validEnd
             || row_annotations[column] == null
             || dc != row_annotations[column].secondaryStructure;
 
+    if (diffupstream || diffdownstream)
+    {
+      // draw glyphline under arrow
+      drawGlyphLine(g, lastSSX, x, y, iconOffset);
+    }
+    g.setColor(STEM_COLOUR);
+
     if (column > 0 && Rna.isClosingParenthesis(dc))
     {
       if (diffupstream)
@@ -202,7 +209,8 @@ public class AnnotationRenderer
          */
         fillPolygon(g, new int[] { lastSSX + 5, lastSSX + 5, lastSSX },
                 new int[]
-                { y + iconOffset, y + 14 + iconOffset, y + 8 + iconOffset },
+                { y + iconOffset + 1, y + 13 + iconOffset,
+                    y + 7 + iconOffset },
                 3);
         x1 += 5;
       }
@@ -220,9 +228,10 @@ public class AnnotationRenderer
          * if annotation ending with an opeing base pair half of the stem, 
          * display a forward arrow
          */
-        fillPolygon(g, new int[] { x2 - 5, x2 - 5, x2 },
+        fillPolygon(g, new int[] { x2 - 6, x2 - 6, x2 - 1 },
                 new int[]
-                { y + iconOffset, y + 14 + iconOffset, y + 8 + iconOffset },
+                { y + iconOffset + 1, y + 13 + iconOffset,
+                    y + 7 + iconOffset },
                 3);
         x2 -= 5;
       }
@@ -232,7 +241,8 @@ public class AnnotationRenderer
       }
     }
     // draw arrow body
-    fillRect(g, x1, y + 4 + iconOffset, x2 - x1, 7);
+    unsetAntialias(g);
+    fillRect(g, x1, y + 4 + iconOffset, x2 - x1, 6);
   }
 
   void drawNotCanonicalAnnot(Graphics g, Color nonCanColor,
@@ -251,7 +261,8 @@ public class AnnotationRenderer
             : row_annotations[column - 1].displayCharacter;
 
     boolean diffupstream = sCol == 0 || row_annotations[sCol - 1] == null
-            || !dc.equals(row_annotations[sCol - 1].displayCharacter);
+            || !dc.equals(row_annotations[sCol - 1].displayCharacter)
+            || !validEnd;
     boolean diffdownstream = !validRes || !validEnd
             || row_annotations[column] == null
             || !dc.equals(row_annotations[column].displayCharacter);
@@ -1267,7 +1278,6 @@ public class AnnotationRenderer
       }
       else
       {
-        // g.setColor(Color.orange);
         fillRoundRect(g, lastSSX, y + 3 + iconOffset, x2 - x1 - ofs, 8, 0,
                 0);
       }
@@ -1278,7 +1288,6 @@ public class AnnotationRenderer
       }
       else
       {
-        // g.setColor(Color.magenta);
         fillRoundRect(g, lastSSX + ofs, y + 3 + iconOffset, x2 - x1 - ofs,
                 8, 0, 0);
       }