X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAnnotationPanel.java;h=86d5c6dacbec1fdb25a40cead49521e1ceb6d244;hb=266c4e2544701f88a8d21294b4a4f4cc42cf76cc;hp=2f444d689943432adc65cfb0b4fc9862ccf00506;hpb=925fb2ee9513a30337cc736996a3487e39d42530;p=jalview.git

diff --git a/src/jalview/gui/AnnotationPanel.java b/src/jalview/gui/AnnotationPanel.java
index 2f444d6..86d5c6d 100755
--- a/src/jalview/gui/AnnotationPanel.java
+++ b/src/jalview/gui/AnnotationPanel.java
@@ -721,7 +721,7 @@ public class AnnotationPanel
 
         if (row.hasText)
         {
-          iconOffset = av.charHeight / 2 + 4;
+          iconOffset =av.charHeight -fm.getDescent();
           y -= av.charHeight;
         }
       }
@@ -821,15 +821,20 @@ public class AnnotationPanel
           }
         }
 
-        if (av.validCharWidth && validRes &&
-            (row.annotations[column].displayCharacter.length() > 0))
+        if (av.validCharWidth && validRes
+            && row.annotations[column].displayCharacter != null
+            && (row.annotations[column].displayCharacter.length() > 0))
         {
 
           int charOffset = (av.charWidth -
                             fm.charWidth(row.annotations[column].
                                          displayCharacter.charAt(
                                              0))) / 2;
-          g.setColor(row.annotations[column].colour);
+
+          if (row.annotations[column].colour == null)
+            g.setColor(Color.black);
+          else
+            g.setColor(row.annotations[column].colour);
 
           if (column == 0 || row.graph > 0)
           {
@@ -1143,7 +1148,11 @@ public class AnnotationPanel
         continue;
       }
 
-      g.setColor(aa.annotations[column].colour);
+      if (aa.annotations[column].colour == null)
+        g.setColor(Color.black);
+      else
+        g.setColor(aa.annotations[column].colour);
+
       y1 = y -
           (int) ( ( (aa.annotations[column - 1].value - min) / range) * graphHeight);
       y2 = y -
@@ -1217,7 +1226,11 @@ public class AnnotationPanel
         continue;
       }
 
-      g.setColor(aa.annotations[column].colour);
+      if (aa.annotations[column].colour == null)
+        g.setColor(Color.black);
+      else
+        g.setColor(aa.annotations[column].colour);
+
       y1 = y -
           (int) ( ( (aa.annotations[column].value - min) / (range)) * aa.graphHeight);
 
@@ -1264,7 +1277,10 @@ public class AnnotationPanel
     {
       if (aa.annotations[j] != null)
       {
-        g.setColor(aa.annotations[j].colour);
+        if (aa.annotations[j].colour == null)
+          g.setColor(Color.black);
+        else
+          g.setColor(aa.annotations[j].colour);
 
         height = (int) ( (aa.annotations[j].value / aa.graphMax) * y);
         if (height > y)