JAL-1601 Expand secondary structure prediction tests

[jalview.git] / src / jalview / datamodel / AlignmentAnnotation.java

diff --git a/src/jalview/datamodel/AlignmentAnnotation.java b/src/jalview/datamodel/AlignmentAnnotation.java
index 0e0239a..40dfdd9 100755 (executable)
--- a/src/jalview/datamodel/AlignmentAnnotation.java
+++ b/src/jalview/datamodel/AlignmentAnnotation.java
@@ -854,15 +854,15 @@ public class AlignmentAnnotation
     }
     if (startRes >= annotations.length)
     {
-      startRes = annotations.length - 1;
+      startRes = annotations.length;
     }
-    if (endRes >= annotations.length)
+    if (endRes < 0)
     {
-      endRes = annotations.length - 1;
+      endRes = -1;
     }
-    if (annotations == null)
+    if (endRes >= annotations.length)
     {
-      return;
+      endRes = annotations.length - 1;
     }
     Annotation[] temp = new Annotation[endRes - startRes + 1];
     if (startRes < annotations.length)
@@ -1625,6 +1625,8 @@ public class AlignmentAnnotation
   private void removeHiddenAnnotation(int start, int end,
           HiddenColumns hiddenColumns)
   {
+    start = Math.min(Math.max(0, start), annotations.length);
+    end = Math.min(Math.max(-1, end), annotations.length - 1);
     // mangle the alignmentAnnotation annotation array
     ArrayList<Annotation[]> annels = new ArrayList<>();
     Annotation[] els = null;
@@ -1744,6 +1746,16 @@ public class AlignmentAnnotation
     return aa;
   }
 
+  public String getLabel()
+  {
+    return label;
+  }
+
+  public Annotation[] getAnnotations()
+  {
+    return annotations;
+  }
+
   public double getBitScore()
   {
     return bitScore;